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Mathematics Faculty: Publications since January 2017

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%% Agarwal, Pankaj K.   
@article{fds337580,
   Author = {Agarwal, PK and Kyle, FOX and Salzman, O},
   Title = {An efficient algorithm for computing high-quality paths amid
             polygonal obstacles},
   Journal = {Acm Transactions on Algorithms},
   Volume = {14},
   Number = {4},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1145/3230650},
   Abstract = {© 2018 ACM. We study a path-planning problem amid a set O
             of obstacles in R2, in which we wish to compute a short path
             between two points while also maintaining a high clearance
             from O; the clearance of a point is its distance from a
             nearest obstacle in O. Specifically, the problem asks for a
             path minimizing the reciprocal of the clearance integrated
             over the length of the path. We present the first
             polynomial-time approximation scheme for this problem. Let n
             be the total number of obstacle vertices and let ε ∈ (0,
             1]. Our algorithm computes in time O(nε22 lognε ) a path
             of total cost at most (1 + ε) times the cost of the optimal
             path.},
   Doi = {10.1145/3230650},
   Key = {fds337580}
}

@article{fds337042,
   Author = {Agarwal, PK and Kaplan, H and Sharir, M},
   Title = {Union of hypercubes and 3D minkowski sums with random
             sizes},
   Journal = {Leibniz International Proceedings in Informatics,
             Lipics},
   Volume = {107},
   Year = {2018},
   Month = {July},
   ISBN = {9783959770767},
   url = {http://dx.doi.org/10.4230/LIPIcs.ICALP.2018.10},
   Abstract = {© Pankaj K. Agarwal, Haim Kaplan, and Micha Sharir;. Let T
             = (1n) be a set of of n pairwise-disjoint triangles in R3,
             and let B be a convex polytope in R3with a constant number
             of faces. For each i, let Ci=iriB denote the Minkowski sum
             ofiwith a copy of B scaled by ri> 0. We show that if the
             scaling factors r1, . . ., rnare chosen randomly then the
             expected complexity of the union of C1, . . ., Cnis
             O(n2+ε), for any ε > 0; the constant of proportionality
             depends on ε and the complexity of B. The worst-case bound
             can be (n3). We also consider a special case of this problem
             in which T is a set of points in R3and B is a unit cube in
             R3, i.e., each Ciis a cube of side-length 2ri. We show that
             if the scaling factors are chosen randomly then the expected
             complexity of the union of the cubes is O(n log2n), and it
             improves to O(n log n) if the scaling factors are chosen
             randomly from a “well-behaved” probability density
             function (pdf). We also extend the latter results to higher
             dimensions. For any fixed odd value of d, we show that the
             expected complexity of the union of the hypercubes is O(nd/2
             log n) and the bound improves to O(nd/2) if the scaling
             factors are chosen from a “well-behaved” pdf. The
             worst-case bounds are (n2) in R3, and (nd/2) in higher
             dimensions.},
   Doi = {10.4230/LIPIcs.ICALP.2018.10},
   Key = {fds337042}
}

@article{fds331366,
   Author = {Agarwal, PK and Kumar, N and Sintos, S and Suri, S},
   Title = {Range-max queries on uncertain data},
   Journal = {Journal of Computer and System Sciences},
   Volume = {94},
   Pages = {118-134},
   Year = {2018},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.jcss.2017.09.006},
   Abstract = {© 2017. Let P be a set of n uncertain points in Rd, where
             each point pi P is associated with a real value vi and
             exists with probability αi (0,1] independently of the other
             points. We present algorithms for building an index on P so
             that for a d-dimensional query rectangle ρ, the expected
             maximum value or the most-likely maximum value in ρ can be
             computed quickly. Our main contributions include the
             following: (i) The first index of sub-quadratic size to
             achieve a sub-linear query time in any dimension. (ii) A
             conditional lower bound for most-likely range-max queries,
             based on the conjectured hardness of the set-intersection
             problem. (iii) A near-linear-size index for estimating the
             expected range-max value within approximation factor 1/2 in
             O(polylog(n)) time. (iv) Extensions of our algorithm to more
             general uncertainty models and for computing the top-k
             values of the range-max.},
   Doi = {10.1016/j.jcss.2017.09.006},
   Key = {fds331366}
}

@article{fds336323,
   Author = {Agarwal, PK and Arge, L and Staals, F},
   Title = {Improved dynamic geodesic nearest neighbor searching in a
             simple polygon},
   Journal = {Leibniz International Proceedings in Informatics,
             Lipics},
   Volume = {99},
   Pages = {41-414},
   Year = {2018},
   Month = {June},
   url = {http://dx.doi.org/10.4230/LIPIcs.SoCG.2018.4},
   Abstract = {© Pankaj K. Agarwal, Lars Arge, and Frank Staals; licensed
             under Creative Commons License CC-BY 34th Symposium on
             Computational Geometry (SoCG 2018). We present an efficient
             dynamic data structure that supports geodesic nearest
             neighbor queries for a set S of point sites in a static
             simple polygon P. Our data structure allows us to insert a
             new site in S, delete a site from S, and ask for the site in
             S closest to an arbitrary query point q ∈ P. All distances
             are measured using the geodesic distance, that is, the
             length of the shortest path that is completely contained in
             P. Our data structure achieves polylogarithmic update and
             query times, and uses O(n log3nlog m + m) space, where n is
             the number of sites in S and m is the number of vertices in
             P. The crucial ingredient in our data structure is an
             implicit representation of a vertical shallow cutting of the
             geodesic distance functions. We show that such an implicit
             representation exists, and that we can compute it
             efficiently.},
   Doi = {10.4230/LIPIcs.SoCG.2018.4},
   Key = {fds336323}
}

@article{fds336324,
   Author = {Agarwal, PK and Kumar, N and Sintos, S and Suri, S},
   Title = {Computing shortest paths in the plane with removable
             obstacles},
   Journal = {Leibniz International Proceedings in Informatics,
             Lipics},
   Volume = {101},
   Pages = {51-515},
   Year = {2018},
   Month = {June},
   ISBN = {9783959770682},
   url = {http://dx.doi.org/10.4230/LIPIcs.SWAT.2018.5},
   Abstract = {© Pankaj Agarwal, Neeraj Kumar, Stavros Sintos, and Subhash
             Suri. We consider the problem of computing a Euclidean
             shortest path in the presence of removable obstacles in the
             plane. In particular, we have a collection of
             pairwise-disjoint polygonal obstacles, each of which may be
             removed at some cost ci> 0. Given a cost budget C > 0, and a
             pair of points s, t, which obstacles should be removed to
             minimize the path length from s to t in the remaining
             workspace? We show that this problem is NP-hard even if the
             obstacles are vertical line segments. Our main result is a
             fully-polynomial time approximation scheme (FPTAS) for the
             case of convex polygons. Specifically, we compute an (1 +
             )-approximate shortest path in time Onh2log n lognwith
             removal cost at most (1 + )C, where h is the number of
             obstacles, n is the total number of obstacle vertices, and
             ∈ (0, 1) is a user-specified parameter. Our approximation
             scheme also solves a shortest path problem for a stochastic
             model of obstacles, where each obstacle’s presence is an
             independent event with a known probability. Finally, we also
             present a data structure that can answer s–t path queries
             in polylogarithmic time, for any pair of points s, t in the
             plane.},
   Doi = {10.4230/LIPIcs.SWAT.2018.5},
   Key = {fds336324}
}

@article{fds336325,
   Author = {Agarwal, PK and Fox, K and Munagala, K and Nath, A and Pan, J and Taylor,
             E},
   Title = {Subtrajectory clustering: Models and algorithms},
   Journal = {Proceedings of the Acm Sigact Sigmod Sigart Symposium on
             Principles of Database Systems},
   Pages = {75-87},
   Year = {2018},
   Month = {May},
   ISBN = {9781450347068},
   url = {http://dx.doi.org/10.1145/3196959.3196972},
   Abstract = {© 2018 Association for Computing Machinery. We propose a
             model for subtrajectory clustering'the clustering of
             subsequences of trajectories; each cluster of
             subtrajectories is represented as a pathlet, a sequence of
             points that is not necessarily a subsequence of an input
             trajectory. Given a set of trajectories, our clustering
             model attempts to capture the shared portions between them
             by assuming each trajectory is a concatenation of a small
             set of pathlets, with possible gaps in between. We present a
             single objective function for finding the optimal collection
             of pathlets that best represents the trajectories taking
             into account noise and other artifacts of the data. We show
             that the subtrajectory clustering problem is NP-Hard and
             present fast approximation algorithms for subtrajectory
             clustering. We further improve the running time of our
             algorithm if the input trajectories are “well-behaved."
             Finally, we present experimental results on both real and
             synthetic data sets. We show via visualization and
             quantitative analysis that the algorithm indeed handles the
             desiderata of being robust to variations, being efficient
             and accurate, and being data-driven.},
   Doi = {10.1145/3196959.3196972},
   Key = {fds336325}
}

@article{fds337581,
   Author = {Agarwal, PK and Fox, K and Nath, A and Sidiropoulos, A and Wang,
             Y},
   Title = {Computing the Gromov-Hausdorff Distance for Metric
             Trees},
   Journal = {Acm Transactions on Algorithms},
   Volume = {14},
   Number = {2},
   Pages = {1-20},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1145/3185466},
   Doi = {10.1145/3185466},
   Key = {fds337581}
}

@article{fds333280,
   Author = {Agarwal, PK and Fox, K and Nath, A},
   Title = {Maintaining reeb graphs of triangulated 2-manifolds},
   Journal = {Leibniz International Proceedings in Informatics,
             Lipics},
   Volume = {93},
   Year = {2018},
   Month = {January},
   ISBN = {9783959770552},
   url = {http://dx.doi.org/10.4230/LIPIcs.FSTTCS.2017.8},
   Abstract = {© Pankaj K. Agarwal, Kyle Fox and Abhinandan Nath. Let M be
             a triangulated, orientable 2-manifold of genus g without
             boundary, and let h be a height function over M that is
             linear within each triangle. We present a kinetic data
             structure (KDS) for maintaining the Reeb graph R of h as the
             heights of M’s vertices vary continuously with time.
             Assuming the heights of two vertices of M become equal only
             O(1) times, the KDS processes O((? + g)n polylog n) events;
             n is the number of vertices in M, and ? is the number of
             external events which change the combinatorial structure of
             R. Each event is processed in O(log 2 n) time, and the total
             size of our KDS is O(gn). The KDS can be extended to
             maintain an augmented Reeb graph as well.},
   Doi = {10.4230/LIPIcs.FSTTCS.2017.8},
   Key = {fds333280}
}

@article{fds332953,
   Author = {Rav, M and Lowe, A and Agarwal, PK},
   Title = {Flood Risk Analysis on Terrains},
   Journal = {GIS: Proceedings of the ACM International Symposium on
             Advances in Geographic Information Systems},
   Volume = {2017-November},
   Year = {2017},
   Month = {November},
   ISBN = {9781450354905},
   url = {http://dx.doi.org/10.1145/3139958.3139985},
   Abstract = {© 2017 Copyright held by the owner/author(s). An important
             problem in terrain analysis is modeling how water flows
             across a terrain and creates floods by filling up
             depressions. In this paper we study the flooding query
             problem: Given a rain region R and a query point q on the
             terrain, quickly determine how much rain has to fall in R so
             that q is flooded. Available terrain data is often subject
             to uncertainty which must be incorporated into the terrain
             analysis. For instance, the digital elevation models of
             terrains have to be refined to incorporate underground
             pipes, tunnels, and waterways under bridges, but there is
             often uncertainty in their existence. By representing the
             uncertainty in the terrain data explicitly, we can develop
             methods for flood risk analysis that properly incorporate
             terrain uncertainty when reporting what areas are at risk of
             flooding. We present two results. First, we present a linear
             size data structure that given a terrain (with no data
             uncertainty) can answer the flooding query in O(m log 2 n)
             time, where m is the number of minima of the terrain at
             which rain is falling and n is the number of vertices of the
             terrain. Next, we extend this data structure to handle
             “uncertain” terrains, using a standard Monte Carlo
             method. Given a probability distribution on terrains, our
             data structure solves the problem of determining the
             probability that if a specified amount of rain falls on a
             given region a query point is flooded. We implement our data
             structures and show that they work very well in
             practice.},
   Doi = {10.1145/3139958.3139985},
   Key = {fds332953}
}

@article{fds328588,
   Author = {Agarwal, PK and Har-Peled, S and Suri, S and Yıldız, H and Zhang,
             W},
   Title = {Convex Hulls Under Uncertainty},
   Journal = {Algorithmica},
   Volume = {79},
   Number = {2},
   Pages = {340-367},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1007/s00453-016-0195-y},
   Doi = {10.1007/s00453-016-0195-y},
   Key = {fds328588}
}

@article{fds329363,
   Author = {Agarwal, PK and Rubin, N and Sharir, M},
   Title = {Approximate nearest neighbor search amid higher-dimensional
             flats},
   Journal = {Leibniz International Proceedings in Informatics,
             Lipics},
   Volume = {87},
   Year = {2017},
   Month = {September},
   ISBN = {9783959770491},
   url = {http://dx.doi.org/10.4230/LIPIcs.ESA.2017.4},
   Abstract = {© Pankaj K. Agarwal, Natan Rubin, and Micha Sharir. We
             consider the approximate nearest neighbor (ANN) problem
             where the input set consists of n k-flats in the Euclidean
             Rd, for any fixed parameters 0 ≤ k < d, and where, for
             each query point q, we want to return an input flat whose
             distance from q is at most (1 + ϵ) times the shortest such
             distance, where ϵ > 0 is another prespecified parameter. We
             present an algorithm that achieves this task with
             nk+1(log(n)/ ϵ)O(1) storage and preprocessing (where the
             constant of proportionality in the big-O notation depends on
             d), and can answer a query in O(polylog(n)) time (where the
             power of the logarithm depends on d and k). In particular,
             we need only nearquadratic storage to answer ANN queries
             amid a set of n lines in any fixed-dimensional Euclidean
             space. As a by-product, our approach also yields an
             algorithm, with similar performance bounds, for answering
             exact nearest neighbor queries amid k-flats with respect to
             any polyhedral distance function. Our results are more
             general, in that they also provide a tradeoff between
             storage and query time.},
   Doi = {10.4230/LIPIcs.ESA.2017.4},
   Key = {fds329363}
}

@article{fds328996,
   Author = {Agarwal, PK and Kumar, N and Sintos, S and Suri, S},
   Title = {Efficient algorithms for k-regret minimizing
             sets},
   Journal = {Leibniz International Proceedings in Informatics,
             Lipics},
   Volume = {75},
   Year = {2017},
   Month = {August},
   ISBN = {9783959770361},
   url = {http://dx.doi.org/10.4230/LIPIcs.SEA.2017.7},
   Abstract = {© Pankaj K. Agarwal, Nirman Kumar, Stavros Sintos, and
             Subhash Suri. A regret minimizing set Q is a small size
             representation of a much larger database P so that user
             queries executed on Q return answers whose scores are not
             much worse than those on the full dataset. In particular, a
             k-regret minimizing set has the property that the regret
             ratio between the score of the top-1 item in Q and the score
             of the top-k item in P is minimized, where the score of an
             item is the inner product of the item's attributes with a
             user's weight (preference) vector. The problem is
             challenging because we want to find a single representative
             set Q whose regret ratio is small with respect to all
             possible user weight vectors. We show that k-regret
             minimization is NP-Complete for all dimensions d ≥ 3,
             settling an open problem from Chester et al. [VLDB 2014].
             Our main algorithmic contributions are two approximation
             algorithms, both with provable guarantees, one based on
             coresets and another based on hitting sets. We perform
             extensive experimental evaluation of our algorithms, using
             both real-world and synthetic data, and compare their
             performance against the solution proposed in [VLDB 14] . The
             results show that our algorithms are significantly faster
             and scalable to much larger sets than the greedy algorithm
             of Chester et al. for comparable quality
             answers.},
   Doi = {10.4230/LIPIcs.SEA.2017.7},
   Key = {fds328996}
}

@article{fds329182,
   Author = {Agarwal, PK and Fox, K and Panigrahi, D and Varadarajan, KR and Xiao,
             A},
   Title = {Faster algorithms for the geometric transportation
             problem},
   Journal = {Leibniz International Proceedings in Informatics,
             Lipics},
   Volume = {77},
   Pages = {71-716},
   Year = {2017},
   Month = {June},
   ISBN = {9783959770385},
   url = {http://dx.doi.org/10.4230/LIPIcs.SoCG.2017.7},
   Abstract = {© Pankaj K. Agarwal, Kyle Fox, Debmalya Panigrahi, Kasturi
             R. Varadarajan, and Allen Xiao. Let R, B C Rdfor constant d,
             be two point sets with |R| + |B| = n, and let λ: R∪B →
             ℕ such that Σr∈Rλ(r) = Σb∈Bλ (b) be demand
             functions over R and B. Let d(·, ·) be a suitable distance
             function such as the Lpdistance. The transportation problem
             asks to find a map τ: R × B → ℕ such that Σb∈Bτ(r,
             b) = λ(r), Σr∈Rτ(r, b) = λ(b), and σr∈Rb∈Bτ(r,
             b)d(r, b) is minimized. We present three new results for the
             transportation problem when d(·, ·) is any Lpmetric: •
             For any constant ϵ > 0, an O(n1+ϵ) expected time
             randomized algorithm that returns a transportation map with
             expected cost O(log2(1/ϵ)) times the optimal cost. • For
             any ϵ > 0, a (1 + ϵ)-approximation in O(n3/2ϵ-dpolylog(U)
             polylog(n)) time, where U = maxp∈Rcup;Bλ (p). •An exact
             strongly polynomial O(n2polylogn) time algorithm, for d =
             2.},
   Doi = {10.4230/LIPIcs.SoCG.2017.7},
   Key = {fds329182}
}

@article{fds330177,
   Author = {Wu, Y and Agarwal, PK and Li, C and Yang, J and Yu, C},
   Title = {Computational Fact Checking through Query
             Perturbations},
   Journal = {Acm Transactions on Database Systems},
   Volume = {42},
   Number = {1},
   Pages = {1-41},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1145/2996453},
   Doi = {10.1145/2996453},
   Key = {fds330177}
}

@article{fds330829,
   Author = {Wu, Y and Gao, J and Agarwal, PK and Yang, J},
   Title = {Finding diverse, high-value representatives on a surface of
             answers},
   Journal = {Proceedings of the Vldb Endowment},
   Volume = {10},
   Number = {7},
   Pages = {793-804},
   Year = {2017},
   Month = {January},
   Abstract = {© 2017 VLDB Endowment. In many applications, the system
             needs to selectively present a small subset of answers to
             users. The set of all possible answers can be seen as an
             elevation surface over a domain, where the elevation
             measures the quality of each answer, and the dimensions of
             the domain correspond to attributes of the answers with
             which similarity between answers can be measured. This paper
             considers the problem of finding a diverse set of k
             high-quality representatives for such a surface. We show
             that existing methods for diversified top-k and weighted
             clustering problems are inadequate for this problem. We
             propose k-DHR as a better formulation for the problem. We
             show that k-DHR has a submodular and monotone objective
             function, and we develop efficient algorithms for solving
             k-DHR with provable guarantees. We conduct extensive
             experiments to demonstrate the usefulness of the results
             produced by k-DHR for applications in computational
             lead-finding and fact-checking, as well as the efficiency
             and effectiveness of our algorithms.},
   Key = {fds330829}
}

@article{fds330830,
   Author = {Garg, N and Sadiq, M and Agarwal, P},
   Title = {GOASREP: Goal oriented approach for software requirements
             elicitation and prioritization using analytic hierarchy
             process},
   Journal = {Advances in Intelligent Systems and Computing},
   Volume = {516},
   Pages = {281-287},
   Year = {2017},
   Month = {January},
   ISBN = {9789811031557},
   url = {http://dx.doi.org/10.1007/978-981-10-3156-4_28},
   Abstract = {© Springer Nature Singapore Pte Ltd. 2017. Software
             requirements elicitation is a valuable process for the
             identification of software requirements according to the
             need of different types of stake-holders. There are
             different methods for the elicitation of software
             requirements like traditional methods, group elicitation
             methods, goal oriented methods, etc. Among these methods,
             goal oriented methods have received much recognition by
             software requirements engineering community. On the basis of
             our literature review, we identify that “goal oriented
             requirements elicitation processes do not support how to
             select and prioritize the requirements using analytic
             hierarchy process on the basis of the cost and effort
             criteria”. Therefore, in-order to address this issue, we
             proposed a method, i.e. GOASREP, for the elicitation of
             software requirements using “goal oriented approach” and
             the prioritization of the elicited requirements using
             “analytic hierarchy process”. In the proposed method, we
             used function point analysis approach for the estimation of
             the cost of each requirement. COCOMO model has been applied
             to estimate the effort of each requirement. Finally, the
             usage of the GOASREP is explained using Institute
             Examination System.},
   Doi = {10.1007/978-981-10-3156-4_28},
   Key = {fds330830}
}


%% Arlotto, Alessandro   
@article{fds330136,
   Author = {Arlotto, A and Steele, JM},
   Title = {A Central Limit Theorem for Costs in Bulinskaya’s
             Inventory Management Problem When Deliveries Face
             Delays},
   Journal = {Methodology and Computing in Applied Probability},
   Volume = {20},
   Number = {3},
   Pages = {839-854},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1007/s11009-016-9522-7},
   Abstract = {© 2016, Springer Science+Business Media New York. It is
             common in inventory theory to consider policies that
             minimize the expected cost of ordering and holding goods or
             materials. Nevertheless, the realized cost is a random
             variable, and, as the Saint Petersburg Paradox reminds us,
             the expected value does not always capture the full economic
             reality of a decision problem. Here we take the classic
             inventory model of Bulinskaya (Theory of Probability & Its
             Applications, 9, 3, 389–403, 1964), and, by proving an
             appropriate central limit theorem, we show in a reasonably
             rich (and practical) sense that the mean-optimal policies
             are economically appropriate. The motivation and the tools
             are applicable to a large class of Markov decision
             problems.},
   Doi = {10.1007/s11009-016-9522-7},
   Key = {fds330136}
}

@article{fds330134,
   Author = {Arlotto, A and Wei, Y and Xie, X},
   Title = {An adaptive O(log n)-optimal policy for the online selection
             of a monotone subsequence from a random sample},
   Journal = {Random Structures & Algorithms},
   Volume = {52},
   Number = {1},
   Pages = {41-53},
   Publisher = {Wiley},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1002/rsa.20728},
   Abstract = {© 2017 Wiley Periodicals, Inc. Given a sequence of n
             independent random variables with common continuous
             distribution, we propose a simple adaptive online policy
             that selects a monotone increasing subsequence. We show that
             the expected number of monotone increasing selections made
             by such a policy is within (Figure presented.) of optimal.
             Our construction provides a direct and natural way for
             proving the (Figure presented.) -optimality gap. An earlier
             proof of the same result made crucial use of a key
             inequality of Bruss and Delbaen [5] and of
             de-Poissonization.},
   Doi = {10.1002/rsa.20728},
   Key = {fds330134}
}

@article{fds338563,
   Author = {Arlotto, A and Xie, X},
   Title = {Logarithmic regret in the dynamic and stochastic knapsack
             problem.},
   Journal = {Corr},
   Volume = {abs/1809.02016},
   Year = {2018},
   Key = {fds338563}
}

@article{fds330135,
   Author = {Arlotto, A and Frazelle, AE and Wei, Y},
   Title = {Strategic open routing in service networks},
   Journal = {Management Science},
   Publisher = {INFORMS},
   Year = {2018},
   Key = {fds330135}
}

@article{fds330137,
   Author = {Arlotto, A and Gurvich, I},
   Title = {Uniformly bounded regret in the multi-secretary
             problem},
   Year = {2017},
   Month = {October},
   Abstract = {In the secretary problem of Cayley (1875) and Moser (1956),
             $n$ non-negative, independent, random variables with common
             distribution are sequentially presented to a decision maker
             who decides when to stop and collect the most recent
             realization. The goal is to maximize the expected value of
             the collected element. In the $k$-choice variant, the
             decision maker is allowed to make $k \leq n$ selections to
             maximize the expected total value of the selected elements.
             Assuming that the values are drawn from a known distribution
             with finite support, we prove that the best regret---the
             expected gap between the optimal online policy and its
             offline counterpart in which all $n$ values are made visible
             at time $0$---is uniformly bounded in the the number of
             candidates $n$ and the budget $k$. Our proof is
             constructive: we develop an adaptive Budget-Ratio policy
             that achieves this performance. The policy selects or skips
             values depending on where the ratio of the residual budget
             to the remaining time stands relative to multiple thresholds
             that correspond to middle points of the distribution. We
             also prove that being adaptive is crucial: in general, the
             minimal regret among non-adaptive policies grows like the
             square root of $n$. The difference is the value of
             adaptiveness.},
   Key = {fds330137}
}


%% Autry, Eric A.   
@article{fds338506,
   Author = {Autry, EA and Bayliss, A and Volpert, VA},
   Title = {Biological control with nonlocal interactions},
   Journal = {Mathematical Biosciences},
   Volume = {301},
   Pages = {129-146},
   Year = {2018},
   Month = {July},
   url = {http://dx.doi.org/10.1016/j.mbs.2018.05.008},
   Doi = {10.1016/j.mbs.2018.05.008},
   Key = {fds338506}
}

@article{fds338507,
   Author = {Autry, EA and Bayliss, A and Volpert, VA},
   Title = {Traveling waves in a nonlocal, piecewise linear
             reaction–diffusion population model},
   Journal = {Nonlinearity},
   Volume = {30},
   Number = {8},
   Pages = {3304-3331},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1088/1361-6544/aa7b95},
   Doi = {10.1088/1361-6544/aa7b95},
   Key = {fds338507}
}


%% Bendich, Paul L   
@article{fds335533,
   Author = {Garagić, D and Peskoe, J and Liu, F and Claffey, MS and Bendich, P and Hineman, J and Borggren, N and Harer, J and Zulch, P and Rhodes,
             BJ},
   Title = {Upstream fusion of multiple sensing modalities using machine
             learning and topological analysis: An initial
             exploration},
   Journal = {Ieee Aerospace Conference Proceedings},
   Volume = {2018-March},
   Pages = {1-8},
   Year = {2018},
   Month = {June},
   ISBN = {9781538620144},
   url = {http://dx.doi.org/10.1109/AERO.2018.8396737},
   Abstract = {© 2018 IEEE. This paper presents a processing pipeline for
             fusing 'raw' and / or feature-level multi-sensor data -
             upstream fusion - and initial results from this pipeline
             using imagery, radar, and radio frequency (RF) signals data
             to determine which tracked object, among several, hosts an
             emitter of interest. Correctly making this determination
             requires fusing data across these modalities. Our approach
             performs better than standard fusion approaches that make
             detection / characterization decisions for each modality
             individually and then try to fuse those decisions -
             downstream (or post-decision) fusion. Our approach (1) fully
             exploits the inter-modality dependencies and phenomenologies
             inherent in different sensing modes, (2) automatically
             discovers compressive hierarchical representations that
             integrate structural and statistical characteristics to
             enhance target / event discriminability, and (3) completely
             obviates the need to specify features, manifolds, or model
             scope a priori. This approach comprises a unique synthesis
             of Deep Learning (DL), topological analysis over probability
             measure (TAPM), and hierarchical Bayesian non-parametric
             (HBNP) recognition models. Deep Generative Networks (DGNs -
             a deep generative statistical form of DL) create probability
             measures that provide a basis for calculating homologies
             (topological summaries over the probability measures). The
             statistics of the resulting persistence diagrams are inputs
             to HBNP methods that learn to discriminate between target
             types and distinguish emitting targets from non-emitting
             targets, for example. HBNP learning obviates batch-mode
             off-line learning. This approach overcomes the inadequacy of
             pre-defined features as a means for creating efficient,
             discriminating, low-dimensional representations from
             high-dimensional multi-modality sensor data collected under
             difficult, dynamic sensing conditions. The invariant
             properties in the resulting compact representations afford
             multiple compressive sensing benefits, including concise
             information sharing and enhanced performance. Machine
             learning makes adaptivity a central feature of our approach.
             Adaptivity is critical because it enables flexible
             processing that automatically accommodates a broad range of
             challenges that non-adaptive, standard fusion approaches
             would typically require manual intervention to begin to
             address. These include (a) interest in unknown or
             unanticipated targets, (b) desire to be rapidly able to fuse
             between different combinations of sensor modalities, and (c)
             potential need to transfer information between platforms
             that host different sensors. This paper presents results
             that demonstrate our approach enables accurate, real-time
             target detection, tracking, and recognition of known and
             unknown moving or stationary targets or events and their
             activities evolving over space and time.},
   Doi = {10.1109/AERO.2018.8396737},
   Key = {fds335533}
}

@article{fds330929,
   Author = {Tralie, CJ and Smith, A and Borggren, N and Hineman, J and Bendich, P and Zulch, P and Harer, J},
   Title = {Geometric Cross-Modal Comparison of Heterogeneous Sensor
             Data},
   Journal = {Proceedings of the 39th Ieee Aerospace Conference},
   Year = {2018},
   Month = {March},
   Abstract = {In this work, we address the problem of cross-modal
             comparison of aerial data streams. A variety of simulated
             automobile trajectories are sensed using two different
             modalities: full-motion video, and radio-frequency (RF)
             signals received by detectors at various locations. The
             information represented by the two modalities is compared
             using self-similarity matrices (SSMs) corresponding to
             time-ordered point clouds in feature spaces of each of these
             data sources; we note that these feature spaces can be of
             entirely different scale and dimensionality. Several metrics
             for comparing SSMs are explored, including a cutting-edge
             time-warping technique that can simultaneously handle local
             time warping and partial matches, while also controlling for
             the change in geometry between feature spaces of the two
             modalities. We note that this technique is quite general,
             and does not depend on the choice of modalities. In this
             particular setting, we demonstrate that the cross-modal
             distance between SSMs corresponding to the same trajectory
             type is smaller than the cross-modal distance between SSMs
             corresponding to distinct trajectory types, and we formalize
             this observation via precision-recall metrics in
             experiments. Finally, we comment on promising implications
             of these ideas for future integration into
             multiple-hypothesis tracking systems.},
   Key = {fds330929}
}


%% Bertozzi, Andrea L   
@booklet{Greer04a,
   Author = {J. B. Greer and A. L. Bertozzi},
   Title = {H-1 solutions of a class of fourth order nonlinear equations
             for image processing},
   Journal = {Discrete And Continuous Dynamical Systems},
   Volume = {10},
   Number = {1-2},
   Pages = {349 -- 366},
   Year = {2004},
   Key = {Greer04a}
}


%% Bray, Hubert   
@article{fds330841,
   Author = {Bray, H and Roesch, H},
   Title = {Proof of a Null Geometry Penrose Conjecture},
   Journal = {Notices of the American Mathematical Society.},
   Volume = {65},
   Publisher = {American Mathematical Society},
   Year = {2018},
   Month = {February},
   Key = {fds330841}
}


%% Bryant, Robert   
@article{fds325462,
   Author = {Bryant, R and Huang, L and Mo, X},
   Title = {On Finsler surfaces of constant flag curvature with a
             Killing field},
   Journal = {Journal of Geometry and Physics},
   Volume = {116},
   Pages = {345-357},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.geomphys.2017.02.012},
   Doi = {10.1016/j.geomphys.2017.02.012},
   Key = {fds325462}
}


%% Calderbank, Robert   
@article{fds335321,
   Author = {Thompson, A and Calderbank, R},
   Title = {Sparse near-equiangular tight frames with applications in
             full duplex wireless communication},
   Journal = {2017 Ieee Global Conference on Signal and Information
             Processing, Globalsip 2017 Proceedings},
   Volume = {2018-January},
   Pages = {868-872},
   Year = {2018},
   Month = {March},
   ISBN = {9781509059904},
   url = {http://dx.doi.org/10.1109/GlobalSIP.2017.8309084},
   Abstract = {© 2017 IEEE. We construct extremely sparse,
             near-equiangular tight frames which share the same row space
             as certain incomplete Delsarte-Goethals frames. Frames
             combining these properties have application in full duplex
             communication in ad-hoc wireless networks. We highlight
             their computational advantage over similar constructions of
             sparse equiangular tight frames: namely that their
             associated matrix-vector products can be implemented as a
             fast transform.},
   Doi = {10.1109/GlobalSIP.2017.8309084},
   Key = {fds335321}
}

@article{fds335322,
   Author = {Mappouras, G and Vahid, A and Calderbank, R and Hower, DR and Sorin,
             DJ},
   Title = {Jenga: Efficient fault tolerance for stacked
             DRAM},
   Journal = {Proceedings - 35th IEEE International Conference on Computer
             Design, ICCD 2017},
   Pages = {361-368},
   Year = {2017},
   Month = {November},
   ISBN = {9781538622544},
   url = {http://dx.doi.org/10.1109/ICCD.2017.62},
   Abstract = {© 2017 IEEE. In this paper, we introduce Jenga, a new
             scheme for protecting 3D DRAM, specifically high bandwidth
             memory (HBM), from failures in bits, rows, banks, channels,
             dies, and TSVs. By providing redundancy at the granularity
             of a cache block rather than across blocks, as in the
             current state of the art Jenga achieves greater error-free
             performance and lower error recovery latency. We show that
             Jenga's runtime is on average only 1.03 the runtime of our
             Baseline across a range of benchmarks. Additionally, for
             memory intensive benchmarks, Jenga is on average 1.11 faster
             than prior work.},
   Doi = {10.1109/ICCD.2017.62},
   Key = {fds335322}
}

@article{fds335323,
   Author = {Kadhe, S and Calderbank, R},
   Title = {Rate optimal binary linear locally repairable codes with
             small availability},
   Journal = {Ieee International Symposium on Information Theory
             Proceedings},
   Pages = {166-170},
   Year = {2017},
   Month = {August},
   ISBN = {9781509040964},
   url = {http://dx.doi.org/10.1109/ISIT.2017.8006511},
   Abstract = {© 2017 IEEE. A locally repairable code with availability
             has the property that every code symbol can be recovered
             from multiple, disjoint subsets of other symbols of small
             size. In particular, a code symbol is said to have (r,
             t)-availability if it can be recovered from t disjoint
             subsets, each of size at most r. A code with availability is
             said to be rate optimal, if its rate is maximum among the
             class of codes with given locality, availability, and
             alphabet size. This paper focuses on rate-optimal binary,
             linear codes with small availability, and makes three
             contributions. First, it establishes tight upper bounds on
             the rate of binary linear codes with (r, 2) and (2, 3)
             availability. Second, it establishes a uniqueness result for
             binary rate-optimal codes, showing that for certain classes
             of binary linear codes with (r, 2) and (2, 3)-availability,
             any rate-optimal code must be a direct sum of shorter
             rateoptimal codes. Finally, it presents a class of locally
             repairable codes associated with convex polyhedra,
             especially, focusing on the codes associated with the
             Platonic solids. It demonstrates that these codes are
             locally repairable with t = 2, and that the codes associated
             with (geometric) dual polyhedra are (coding theoretic) duals
             of each other.},
   Doi = {10.1109/ISIT.2017.8006511},
   Key = {fds335323}
}

@article{fds335324,
   Author = {Michelusi, N and Nokleby, M and Mitra, U and Calderbank,
             R},
   Title = {Multi-scale spectrum sensing in small-cell mm-wave cognitive
             wireless networks},
   Journal = {Ieee International Conference on Communications},
   Year = {2017},
   Month = {July},
   ISBN = {9781467389990},
   url = {http://dx.doi.org/10.1109/ICC.2017.7996657},
   Abstract = {© 2017 IEEE. In this paper, a multi-scale approach to
             spectrum sensing in cognitive cellular networks is proposed.
             In order to overcome the huge cost incurred in the
             acquisition of full network state information, a
             hierarchical scheme is proposed, based on which local state
             estimates are aggregated up the hierarchy to obtain
             aggregate state information at multiple scales, which are
             then sent back to each cell for local decision making. Thus,
             each cell obtains fine-grained estimates of the channel
             occupancies of nearby cells, but coarse-grained estimates of
             those of distant cells. The performance of the aggregation
             scheme is studied in terms of the trade-off between the
             throughput achievable by secondary users and the
             interference generated by the activity of these secondary
             users to primary users. In order to account for the
             irregular structure of interference patterns arising from
             path loss, shadowing, and blockages, which are especially
             relevant in millimeter wave networks, a greedy algorithm is
             proposed to find a multi-scale aggregation tree to optimize
             the performance. It is shown numerically that this tailored
             hierarchy outperforms a regular tree construction by
             60%.},
   Doi = {10.1109/ICC.2017.7996657},
   Key = {fds335324}
}

@article{fds332945,
   Author = {Cnaan-On, I and Harms, A and Krolik, JL and Calderbank,
             AR},
   Title = {Run-length limited codes for backscatter
             communication},
   Journal = {2015 Ieee International Conference on Acoustics, Speech, and
             Signal Processing (Icassp)},
   Pages = {6110-6114},
   Year = {2017},
   Month = {June},
   ISBN = {9781509041176},
   url = {http://dx.doi.org/10.1109/ICASSP.2017.7953330},
   Abstract = {© 2017 IEEE. In backscatter communications, ultra-low power
             devices signal by modulating the reflection of radio
             frequency signals emitted from an external source. Unlike
             conventional one-way communication, the backscatter channel
             experiences unique self-interference and spread Doppler
             clutter. Run-length limited (RLL) codes provide a method for
             spectrum shaping that requires no hardware changes to the
             communicating devices. The proposed coding framework is
             suitable for any arbitrarily-shaped pulse train or
             continuous wave reader waveform. It exploits the unique
             channel Doppler spread statistics to offer a trade-off
             between interference rejection and data rate. Analysis shows
             that code rates of 1 and 4/5 are achievable when dealing
             with low spread Doppler channels, which is an improvement
             over the current rate 1/2 with current mainstream
             backscatter communication techniques. Simulation results
             with realistic channel assumptions are analyzed and
             discussed to confirm the theoretical analysis.},
   Doi = {10.1109/ICASSP.2017.7953330},
   Key = {fds332945}
}

@article{fds326748,
   Author = {Wang, L and Chen, M and Rodrigues, M and Wilcox, D and Calderbank, R and Carin, L},
   Title = {Information-Theoretic Compressive Measurement
             Design.},
   Journal = {Ieee Transactions on Pattern Analysis and Machine
             Intelligence},
   Volume = {39},
   Number = {6},
   Pages = {1150-1164},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1109/tpami.2016.2568189},
   Abstract = {An information-theoretic projection design framework is
             proposed, of interest for feature design and compressive
             measurements. Both Gaussian and Poisson measurement models
             are considered. The gradient of a proposed
             information-theoretic metric (ITM) is derived, and a
             gradient-descent algorithm is applied in design; connections
             are made to the information bottleneck. The fundamental
             solution structure of such design is revealed in the case of
             a Gaussian measurement model and arbitrary input statistics.
             This new theoretical result reveals how ITM parameter
             settings impact the number of needed projection
             measurements, with this verified experimentally. The ITM
             achieves promising results on real data, for both signal
             recovery and classification.},
   Doi = {10.1109/tpami.2016.2568189},
   Key = {fds326748}
}

@article{fds326881,
   Author = {Hadani, R and Rakib, S and Tsatsanis, M and Monk, A and Goldsmith, AJ and Molisch, AF and Calderbank, R},
   Title = {Orthogonal time frequency space modulation},
   Journal = {Ieee Wireless Communications and Networking Conference,
             Wcnc},
   Year = {2017},
   Month = {May},
   ISBN = {9781509041831},
   url = {http://dx.doi.org/10.1109/WCNC.2017.7925924},
   Abstract = {© 2017 IEEE. A new two-dimensional modulation technique
             called Orthogonal Time Frequency Space (OTFS) modulation
             designed in the delay-Doppler domain is introduced. Through
             this design, which exploits full diversity over time and
             frequency, OTFS coupled with equalization converts the
             fading, time-varying wireless channel experienced by
             modulated signals such as OFDM into a time-independent
             channel with a complex channel gain that is roughly constant
             for all symbols. Thus, transmitter adaptation is not needed.
             This extraction of the full channel diversity allows OTFS to
             greatly simplify system operation and significantly improves
             performance, particular in systems with high Doppler, short
             packets, and large antenna arrays. Simulation results
             indicate at least several dB of block error rate performance
             improvement for OTFS over OFDM in all of these settings. In
             addition these results show that even at very high Dopplers
             (500 km/h), OTFS approaches channel capacity through linear
             scaling of throughput with the MIMO order, whereas the
             performance of OFDM under typical design parameters breaks
             down completely.},
   Doi = {10.1109/WCNC.2017.7925924},
   Key = {fds326881}
}

@article{fds326749,
   Author = {Campbell, K and Carpenter, KLH and Espinosa, S and Hashemi, J and Qiu,
             Q and Tepper, M and Calderbank, R and Sapiro, G and Egger, HL and Baker,
             JP and Dawson, G},
   Title = {Use of a Digital Modified Checklist for Autism in Toddlers -
             Revised with Follow-up to Improve Quality of Screening for
             Autism.},
   Journal = {The Journal of Pediatrics},
   Volume = {183},
   Pages = {133-139.e1},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1016/j.jpeds.2017.01.021},
   Abstract = {OBJECTIVES:To assess changes in quality of care for children
             at risk for autism spectrum disorders (ASD) due to process
             improvement and implementation of a digital screening form.
             STUDY DESIGN:The process of screening for ASD was studied in
             an academic primary care pediatrics clinic before and after
             implementation of a digital version of the Modified
             Checklist for Autism in Toddlers - Revised with Follow-up
             with automated risk assessment. Quality metrics included
             accuracy of documentation of screening results and
             appropriate action for positive screens (secondary screening
             or referral). Participating physicians completed pre- and
             postintervention surveys to measure changes in attitudes
             toward feasibility and value of screening for ASD. Evidence
             of change was evaluated with statistical process control
             charts and χ2 tests. RESULTS:Accurate documentation in the
             electronic health record of screening results increased from
             54% to 92% (38% increase, 95% CI 14%-64%) and appropriate
             action for children screening positive increased from 25% to
             85% (60% increase, 95% CI 35%-85%). A total of 90% of
             participating physicians agreed that the transition to a
             digital screening form improved their clinical assessment of
             autism risk. CONCLUSIONS:Implementation of a tablet-based
             digital version of the Modified Checklist for Autism in
             Toddlers - Revised with Follow-up led to improved quality of
             care for children at risk for ASD and increased
             acceptability of screening for ASD. Continued efforts
             towards improving the process of screening for ASD could
             facilitate rapid, early diagnosis of ASD and advance the
             accuracy of studies of the impact of screening.},
   Doi = {10.1016/j.jpeds.2017.01.021},
   Key = {fds326749}
}


%% Cheng, Cheng   
@article{fds330512,
   Author = {Cheng, C and Jiang, Y and Sun, Q},
   Title = {Spatially distributed sampling and reconstruction},
   Journal = {Applied and Computational Harmonic Analysis},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1016/j.acha.2017.07.007},
   Doi = {10.1016/j.acha.2017.07.007},
   Key = {fds330512}
}

@article{fds330513,
   Author = {Li, L and Cheng, C and Han, D and Sun, Q and Shi, G},
   Title = {Phase Retrieval From Multiple-Window Short-Time Fourier
             Measurements},
   Journal = {Ieee Signal Processing Letters},
   Volume = {24},
   Number = {4},
   Pages = {372-376},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1109/LSP.2017.2663668},
   Doi = {10.1109/LSP.2017.2663668},
   Key = {fds330513}
}


%% Cheng, Xiuyuan   
@article{fds339535,
   Author = {Cheng, X and Rachh, M and Steinerberger, S},
   Title = {On the diffusion geometry of graph laplacians and
             applications},
   Journal = {Applied and Computational Harmonic Analysis},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1016/j.acha.2018.04.001},
   Doi = {10.1016/j.acha.2018.04.001},
   Key = {fds339535}
}

@article{fds330801,
   Author = {Cheng, X and Mishne, G and Steinerberger, S},
   Title = {The geometry of nodal sets and outlier detection},
   Journal = {Journal of Number Theory},
   Volume = {185},
   Pages = {48-64},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1016/j.jnt.2017.09.021},
   Doi = {10.1016/j.jnt.2017.09.021},
   Key = {fds330801}
}

@article{fds339536,
   Author = {Qiu, Q and Cheng, X and Calderbank, AR and Sapiro,
             G},
   Title = {DCFNet: Deep Neural Network with Decomposed Convolutional
             Filters.},
   Journal = {Icml},
   Volume = {80},
   Pages = {4195-4204},
   Publisher = {JMLR.org},
   Editor = {Dy, JG and Krause, A},
   Year = {2018},
   Key = {fds339536}
}

@article{fds330800,
   Author = {Lu, J and Lu, Y and Wang, X and Li, X and Linderman, GC and Wu, C and Cheng,
             X and Mu, L and Zhang, H and Liu, J and Su, M and Zhao, H and Spatz, ES and Spertus, JA and Masoudi, FA and Krumholz, HM and Jiang,
             L},
   Title = {Prevalence, awareness, treatment, and control of
             hypertension in China: data from 1·7 million adults in a
             population-based screening study (China PEACE Million
             Persons Project)},
   Journal = {Lancet (London, England)},
   Volume = {390},
   Number = {10112},
   Pages = {2549-2558},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1016/S0140-6736(17)32478-9},
   Doi = {10.1016/S0140-6736(17)32478-9},
   Key = {fds330800}
}


%% Dasgupta, Samit   
@article{fds339636,
   Author = {Dasgupta, S and Kakde, M and Ventullo, K},
   Title = {On the Gross-Stark Conjecture},
   Journal = {Annals of Mathematics},
   Volume = {188},
   Number = {3},
   Pages = {833-870},
   Year = {2018},
   Month = {November},
   url = {http://dx.doi.org/10.4007/annals.2018.188.3.3},
   Abstract = {© 2018 Department of Mathematics, Princeton University. In
             1980, Gross conjectured a formula for the expected leading
             term at s=0 of the Deligne-Ribet p-adic L-function
             associated to a totally even character ϕ of a totally real
             field F. The conjecture states that after scaling by
             L(ϕω-1,0), this value is equal to a p-adic regulator of
             units in the abelian extension of F cut out by ϕω-1. In
             this paper, we prove Gross's conjecture.},
   Doi = {10.4007/annals.2018.188.3.3},
   Key = {fds339636}
}

@article{fds338508,
   Author = {Dasgupta, S and Voight, J},
   Title = {Sylvester’s problem and mock Heegner points},
   Journal = {Proceedings of the American Mathematical
             Society},
   Volume = {146},
   Number = {8},
   Pages = {3257-3273},
   Year = {2018},
   Month = {March},
   url = {http://dx.doi.org/10.1090/proc/14008},
   Doi = {10.1090/proc/14008},
   Key = {fds338508}
}

@article{fds339289,
   Author = {Dasgupta, S and Spieß, M},
   Title = {Partial zeta values, Gross's tower of fields conjecture, and
             Gross-Stark units},
   Journal = {Journal of the European Mathematical Society},
   Volume = {20},
   Number = {11},
   Pages = {2643-2683},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.4171/JEMS/821},
   Abstract = {© European Mathematical Society 2018. We prove a conjecture
             of Gross regarding the “order of vanishing” of
             Stickelberger elements relative to an abelian tower of
             fields and give a cohomological construction of the
             conjectural Gross-Stark units. This is achieved by
             introducing an integral version of the Eisenstein
             cocycle.},
   Doi = {10.4171/JEMS/821},
   Key = {fds339289}
}


%% Daubechies, Ingrid   
@article{fds329931,
   Author = {Gao, T and Yapuncich, GS and Daubechies, I and Mukherjee, S and Boyer,
             DM},
   Title = {Development and Assessment of Fully Automated and Globally
             Transitive Geometric Morphometric Methods, With Application
             to a Biological Comparative Dataset With High Interspecific
             Variation.},
   Journal = {Anatomical Record (Hoboken, N.J. : 2007)},
   Volume = {301},
   Number = {4},
   Pages = {636-658},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1002/ar.23700},
   Abstract = {Automated geometric morphometric methods are promising tools
             for shape analysis in comparative biology, improving
             researchers' abilities to quantify variation extensively (by
             permitting more specimens to be analyzed) and intensively
             (by characterizing shapes with greater fidelity). Although
             use of these methods has increased, published automated
             methods have some notable limitations: pairwise
             correspondences are frequently inaccurate and pairwise
             mappings are not globally consistent (i.e., they lack
             transitivity across the full sample). Here, we reassess the
             accuracy of published automated methods-cPDist (Boyer et al.
             Proc Nat Acad Sci 108 () 18221-18226) and auto3Dgm (Boyer et
             al.: Anat Rec 298 () 249-276)-and evaluate several
             modifications to these methods. We show that a substantial
             percentage of alignments and pairwise maps between specimens
             of dissimilar geometries were inaccurate in the study of
             Boyer et al. (Proc Nat Acad Sci 108 () 18221-18226), despite
             a taxonomically partitioned variance structure of continuous
             Procrustes distances. We show these inaccuracies are
             remedied using a globally informed methodology within a
             collection of shapes, rather than relying on pairwise
             comparisons (c.f. Boyer et al.: Anat Rec 298 () 249-276).
             Unfortunately, while global information generally enhances
             maps between dissimilar objects, it can degrade the quality
             of correspondences between similar objects due to the
             accumulation of numerical error. We explore a number of
             approaches to mitigate this degradation, quantify their
             performance, and compare the generated pairwise maps (and
             the shape space characterized by these maps) to a "ground
             truth" obtained from landmarks manually collected by
             geometric morphometricians. Novel methods both improve the
             quality of the pairwise correspondences relative to cPDist
             and achieve a taxonomic distinctiveness comparable to
             auto3Dgm. Anat Rec, 301:636-658, 2018. © 2017 Wiley
             Periodicals, Inc.},
   Doi = {10.1002/ar.23700},
   Key = {fds329931}
}

@article{fds333315,
   Author = {Xu, J and Yang, H and Daubechies, I},
   Title = {Recursive diffeomorphism-based regression for shape
             functions},
   Journal = {Siam Journal on Mathematical Analysis},
   Volume = {50},
   Number = {1},
   Pages = {5-32},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1097535},
   Abstract = {© 2018 Society for Industrial and Applied Mathematics. This
             paper proposes a recursive diffeomorphism-based regression
             method for the one-dimensional generalized mode
             decomposition problem that aims at extracting generalized
             modes α k (t)s k (2πN k φ k (t)) from their superposition
             K k =1 α k (t)s k (2πN k φ k (t)). We assume that the
             instantaneous information, e.g., α k (t) and N k φ k (t),
             is determined by, e.g., a one-dimensional synchrosqueezed
             transform or some other methods. Our main contribution is to
             propose a novel approach based on diffeomorphisms and
             nonparametric regression to estimate wave shape functions s
             k (t). This leads to a framework for the generalized mode
             decomposition problem under a weak well-separation
             condition. Numerical examples of synthetic and real data are
             provided to demonstrate the successful application of our
             approach.},
   Doi = {10.1137/16M1097535},
   Key = {fds333315}
}

@article{fds339576,
   Author = {Alaifari, R and Daubechies, I and Grohs, P and Yin,
             R},
   Title = {Stable Phase Retrieval in Infinite Dimensions},
   Journal = {Foundations of Computational Mathematics},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1007/s10208-018-9399-7},
   Abstract = {© 2018, The Author(s). The problem of phase retrieval is to
             determine a signal f∈ H, with H a Hilbert space, from
             intensity measurements | F(ω) | , where F(ω) : = ⟨ f,
             φω⟩ are measurements of f with respect to a measurement
             system (φω)ω∈Ω⊂H. Although phase retrieval is always
             stable in the finite-dimensional setting whenever it is
             possible (i.e. injectivity implies stability for the inverse
             problem), the situation is drastically different if H is
             infinite-dimensional: in that case phase retrieval is never
             uniformly stable (Alaifari and Grohs in SIAM J Math Anal
             49(3):1895–1911, 2017; Cahill et al. in Trans Am Math Soc
             Ser B 3(3):63–76, 2016); moreover, the stability
             deteriorates severely in the dimension of the problem
             (Cahill et al. 2016). On the other hand, all empirically
             observed instabilities are of a certain type: they occur
             whenever the function |F| of intensity measurements is
             concentrated on disjoint sets Dj⊂ Ω , i.e. when
             F=∑j=1kFj where each Fj is concentrated on Dj (and k≥
             2). Motivated by these considerations, we propose a new
             paradigm for stable phase retrieval by considering the
             problem of reconstructing F up to a phase factor that is not
             global, but that can be different for each of the subsets
             Dj, i.e. recovering F up to the equivalence
             F∼∑j=1keiαjFj.We present concrete applications (for
             example in audio processing) where this new notion of
             stability is natural and meaningful and show that in this
             setting stable phase retrieval can actually be achieved, for
             instance, if the measurement system is a Gabor frame or a
             frame of Cauchy wavelets.},
   Doi = {10.1007/s10208-018-9399-7},
   Key = {fds339576}
}

@article{fds332858,
   Author = {Alaifari, R and Daubechies, I and Grohs, P and Thakur,
             G},
   Title = {Reconstructing Real-Valued Functions from Unsigned
             Coefficients with Respect to Wavelet and Other
             Frames},
   Journal = {Journal of Fourier Analysis and Applications},
   Volume = {23},
   Number = {6},
   Pages = {1480-1494},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1007/s00041-016-9513-7},
   Doi = {10.1007/s00041-016-9513-7},
   Key = {fds332858}
}

@article{fds325388,
   Author = {Deligiannis, N and Mota, JFC and Cornelis, B and Rodrigues, MRD and Daubechies, I},
   Title = {Multi-Modal Dictionary Learning for Image Separation With
             Application in Art Investigation.},
   Journal = {Ieee Transactions on Image Processing : a Publication of the
             Ieee Signal Processing Society},
   Volume = {26},
   Number = {2},
   Pages = {751-764},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1109/tip.2016.2623484},
   Abstract = {In support of art investigation, we propose a new source
             separation method that unmixes a single X-ray scan acquired
             from double-sided paintings. In this problem, the X-ray
             signals to be separated have similar morphological
             characteristics, which brings previous source separation
             methods to their limits. Our solution is to use photographs
             taken from the front-and back-side of the panel to drive the
             separation process. The crux of our approach relies on the
             coupling of the two imaging modalities (photographs and
             X-rays) using a novel coupled dictionary learning framework
             able to capture both common and disparate features across
             the modalities using parsimonious representations; the
             common component captures features shared by the multi-modal
             images, whereas the innovation component captures
             modality-specific information. As such, our model enables
             the formulation of appropriately regularized convex
             optimization procedures that lead to the accurate separation
             of the X-rays. Our dictionary learning framework can be
             tailored both to a single- and a multi-scale framework, with
             the latter leading to a significant performance improvement.
             Moreover, to improve further on the visual quality of the
             separated images, we propose to train coupled dictionaries
             that ignore certain parts of the painting corresponding to
             craquelure. Experimentation on synthetic and real data -
             taken from digital acquisition of the Ghent Altarpiece
             (1432) - confirms the superiority of our method against the
             state-of-the-art morphological component analysis technique
             that uses either fixed or trained dictionaries to perform
             image separation.},
   Doi = {10.1109/tip.2016.2623484},
   Key = {fds325388}
}

@article{fds324089,
   Author = {Cornelis, B and Yang, H and Goodfriend, A and Ocon, N and Lu, J and Daubechies, I},
   Title = {Removal of Canvas Patterns in Digital Acquisitions of
             Paintings.},
   Journal = {Ieee Transactions on Image Processing : a Publication of the
             Ieee Signal Processing Society},
   Volume = {26},
   Number = {1},
   Pages = {160-171},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1109/tip.2016.2621413},
   Abstract = {We address the removal of canvas artifacts from
             high-resolution digital photographs and X-ray images of
             paintings on canvas. Both imaging modalities are common
             investigative tools in art history and art conservation.
             Canvas artifacts manifest themselves very differently
             according to the acquisition modality; they can hamper the
             visual reading of the painting by art experts, for instance,
             in preparing a restoration campaign. Computer-aided canvas
             removal is desirable for restorers when the painting on
             canvas they are preparing to restore has acquired over the
             years a much more salient texture. We propose a new
             algorithm that combines a cartoon-texture decomposition
             method with adaptive multiscale thresholding in the
             frequency domain to isolate and suppress the canvas
             components. To illustrate the strength of the proposed
             method, we provide various examples, for acquisitions in
             both imaging modalities, for paintings with different types
             of canvas and from different periods. The proposed algorithm
             outperforms previous methods proposed for visual photographs
             such as morphological component analysis and Wiener
             filtering and it also works for the digital removal of
             canvas artifacts in X-ray images.},
   Doi = {10.1109/tip.2016.2621413},
   Key = {fds324089}
}

@article{fds329099,
   Author = {Voronin, S and Daubechies, I},
   Title = {An iteratively reweighted least squares algorithm for sparse
             regularization},
   Volume = {693},
   Pages = {391-411},
   Booktitle = {Contemporary Mathematics},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1090/conm/693/13941},
   Abstract = {© 2017 by the authors. We present a new algorithm and the
             corresponding convergence analysis for the regularization of
             linear inverse problems with sparsity constraints, applied
             to a new generalized sparsity promoting functional. The
             algorithm is based on the idea of iteratively reweighted
             least squares, reducing the minimization at every iteration
             step to that of a functional including only ℓ 2 -norms.
             This amounts to smoothing of the absolute value function
             that appears in the generalized sparsity promoting penalty
             we consider, with the smoothing becoming iteratively less
             pronounced. We demonstrate that the sequence of iterates of
             our algorithm converges to a limit that minimizes the
             original functional.},
   Doi = {10.1090/conm/693/13941},
   Key = {fds329099}
}

@article{fds327595,
   Author = {Yin, R and Gao, T and Lu, YM and Daubechies, I},
   Title = {A Tale of Two Bases: Local-Nonlocal Regularization on Image
             Patches with Convolution Framelets},
   Journal = {Siam Journal on Imaging Sciences},
   Volume = {10},
   Number = {2},
   Pages = {711-750},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1091447},
   Doi = {10.1137/16M1091447},
   Key = {fds327595}
}

@article{fds328056,
   Author = {Fodor, G and Cornelis, B and Yin, R and Dooms, A and Daubechies,
             I},
   Title = {Cradle Removal in X-Ray Images of Panel Paintings},
   Journal = {Image Processing On Line},
   Volume = {7},
   Pages = {23-42},
   Year = {2017},
   url = {http://dx.doi.org/10.5201/ipol.2017.174},
   Doi = {10.5201/ipol.2017.174},
   Key = {fds328056}
}


%% Dolbow, John E.   
@article{fds337737,
   Author = {Peco, C and Liu, Y and Rhea, C and Dolbow, JE},
   Title = {Models and simulations of surfactant-driven fracture in
             particle rafts},
   Journal = {International Journal of Solids and Structures},
   Volume = {156-157},
   Pages = {194-209},
   Year = {2019},
   Month = {January},
   url = {http://dx.doi.org/10.1016/j.ijsolstr.2018.08.014},
   Abstract = {© 2018 Elsevier Ltd A continuum-based model for the
             surfactant-driven fracture of closely-packed particle rafts
             is extended to examine the influence of micro-scale density
             variability. The model treats the particle monolayer as an
             elastic sheet endowed with a critical fracture energy that
             can be reduced through interaction with a flowing
             surfactant. In addition to the displacement of the
             monolayer, the model employs a surfactant damage field that
             serves as both an indicator function for the surfactant
             concentration as well as the damage to the monolayer.
             Spatial variability in the particle packing is incorporated
             in the model through a continuum mapping approach. The
             formulation gives rise to a coupled system of nonlinear
             partial differential equations with an irreversibility
             constraint. The evolution equations are recast in
             variational form and discretized with an adaptive finite
             element method. Simulations are provided to demonstrate
             convergence of the model, illustrate the sensitivity of the
             fracture process to variations in the initial packing
             fraction field, and make comparisons with experimental
             observations. The results indicate that crack bifurcations
             can occur in regions with spatially uniform packing as well
             as spatially variable packing, suggesting that both the
             macro-scale mechanics and the random aspects of the packing
             contribute to these instabilities. The model is also used to
             predict the response of these systems to multiple injection
             sources and obstacles in the domains. Finally, the model is
             extended to non-planar surfaces as a means to study systems
             in which confinement and jamming can only occur due to
             multiple injection sites.},
   Doi = {10.1016/j.ijsolstr.2018.08.014},
   Key = {fds337737}
}

@article{fds332774,
   Author = {Zhang, Z and Jiang, W and Dolbow, JE and Spencer,
             BW},
   Title = {A modified moment-fitted integration scheme for X-FEM
             applications with history-dependent material
             data},
   Journal = {Computational Mechanics},
   Volume = {62},
   Number = {2},
   Pages = {233-252},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1007/s00466-018-1544-2},
   Abstract = {© 2018 Springer-Verlag GmbH Germany, part of Springer
             Nature We present a strategy for the numerical integration
             of partial elements with the eXtended finite element method
             (X-FEM). The new strategy is specifically designed for
             problems with propagating cracks through a bulk material
             that exhibits inelasticity. Following a standard approach
             with the X-FEM, as the crack propagates new partial elements
             are created. We examine quadrature rules that have
             sufficient accuracy to calculate stiffness matrices
             regardless of the orientation of the crack with respect to
             the element. This permits the number of integration points
             within elements to remain constant as a crack propagates,
             and for state data to be easily transferred between
             successive discretizations. In order to maintain weights
             that are strictly positive, we propose an approach that
             blends moment-fitted weights with volume-fraction based
             weights. To demonstrate the efficacy of this simple
             approach, we present results from numerical tests and
             examples with both elastic and plastic material
             response.},
   Doi = {10.1007/s00466-018-1544-2},
   Key = {fds332774}
}

@article{fds329137,
   Author = {Peco, C and Chen, W and Liu, Y and Bandi, MM and Dolbow, JE and Fried,
             E},
   Title = {Influence of surface tension in the surfactant-driven
             fracture of closely-packed particulate monolayers.},
   Journal = {Soft Matter},
   Volume = {13},
   Number = {35},
   Pages = {5832-5841},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1039/c7sm01245d},
   Abstract = {A phase-field model is used to capture the surfactant-driven
             formation of fracture patterns in particulate monolayers.
             The model is intended for the regime of closely-packed
             systems in which the mechanical response of the monolayer
             can be approximated as that of a linearly elastic solid. The
             model approximates the loss in tensile strength of the
             monolayer with increasing surfactant concentration through
             the evolution of a damage field. Initial-boundary value
             problems are constructed and spatially discretized with
             finite element approximations to the displacement and
             surfactant damage fields. A comparison between model-based
             simulations and existing experimental observations indicates
             a qualitative match in both the fracture patterns and
             temporal scaling of the fracture process. The importance of
             surface tension differences is quantified by means of a
             dimensionless parameter, revealing thresholds that separate
             different regimes of fracture. These findings are supported
             by newly performed experiments that validate the model and
             demonstrate the strong sensitivity of the fracture pattern
             to differences in surface tension.},
   Doi = {10.1039/c7sm01245d},
   Key = {fds329137}
}

@article{fds322100,
   Author = {Zhang, Z and Dolbow, JE},
   Title = {Remeshing strategies for large deformation problems with
             frictional contact and nearly incompressible
             materials},
   Journal = {International Journal for Numerical Methods in
             Engineering},
   Volume = {109},
   Number = {9},
   Pages = {1289-1314},
   Year = {2017},
   Month = {March},
   url = {http://dx.doi.org/10.1002/nme.5325},
   Doi = {10.1002/nme.5325},
   Key = {fds322100}
}

@article{fds323719,
   Author = {Stershic, AJ and Dolbow, JE and Moës, N},
   Title = {The Thick Level-Set model for dynamic fragmentation},
   Journal = {Engineering Fracture Mechanics},
   Volume = {172},
   Pages = {39-60},
   Year = {2017},
   Month = {March},
   url = {http://dx.doi.org/10.1016/j.engfracmech.2016.12.012},
   Doi = {10.1016/j.engfracmech.2016.12.012},
   Key = {fds323719}
}


%% Dunson, David B.   
@article{fds338057,
   Author = {Srivastava, S and Li, C and Dunson, DB},
   Title = {Scalable Bayes via barycenter in Wasserstein
             space},
   Journal = {Journal of Machine Learning Research},
   Volume = {19},
   Pages = {1-35},
   Year = {2018},
   Month = {August},
   Abstract = {© 2018 Sanvesh Srivastava, Cheng Li and David B. Dunson.
             Divide-and-conquer based methods for Bayesian inference
             provide a general approach for tractable posterior inference
             when the sample size is large. These methods divide the data
             into smaller subsets, sample from the posterior distribution
             of parameters in parallel on all the subsets, and combine
             posterior samples from all the subsets to approximate the
             full data posterior distribution. The smaller size of any
             subset compared to the full data implies that posterior
             sampling on any subset is computationally more efficient
             than sampling from the true posterior distribution. Since
             the combination step takes negligible time relative to
             sampling, posterior computations can be scaled to massive
             data by dividing the full data into sufficiently large
             number of data subsets. One such approach relies on the
             geometry of posterior distributions estimated across
             different subsets and combines them through their barycenter
             in a Wasserstein space of probability measures. We provide
             theoretical guarantees on the accuracy of approximation that
             are valid in many applications. We show that the geometric
             method approximates the full data posterior distribution
             better than its competitors across diverse simulations and
             reproduces known results when applied to a movie ratings
             database.},
   Key = {fds338057}
}

@article{fds339365,
   Author = {van den Boom, W and Mao, C and Schroeder, RA and Dunson,
             DB},
   Title = {Extrema-weighted feature extraction for functional
             data.},
   Journal = {Bioinformatics (Oxford, England)},
   Volume = {34},
   Number = {14},
   Pages = {2457-2464},
   Year = {2018},
   Month = {July},
   url = {http://dx.doi.org/10.1093/bioinformatics/bty120},
   Abstract = {Although there is a rich literature on methods for assessing
             the impact of functional predictors, the focus has been on
             approaches for dimension reduction that do not suit certain
             applications. Examples of standard approaches include
             functional linear models, functional principal components
             regression and cluster-based approaches, such as latent
             trajectory analysis. This article is motivated by
             applications in which the dynamics in a predictor, across
             times when the value is relatively extreme, are particularly
             informative about the response. For example, physicians are
             interested in relating the dynamics of blood pressure
             changes during surgery to post-surgery adverse outcomes, and
             it is thought that the dynamics are more important when
             blood pressure is significantly elevated or lowered.We
             propose a novel class of extrema-weighted feature (XWF)
             extraction models. Key components in defining XWFs include
             the marginal density of the predictor, a function
             up-weighting values at extreme quantiles of this marginal,
             and functionals characterizing local dynamics. Algorithms
             are proposed for fitting of XWF-based regression and
             classification models, and are compared with current methods
             for functional predictors in simulations and a blood
             pressure during surgery application. XWFs find features of
             intraoperative blood pressure trajectories that are
             predictive of postoperative mortality. By their nature, most
             of these features cannot be found by previous methods.The R
             package 'xwf' is available at the CRAN repository:
             https://cran.r-project.org/package=xwf.Supplementary data
             are available at Bioinformatics online.},
   Doi = {10.1093/bioinformatics/bty120},
   Key = {fds339365}
}

@article{fds335794,
   Author = {Shterev, ID and Dunson, DB and Chan, C and Sempowski,
             GD},
   Title = {Bayesian Multi-Plate High-Throughput Screening of
             Compounds.},
   Journal = {Scientific Reports},
   Volume = {8},
   Number = {1},
   Pages = {9551},
   Year = {2018},
   Month = {June},
   url = {http://dx.doi.org/10.1038/s41598-018-27531-w},
   Abstract = {High-throughput screening of compounds (chemicals) is an
             essential part of drug discovery, involving thousands to
             millions of compounds, with the purpose of identifying
             candidate hits. Most statistical tools, including the
             industry standard B-score method, work on individual
             compound plates and do not exploit cross-plate correlation
             or statistical strength among plates. We present a new
             statistical framework for high-throughput screening of
             compounds based on Bayesian nonparametric modeling. The
             proposed approach is able to identify candidate hits from
             multiple plates simultaneously, sharing statistical strength
             among plates and providing more robust estimates of compound
             activity. It can flexibly accommodate arbitrary
             distributions of compound activities and is applicable to
             any plate geometry. The algorithm provides a principled
             statistical approach for hit identification and false
             discovery rate control. Experiments demonstrate significant
             improvements in hit identification sensitivity and
             specificity over the B-score and R-score methods, which are
             highly sensitive to threshold choice. These improvements are
             maintained at low hit rates. The framework is implemented as
             an efficient R extension package BHTSpack and is suitable
             for large scale data sets.},
   Doi = {10.1038/s41598-018-27531-w},
   Key = {fds335794}
}

@article{fds335795,
   Author = {Johndrow, JE and Lum, K and Dunson, DB},
   Title = {Theoretical limits of microclustering for record
             linkage.},
   Journal = {Biometrika},
   Volume = {105},
   Number = {2},
   Pages = {431-446},
   Year = {2018},
   Month = {June},
   url = {http://dx.doi.org/10.1093/biomet/asy003},
   Abstract = {There has been substantial recent interest in record
             linkage, where one attempts to group the records pertaining
             to the same entities from one or more large databases that
             lack unique identifiers. This can be viewed as a type of
             microclustering, with few observations per cluster and a
             very large number of clusters. We show that the problem is
             fundamentally hard from a theoretical perspective and, even
             in idealized cases, accurate entity resolution is
             effectively impossible unless the number of entities is
             small relative to the number of records and/or the
             separation between records from different entities is
             extremely large. These results suggest conservatism in
             interpretation of the results of record linkage, support
             collection of additional data to more accurately
             disambiguate the entities, and motivate a focus on coarser
             inference. For example, results from a simulation study
             suggest that sometimes one may obtain accurate results for
             population size estimation even when fine-scale entity
             resolution is inaccurate.},
   Doi = {10.1093/biomet/asy003},
   Key = {fds335795}
}

@article{fds337687,
   Author = {Miller, JW and Dunson, DB},
   Title = {Robust Bayesian inference via coarsening},
   Journal = {Journal of the American Statistical Association},
   Pages = {1-31},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1080/01621459.2018.1469995},
   Doi = {10.1080/01621459.2018.1469995},
   Key = {fds337687}
}

@article{fds333512,
   Author = {Zhang, Z and Descoteaux, M and Zhang, J and Girard, G and Chamberland,
             M and Dunson, D and Srivastava, A and Zhu, H},
   Title = {Mapping population-based structural connectomes.},
   Journal = {Neuroimage},
   Volume = {172},
   Pages = {130-145},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1016/j.neuroimage.2017.12.064},
   Abstract = {Advances in understanding the structural connectomes of
             human brain require improved approaches for the
             construction, comparison and integration of high-dimensional
             whole-brain tractography data from a large number of
             individuals. This article develops a population-based
             structural connectome (PSC) mapping framework to address
             these challenges. PSC simultaneously characterizes a large
             number of white matter bundles within and across different
             subjects by registering different subjects' brains based on
             coarse cortical parcellations, compressing the bundles of
             each connection, and extracting novel connection weights. A
             robust tractography algorithm and streamline post-processing
             techniques, including dilation of gray matter regions,
             streamline cutting, and outlier streamline removal are
             applied to improve the robustness of the extracted
             structural connectomes. The developed PSC framework can be
             used to reproducibly extract binary networks, weighted
             networks and streamline-based brain connectomes. We apply
             the PSC to Human Connectome Project data to illustrate its
             application in characterizing normal variations and
             heritability of structural connectomes in healthy
             subjects.},
   Doi = {10.1016/j.neuroimage.2017.12.064},
   Key = {fds333512}
}

@article{fds332810,
   Author = {van den Boom, W and Schroeder, RA and Manning, MW and Setji, TL and Fiestan, G-O and Dunson, DB},
   Title = {Effect of A1C and Glucose on Postoperative Mortality in
             Noncardiac and Cardiac Surgeries.},
   Journal = {Diabetes Care},
   Volume = {41},
   Number = {4},
   Pages = {782-788},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.2337/dc17-2232},
   Abstract = {Hemoglobin A1c (A1C) is used in assessment of patients for
             elective surgeries because hyperglycemia increases risk of
             adverse events. However, the interplay of A1C, glucose, and
             surgical outcomes remains unclarified, with often only two
             of these three factors considered simultaneously. We
             assessed the association of preoperative A1C with
             perioperative glucose control and their relationship with
             30-day mortality.Retrospective analysis on 431,480 surgeries
             within the Duke University Health System determined the
             association of preoperative A1C with perioperative glucose
             (averaged over the first 3 postoperative days) and 30-day
             mortality among 6,684 noncardiac and 6,393 cardiac surgeries
             with A1C and glucose measurements. A generalized additive
             model was used, enabling nonlinear relationships.A1C and
             glucose were strongly associated. Glucose and mortality were
             positively associated for noncardiac cases: 1.0% mortality
             at mean glucose of 100 mg/dL and 1.6% at mean glucose of 200
             mg/dL. For cardiac procedures, there was a striking U-shaped
             relationship between glucose and mortality, ranging from
             4.5% at 100 mg/dL to a nadir of 1.5% at 140 mg/dL and rising
             again to 6.9% at 200 mg/dL. A1C and 30-day mortality were
             not associated when controlling for glucose in noncardiac or
             cardiac procedures.Although A1C is positively associated
             with perioperative glucose, it is not associated with
             increased 30-day mortality after controlling for glucose.
             Perioperative glucose predicts 30-day mortality, linearly in
             noncardiac and nonlinearly in cardiac procedures. This
             confirms that perioperative glucose control is related to
             surgical outcomes but that A1C, reflecting antecedent
             glycemia, is a less useful predictor.},
   Doi = {10.2337/dc17-2232},
   Key = {fds332810}
}

@article{fds335793,
   Author = {Sarkar, A and Chabout, J and Macopson, JJ and Jarvis, ED and Dunson,
             DB},
   Title = {Bayesian Semiparametric Mixed Effects Markov Models With
             Application to Vocalization Syntax},
   Journal = {Journal of the American Statistical Association},
   Pages = {1-13},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1080/01621459.2018.1423986},
   Abstract = {© 2018 American Statistical Association Studying the
             neurological, genetic, and evolutionary basis of human vocal
             communication mechanisms using animal vocalization models is
             an important field of neuroscience. The datasets typically
             comprise structured sequences of syllables or “songs”
             produced by animals from different genotypes under different
             social contexts. It has been difficult to come up with
             sophisticated statistical methods that appropriately model
             animal vocal communication syntax. We address this need by
             developing a novel Bayesian semiparametric framework for
             inference in such datasets. Our approach is built on a novel
             class of mixed effects Markov transition models for the
             songs that accommodate exogenous influences of genotype and
             context as well as animal-specific heterogeneity. Crucial
             advantages of the proposed approach include its ability to
             provide insights into key scientific queries related to
             global and local influences of the exogenous predictors on
             the transition dynamics via automated tests of hypotheses.
             The methodology is illustrated using simulation experiments
             and the aforementioned motivating application in
             neuroscience. Supplementary materials for this article,
             including a standardized description of the materials
             available for reproducing the work, are available as an
             online supplement.},
   Doi = {10.1080/01621459.2018.1423986},
   Key = {fds335793}
}

@article{fds339305,
   Author = {Guhaniyogi, R and Qamar, S and Dunson, DB},
   Title = {Bayesian Conditional Density Filtering},
   Journal = {Journal of Computational and Graphical Statistics : a Joint
             Publication of American Statistical Association, Institute
             of Mathematical Statistics, Interface Foundation of North
             America},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1080/10618600.2017.1422431},
   Doi = {10.1080/10618600.2017.1422431},
   Key = {fds339305}
}

@article{fds333225,
   Author = {Dunson, DB},
   Title = {Statistics in the big data era: Failures of the
             machine},
   Journal = {Statistics & Probability Letters},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1016/j.spl.2018.02.028},
   Abstract = {© 2018. There is vast interest in automated methods for
             complex data analysis. However, there is a lack of
             consideration of (1) interpretability, (2) uncertainty
             quantification, (3) applications with limited training data,
             and (4) selection bias. Statistical methods can achieve
             (1)-(4) with a change in focus.},
   Doi = {10.1016/j.spl.2018.02.028},
   Key = {fds333225}
}

@article{fds335796,
   Author = {Bertrán, MA and Martínez, NL and Wang, Y and Dunson, D and Sapiro, G and Ringach, D},
   Title = {Active learning of cortical connectivity from two-photon
             imaging data.},
   Journal = {Plos One},
   Volume = {13},
   Number = {5},
   Pages = {e0196527},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0196527},
   Abstract = {Understanding how groups of neurons interact within a
             network is a fundamental question in system neuroscience.
             Instead of passively observing the ongoing activity of a
             network, we can typically perturb its activity, either by
             external sensory stimulation or directly via techniques such
             as two-photon optogenetics. A natural question is how to use
             such perturbations to identify the connectivity of the
             network efficiently. Here we introduce a method to infer
             sparse connectivity graphs from in-vivo, two-photon imaging
             of population activity in response to external stimuli. A
             novel aspect of the work is the introduction of a
             recommended distribution, incrementally learned from the
             data, to optimally refine the inferred network. Unlike
             existing system identification techniques, this "active
             learning" method automatically focuses its attention on key
             undiscovered areas of the network, instead of targeting
             global uncertainty indicators like parameter variance. We
             show how active learning leads to faster inference while, at
             the same time, provides confidence intervals for the network
             parameters. We present simulations on artificial small-world
             networks to validate the methods and apply the method to
             real data. Analysis of frequency of motifs recovered show
             that cortical networks are consistent with a small-world
             topology model.},
   Doi = {10.1371/journal.pone.0196527},
   Key = {fds335796}
}

@article{fds332378,
   Author = {Minsker, S and Srivastava, S and Lin, L and Dunson,
             DB},
   Title = {Robust and scalable bayes via a median of subset posterior
             measures},
   Journal = {Journal of Machine Learning Research},
   Volume = {18},
   Pages = {1-40},
   Year = {2017},
   Month = {December},
   Abstract = {© 2017 Stanislav Minsker, Sanvesh Srivastava, Lizhen Lin
             and David B. Dunson. We propose a novel approach to Bayesian
             analysis that is provably robust to outliers in the data and
             often has computational advantages over standard methods.
             Our technique is based on splitting the data into
             non-overlapping subgroups, evaluating the posterior
             distribution given each independent subgroup, and then
             combining the resulting measures. The main novelty of our
             approach is the proposed aggregation step, which is based on
             the evaluation of a median in the space of probability
             measures equipped with a suitable collection of distances
             that can be quickly and efficiently evaluated in practice.
             We present both theoretical and numerical evidence
             illustrating the improvements achieved by our
             method.},
   Key = {fds332378}
}

@article{fds332363,
   Author = {Wheeler, MW and Dunson, DB and Herring, AH},
   Title = {Bayesian Local Extremum Splines.},
   Journal = {Biometrika},
   Volume = {104},
   Number = {4},
   Pages = {939-952},
   Publisher = {Oxford University Press (OUP)},
   Year = {2017},
   Month = {December},
   Abstract = {We consider shape restricted nonparametric regression on a
             closed set [Formula: see text], where it is reasonable to
             assume the function has no more than H local extrema
             interior to [Formula: see text]. Following a Bayesian
             approach we develop a nonparametric prior over a novel class
             of local extremum splines. This approach is shown to be
             consistent when modeling any continuously differentiable
             function within the class considered, and is used to develop
             methods for testing hypotheses on the shape of the curve.
             Sampling algorithms are developed, and the method is applied
             in simulation studies and data examples where the shape of
             the curve is of interest.},
   Key = {fds332363}
}

@article{fds332886,
   Author = {Shang, Y and Dunson, D and Song, J-S},
   Title = {Exploiting Big Data in Logistics Risk Assessment via
             Bayesian Nonparametrics},
   Journal = {Operations Research},
   Volume = {65},
   Number = {6},
   Pages = {1574-1588},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1287/opre.2017.1612},
   Doi = {10.1287/opre.2017.1612},
   Key = {fds332886}
}

@article{fds332379,
   Author = {Durante, D and Dunson, DB and Vogelstein, JT},
   Title = {Rejoinder: Nonparametric Bayes Modeling of Populations of
             Networks},
   Journal = {Journal of the American Statistical Association},
   Volume = {112},
   Number = {520},
   Pages = {1547-1552},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1080/01621459.2017.1395643},
   Doi = {10.1080/01621459.2017.1395643},
   Key = {fds332379}
}

@article{fds327388,
   Author = {Durante, D and Dunson, DB and Vogelstein, JT},
   Title = {Nonparametric Bayes Modeling of Populations of
             Networks},
   Journal = {Journal of the American Statistical Association},
   Volume = {112},
   Number = {520},
   Pages = {1516-1530},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1080/01621459.2016.1219260},
   Abstract = {© 2017 American Statistical Association Replicated network
             data are increasingly available in many research fields. For
             example, in connectomic applications, interconnections among
             brain regions are collected for each patient under study,
             motivating statistical models which can flexibly
             characterize the probabilistic generative mechanism
             underlying these network-valued data. Available models for a
             single network are not designed specifically for inference
             on the entire probability mass function of a network-valued
             random variable and therefore lack flexibility in
             characterizing the distribution of relevant topological
             structures. We propose a flexible Bayesian nonparametric
             approach for modeling the population distribution of
             network-valued data. The joint distribution of the edges is
             defined via a mixture model that reduces dimensionality and
             efficiently incorporates network information within each
             mixture component by leveraging latent space
             representations. The formulation leads to an efficient Gibbs
             sampler and provides simple and coherent strategies for
             inference and goodness-of-fit assessments. We provide
             theoretical results on the flexibility of our model and
             illustrate improved performance—compared to
             state-of-the-art models—in simulations and application to
             human brain networks. Supplementary materials for this
             article are available online.},
   Doi = {10.1080/01621459.2016.1219260},
   Key = {fds327388}
}

@article{fds329352,
   Author = {Reddy, A and Zhang, J and Davis, NS and Moffitt, AB and Love, CL and Waldrop, A and Leppa, S and Pasanen, A and Meriranta, L and Karjalainen-Lindsberg, M-L and Nørgaard, P and Pedersen, M and Gang,
             AO and Høgdall, E and Heavican, TB and Lone, W and Iqbal, J and Qin, Q and Li, G and Kim, SY and Healy, J and Richards, KL and Fedoriw, Y and Bernal-Mizrachi, L and Koff, JL and Staton, AD and Flowers, CR and Paltiel, O and Goldschmidt, N and Calaminici, M and Clear, A and Gribben, J and Nguyen, E and Czader, MB and Ondrejka, SL and Collie, A and Hsi, ED and Tse, E and Au-Yeung, RKH and Kwong, Y-L and Srivastava, G and Choi, WWL and Evens, AM and Pilichowska, M and Sengar, M and Reddy, N and Li, S and Chadburn, A and Gordon, LI and Jaffe, ES and Levy, S and Rempel,
             R and Tzeng, T and Happ, LE and Dave, T and Rajagopalan, D and Datta, J and Dunson, DB and Dave, SS},
   Title = {Genetic and Functional Drivers of Diffuse Large B Cell
             Lymphoma.},
   Journal = {Cell},
   Volume = {171},
   Number = {2},
   Pages = {481-494.e15},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1016/j.cell.2017.09.027},
   Abstract = {Diffuse large B cell lymphoma (DLBCL) is the most common
             form of blood cancer and is characterized by a striking
             degree of genetic and clinical heterogeneity. This
             heterogeneity poses a major barrier to understanding the
             genetic basis of the disease and its response to therapy.
             Here, we performed an integrative analysis of whole-exome
             sequencing and transcriptome sequencing in a cohort of 1,001
             DLBCL patients to comprehensively define the landscape of
             150 genetic drivers of the disease. We characterized the
             functional impact of these genes using an unbiased CRISPR
             screen of DLBCL cell lines to define oncogenes that promote
             cell growth. A prognostic model comprising these genetic
             alterations outperformed current established methods: cell
             of origin, the International Prognostic Index comprising
             clinical variables, and dual MYC and BCL2 expression. These
             results comprehensively define the genetic drivers and their
             functional roles in DLBCL to identify new therapeutic
             opportunities in the disease.},
   Doi = {10.1016/j.cell.2017.09.027},
   Key = {fds329352}
}

@article{fds329109,
   Author = {Li, C and Srivastava, S and Dunson, DB},
   Title = {Simple, scalable and accurate posterior interval
             estimation},
   Journal = {Biometrika},
   Volume = {104},
   Number = {3},
   Pages = {665-680},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1093/biomet/asx033},
   Abstract = {© 2017 Biometrika Trust. Standard posterior sampling
             algorithms, such as Markov chain Monte Carlo procedures,
             face major challenges in scaling up to massive datasets. We
             propose a simple and general posterior interval estimation
             algorithm to rapidly and accurately estimate quantiles of
             the posterior distributions for one-dimensional functionals.
             Our algorithm runs Markov chain Monte Carlo in parallel for
             subsets of the data, and then averages quantiles estimated
             from each subset. We provide strong theoretical guarantees
             and show that the credible intervals from our algorithm
             asymptotically approximate those from the full posterior in
             the leading parametric order. Our algorithm has a better
             balance of accuracy and efficiency than its competitors
             across a variety of simulations and a real-data
             example.},
   Doi = {10.1093/biomet/asx033},
   Key = {fds329109}
}

@article{fds323700,
   Author = {Lock, EF and Dunson, DB},
   Title = {Bayesian genome- and epigenome-wide association studies with
             gene level dependence.},
   Journal = {Biometrics},
   Volume = {73},
   Number = {3},
   Pages = {1018-1028},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1111/biom.12649},
   Abstract = {High-throughput genetic and epigenetic data are often
             screened for associations with an observed phenotype. For
             example, one may wish to test hundreds of thousands of
             genetic variants, or DNA methylation sites, for an
             association with disease status. These genomic variables can
             naturally be grouped by the gene they encode, among other
             criteria. However, standard practice in such applications is
             independent screening with a universal correction for
             multiplicity. We propose a Bayesian approach in which the
             prior probability of an association for a given genomic
             variable depends on its gene, and the gene-specific
             probabilities are modeled nonparametrically. This
             hierarchical model allows for appropriate gene and
             genome-wide multiplicity adjustments, and can be
             incorporated into a variety of Bayesian association
             screening methodologies with negligible increase in
             computational complexity. We describe an application to
             screening for differences in DNA methylation between lower
             grade glioma and glioblastoma multiforme tumor samples from
             The Cancer Genome Atlas. Software is available via the
             package BayesianScreening for R: github.com/lockEF/BayesianScreening.},
   Doi = {10.1111/biom.12649},
   Key = {fds323700}
}

@article{fds329110,
   Author = {Srivastava, S and Engelhardt, BE and Dunson, DB},
   Title = {Expandable factor analysis.},
   Journal = {Biometrika},
   Volume = {104},
   Number = {3},
   Pages = {649-663},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1093/biomet/asx030},
   Abstract = {Bayesian sparse factor models have proven useful for
             characterizing dependence in multivariate data, but scaling
             computation to large numbers of samples and dimensions is
             problematic. We propose expandable factor analysis for
             scalable inference in factor models when the number of
             factors is unknown. The method relies on a continuous
             shrinkage prior for efficient maximum a posteriori
             estimation of a low-rank and sparse loadings matrix. The
             structure of the prior leads to an estimation algorithm that
             accommodates uncertainty in the number of factors. We
             propose an information criterion to select the
             hyperparameters of the prior. Expandable factor analysis has
             better false discovery rates and true positive rates than
             its competitors across diverse simulation settings. We apply
             the proposed approach to a gene expression study of ageing
             in mice, demonstrating superior results relative to four
             competing methods.},
   Doi = {10.1093/biomet/asx030},
   Key = {fds329110}
}

@article{fds329353,
   Author = {Guhaniyogi, R and Qamar, S and Dunson, DB},
   Title = {Bayesian tensor regression},
   Journal = {Journal of Machine Learning Research},
   Volume = {18},
   Pages = {1-31},
   Year = {2017},
   Month = {August},
   Abstract = {©2017 Rajarshi Guhaniyogi and Shaan Qamar and David B.
             Dunson. We propose a Bayesian approach to regression with a
             scalar response on vector and tensor covariates.
             Vectorization of the tensor prior to analysis fails to
             exploit the structure, often leading to poor estimation and
             predictive performance. We introduce a novel class of
             multiway shrinkage priors for tensor coefficients in the
             regression setting and present posterior consistency results
             under mild conditions. A computationally efficient Markov
             chain Monte Carlo algorithm is developed for posterior
             computation. Simulation studies illustrate substantial gains
             over existing tensor regression methods in terms of
             estimation and parameter inference. Our approach is further
             illustrated in a neuroimaging application.},
   Key = {fds329353}
}

@article{fds326919,
   Author = {Schaich Borg and J and Srivastava, S and Lin, L and Heffner, J and Dunson,
             D and Dzirasa, K and de Lecea, L},
   Title = {Rat intersubjective decisions are encoded by
             frequency-specific oscillatory contexts.},
   Journal = {Brain and Behavior},
   Volume = {7},
   Number = {6},
   Pages = {e00710},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1002/brb3.710},
   Abstract = {It is unknown how the brain coordinates decisions to
             withstand personal costs in order to prevent other
             individuals' distress. Here we test whether local field
             potential (LFP) oscillations between brain regions create
             "neural contexts" that select specific brain functions and
             encode the outcomes of these types of intersubjective
             decisions.Rats participated in an "Intersubjective Avoidance
             Test" (IAT) that tested rats' willingness to enter an
             innately aversive chamber to prevent another rat from
             getting shocked. c-Fos immunoreactivity was used to screen
             for brain regions involved in IAT performance. Multi-site
             local field potential (LFP) recordings were collected
             simultaneously and bilaterally from five brain regions
             implicated in the c-Fos studies while rats made decisions in
             the IAT. Local field potential recordings were analyzed
             using an elastic net penalized regression framework.Rats
             voluntarily entered an innately aversive chamber to prevent
             another rat from getting shocked, and c-Fos immunoreactivity
             in brain regions known to be involved in human
             empathy-including the anterior cingulate, insula, orbital
             frontal cortex, and amygdala-correlated with the magnitude
             of "intersubjective avoidance" each rat displayed. Local
             field potential recordings revealed that optimal accounts of
             rats' performance in the task require specific frequencies
             of LFP oscillations between brain regions in addition to
             specific frequencies of LFP oscillations within brain
             regions. Alpha and low gamma coherence between spatially
             distributed brain regions predicts more intersubjective
             avoidance, while theta and high gamma coherence between a
             separate subset of brain regions predicts less
             intersubjective avoidance. Phase relationship analyses
             indicated that choice-relevant coherence in the alpha range
             reflects information passed from the amygdala to cortical
             structures, while coherence in the theta range reflects
             information passed in the reverse direction.These results
             indicate that the frequency-specific "neural context"
             surrounding brain regions involved in social cognition
             encodes outcomes of decisions that affect others, above and
             beyond signals from any set of brain regions in
             isolation.},
   Doi = {10.1002/brb3.710},
   Key = {fds326919}
}

@article{fds327028,
   Author = {Zhu, B and Dunson, DB},
   Title = {Bayesian Functional Data Modeling for Heterogeneous
             Volatility},
   Journal = {Bayesian Analysis},
   Volume = {12},
   Number = {2},
   Pages = {335-350},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1214/16-BA1004},
   Doi = {10.1214/16-BA1004},
   Key = {fds327028}
}

@article{fds327029,
   Author = {Wang, L and Durante, D and Jung, RE and Dunson, DB},
   Title = {Bayesian network-response regression.},
   Journal = {Bioinformatics (Oxford, England)},
   Volume = {33},
   Number = {12},
   Pages = {1859-1866},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1093/bioinformatics/btx050},
   Abstract = {There is increasing interest in learning how human brain
             networks vary as a function of a continuous trait, but
             flexible and efficient procedures to accomplish this goal
             are limited. We develop a Bayesian semiparametric model,
             which combines low-rank factorizations and flexible Gaussian
             process priors to learn changes in the conditional
             expectation of a network-valued random variable across the
             values of a continuous predictor, while including
             subject-specific random effects.The formulation leads to a
             general framework for inference on changes in brain network
             structures across human traits, facilitating borrowing of
             information and coherently characterizing uncertainty. We
             provide an efficient Gibbs sampler for posterior computation
             along with simple procedures for inference, prediction and
             goodness-of-fit assessments. The model is applied to learn
             how human brain networks vary across individuals with
             different intelligence scores. Results provide interesting
             insights on the association between intelligence and brain
             connectivity, while demonstrating good predictive
             performance.Source code implemented in R and data are
             available at https://github.com/wangronglu/BNRR.rl.wang@duke.edu.Supplementary
             data are available at Bioinformatics online.},
   Doi = {10.1093/bioinformatics/btx050},
   Key = {fds327029}
}

@article{fds329991,
   Author = {Ovaskainen, O and Tikhonov, G and Norberg, A and Guillaume Blanchet,
             F and Duan, L and Dunson, D and Roslin, T and Abrego,
             N},
   Title = {How to make more out of community data? A conceptual
             framework and its implementation as models and
             software.},
   Journal = {Ecology Letters},
   Volume = {20},
   Number = {5},
   Pages = {561-576},
   Year = {2017},
   Month = {May},
   url = {http://dx.doi.org/10.1111/ele.12757},
   Abstract = {Community ecology aims to understand what factors determine
             the assembly and dynamics of species assemblages at
             different spatiotemporal scales. To facilitate the
             integration between conceptual and statistical approaches in
             community ecology, we propose Hierarchical Modelling of
             Species Communities (HMSC) as a general, flexible framework
             for modern analysis of community data. While
             non-manipulative data allow for only correlative and not
             causal inference, this framework facilitates the formulation
             of data-driven hypotheses regarding the processes that
             structure communities. We model environmental filtering by
             variation and covariation in the responses of individual
             species to the characteristics of their environment, with
             potential contingencies on species traits and phylogenetic
             relationships. We capture biotic assembly rules by
             species-to-species association matrices, which may be
             estimated at multiple spatial or temporal scales. We
             operationalise the HMSC framework as a hierarchical Bayesian
             joint species distribution model, and implement it as R- and
             Matlab-packages which enable computationally efficient
             analyses of large data sets. Armed with this tool, community
             ecologists can make sense of many types of data, including
             spatially explicit data and time-series data. We illustrate
             the use of this framework through a series of diverse
             ecological examples.},
   Doi = {10.1111/ele.12757},
   Key = {fds329991}
}

@article{fds329990,
   Author = {Ovaskainen, O and Tikhonov, G and Dunson, D and Grøtan, V and Engen, S and Sæther, B-E and Abrego, N},
   Title = {How are species interactions structured in species-rich
             communities? A new method for analysing time-series
             data.},
   Journal = {Proceedings of the Royal Society B: Biological
             Sciences},
   Volume = {284},
   Number = {1855},
   Pages = {20170768-20170768},
   Year = {2017},
   Month = {May},
   url = {http://dx.doi.org/10.1098/rspb.2017.0768},
   Abstract = {Estimation of intra- and interspecific interactions from
             time-series on species-rich communities is challenging due
             to the high number of potentially interacting species pairs.
             The previously proposed sparse interactions model overcomes
             this challenge by assuming that most species pairs do not
             interact. We propose an alternative model that does not
             assume that any of the interactions are necessarily zero,
             but summarizes the influences of individual species by a
             small number of community-level drivers. The community-level
             drivers are defined as linear combinations of species
             abundances, and they may thus represent e.g. the total
             abundance of all species or the relative proportions of
             different functional groups. We show with simulated and real
             data how our approach can be used to compare different
             hypotheses on community structure. In an empirical example
             using aquatic microorganisms, the community-level drivers
             model clearly outperformed the sparse interactions model in
             predicting independent validation data.},
   Doi = {10.1098/rspb.2017.0768},
   Key = {fds329990}
}

@article{fds327282,
   Author = {Moffitt, AB and Ondrejka, SL and McKinney, M and Rempel, RE and Goodlad,
             JR and Teh, CH and Leppa, S and Mannisto, S and Kovanen, PE and Tse, E and Au-Yeung, RKH and Kwong, Y-L and Srivastava, G and Iqbal, J and Yu, J and Naresh, K and Villa, D and Gascoyne, RD and Said, J and Czader, MB and Chadburn, A and Richards, KL and Rajagopalan, D and Davis, NS and Smith,
             EC and Palus, BC and Tzeng, TJ and Healy, JA and Lugar, PL and Datta, J and Love, C and Levy, S and Dunson, DB and Zhuang, Y and Hsi, ED and Dave,
             SS},
   Title = {Enteropathy-associated T cell lymphoma subtypes are
             characterized by loss of function of SETD2.},
   Journal = {The Journal of Experimental Medicine},
   Volume = {214},
   Number = {5},
   Pages = {1371-1386},
   Year = {2017},
   Month = {May},
   url = {http://dx.doi.org/10.1084/jem.20160894},
   Abstract = {Enteropathy-associated T cell lymphoma (EATL) is a lethal,
             and the most common, neoplastic complication of celiac
             disease. Here, we defined the genetic landscape of EATL
             through whole-exome sequencing of 69 EATL tumors. SETD2 was
             the most frequently silenced gene in EATL (32% of cases).
             The JAK-STAT pathway was the most frequently mutated
             pathway, with frequent mutations in STAT5B as well as JAK1,
             JAK3, STAT3, and SOCS1 We also identified mutations in KRAS,
             TP53, and TERT Type I EATL and type II EATL (monomorphic
             epitheliotropic intestinal T cell lymphoma) had highly
             overlapping genetic alterations indicating shared mechanisms
             underlying their pathogenesis. We modeled the effects of
             SETD2 loss in vivo by developing a T cell-specific knockout
             mouse. These mice manifested an expansion of γδ T cells,
             indicating novel roles for SETD2 in T cell development and
             lymphomagenesis. Our data render the most comprehensive
             genetic portrait yet of this uncommon but lethal disease and
             may inform future classification schemes.},
   Doi = {10.1084/jem.20160894},
   Key = {fds327282}
}

@article{fds329111,
   Author = {Durante, D and Paganin, S and Scarpa, B and Dunson,
             DB},
   Title = {Bayesian modelling of networks in complex business
             intelligence problems},
   Journal = {Journal of the Royal Statistical Society. Series C, Applied
             Statistics},
   Volume = {66},
   Number = {3},
   Pages = {555-580},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1111/rssc.12168},
   Doi = {10.1111/rssc.12168},
   Key = {fds329111}
}

@article{fds326037,
   Author = {McKinney, M and Moffitt, AB and Gaulard, P and Travert, M and De Leval,
             L and Nicolae, A and Raffeld, M and Jaffe, ES and Pittaluga, S and Xi, L and Heavican, T and Iqbal, J and Belhadj, K and Delfau-Larue, MH and Fataccioli, V and Czader, MB and Lossos, IS and Chapman-Fredricks,
             JR and Richards, KL and Fedoriw, Y and Ondrejka, SL and Hsi, ED and Low, L and Weisenburger, D and Chan, WC and Mehta-Shah, N and Horwitz, S and Bernal-Mizrachi, L and Flowers, CR and Beaven, AW and Parihar, M and Baseggio, L and Parrens, M and Moreau, A and Sujobert, P and Pilichowska, M and Evens, AM and Chadburn, A and Au-Yeung, RKH and Srivastava, G and Choi, WWL and Goodlad, JR and Aurer, I and Basic-Kinda, S and Gascoyne, RD and Davis, NS and Li, G and Zhang, J and Rajagopalan, D and Reddy, A and Love, C and Levy, S and Zhuang, Y and Datta, J and Dunson, DB and Davé, SS},
   Title = {The Genetic Basis of Hepatosplenic T-cell
             Lymphoma.},
   Journal = {Cancer Discovery},
   Volume = {7},
   Number = {4},
   Pages = {369-379},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1158/2159-8290.cd-16-0330},
   Abstract = {Hepatosplenic T-cell lymphoma (HSTL) is a rare and lethal
             lymphoma; the genetic drivers of this disease are unknown.
             Through whole-exome sequencing of 68 HSTLs, we define
             recurrently mutated driver genes and copy-number alterations
             in the disease. Chromatin-modifying genes, including SETD2,
             INO80, and ARID1B, were commonly mutated in HSTL, affecting
             62% of cases. HSTLs manifest frequent mutations in STAT5B
             (31%), STAT3 (9%), and PIK3CD (9%), for which there
             currently exist potential targeted therapies. In addition,
             we noted less frequent events in EZH2, KRAS, and TP53SETD2
             was the most frequently silenced gene in HSTL. We
             experimentally demonstrated that SETD2 acts as a tumor
             suppressor gene. In addition, we found that mutations in
             STAT5B and PIK3CD activate critical signaling pathways
             important to cell survival in HSTL. Our work thus defines
             the genetic landscape of HSTL and implicates gene mutations
             linked to HSTL pathogenesis and potential treatment
             targets.Significance: We report the first systematic
             application of whole-exome sequencing to define the genetic
             basis of HSTL, a rare but lethal disease. Our work defines
             SETD2 as a tumor suppressor gene in HSTL and implicates
             genes including INO80 and PIK3CD in the disease. Cancer
             Discov; 7(4); 369-79. ©2017 AACR.See related commentary by
             Yoshida and Weinstock, p. 352This article is highlighted in
             the In This Issue feature, p. 339.},
   Doi = {10.1158/2159-8290.cd-16-0330},
   Key = {fds326037}
}

@article{fds329992,
   Author = {Tikhonov, G and Abrego, N and Dunson, D and Ovaskainen,
             O},
   Title = {Using joint species distribution models for evaluating how
             species-to-species associations depend on the environmental
             context},
   Journal = {Methods in Ecology and Evolution},
   Volume = {8},
   Number = {4},
   Pages = {443-452},
   Editor = {Warton, D},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1111/2041-210X.12723},
   Doi = {10.1111/2041-210X.12723},
   Key = {fds329992}
}

@article{fds326219,
   Author = {Dunson, DB},
   Title = {Toward Automated Prior Choice},
   Journal = {Statistical Science},
   Volume = {32},
   Number = {1},
   Pages = {41-43},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1214/16-STS607},
   Doi = {10.1214/16-STS607},
   Key = {fds326219}
}

@article{fds333226,
   Author = {Abrego, N and Dunson, D and Halme, P and Salcedo, I and Ovaskainen,
             O},
   Title = {Wood-inhabiting fungi with tight associations with other
             species have declined as a response to forest
             management},
   Journal = {Oikos},
   Volume = {126},
   Number = {2},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1111/oik.03674},
   Doi = {10.1111/oik.03674},
   Key = {fds333226}
}

@article{fds325339,
   Author = {Johndrow, JE and Bhattacharya, A and Dunson, DB},
   Title = {TENSOR DECOMPOSITIONS AND SPARSE LOG-LINEAR
             MODELS.},
   Journal = {The Annals of Statistics},
   Volume = {45},
   Number = {1},
   Pages = {1-38},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1214/15-aos1414},
   Abstract = {Contingency table analysis routinely relies on log-linear
             models, with latent structure analysis providing a common
             alternative. Latent structure models lead to a reduced rank
             tensor factorization of the probability mass function for
             multivariate categorical data, while log-linear models
             achieve dimensionality reduction through sparsity. Little is
             known about the relationship between these notions of
             dimensionality reduction in the two paradigms. We derive
             several results relating the support of a log-linear model
             to nonnegative ranks of the associated probability tensor.
             Motivated by these findings, we propose a new collapsed
             Tucker class of tensor decompositions, which bridge existing
             PARAFAC and Tucker decompositions, providing a more flexible
             framework for parsimoniously characterizing multivariate
             categorical data. Taking a Bayesian approach to inference,
             we illustrate empirical advantages of the new
             decompositions.},
   Doi = {10.1214/15-aos1414},
   Key = {fds325339}
}

@article{fds326570,
   Author = {Lin, L and St Thomas and B and Zhu, H and Dunson, DB},
   Title = {Extrinsic local regression on manifold-valued
             data.},
   Journal = {Journal of the American Statistical Association},
   Volume = {112},
   Number = {519},
   Pages = {1261-1273},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1080/01621459.2016.1208615},
   Abstract = {We propose an extrinsic regression framework for modeling
             data with manifold valued responses and Euclidean
             predictors. Regression with manifold responses has wide
             applications in shape analysis, neuroscience, medical
             imaging and many other areas. Our approach embeds the
             manifold where the responses lie onto a higher dimensional
             Euclidean space, obtains a local regression estimate in that
             space, and then projects this estimate back onto the image
             of the manifold. Outside the regression setting both
             intrinsic and extrinsic approaches have been proposed for
             modeling i.i.d manifold-valued data. However, to our
             knowledge our work is the first to take an extrinsic
             approach to the regression problem. The proposed extrinsic
             regression framework is general, computationally efficient
             and theoretically appealing. Asymptotic distributions and
             convergence rates of the extrinsic regression estimates are
             derived and a large class of examples are considered
             indicating the wide applicability of our
             approach.},
   Doi = {10.1080/01621459.2016.1208615},
   Key = {fds326570}
}

@article{fds336993,
   Author = {Durante, D and Dunson, DB and Vogelstein, JT},
   Title = {Nonparametric Bayes Modeling of Populations of
             Networks},
   Journal = {Journal of the American Statistical Association},
   Volume = {112},
   Number = {520},
   Pages = {1516-1530},
   Year = {2017},
   url = {http://dx.doi.org/10.1080/01621459.2017.1219260},
   Doi = {10.1080/01621459.2017.1219260},
   Key = {fds336993}
}

@article{fds325977,
   Author = {Lin, L and Rao, V and Dunson, D},
   Title = {Bayesian nonparametric inference on the Stiefel
             manifold},
   Journal = {Statistica Sinica},
   Year = {2017},
   url = {http://dx.doi.org/10.5705/ss.202016.0017},
   Doi = {10.5705/ss.202016.0017},
   Key = {fds325977}
}


%% Durrett, Richard T.   
@article{fds337720,
   Author = {Ma, R and Durrett, R},
   Title = {A simple evolutionary game arising from the study of the
             role of igf-II in pancreatic cancer},
   Journal = {The Annals of Applied Probability},
   Volume = {28},
   Number = {5},
   Pages = {2896-2921},
   Year = {2018},
   Month = {October},
   url = {http://dx.doi.org/10.1214/17-AAP1378},
   Abstract = {© Institute of Mathematical Statistics, 2018. We study an
             evolutionary game in which a producer at x gives birth at
             rate 1 to an offspring sent to a randomly chosen point in x
             + Nc, while a cheater at x gives birth at rate λ > 1 times
             the fraction of producers in x + Nd and sends its offspring
             to a randomly chosen point in x + Nc. We first study this
             game on the d-dimensional torus (Z mod L)d with Nd = (Z mod
             L)d and Nc = the 2d nearest neighbors. If we let L → ∞
             then t → ∞ the fraction of producers converges to 1/λ.
             In d ≥ 3 the limiting finite dimensional distributions
             converge as t → ∞ to the voter model equilibrium with
             density 1/λ. We next reformulate the system as an
             evolutionary game with “birth-death” updating and take
             Nc = Nd = N. Using results for voter model perturbations we
             show that in d = 3 with N = the six nearest neighbors, the
             density of producers converges to (2/λ) − 0.5 for 4/3 <
             λ < 4. Producers take over the system when λ < 4/3 and die
             out when λ > 4. In d = 2 with N = [−clog N, clog N]2
             there are similar phase transitions, with coexistence
             occurring when (1 + 2θ)/(1 + θ) < λ < (1 + 2θ)/θ where
             θ = (e3/(πc2) − 1)/2.},
   Doi = {10.1214/17-AAP1378},
   Key = {fds337720}
}

@article{fds335535,
   Author = {Wang, Z and Durrett, R},
   Title = {Extrapolating weak selection in evolutionary
             games.},
   Journal = {Journal of Mathematical Biology},
   Year = {2018},
   Month = {July},
   url = {http://dx.doi.org/10.1007/s00285-018-1270-6},
   Abstract = {This work is inspired by a 2013 paper from Arne Traulsen's
             lab at the Max Plank Institute for Evolutionary Biology (Wu
             et al. in PLoS Comput Biol 9:e1003381, 2013). They studied
             evolutionary games when the mutation rate is so small that
             each mutation goes to fixation before the next one occurs.
             It has been shown that for [Formula: see text] games the
             ranking of the strategies does not change as strength of
             selection is increased (Wu et al. in Phys Rev 82:046106,
             2010). The point of the 2013 paper is that when there are
             three or more strategies the ordering can change as
             selection is increased. Wu et al. (2013) did numerical
             computations for a fixed population size N. Here, we will
             instead let the strength of selection [Formula: see text]
             where c is fixed and let [Formula: see text] to obtain
             formulas for the invadability probabilities [Formula: see
             text] that determine the rankings. These formulas, which are
             integrals on [0, 1], are intractable calculus problems, but
             can be easily evaluated numerically. Here, we use them to
             derive simple formulas for the ranking order when c is small
             or c is large.},
   Doi = {10.1007/s00285-018-1270-6},
   Key = {fds335535}
}

@article{fds339723,
   Author = {Talkington, A and Dantoin, C and Durrett, R},
   Title = {Ordinary Differential Equation Models for Adoptive
             Immunotherapy.},
   Journal = {Bulletin of Mathematical Biology},
   Volume = {80},
   Number = {5},
   Pages = {1059-1083},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1007/s11538-017-0263-8},
   Abstract = {Modified T cells that have been engineered to recognize the
             CD19 surface marker have recently been shown to be very
             successful at treating acute lymphocytic leukemias. Here, we
             explore four previous approaches that have used ordinary
             differential equations to model this type of therapy,
             compare their properties, and modify the models to address
             their deficiencies. Although the four models treat the
             workings of the immune system in slightly different ways,
             they all predict that adoptive immunotherapy can be
             successful to move a patient from the large tumor fixed
             point to an equilibrium with little or no
             tumor.},
   Doi = {10.1007/s11538-017-0263-8},
   Key = {fds339723}
}

@article{fds330932,
   Author = {Huo, R and Durrett, R},
   Title = {Latent voter model on locally tree-like random
             graphs},
   Journal = {Stochastic Processes and Their Applications},
   Volume = {128},
   Number = {5},
   Pages = {1590-1614},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1016/j.spa.2017.08.004},
   Doi = {10.1016/j.spa.2017.08.004},
   Key = {fds330932}
}

@article{fds339577,
   Author = {Beckman, E and Dinan, E and Durrett, R and Huo, R and Junge,
             M},
   Title = {Asymptotic behavior of the brownian frog
             model},
   Journal = {Electronic Journal of Probability},
   Volume = {23},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1214/18-EJP215},
   Abstract = {© 2018, University of Washington. All rights reserved. We
             introduce an extension of the frog model to Euclidean space
             and prove properties for the spread of active particles. Fix
             r>0 and place a particle at each point x of a unit intensity
             Poisson point process P⊆ℝd−B(0,r). Around each point
             in P, put a ball of radius r. A particle at the origin
             performs Brownian motion. When it hits the ball around x for
             some x ∈ P, new particles begin independent Brownian
             motions from the centers of the balls in the cluster
             containing x. Subsequent visits to the cluster do nothing.
             This waking process continues indefinitely. For r smaller
             than the critical threshold of continuum percolation, we
             show that the set of activated points in P approximates a
             linearly expanding ball. Moreover, in any fixed ball the set
             of active particles converges to a unit intensity Poisson
             point process.},
   Doi = {10.1214/18-EJP215},
   Key = {fds339577}
}

@article{fds339578,
   Author = {Basak, A and Durrett, R and Foxall, E},
   Title = {Diffusion limit for the partner model at the critical
             value},
   Journal = {Electronic Journal of Probability},
   Volume = {23},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1214/18-EJP229},
   Abstract = {© 2018, University of Washington. All rights reserved.
             population with random formation and dissolution of
             partnerships, and with disease transmission only occuring
             within partnerships. Foxall, Edwards, and van den Driessche
             [7] found the critical value and studied the subcritical and
             supercritical regimes. Recently Foxall [4] has shown that
             (if there are enough initial infecteds I0) the extinction
             time in the critical model is of order √N. Here we improve
             that result by proving the convergence of
             iN(t)=I(√Nt)/√N to a limiting diffusion. We do this by
             showing that within a short time, this four dimensional
             process collapses to two dimensions: the number of SI and II
             partnerships are constant multiples of the the number of
             infected singles. The other variable, the total number of
             singles, fluctuates around its equilibrium like an
             Ornstein-Uhlenbeck process of magnitude √N on the original
             time scale and averages out of the limit theorem for iN(t).
             As a by-product of our proof we show that if τN is the
             extinction time of iN(t) (on the √N time scale) then τN
             has a limit.},
   Doi = {10.1214/18-EJP229},
   Key = {fds339578}
}

@article{fds339329,
   Author = {Cristali, I and Ranjan, V and Steinberg, J and Beckman, E and Durrett,
             R and Junge, M and Nolen, J},
   Title = {Block size in geometric(P)-biased permutations},
   Journal = {Electronic Communications in Probability},
   Volume = {23},
   Pages = {1-10},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1214/18-ECP182},
   Abstract = {© 2018, University of Washington. All rights reserved. Fix
             a probability distribution p = (p1, p2, …) on the positive
             integers. The first block in a p-biased permutation can be
             visualized in terms of raindrops that land at each positive
             integer j with probability pj. It is the first point K so
             that all sites in [1, K] are wet and all sites in (K, ∞)
             are dry. For the geometric distribution pj = p(1 − p)j−1
             we show that p log K converges in probability to an explicit
             constant as p tends to 0. Additionally, we prove that if p
             has a stretch exponential distribution, then K is infinite
             with positive probability.},
   Doi = {10.1214/18-ECP182},
   Key = {fds339329}
}

@article{fds330931,
   Author = {Lopatkin, AJ and Meredith, HR and Srimani, JK and Pfeiffer, C and Durrett, R and You, L},
   Title = {Persistence and reversal of plasmid-mediated antibiotic
             resistance.},
   Journal = {Nature Communications},
   Volume = {8},
   Number = {1},
   Pages = {1689},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1038/s41467-017-01532-1},
   Abstract = {In the absence of antibiotic-mediated selection, sensitive
             bacteria are expected to displace their resistant
             counterparts if resistance genes are costly. However, many
             resistance genes persist for long periods in the absence of
             antibiotics. Horizontal gene transfer (primarily
             conjugation) could explain this persistence, but it has been
             suggested that very high conjugation rates would be
             required. Here, we show that common conjugal plasmids, even
             when costly, are indeed transferred at sufficiently high
             rates to be maintained in the absence of antibiotics in
             Escherichia coli. The notion is applicable to nine plasmids
             from six major incompatibility groups and mixed populations
             carrying multiple plasmids. These results suggest that
             reducing antibiotic use alone is likely insufficient for
             reversing resistance. Therefore, combining conjugation
             inhibition and promoting plasmid loss would be an effective
             strategy to limit conjugation-assisted persistence of
             antibiotic resistance.},
   Doi = {10.1038/s41467-017-01532-1},
   Key = {fds330931}
}

@article{fds329932,
   Author = {Gleeson, JP and Durrett, R},
   Title = {Temporal profiles of avalanches on networks.},
   Journal = {Nature Communications},
   Volume = {8},
   Number = {1},
   Pages = {1227},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1038/s41467-017-01212-0},
   Abstract = {An avalanche or cascade occurs when one event causes one or
             more subsequent events, which in turn may cause further
             events in a chain reaction. Avalanching dynamics are studied
             in many disciplines, with a recent focus on average
             avalanche shapes, i.e., the temporal profiles of avalanches
             of fixed duration. At the critical point of the dynamics,
             the rescaled average avalanche shapes for different
             durations collapse onto a single universal curve. We apply
             Markov branching process theory to derive an equation
             governing the average avalanche shape for cascade dynamics
             on networks. Analysis of the equation at criticality
             demonstrates that nonsymmetric average avalanche shapes (as
             observed in some experiments) occur for certain combinations
             of dynamics and network topology. We give examples using
             numerical simulations of models for information spreading,
             neural dynamics, and behavior adoption and we propose simple
             experimental tests to quantify whether cascading systems are
             in the critical state.},
   Doi = {10.1038/s41467-017-01212-0},
   Key = {fds329932}
}

@article{fds329933,
   Author = {Tomasetti, C and Durrett, R and Kimmel, M and Lambert, A and Parmigiani,
             G and Zauber, A and Vogelstein, B},
   Title = {Role of stem-cell divisions in cancer risk},
   Journal = {Nature},
   Volume = {548},
   Number = {7666},
   Pages = {E13-E14},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1038/nature23302},
   Doi = {10.1038/nature23302},
   Key = {fds329933}
}

@article{fds327001,
   Author = {Nanda, M and Durrett, R},
   Title = {Spatial evolutionary games with weak selection},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {114},
   Number = {23},
   Pages = {6046-6051},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1073/pnas.1620852114},
   Doi = {10.1073/pnas.1620852114},
   Key = {fds327001}
}

@article{fds323833,
   Author = {Bessonov, M and Durrett, R},
   Title = {Phase transitions for a planar quadratic contact
             process},
   Journal = {Advances in Applied Mathematics},
   Volume = {87},
   Pages = {82-107},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.aam.2017.01.002},
   Doi = {10.1016/j.aam.2017.01.002},
   Key = {fds323833}
}


%% Dym, Nadav   
@article{fds338328,
   Author = {Lazar, R and Dym, N and Kushinsky, Y and Huang, Z and Ju, T and Lipman,
             Y},
   Title = {Robust optimization for topological surface
             reconstruction},
   Journal = {Acm Transactions on Graphics},
   Volume = {37},
   Number = {4},
   Pages = {46:1-46:1},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1145/3197517.3201348},
   Abstract = {© 2018 Copyright held by the owner/author(s). Surface
             reconstruction is one of the central problems in computer
             graphics. Existing research on this problem has primarily
             focused on improving the geometric aspects of the
             reconstruction (e.g., smoothness, features, element quality,
             etc.), and little attention has been paid to ensure it also
             has desired topological properties (e.g., connectedness and
             genus). In this paper, we propose a novel and general
             optimization method for surface reconstruction under
             topological constraints. The input to our method is a
             prescribed genus for the reconstructed surface, a partition
             of the ambient volume into cells, and a set of possible
             surface candidates and their associated energy within each
             cell. Our method computes one candidate per cell so that
             their union is a connected surface with the prescribed genus
             that minimizes the total energy. We formulate the task as an
             integer program, and propose a novel solution that combines
             convex relaxations within a branch and bound framework. As
             our method is oblivious of the type of input cells, surface
             candidates, and energy, it can be applied to a variety of
             reconstruction scenarios, and we explore two of them in the
             paper: Reconstruction from cross-section slices and
             iso-surfacing an intensity volume. In the first scenario,
             our method outperforms an existing topology-aware method
             particularly for complex inputs and higher genus
             constraints. In the second scenario, we demonstrate the
             benefit of topology control over classical
             topology-oblivious methods such as Marching
             Cubes.},
   Doi = {10.1145/3197517.3201348},
   Key = {fds338328}
}

@article{fds338329,
   Author = {Dym, N and Maron, H and Lipman, Y},
   Title = {DS++},
   Journal = {Acm Transactions on Graphics},
   Volume = {36},
   Number = {6},
   Pages = {1-14},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1145/3130800.3130826},
   Doi = {10.1145/3130800.3130826},
   Key = {fds338329}
}

@article{fds338330,
   Author = {Maron, H and Galun, M and Aigerman, N and Trope, M and Dym, N and Yumer, E and Kim, VG and Lipman, Y},
   Title = {Convolutional neural networks on surfaces via seamless toric
             covers},
   Journal = {Acm Transactions on Graphics},
   Volume = {36},
   Number = {4},
   Pages = {1-10},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1145/3072959.3073616},
   Doi = {10.1145/3072959.3073616},
   Key = {fds338330}
}

@article{fds338331,
   Author = {Dym, N and Lipman, Y},
   Title = {Exact Recovery with Symmetries for Procrustes
             Matching},
   Journal = {Siam Journal on Optimization},
   Volume = {27},
   Number = {3},
   Pages = {1513-1530},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1078628},
   Doi = {10.1137/16M1078628},
   Key = {fds338331}
}

@article{fds338332,
   Author = {Dym, N and Lipman, Y and Slutsky, R},
   Title = {A Linear Variational Principle for Riemann Mapping and
             Discrete Conformality.},
   Journal = {Corr},
   Volume = {abs/1711.02221},
   Year = {2017},
   Key = {fds338332}
}


%% Fernandes de Oliveira, Goncalo M.   
@article{fds323834,
   Author = {Oliveira, G},
   Title = {Gerbes on G2 manifolds},
   Journal = {Journal of Geometry and Physics},
   Volume = {114},
   Pages = {570-580},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1016/j.geomphys.2017.01.007},
   Doi = {10.1016/j.geomphys.2017.01.007},
   Key = {fds323834}
}


%% Getz, Jayce R.   
@article{fds320413,
   Author = {Getz, JR},
   Title = {Nonabelian fourier transforms for spherical
             representations},
   Journal = {Pacific Journal of Mathematics},
   Volume = {294},
   Number = {2},
   Pages = {351-373},
   Publisher = {Mathematical Sciences Publishers},
   Year = {2018},
   Month = {January},
   url = {arXiv:1506.09128},
   Abstract = {© 2018 Mathematical Sciences Publishers. Braverman and
             Kazhdan have introduced an influential conjecture on local
             functional equations for general Langlands L-functions. It
             is related to L. Lafforgue's equally influential conjectural
             construction of kernels for functorial transfers. We
             formulate and prove a version of Braverman and Kazhdan's
             conjecture for spherical representations over an archimedean
             field that is suitable for application to the trace formula.
             We then give a global application related to Langlands'
             beyond endoscopy proposal. It is motivated by Ngô's
             suggestion that one combine nonabelian Fourier transforms
             with the trace formula in order to prove the functional
             equations of Langlands L-functions in general.},
   Doi = {10.2140/pjm.2018.294.351},
   Key = {fds320413}
}


%% Hahn, Heekyoung   
@article{fds339331,
   Author = {Hahn, H and Huh, J and Lim, E and Sohn, J},
   Title = {From partition identities to a combinatorial approach to
             explicit Satake inversions},
   Journal = {Annals of Combinatorics},
   Volume = {22},
   Pages = {543-562},
   Publisher = {Springer Verlag},
   Year = {2018},
   Month = {June},
   url = {http://dx.doi.org/10.1007/s00026-018-0391-3},
   Doi = {10.1007/s00026-018-0391-3},
   Key = {fds339331}
}


%% Hain, Richard   
@article{fds337126,
   Author = {Brown, F and Hain, R},
   Title = {Algebraic de Rham theory for weakly holomorphic modular
             forms of level one},
   Journal = {Algebra & Number Theory},
   Volume = {12},
   Number = {3},
   Pages = {723-750},
   Year = {2018},
   url = {http://dx.doi.org/10.2140/ant.2018.12.723},
   Doi = {10.2140/ant.2018.12.723},
   Key = {fds337126}
}

@article{fds320425,
   Author = {Hain, R},
   Title = {Deligne-Beilinson Cohomology of Affine Groups},
   Booktitle = {Hodge Theory and $L^2$-analysis},
   Publisher = {International Press},
   Editor = {Ji, L},
   Year = {2017},
   ISBN = {1571463518},
   url = {http://arxiv.org/abs/1507.03144},
   Abstract = {The goal of this paper is to develop the theory of
             Deligne-Beilinson cohomology of affine groups with a mixed
             Hodge structure. The motivation comes from Hodge theory and
             the study of motives, where such groups appear. Several of
             Francis Brown's period computations (arXiv:1407.5167) are
             interpreted as elements of the DB cohomology of the relative
             unipotent completion of $SL_2(Z)$ and their cup products.
             The results in this paper are used in arXiv:1403.6443 where
             they are used to prove that Pollack's quadratic relations
             are motivic.},
   Key = {fds320425}
}


%% Harer, John   
@article{fds335536,
   Author = {Garagić, D and Peskoe, J and Liu, F and Claffey, MS and Bendich, P and Hineman, J and Borggren, N and Harer, J and Zulch, P and Rhodes,
             BJ},
   Title = {Upstream fusion of multiple sensing modalities using machine
             learning and topological analysis: An initial
             exploration},
   Journal = {Ieee Aerospace Conference Proceedings},
   Volume = {2018-March},
   Pages = {1-8},
   Year = {2018},
   Month = {June},
   ISBN = {9781538620144},
   url = {http://dx.doi.org/10.1109/AERO.2018.8396737},
   Abstract = {© 2018 IEEE. This paper presents a processing pipeline for
             fusing 'raw' and / or feature-level multi-sensor data -
             upstream fusion - and initial results from this pipeline
             using imagery, radar, and radio frequency (RF) signals data
             to determine which tracked object, among several, hosts an
             emitter of interest. Correctly making this determination
             requires fusing data across these modalities. Our approach
             performs better than standard fusion approaches that make
             detection / characterization decisions for each modality
             individually and then try to fuse those decisions -
             downstream (or post-decision) fusion. Our approach (1) fully
             exploits the inter-modality dependencies and phenomenologies
             inherent in different sensing modes, (2) automatically
             discovers compressive hierarchical representations that
             integrate structural and statistical characteristics to
             enhance target / event discriminability, and (3) completely
             obviates the need to specify features, manifolds, or model
             scope a priori. This approach comprises a unique synthesis
             of Deep Learning (DL), topological analysis over probability
             measure (TAPM), and hierarchical Bayesian non-parametric
             (HBNP) recognition models. Deep Generative Networks (DGNs -
             a deep generative statistical form of DL) create probability
             measures that provide a basis for calculating homologies
             (topological summaries over the probability measures). The
             statistics of the resulting persistence diagrams are inputs
             to HBNP methods that learn to discriminate between target
             types and distinguish emitting targets from non-emitting
             targets, for example. HBNP learning obviates batch-mode
             off-line learning. This approach overcomes the inadequacy of
             pre-defined features as a means for creating efficient,
             discriminating, low-dimensional representations from
             high-dimensional multi-modality sensor data collected under
             difficult, dynamic sensing conditions. The invariant
             properties in the resulting compact representations afford
             multiple compressive sensing benefits, including concise
             information sharing and enhanced performance. Machine
             learning makes adaptivity a central feature of our approach.
             Adaptivity is critical because it enables flexible
             processing that automatically accommodates a broad range of
             challenges that non-adaptive, standard fusion approaches
             would typically require manual intervention to begin to
             address. These include (a) interest in unknown or
             unanticipated targets, (b) desire to be rapidly able to fuse
             between different combinations of sensor modalities, and (c)
             potential need to transfer information between platforms
             that host different sensors. This paper presents results
             that demonstrate our approach enables accurate, real-time
             target detection, tracking, and recognition of known and
             unknown moving or stationary targets or events and their
             activities evolving over space and time.},
   Doi = {10.1109/AERO.2018.8396737},
   Key = {fds335536}
}

@article{fds332374,
   Author = {Tralie, CJ and Smith, A and Borggren, N and Hineman, J and Bendich, P and Zulch, P and Harer, J},
   Title = {Geometric Cross-Modal Comparison of Heterogeneous Sensor
             Data},
   Journal = {Proceedings of the 39th Ieee Aerospace Conference},
   Year = {2018},
   Month = {March},
   Abstract = {In this work, we address the problem of cross-modal
             comparison of aerial data streams. A variety of simulated
             automobile trajectories are sensed using two different
             modalities: full-motion video, and radio-frequency (RF)
             signals received by detectors at various locations. The
             information represented by the two modalities is compared
             using self-similarity matrices (SSMs) corresponding to
             time-ordered point clouds in feature spaces of each of these
             data sources; we note that these feature spaces can be of
             entirely different scale and dimensionality. Several metrics
             for comparing SSMs are explored, including a cutting-edge
             time-warping technique that can simultaneously handle local
             time warping and partial matches, while also controlling for
             the change in geometry between feature spaces of the two
             modalities. We note that this technique is quite general,
             and does not depend on the choice of modalities. In this
             particular setting, we demonstrate that the cross-modal
             distance between SSMs corresponding to the same trajectory
             type is smaller than the cross-modal distance between SSMs
             corresponding to distinct trajectory types, and we formalize
             this observation via precision-recall metrics in
             experiments. Finally, we comment on promising implications
             of these ideas for future integration into
             multiple-hypothesis tracking systems.},
   Key = {fds332374}
}

@article{fds330518,
   Author = {Hughes, ME and Abruzzi, KC and Allada, R and Anafi, R and Arpat, AB and Asher, G and Baldi, P and de Bekker, C and Bell-Pedersen, D and Blau, J and Brown, S and Ceriani, MF and Chen, Z and Chiu, JC and Cox, J and Crowell,
             AM and DeBruyne, JP and Dijk, D-J and DiTacchio, L and Doyle, FJ and Duffield, GE and Dunlap, JC and Eckel-Mahan, K and Esser, KA and FitzGerald, GA and Forger, DB and Francey, LJ and Fu, Y-H and Gachon, F and Gatfield, D and de Goede, P and Golden, SS and Green, C and Harer, J and Harmer, S and Haspel, J and Hastings, MH and Herzel, H and Herzog, ED and Hoffmann, C and Hong, C and Hughey, JJ and Hurley, JM and de la Iglesia,
             HO and Johnson, C and Kay, SA and Koike, N and Kornacker, K and Kramer, A and Lamia, K and Leise, T and Lewis, SA and Li, J and Li, X and Liu, AC and Loros,
             JJ and Martino, TA and Menet, JS and Merrow, M and Millar, AJ and Mockler,
             T and Naef, F and Nagoshi, E and Nitabach, MN and Olmedo, M and Nusinow,
             DA and Ptáček, LJ and Rand, D and Reddy, AB and Robles, MS and Roenneberg, T and Rosbash, M and Ruben, MD and Rund, SSC and Sancar, A and Sassone-Corsi, P and Sehgal, A and Sherrill-Mix, S and Skene, DJ and Storch, K-F and Takahashi, JS and Ueda, HR and Wang, H and Weitz, C and Westermark, PO and Wijnen, H and Xu, Y and Wu, G and Yoo, S-H and Young, M and Zhang, EE and Zielinski, T and Hogenesch, JB},
   Title = {Guidelines for Genome-Scale Analysis of Biological
             Rhythms.},
   Journal = {Journal of Biological Rhythms},
   Volume = {32},
   Number = {5},
   Pages = {380-393},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1177/0748730417728663},
   Abstract = {Genome biology approaches have made enormous contributions
             to our understanding of biological rhythms, particularly in
             identifying outputs of the clock, including RNAs, proteins,
             and metabolites, whose abundance oscillates throughout the
             day. These methods hold significant promise for future
             discovery, particularly when combined with computational
             modeling. However, genome-scale experiments are costly and
             laborious, yielding "big data" that are conceptually and
             statistically difficult to analyze. There is no obvious
             consensus regarding design or analysis. Here we discuss the
             relevant technical considerations to generate reproducible,
             statistically sound, and broadly useful genome-scale data.
             Rather than suggest a set of rigid rules, we aim to codify
             principles by which investigators, reviewers, and readers of
             the primary literature can evaluate the suitability of
             different experimental designs for measuring different
             aspects of biological rhythms. We introduce CircaInSilico, a
             web-based application for generating synthetic genome
             biology data to benchmark statistical methods for studying
             biological rhythms. Finally, we discuss several unmet
             analytical needs, including applications to clinical
             medicine, and suggest productive avenues to address
             them.},
   Doi = {10.1177/0748730417728663},
   Key = {fds330518}
}


%% He, Siming   
@article{fds337289,
   Author = {He, S},
   Title = {Suppression of blow-up in parabolic–parabolic
             Patlak–Keller–Segel via strictly monotone shear
             flows},
   Journal = {Nonlinearity},
   Volume = {31},
   Number = {8},
   Pages = {3651-3688},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1088/1361-6544/aac1ce},
   Doi = {10.1088/1361-6544/aac1ce},
   Key = {fds337289}
}

@article{fds339828,
   Author = {He, S and Tadmor, E},
   Title = {Suppressing Chemotactic Blow-Up Through a Fast Splitting
             Scenario on the Plane},
   Journal = {Archive for Rational Mechanics and Analysis},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1007/s00205-018-01336-7},
   Abstract = {© 2018, Springer-Verlag GmbH Germany, part of Springer
             Nature. We revisit the question of global regularity for the
             Patlak–Keller–Segel (PKS) chemotaxis model. The
             classical 2D parabolic-elliptic model blows up for initial
             mass M> 8 π. We consider a more realistic scenario which
             takes into account the flow of the ambient environment
             induced by harmonic potentials, and thus retain the
             identical elliptic structure as in the original PKS.
             Surprisingly, we find that already the simplest case of
             linear stationary vector field, Ax⊤, with large enough
             amplitude A, prevents chemotactic blow-up. Specifically, the
             presence of such an ambient fluid transport creates what we
             call a ‘fast splitting scenario’, which competes with
             the focusing effect of aggregation so that ‘enough mass’
             is pushed away from concentration along the x1-axis, thus
             avoiding a finite time blow-up, at least for M< 16 π. Thus,
             the enhanced ambient flow doubles the amount of allowable
             mass which evolve to global smooth solutions.},
   Doi = {10.1007/s00205-018-01336-7},
   Key = {fds339828}
}

@article{fds337290,
   Author = {He, S and Tadmor, E},
   Title = {Global regularity of two-dimensional flocking
             hydrodynamics},
   Journal = {Comptes Rendus Mathematique},
   Volume = {355},
   Number = {7},
   Pages = {795-805},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1016/j.crma.2017.05.008},
   Doi = {10.1016/j.crma.2017.05.008},
   Key = {fds337290}
}

@article{fds337281,
   Author = {Bedrossian, J and He, S},
   Title = {Suppression of Blow-Up in Patlak--Keller--Segel Via Shear
             Flows},
   Journal = {Siam Journal on Mathematical Analysis},
   Volume = {49},
   Number = {6},
   Pages = {4722-4766},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1093380},
   Doi = {10.1137/16M1093380},
   Key = {fds337281}
}


%% Herschlag, Gregory J.   
@article{fds330268,
   Author = {Cao, Y and Feng, Y and Ryser, MD and Zhu, K and Herschlag, G and Cao, C and Marusak, K and Zauscher, S and You, L},
   Title = {Programmable assembly of pressure sensors using
             pattern-forming bacteria.},
   Journal = {Nature Biotechnology},
   Volume = {35},
   Number = {11},
   Pages = {1087-1093},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1038/nbt.3978},
   Abstract = {Biological systems can generate microstructured materials
             that combine organic and inorganic components and possess
             diverse physical and chemical properties. However, these
             natural processes in materials fabrication are not readily
             programmable. Here, we use a synthetic-biology approach to
             assemble patterned materials. We demonstrate programmable
             fabrication of three-dimensional (3D) materials by printing
             engineered self-patterning bacteria on permeable membranes
             that serve as a structural scaffold. Application of gold
             nanoparticles to the colonies creates hybrid
             organic-inorganic dome structures. The dynamics of the dome
             structures' response to pressure is determined by their
             geometry (colony size, dome height, and pattern), which is
             easily modified by varying the properties of the membrane
             (e.g., pore size and hydrophobicity). We generate resettable
             pressure sensors that process signals in response to varying
             pressure intensity and duration.},
   Doi = {10.1038/nbt.3978},
   Key = {fds330268}
}

@article{fds335537,
   Author = {Herschlag, G and Ravier, R and Mattingly, JC},
   Title = {Evaluating Partisan Gerrymandering in Wisconsin},
   Year = {2017},
   Month = {September},
   Abstract = {We examine the extent of gerrymandering for the 2010 General
             Assembly district map of Wisconsin. We find that there is
             substantial variability in the election outcome depending on
             what maps are used. We also found robust evidence that the
             district maps are highly gerrymandered and that this
             gerrymandering likely altered the partisan make up of the
             Wisconsin General Assembly in some elections. Compared to
             the distribution of possible redistricting plans for the
             General Assembly, Wisconsin's chosen plan is an outlier in
             that it yields results that are highly skewed to the
             Republicans when the statewide proportion of Democratic
             votes comprises more than 50-52% of the overall vote (with
             the precise threshold depending on the election considered).
             Wisconsin's plan acts to preserve the Republican majority by
             providing extra Republican seats even when the Democratic
             vote increases into the range when the balance of power
             would shift for the vast majority of redistricting
             plans.},
   Key = {fds335537}
}


%% Junge, Matthew S   
@article{fds335538,
   Author = {Johnson, T and Junge, M},
   Title = {Stochastic orders and the frog model},
   Journal = {Annales De L'Institut Henri Poincaré, Probabilités Et
             Statistiques},
   Volume = {54},
   Number = {2},
   Pages = {1013-1030},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1214/17-AIHP830},
   Doi = {10.1214/17-AIHP830},
   Key = {fds335538}
}

@article{fds338420,
   Author = {Foxall, E and Hutchcroft, T and Junge, M},
   Title = {Coalescing random walk on unimodular graphs},
   Journal = {Electronic Communications in Probability},
   Volume = {23},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1214/18-ECP136},
   Abstract = {© 2018, University of Washington. All rights reserved.
             Coalescing random walk on a unimodular random rooted graph
             for which the root has finite expected degree visits each
             site infinitely often almost surely. A corollary is that an
             opinion in the voter model on such graphs has infinite
             expected lifetime. Additionally, we deduce an adaptation of
             our main theorem that holds uniformly for coalescing random
             walk on finite random unimodular graphs with degree
             distribution stochastically dominated by a probability
             measure with finite mean.},
   Doi = {10.1214/18-ECP136},
   Key = {fds338420}
}

@article{fds339580,
   Author = {Beckman, E and Dinan, E and Durrett, R and Huo, R and Junge,
             M},
   Title = {Asymptotic behavior of the brownian frog
             model},
   Journal = {Electronic Journal of Probability},
   Volume = {23},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1214/18-EJP215},
   Abstract = {© 2018, University of Washington. All rights reserved. We
             introduce an extension of the frog model to Euclidean space
             and prove properties for the spread of active particles. Fix
             r>0 and place a particle at each point x of a unit intensity
             Poisson point process P⊆ℝd−B(0,r). Around each point
             in P, put a ball of radius r. A particle at the origin
             performs Brownian motion. When it hits the ball around x for
             some x ∈ P, new particles begin independent Brownian
             motions from the centers of the balls in the cluster
             containing x. Subsequent visits to the cluster do nothing.
             This waking process continues indefinitely. For r smaller
             than the critical threshold of continuum percolation, we
             show that the set of activated points in P approximates a
             linearly expanding ball. Moreover, in any fixed ball the set
             of active particles converges to a unit intensity Poisson
             point process.},
   Doi = {10.1214/18-EJP215},
   Key = {fds339580}
}

@article{fds339742,
   Author = {Cristali, I and Ranjan, V and Steinberg, J and Beckman, E and Durrett,
             R and Junge, M and Nolen, J},
   Title = {Block size in geometric(P)-biased permutations},
   Journal = {Electronic Communications in Probability},
   Volume = {23},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1214/18-ECP182},
   Abstract = {© 2018, University of Washington. All rights reserved. Fix
             a probability distribution p = (p1, p2, …) on the positive
             integers. The first block in a p-biased permutation can be
             visualized in terms of raindrops that land at each positive
             integer j with probability pj. It is the first point K so
             that all sites in [1, K] are wet and all sites in (K, ∞)
             are dry. For the geometric distribution pj = p(1 − p)j−1
             we show that p log K converges in probability to an explicit
             constant as p tends to 0. Additionally, we prove that if p
             has a stretch exponential distribution, then K is infinite
             with positive probability.},
   Doi = {10.1214/18-ECP182},
   Key = {fds339742}
}

@article{fds329100,
   Author = {Hoffman, C and Johnson, T and Junge, M},
   Title = {Recurrence and transience for the frog model on
             trees},
   Journal = {The Annals of Probability},
   Volume = {45},
   Number = {5},
   Pages = {2826-2854},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1214/16-AOP1125},
   Doi = {10.1214/16-AOP1125},
   Key = {fds329100}
}


%% Kiselev, Alexander A.   
@article{fds335539,
   Author = {Do, T and Kiselev, A and Ryzhik, L and Tan, C},
   Title = {Global Regularity for the Fractional Euler Alignment
             System},
   Journal = {Archive for Rational Mechanics and Analysis},
   Volume = {228},
   Number = {1},
   Pages = {1-37},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1007/s00205-017-1184-2},
   Doi = {10.1007/s00205-017-1184-2},
   Key = {fds335539}
}

@article{fds330278,
   Author = {Kiselev, A and Tan, C},
   Title = {Finite time blow up in the hyperbolic Boussinesq
             system},
   Journal = {Advances in Mathematics},
   Volume = {325},
   Pages = {34-55},
   Year = {2018},
   Month = {February},
   url = {http://dx.doi.org/10.1016/j.aim.2017.11.019},
   Abstract = {© 2017 Elsevier Inc. In recent work of Luo and Hou [10], a
             new scenario for finite time blow up in solutions of 3D
             Euler equation has been proposed. The scenario involves a
             ring of hyperbolic points of the flow located at the
             boundary of a cylinder. In this paper, we propose a two
             dimensional model that we call “hyperbolic Boussinesq
             system”. This model is designed to provide insight into
             the hyperbolic point blow up scenario. The model features an
             incompressible velocity vector field, a simplified
             Biot–Savart law, and a simplified term modeling buoyancy.
             We prove that finite time blow up happens for a natural
             class of initial data.},
   Doi = {10.1016/j.aim.2017.11.019},
   Key = {fds330278}
}

@article{fds330279,
   Author = {Choi, K and Hou, TY and Kiselev, A and Luo, G and Sverak, V and Yao,
             Y},
   Title = {On the Finite-Time Blowup of a One-Dimensional Model for the
             Three-Dimensional Axisymmetric Euler Equations},
   Journal = {Communications on Pure and Applied Mathematics},
   Volume = {70},
   Number = {11},
   Pages = {2218-2243},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1002/cpa.21697},
   Doi = {10.1002/cpa.21697},
   Key = {fds330279}
}

@article{fds330280,
   Author = {Kiselev, A and Yao, Y and Zlatoš, A},
   Title = {Local Regularity for the Modified SQG Patch
             Equation},
   Journal = {Communications on Pure and Applied Mathematics},
   Volume = {70},
   Number = {7},
   Pages = {1253-1315},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1002/cpa.21677},
   Doi = {10.1002/cpa.21677},
   Key = {fds330280}
}


%% Kovalsky, Shahar   
@article{fds329934,
   Author = {Aigerman, N and Kovalsky, SZ and Lipman, Y},
   Title = {Spherical orbifold tutte embeddings},
   Journal = {Acm Transactions on Graphics},
   Volume = {36},
   Number = {4},
   Pages = {1-13},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1145/3072959.3073615},
   Doi = {10.1145/3072959.3073615},
   Key = {fds329934}
}

@article{fds329935,
   Author = {Shtengel, A and Poranne, R and Sorkine-Hornung, O and Kovalsky, SZ and Lipman, Y},
   Title = {Geometric optimization via composite majorization},
   Journal = {Acm Transactions on Graphics},
   Volume = {36},
   Number = {4},
   Pages = {1-11},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1145/3072959.3073618},
   Doi = {10.1145/3072959.3073618},
   Key = {fds329935}
}


%% Layton, Anita T.   
@article{fds338526,
   Author = {Li, Q and McDonough, AA and Layton, HE and Layton,
             AT},
   Title = {Functional implications of sexual dimorphism of transporter
             patterns along the rat proximal tubule: modeling and
             analysis.},
   Journal = {American Journal of Physiology. Renal Physiology},
   Volume = {315},
   Number = {3},
   Pages = {F692-F700},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1152/ajprenal.00171.2018},
   Abstract = {The goal of this study is to investigate the functional
             implications of the sexual dimorphism in transporter
             patterns along the proximal tubule. To do so, we have
             developed sex-specific computational models of solute and
             water transport in the proximal convoluted tubule of the rat
             kidney. The models account for the sex differences in
             expression levels of the apical and basolateral
             transporters, in single-nephron glomerular filtration rate,
             and in tubular dimensions. Model simulations predict that
             70.6 and 38.7% of the filtered volume is reabsorbed by the
             proximal tubule of the male and female rat kidneys,
             respectively. The lower fractional volume reabsorption in
             females can be attributed to their smaller transport area
             and lower aquaporin-1 expression level. The latter also
             results in a larger contribution of the paracellular pathway
             to water transport. Correspondingly similar fractions (70.9
             and 39.2%) of the filtered Na+ are reabsorbed by the male
             and female proximal tubule models, respectively. The lower
             fractional Na+ reabsorption in females is due primarily to
             their smaller transport area and lower Na+/H+ exchanger
             isoform 3 and claudin-2 expression levels. Notably, unlike
             most Na+ transporters, whose expression levels are lower in
             females, Na+-glucose cotransporter 2 (SGLT2) expression
             levels are 2.5-fold higher in females. Model simulations
             suggest that the higher SGLT2 expression in females may
             compensate for their lower tubular transport area to achieve
             a hyperglycemic tolerance similar to that of
             males.},
   Doi = {10.1152/ajprenal.00171.2018},
   Key = {fds338526}
}

@article{fds339517,
   Author = {Wei, N and Gumz, ML and Layton, AT},
   Title = {Predicted effect of circadian clock modulation of NHE3 of a
             proximal tubule cell on sodium transport.},
   Journal = {American Journal of Physiology. Renal Physiology},
   Volume = {315},
   Number = {3},
   Pages = {F665-F676},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1152/ajprenal.00008.2018},
   Abstract = {Major renal functions such as renal blood flow, glomerular
             filtration rate, and urinary excretion are known to exhibit
             circadian oscillations. However, the underlying mechanisms
             that govern these variations have yet to be fully
             elucidated. To better understand the impact of the circadian
             clock on renal solute and water transport, we have developed
             a computational model of the renal circadian clock and
             coupled that model to an epithelial transport model of the
             proximal convoluted cell of the rat kidney. The activity of
             the Na+-H+ exchanger 3 (NHE3) is assumed to be regulated by
             changes in transcription of the NHE3 mRNA due to regulation
             by circadian clock proteins. The model predicts the rhythmic
             oscillations in NHE3 activity, which gives rise to
             significant daily fluctuations in Na+ and water transport of
             the proximal tubule cell. Additionally, the model predicts
             that 1) mutation in period 2 (Per2) or cryptochrome 1 (Cry1)
             preserves the circadian rhythm and modestly raises Na+
             reabsorption; 2) mutation in Bmal1 or CLOCK eliminates the
             circadian rhythm and modestly lowers Na+ reabsorption; 3)
             mutation in Rev-Erb or ROR-related orphan receptor (Ror) has
             minimal impact on the circadian oscillations. The model
             represents the first step in building a tool set aimed at
             increasing our understanding of how the molecular clock
             affects renal ion transport and renal function, which likely
             has important implications for kidney disease.},
   Doi = {10.1152/ajprenal.00008.2018},
   Key = {fds339517}
}

@article{fds339829,
   Author = {Layton, AT and Vallon, V},
   Title = {Renal tubular solute transport and oxygen consumption:
             insights from computational models.},
   Journal = {Current Opinion in Nephrology and Hypertension},
   Volume = {27},
   Number = {5},
   Pages = {384-389},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1097/mnh.0000000000000435},
   Abstract = {To maintain electrolyte homeostasis, the kidneys reabsorb
             more than 99% of the filtered Na under physiological
             conditions, resulting in less than 1% of the filtered Na
             excreted in urine. In contrast, due to distal tubular
             secretion, urinary K output may exceed filtered load. This
             review focuses on a relatively new methodology for
             investigating renal epithelial transport, computational
             modelling and highlights recent insights regarding renal Na
             and K transport and O2 consumption under pathophysiological
             conditions, with a focus on nephrectomy.Recent modelling
             studies investigated the extent to which the adaptive
             response to nephrectomy, which includes elevation in
             single-nephron glomerular filtration rate and tubular
             transport capacity, may achieve balance but increases O2
             consumption per nephron. Simulation results pointed to
             potential mechanisms in a hemi-nephrectomized rat that may
             attenuate the natriuresis response under K load, or that may
             augment the natriuretic, diuretic and kaliuretic effects of
             sodium glucose cotransporter 2 inhibition.Computational
             models provide a systemic approach for investigating system
             perturbations, such as those induced by drug administration
             or genetic alterations. Thus, computational models can be a
             great asset in data interpretation concerning (but not
             limited to) renal tubular transport and metabolism.},
   Doi = {10.1097/mnh.0000000000000435},
   Key = {fds339829}
}

@article{fds336409,
   Author = {Layton, AT},
   Title = {Sweet success? SGLT2 inhibitors and diabetes.},
   Journal = {American Journal of Physiology. Renal Physiology},
   Volume = {314},
   Number = {6},
   Pages = {F1034-F1035},
   Year = {2018},
   Month = {June},
   url = {http://dx.doi.org/10.1152/ajprenal.00557.2017},
   Doi = {10.1152/ajprenal.00557.2017},
   Key = {fds336409}
}

@article{fds336410,
   Author = {Leete, J and Gurley, S and Layton, AT},
   Title = {Modeling sex differences in the renin angiotensin system and
             the efficacy of antihypertensive therapies},
   Journal = {Computers & Chemical Engineering},
   Volume = {112},
   Pages = {253-264},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1016/j.compchemeng.2018.02.009},
   Abstract = {© 2018 Elsevier Ltd The renin angiotensin system is a major
             regulator of blood pressure and a target for many
             anti-hypertensive therapies; yet the efficacy of these
             treatments varies between the sexes. We use published data
             for systemic RAS hormones to build separate models for four
             groups of rats: male normotensive, male hypertensive, female
             normotensive, and female hypertensive rats. We found that
             plasma renin activity, angiotensinogen production rate,
             angiotensin converting enzyme activity, and neutral
             endopeptidase activity differ significantly among the four
             groups of rats. Model results indicate that angiotensin
             converting enzyme inhibitors and angiotensin receptor
             blockers induce similar percentage decreases in angiotensin
             I and II between groups, but substantially different
             absolute decreases. We further propose that a major
             difference between the male and female RAS may be the
             strength of the feedback mechanism, by which receptor bound
             angiotensin II impacts the production of
             renin.},
   Doi = {10.1016/j.compchemeng.2018.02.009},
   Key = {fds336410}
}

@article{fds336411,
   Author = {Layton, AT and Edwards, A and Vallon, V},
   Title = {Renal potassium handling in rats with subtotal nephrectomy:
             modeling and analysis.},
   Journal = {American Journal of Physiology. Renal Physiology},
   Volume = {314},
   Number = {4},
   Pages = {F643-F657},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1152/ajprenal.00460.2017},
   Abstract = {We sought to decipher the mechanisms underlying the kidney's
             response to changes in K+ load and intake, under
             physiological and pathophysiological conditions. To
             accomplish that goal, we applied a published computational
             model of epithelial transport along rat nephrons in a sham
             rat, an uninephrectomized (UNX) rat, and a
             5/6-nephrectomized (5/6-NX) rat that also considers
             adaptations in glomerular filtration rate and tubular
             growth. Model simulations of an acute K+ load indicate that
             elevated expression levels and activities of Na+/K+-ATPase,
             epithelial sodium channels, large-conductance Ca2+-activated
             K+ channels, and renal outer medullary K+ channels, together
             with downregulation of sodium-chloride cotransporters (NCC),
             increase K+ secretion along the connecting tubule, resulting
             in a >6-fold increase in urinary K+ excretion in sham rats,
             which substantially exceeds the filtered K+ load. In the UNX
             and 5/6-NX models, the acute K+ load is predicted to
             increase K+ excretion, but at significantly reduced levels
             compared with sham. Acute K+ load is accompanied by
             natriuresis in sham rats. Model simulations suggest that the
             lesser natriuretic effect observed in the nephrectomized
             groups may be explained by impaired NCC downregulation in
             these kidneys. At a single-nephron level, a high K+ intake
             raises K+ secretion along the connecting tubule and
             reabsorption along the collecting duct in sham, and even
             more in UNX and 5/6-NX. However, the increased K+ secretion
             per tubule fails to sufficiently compensate for the
             reduction in nephron number, such that nephrectomized rats
             have an impaired ability to excrete an acute or chronic K+
             load.},
   Doi = {10.1152/ajprenal.00460.2017},
   Key = {fds336411}
}

@article{fds336412,
   Author = {Layton, AT and Vallon, V},
   Title = {Cardiovascular benefits of SGLT2 inhibition in diabetes and
             chronic kidney diseases.},
   Journal = {Acta Physiologica},
   Volume = {222},
   Number = {4},
   Pages = {e13050},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1111/apha.13050},
   Doi = {10.1111/apha.13050},
   Key = {fds336412}
}

@article{fds336413,
   Author = {Wei, N and Layton, AT},
   Title = {Theoretical assessment of the Ca2+ oscillations in the
             afferent arteriole smooth muscle cell of the rat
             kidney},
   Journal = {International Journal of Biomathematics},
   Volume = {11},
   Number = {03},
   Pages = {1850043-1850043},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1142/S1793524518500432},
   Doi = {10.1142/S1793524518500432},
   Key = {fds336413}
}

@article{fds329189,
   Author = {Edwards, A and Layton, AT},
   Title = {Cell Volume Regulation in the Proximal Tubule of Rat Kidney
             : Proximal Tubule Cell Volume Regulation.},
   Journal = {Bulletin of Mathematical Biology},
   Volume = {79},
   Number = {11},
   Pages = {2512-2533},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1007/s11538-017-0338-6},
   Abstract = {We developed a dynamic model of a rat proximal convoluted
             tubule cell in order to investigate cell volume regulation
             mechanisms in this nephron segment. We examined whether
             regulatory volume decrease (RVD), which follows exposure to
             a hyposmotic peritubular solution, can be achieved solely
             via stimulation of basolateral K[Formula: see text] and
             [Formula: see text] channels and [Formula: see
             text]-[Formula: see text] cotransporters. We also determined
             whether regulatory volume increase (RVI), which follows
             exposure to a hyperosmotic peritubular solution under
             certain conditions, may be accomplished by activating
             basolateral [Formula: see text]/H[Formula: see text]
             exchangers. Model predictions were in good agreement with
             experimental observations in mouse proximal tubule cells
             assuming that a 10% increase in cell volume induces a
             fourfold increase in the expression of basolateral
             K[Formula: see text] and [Formula: see text] channels and
             [Formula: see text]-[Formula: see text] cotransporters. Our
             results also suggest that in response to a hyposmotic
             challenge and subsequent cell swelling, [Formula: see
             text]-[Formula: see text] cotransporters are more efficient
             than basolateral K[Formula: see text] and [Formula: see
             text] channels at lowering intracellular osmolality and
             reducing cell volume. Moreover, both RVD and RVI are
             predicted to stabilize net transcellular [Formula: see text]
             reabsorption, that is, to limit the net [Formula: see text]
             flux decrease during a hyposmotic challenge or the net
             [Formula: see text] flux increase during a hyperosmotic
             challenge.},
   Doi = {10.1007/s11538-017-0338-6},
   Key = {fds329189}
}

@article{fds328946,
   Author = {Burt, T and Noveck, RJ and MacLeod, DB and Layton, AT and Rowland, M and Lappin, G},
   Title = {Intra-Target Microdosing (ITM): A Novel Drug Development
             Approach Aimed at Enabling Safer and Earlier Translation of
             Biological Insights Into Human Testing.},
   Journal = {Clinical and Translational Science},
   Volume = {10},
   Number = {5},
   Pages = {337-350},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1111/cts.12464},
   Doi = {10.1111/cts.12464},
   Key = {fds328946}
}

@article{fds320879,
   Author = {Sgouralis, I and Evans, RG and Layton, AT},
   Title = {Renal medullary and urinary oxygen tension during
             cardiopulmonary bypass in the rat.},
   Journal = {Mathematical Medicine and Biology : a Journal of the
             Ima},
   Volume = {34},
   Number = {3},
   Pages = {313-333},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1093/imammb/dqw010},
   Abstract = {Renal hypoxia could result from a mismatch in renal oxygen
             supply and demand, particularly in the renal medulla.
             Medullary hypoxic damage is believed to give rise to acute
             kidney injury, which is a prevalent complication of cardiac
             surgery performed on cardiopulmonary bypass (CPB). To
             determine the mechanisms that could lead to medullary
             hypoxia during CPB in the rat kidney, we developed a
             mathematical model which incorporates (i) autoregulation of
             renal blood flow and glomerular filtration rate, (ii)
             detailed oxygen transport and utilization in the renal
             medulla and (iii) oxygen transport along the ureter. Within
             the outer medulla, the lowest interstitial tissue P$_{\rm
             O2}$, which is an indicator of renal hypoxia, is predicted
             near the thick ascending limbs. Interstitial tissue P$_{\rm
             O2}$ exhibits a general decrease along the inner medullary
             axis, but urine P$_{\rm O2}$ increases significantly along
             the ureter. Thus, bladder urinary P$_{\rm O2}$ is predicted
             to be substantially higher than medullary P$_{\rm O2}$. The
             model is used to identify the phase of cardiac surgery
             performed on CPB that is associated with the highest risk
             for hypoxic kidney injury. Simulation results indicate that
             the outer medulla's vulnerability to hypoxic injury depends,
             in part, on the extent to which medullary blood flow is
             autoregulated. With imperfect medullary blood flow
             autoregulation, the model predicts that the rewarming phase
             of CPB, in which medullary blood flow is low but medullary
             oxygen consumption remains high, is the phase in which the
             kidney is most likely to suffer hypoxic injury.},
   Doi = {10.1093/imammb/dqw010},
   Key = {fds320879}
}

@article{fds328036,
   Author = {Chen, Y and Sullivan, JC and Edwards, A and Layton,
             AT},
   Title = {Sex-specific computational models of the spontaneously
             hypertensive rat kidneys: factors affecting nitric oxide
             bioavailability.},
   Journal = {American Journal of Physiology. Renal Physiology},
   Volume = {313},
   Number = {2},
   Pages = {F174-F183},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1152/ajprenal.00482.2016},
   Abstract = {The goals of this study were to 1) develop a computational
             model of solute transport and oxygenation in the kidney of
             the female spontaneously hypertensive rat (SHR), and 2)
             apply that model to investigate sex differences in nitric
             oxide (NO) levels in SHR and their effects on medullary
             oxygenation and oxidative stress. To accomplish these goals,
             we first measured NO synthase (NOS) 1 and NOS3 protein
             expression levels in total renal microvessels of male and
             female SHR. We found that the expression of both NOS1 and
             NOS3 is higher in the renal vasculature of females compared
             with males. To predict the implications of that finding on
             medullary oxygenation and oxidative stress levels, we
             developed a detailed computational model of the female SHR
             kidney. The model was based on a published male kidney model
             and represents solute transport and the biochemical
             reactions among O2, NO, and superoxide ([Formula: see text])
             in the renal medulla. Model simulations conducted using both
             male and female SHR kidney models predicted significant
             radial gradients in interstitial fluid oxygen tension (Po2)
             and NO and [Formula: see text] concentration in the outer
             medulla and upper inner medulla. The models also predicted
             that increases in endothelial NO-generating capacity, even
             when limited to specific vascular segments, may
             substantially raise medullary NO and Po2 levels. Other
             potential sex differences in SHR, including [Formula: see
             text] production rate, are predicted to significantly impact
             oxidative stress levels, but effects on NO concentration and
             Po2 are limited.},
   Doi = {10.1152/ajprenal.00482.2016},
   Key = {fds328036}
}

@article{fds328608,
   Author = {Layton, AT and Edwards, A and Vallon, V},
   Title = {Adaptive changes in GFR, tubular morphology, and transport
             in subtotal nephrectomized kidneys: modeling and
             analysis.},
   Journal = {American Journal of Physiology. Renal Physiology},
   Volume = {313},
   Number = {2},
   Pages = {F199-F209},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1152/ajprenal.00018.2017},
   Abstract = {Removal of renal mass stimulates anatomical and functional
             adaptations in the surviving nephrons, including elevations
             in single-nephron glomerular filtration rate (SNGFR) and
             tubular hypertrophy. A goal of this study is to assess the
             extent to which the concomitant increases in filtered load
             and tubular transport capacity preserve homeostasis of water
             and salt. To accomplish that goal, we developed
             computational models to simulate solute transport and
             metabolism along nephron populations in a uninephrectomized
             (UNX) rat and a 5/6-nephrectomized (5/6-NX) rat. Model
             simulations indicate that nephrectomy-induced SNGFR increase
             and tubular hypertrophy go a long way to normalize
             excretion, but alone are insufficient to fully maintain salt
             balance. We then identified increases in the protein density
             of Na+-K+-ATPase, Na+-K+-2Cl- cotransporter, Na+-Cl-
             cotransporter, and epithelial Na+ channel, such that the UNX
             and 5/6-NX models predict urine flow and urinary Na+ and K+
             excretions that are similar to sham levels. The models
             predict that, in the UNX and 5/6-NX kidneys, fractional
             water and salt reabsorption is similar to sham along the
             initial nephron segments (i.e., from the proximal tubule to
             the distal convoluted tubule), with a need to further reduce
             Na+ reabsorption and increase K+ secretion primarily along
             the connecting tubules and collecting ducts to achieve
             balance. Additionally, the models predict that, given the
             substantially elevated filtered and thus transport load
             among each of the surviving nephrons, oxygen consumption per
             nephron segment in a UNX or 5/6-NX kidney increases
             substantially. But due to the reduced nephron population,
             whole animal renal oxygen consumption is lower. The
             efficiency of tubular Na+ transport in the UNX and 5/6-NX
             kidneys is predicted to be similar to sham.},
   Doi = {10.1152/ajprenal.00018.2017},
   Key = {fds328608}
}

@article{fds326523,
   Author = {Chen, Y and Fry, BC and Layton, AT},
   Title = {Modeling glucose metabolism and lactate production in the
             kidney.},
   Journal = {Mathematical Biosciences},
   Volume = {289},
   Pages = {116-129},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1016/j.mbs.2017.04.008},
   Abstract = {The metabolism of glucose provides most of the ATP required
             for energy-dependent transport processes. In the inner
             medulla of the mammalian kidney, limited blood flow and O2
             supply yield low oxygen tension; therefore, a substantial
             fraction of the glucose metabolism in that region is
             anaerobic. Lactate is considered to be a waste product of
             anaerobic glycolysis, which yields two lactate molecules for
             each glucose molecule consumed, thereby likely leading to
             the production and accumulation of a significant amount of
             lactate in the inner medulla. To gain insights into the
             transport and metabolic processes in the kidney, we have
             developed a detailed mathematical model of the renal medulla
             of the rat kidney. The model represents the radial
             organization of the renal tubules and vessels, which centers
             around the vascular bundles in the outer medulla and around
             clusters of collecting ducts in the inner medulla. Model
             simulations yield significant radial gradients in
             interstitial fluid oxygen tension and glucose and lactate
             concentrations in the outer medulla and upper inner medulla.
             In the deep inner medulla, interstitial fluid concentrations
             become much more homogeneous, as the radial organization of
             tubules and vessels is not distinguishable. Using this
             model, we have identified parameters concerning glucose
             transport and basal metabolism, as well as lactate
             production via anaerobic glycolysis, that yield predicted
             blood glucose and lactate concentrations consistent with
             experimental measurements in the papillary tip. In addition,
             simulations indicate that the radial organization of the rat
             kidney may affect lactate buildup in the inner
             medulla.},
   Doi = {10.1016/j.mbs.2017.04.008},
   Key = {fds326523}
}

@article{fds325778,
   Author = {Layton, AT},
   Title = {A new microscope for the kidney: mathematics.},
   Journal = {American Journal of Physiology. Renal Physiology},
   Volume = {312},
   Number = {4},
   Pages = {F671-F672},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1152/ajprenal.00648.2016},
   Doi = {10.1152/ajprenal.00648.2016},
   Key = {fds325778}
}

@article{fds323660,
   Author = {Jiang, T and Li, Y and Layton, AT and Wang, W and Sun, Y and Li, M and Zhou,
             H and Yang, B},
   Title = {Generation and phenotypic analysis of mice lacking all urea
             transporters.},
   Journal = {Kidney International},
   Volume = {91},
   Number = {2},
   Pages = {338-351},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1016/j.kint.2016.09.017},
   Abstract = {Urea transporters (UT) are a family of transmembrane
             urea-selective channel proteins expressed in multiple
             tissues and play an important role in the urine
             concentrating mechanism of the mammalian kidney. UT
             inhibitors have diuretic activity and could be developed as
             novel diuretics. To determine if functional deficiency of
             all UTs in all tissues causes physiological abnormality, we
             established a novel mouse model in which all UTs were
             knocked out by deleting an 87 kb of DNA fragment containing
             most parts of Slc14a1 and Slc14a2 genes. Western blot
             analysis and immunofluorescence confirmed that there is no
             expression of urea transporter in these all-UT-knockout
             mice. Daily urine output was nearly 3.5-fold higher, with
             significantly lower urine osmolality in all-UT-knockout mice
             than that in wild-type mice. All-UT-knockout mice were not
             able to increase urinary urea concentration and osmolality
             after water deprivation, acute urea loading, or high protein
             intake. A computational model that simulated UT-knockout
             mouse models identified the individual contribution of each
             UT in urine concentrating mechanism. Knocking out all UTs
             also decreased the blood pressure and promoted the
             maturation of the male reproductive system. Thus, functional
             deficiency of all UTs caused a urea-selective
             urine-concentrating defect with little physiological
             abnormality in extrarenal organs.},
   Doi = {10.1016/j.kint.2016.09.017},
   Key = {fds323660}
}


%% Layton, Harold   
@article{fds338525,
   Author = {Li, Q and McDonough, AA and Layton, HE and Layton,
             AT},
   Title = {Functional implications of sexual dimorphism of transporter
             patterns along the rat proximal tubule: modeling and
             analysis.},
   Journal = {American Journal of Physiology. Renal Physiology},
   Volume = {315},
   Number = {3},
   Pages = {F692-F700},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1152/ajprenal.00171.2018},
   Abstract = {The goal of this study is to investigate the functional
             implications of the sexual dimorphism in transporter
             patterns along the proximal tubule. To do so, we have
             developed sex-specific computational models of solute and
             water transport in the proximal convoluted tubule of the rat
             kidney. The models account for the sex differences in
             expression levels of the apical and basolateral
             transporters, in single-nephron glomerular filtration rate,
             and in tubular dimensions. Model simulations predict that
             70.6 and 38.7% of the filtered volume is reabsorbed by the
             proximal tubule of the male and female rat kidneys,
             respectively. The lower fractional volume reabsorption in
             females can be attributed to their smaller transport area
             and lower aquaporin-1 expression level. The latter also
             results in a larger contribution of the paracellular pathway
             to water transport. Correspondingly similar fractions (70.9
             and 39.2%) of the filtered Na+ are reabsorbed by the male
             and female proximal tubule models, respectively. The lower
             fractional Na+ reabsorption in females is due primarily to
             their smaller transport area and lower Na+/H+ exchanger
             isoform 3 and claudin-2 expression levels. Notably, unlike
             most Na+ transporters, whose expression levels are lower in
             females, Na+-glucose cotransporter 2 (SGLT2) expression
             levels are 2.5-fold higher in females. Model simulations
             suggest that the higher SGLT2 expression in females may
             compensate for their lower tubular transport area to achieve
             a hyperglycemic tolerance similar to that of
             males.},
   Doi = {10.1152/ajprenal.00171.2018},
   Key = {fds338525}
}


%% Levine, Adam S.   
@article{fds328057,
   Author = {Baldwin, JA and Levine, AS and Sarkar, S},
   Title = {Khovanov homology and knot Floer homology for pointed
             links},
   Journal = {Journal of Knot Theory and Its Ramifications},
   Volume = {26},
   Number = {02},
   Pages = {1740004-1740004},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1142/S0218216517400041},
   Doi = {10.1142/S0218216517400041},
   Key = {fds328057}
}


%% Li, Lei   
@article{fds329321,
   Author = {Li, L and Liu, J-G and Lu, J},
   Title = {Fractional Stochastic Differential Equations Satisfying
             Fluctuation-Dissipation Theorem},
   Journal = {Journal of Statistical Physics},
   Volume = {169},
   Number = {2},
   Pages = {316-339},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1007/s10955-017-1866-z},
   Doi = {10.1007/s10955-017-1866-z},
   Key = {fds329321}
}

@article{fds327370,
   Author = {Li, L and Xu, X and Spagnolie, SE},
   Title = {A Locally Gradient-Preserving Reinitialization for Level Set
             Functions},
   Journal = {Journal of Scientific Computing},
   Volume = {71},
   Number = {1},
   Pages = {274-302},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1007/s10915-016-0299-1},
   Doi = {10.1007/s10915-016-0299-1},
   Key = {fds327370}
}

@article{fds331594,
   Author = {Li, L and Liu, J-G},
   Title = {A note on deconvolution with completely monotone sequences
             and discrete fractional calculus},
   Journal = {Quarterly of Applied Mathematics},
   Pages = {1-1},
   Year = {2017},
   url = {http://dx.doi.org/10.1090/qam/1479},
   Doi = {10.1090/qam/1479},
   Key = {fds331594}
}


%% Li, Yingzhou   
@article{fds329936,
   Author = {Li, Y and Ying, L},
   Title = {Distributed-memory hierarchical interpolative
             factorization},
   Journal = {Research in the Mathematical Sciences},
   Volume = {4},
   Number = {1},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1186/s40687-017-0100-6},
   Doi = {10.1186/s40687-017-0100-6},
   Key = {fds329936}
}

@article{fds329937,
   Author = {Zhang, L and Sun, L and Guan, Z and Lee, S and Li, Y and Deng, HD and Li, Y and Ahlborg, NL and Boloor, M and Melosh, NA and Chueh,
             WC},
   Title = {Quantifying and Elucidating Thermally Enhanced Minority
             Carrier Diffusion Length Using Radius-Controlled Rutile
             Nanowires.},
   Journal = {Nano Letters},
   Volume = {17},
   Number = {9},
   Pages = {5264-5272},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1021/acs.nanolett.7b01504},
   Abstract = {The minority carrier diffusion length (LD) is a crucial
             property that determines the performance of light absorbers
             in photoelectrochemical (PEC) cells. Many transition-metal
             oxides are stable photoanodes for solar water splitting but
             exhibit a small to moderate LD, ranging from a few
             nanometers (such as α-Fe2O3 and TiO2) to a few tens of
             nanometers (such as BiVO4). Under operating conditions, the
             temperature of PEC cells can deviate substantially from
             ambient, yet the temperature dependence of LD has not been
             quantified. In this work, we show that measuring the
             photocurrent as a function of both temperature and absorber
             dimensions provides a quantitative method for evaluating the
             temperature-dependent minority carrier transport. By
             measuring photocurrents of nonstoichiometric rutile TiO2-x
             nanowires as a function of wire radius (19-75 nm) and
             temperature (10-70 °C), we extract the minority carrier
             diffusion length along with its activation energy. The
             minority carrier diffusion length in TiO2-x increases from 5
             nm at 25 °C to 10 nm at 70 °C, implying that enhanced
             carrier mobility outweighs the increase in the recombination
             rate with temperature. Additionally, by comparing the
             temperature-dependent photocurrent in BiVO4, TiO2, and
             α-Fe2O3, we conclude that the ratio of the minority carrier
             diffusion length to the depletion layer width determines the
             extent of temperature enhancement, and reconcile the
             widespread temperature coefficients, which ranged from 0.6
             to 1.7% K-1. This insight provides a general design rule to
             select light absorbers for large thermally activated
             photocurrents and to predict PEC cell characteristics at a
             range of temperatures encountered during realistic device
             operation.},
   Doi = {10.1021/acs.nanolett.7b01504},
   Key = {fds329937}
}

@article{fds328965,
   Author = {Li, Y and Yang, H and Ying, L},
   Title = {Multidimensional butterfly factorization},
   Journal = {Applied and Computational Harmonic Analysis},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1016/j.acha.2017.04.002},
   Doi = {10.1016/j.acha.2017.04.002},
   Key = {fds328965}
}

@article{fds328966,
   Author = {Li, Y and Yang, H},
   Title = {Interpolative Butterfly Factorization},
   Journal = {Siam Journal on Scientific Computing},
   Volume = {39},
   Number = {2},
   Pages = {A503-A531},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1074941},
   Doi = {10.1137/16M1074941},
   Key = {fds328966}
}


%% Liu, Jian-Guo   
@article{fds335603,
   Author = {Feng, Y and Li, L and Liu, J-G and Xu, X},
   Title = {A note on one-dimensional time fractional
             ODEs},
   Journal = {Applied Mathematics Letters},
   Volume = {83},
   Pages = {87-94},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1016/j.aml.2018.03.015},
   Doi = {10.1016/j.aml.2018.03.015},
   Key = {fds335603}
}

@article{fds335604,
   Author = {Li, L and Liu, J-G and Wang, L},
   Title = {Cauchy problems for Keller–Segel type time–space
             fractional diffusion equation},
   Journal = {Journal of Differential Equations},
   Volume = {265},
   Number = {3},
   Pages = {1044-1096},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1016/j.jde.2018.03.025},
   Abstract = {© 2018 Elsevier Inc. This paper investigates Cauchy
             problems for nonlinear fractional time–space generalized
             Keller–Segel equation Dtβ0cρ+(−△)[Formula
             presented]ρ+∇⋅(ρB(ρ))=0, where Caputo derivative
             Dtβ0cρ models memory effects in time, fractional Laplacian
             (−△)[Formula presented]ρ represents Lévy diffusion and
             B(ρ)=−sn,γ∫Rn[Formula presented]ρ(y)dy is the Riesz
             potential with a singular kernel which takes into account
             the long rang interaction. We first establish
             Lr−Lqestimates and weighted estimates of the fundamental
             solutions (P(x,t),Y(x,t)) (or equivalently, the solution
             operators (Sαβ(t),Tαβ(t))). Then, we prove the existence
             and uniqueness of the mild solutions when initial data are
             in Lpspaces, or the weighted spaces. Similar to
             Keller–Segel equations, if the initial data are small in
             critical space Lpc(Rn) (pc=[Formula presented]), we
             construct the global existence. Furthermore, we prove the
             L1integrability and integral preservation when the initial
             data are in L1(Rn)∩Lp(Rn) or L1(Rn)∩Lpc(Rn). Finally,
             some important properties of the mild solutions including
             the nonnegativity preservation, mass conservation and blowup
             behaviors are established.},
   Doi = {10.1016/j.jde.2018.03.025},
   Key = {fds335604}
}

@article{fds335605,
   Author = {Liu, JG and Tang, M and Wang, L and Zhou, Z},
   Title = {An accurate front capturing scheme for tumor growth models
             with a free boundary limit},
   Journal = {Journal of Computational Physics},
   Volume = {364},
   Pages = {73-94},
   Year = {2018},
   Month = {July},
   url = {http://dx.doi.org/10.1016/j.jcp.2018.03.013},
   Abstract = {© 2018 Elsevier Inc. We consider a class of tumor growth
             models under the combined effects of density-dependent
             pressure and cell multiplication, with a free boundary model
             as its singular limit when the pressure-density relationship
             becomes highly nonlinear. In particular, the constitutive
             law connecting pressure p and density ρ is p(ρ)=[Formula
             presented]ρm−1, and when m≫1, the cell density ρ may
             evolve its support according to a pressure-driven geometric
             motion with sharp interface along its boundary. The
             nonlinearity and degeneracy in the diffusion bring great
             challenges in numerical simulations. Prior to the present
             paper, there is lack of standard mechanism to numerically
             capture the front propagation speed as m≫1. In this paper,
             we develop a numerical scheme based on a novel
             prediction-correction reformulation that can accurately
             approximate the front propagation even when the nonlinearity
             is extremely strong. We show that the semi-discrete scheme
             naturally connects to the free boundary limit equation as
             m→∞. With proper spatial discretization, the fully
             discrete scheme has improved stability, preserves
             positivity, and can be implemented without nonlinear
             solvers. Finally, extensive numerical examples in both one
             and two dimensions are provided to verify the claimed
             properties in various applications.},
   Doi = {10.1016/j.jcp.2018.03.013},
   Key = {fds335605}
}

@article{fds335606,
   Author = {Chen, K and Li, Q and Liu, J-G},
   Title = {Online learning in optical tomography: a stochastic
             approach},
   Journal = {Inverse Problems},
   Volume = {34},
   Number = {7},
   Pages = {075010-075010},
   Year = {2018},
   Month = {July},
   url = {http://dx.doi.org/10.1088/1361-6420/aac220},
   Doi = {10.1088/1361-6420/aac220},
   Key = {fds335606}
}

@article{fds335607,
   Author = {Gao, Y and Liu, J-G and Lu, XY and Xu, X},
   Title = {Maximal monotone operator theory and its applications to
             thin film equation in epitaxial growth on vicinal
             surface},
   Journal = {Calculus of Variations and Partial Differential
             Equations},
   Volume = {57},
   Number = {2},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1007/s00526-018-1326-x},
   Doi = {10.1007/s00526-018-1326-x},
   Key = {fds335607}
}

@article{fds333565,
   Author = {Liu, J-G and Xu, X},
   Title = {Partial regularity of weak solutions to a PDE system with
             cubic nonlinearity},
   Journal = {Journal of Differential Equations},
   Volume = {264},
   Number = {8},
   Pages = {5489-5526},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1016/j.jde.2018.01.001},
   Abstract = {© 2018 Elsevier Inc. In this paper we investigate
             regularity properties of weak solutions to a PDE system that
             arises in the study of biological transport networks. The
             system consists of a possibly singular elliptic equation for
             the scalar pressure of the underlying biological network
             coupled to a diffusion equation for the conductance vector
             of the network. There are several different types of
             nonlinearities in the system. Of particular mathematical
             interest is a term that is a polynomial function of
             solutions and their partial derivatives and this polynomial
             function has degree three. That is, the system contains a
             cubic nonlinearity. Only weak solutions to the system have
             been shown to exist. The regularity theory for the system
             remains fundamentally incomplete. In particular, it is not
             known whether or not weak solutions develop singularities.
             In this paper we obtain a partial regularity theorem, which
             gives an estimate for the parabolic Hausdorff dimension of
             the set of possible singular points.},
   Doi = {10.1016/j.jde.2018.01.001},
   Key = {fds333565}
}

@article{fds333566,
   Author = {Li, L and Liu, J-G},
   Title = {p -Euler equations and p -Navier–Stokes
             equations},
   Journal = {Journal of Differential Equations},
   Volume = {264},
   Number = {7},
   Pages = {4707-4748},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1016/j.jde.2017.12.023},
   Abstract = {© 2017 Elsevier Inc. We propose in this work new systems of
             equations which we call p-Euler equations and
             p-Navier-Stokes equations. p-Euler equations are derived as
             the Euler-Lagrange equations for the action represented by
             the Benamou-Brenier characterization of Wasserstein-p
             distances, with incompressibility constraint. p-Euler
             equations have similar structures with the usual Euler
             equations but the 'momentum' is the signed (p-1)-th power of
             the velocity. In the 2D case, the p-Euler equations have
             streamfunction-vorticity formulation, where the vorticity is
             given by the p-Laplacian of the streamfunction. By adding
             diffusion presented by γ-Laplacian of the velocity, we
             obtain what we call p-Navier-Stokes equations. If γ=p, the
             a priori energy estimates for the velocity and momentum have
             dual symmetries. Using these energy estimates and a
             time-shift estimate, we show the global existence of weak
             solutions for the p-Navier-Stokes equations in Rd for γ=p
             and p≥d≥2 through a compactness criterion.},
   Doi = {10.1016/j.jde.2017.12.023},
   Key = {fds333566}
}

@article{fds338622,
   Author = {Feng, Y and Li, L and Liu, JG},
   Title = {Semigroups of stochastic gradient descent and online
             principal component analysis: Properties and diffusion
             approximations},
   Journal = {Communications in Mathematical Sciences},
   Volume = {16},
   Number = {3},
   Pages = {777-789},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.4310/CMS.2018.v16.n3.a7},
   Abstract = {© 2018 International Press. We study the Markov semigroups
             for two important algorithms from machine learning:
             stochastic gradient descent (SGD) and online principal
             component analysis (PCA). We investigate the effects of
             small jumps on the properties of the semigroups. Properties
             including regularity preserving, L∞contraction are
             discussed. These semigroups are the dual of the semigroups
             for evolution of probability, while the latter are
             L1contracting and positivity preserving. Using these
             properties, we show that stochastic differential equations
             (SDEs) in Rd (on the sphere Sd-1) can be used to approximate
             SGD (online PCA) weakly. These SDEs may be used to provide
             some insights of the behaviors of these algorithms.},
   Doi = {10.4310/CMS.2018.v16.n3.a7},
   Key = {fds338622}
}

@article{fds338623,
   Author = {Li, L and Liu, JG},
   Title = {Some compactness criteria for weak solutions of time
             fractional pdes},
   Journal = {Siam Journal on Mathematical Analysis},
   Volume = {50},
   Number = {4},
   Pages = {3963-3995},
   Publisher = {SIAM PUBLICATIONS},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1137/17M1145549},
   Abstract = {© 2018 Society for Industrial and Applied Mathematics. The
             Aubin-Lions lemma and its variants play crucial roles for
             the existence of weak solutions of nonlinear evolutionary
             PDEs. In this paper, we aim to develop some compactness
             criteria that are analogies of the Aubin-Lions lemma for the
             existence of weak solutions to time fractional PDEs. We
             first define the weak Caputo derivatives of order γ ϵ (0;
             1) for functions valued in general Banach spaces, consistent
             with the traditional definition if the space is Rd and
             functions are absolutely continuous. Based on a
             Volterra-type integral form, we establish some time
             regularity estimates of the functions provided that the weak
             Caputo derivatives are in certain spaces. The compactness
             criteria are then established using the time regularity
             estimates. The existence of weak solutions for a special
             case of time fractional compressible Navier-Stokes equations
             with constant density and time fractional Keller-Segel
             equations in R2 are then proved as model problems. This work
             provides a framework for studying weak solutions of
             nonlinear time fractional PDEs.},
   Doi = {10.1137/17M1145549},
   Key = {fds338623}
}

@article{fds335608,
   Author = {Gao, Y and Li, L and Liu, J-G},
   Title = {A Dispersive Regularization for the Modified Camassa--Holm
             Equation},
   Journal = {Siam Journal on Mathematical Analysis},
   Volume = {50},
   Number = {3},
   Pages = {2807-2838},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1137/17M1132756},
   Doi = {10.1137/17M1132756},
   Key = {fds335608}
}

@article{fds335609,
   Author = {Li, L and Liu, J-G},
   Title = {A Generalized Definition of Caputo Derivatives and Its
             Application to Fractional ODEs},
   Journal = {Siam Journal on Mathematical Analysis},
   Volume = {50},
   Number = {3},
   Pages = {2867-2900},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1137/17M1160318},
   Doi = {10.1137/17M1160318},
   Key = {fds335609}
}

@article{fds329519,
   Author = {Li, L and Liu, J-G and Lu, J},
   Title = {Fractional Stochastic Differential Equations Satisfying
             Fluctuation-Dissipation Theorem},
   Journal = {Journal of Statistical Physics},
   Volume = {169},
   Number = {2},
   Pages = {316-339},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1007/s10955-017-1866-z},
   Doi = {10.1007/s10955-017-1866-z},
   Key = {fds329519}
}

@article{fds333569,
   Author = {Liu, J-G and Wang, L and Zhou, Z},
   Title = {Positivity-preserving and asymptotic preserving method for
             2D Keller-Segal equations},
   Journal = {Mathematics of Computation},
   Volume = {87},
   Number = {311},
   Pages = {1165-1189},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1090/mcom/3250},
   Doi = {10.1090/mcom/3250},
   Key = {fds333569}
}

@article{fds333568,
   Author = {Coquel, F and Jin, S and Liu, J-G and Wang, L},
   Title = {Entropic sub-cell shock capturing schemes via Jin-Xin
             relaxation and Glimm front sampling for scalar conservation
             laws},
   Journal = {Mathematics of Computation},
   Volume = {87},
   Number = {311},
   Pages = {1083-1126},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1090/mcom/3253},
   Doi = {10.1090/mcom/3253},
   Key = {fds333568}
}

@article{fds329520,
   Author = {Liu, J-G and Ma, Z and Zhou, Z},
   Title = {Explicit and Implicit TVD Schemes for Conservation Laws with
             Caputo Derivatives},
   Journal = {Journal of Scientific Computing},
   Volume = {72},
   Number = {1},
   Pages = {291-313},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1007/s10915-017-0356-4},
   Doi = {10.1007/s10915-017-0356-4},
   Key = {fds329520}
}

@article{fds329521,
   Author = {Gao, Y and Ji, H and Liu, J-G and Witelski, TP},
   Title = {Global existence of solutions to a tear film model with
             locally elevated evaporation rates},
   Journal = {Physica D: Nonlinear Phenomena},
   Volume = {350},
   Pages = {13-25},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1016/j.physd.2017.03.005},
   Doi = {10.1016/j.physd.2017.03.005},
   Key = {fds329521}
}

@article{fds329522,
   Author = {Gao, Y and Liu, J-G and Lu, J},
   Title = {Continuum Limit of a Mesoscopic Model with Elasticity of
             Step Motion on Vicinal Surfaces},
   Journal = {Journal of Nonlinear Science},
   Volume = {27},
   Number = {3},
   Pages = {873-926},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1007/s00332-016-9354-1},
   Doi = {10.1007/s00332-016-9354-1},
   Key = {fds329522}
}

@article{fds325700,
   Author = {Degond, P and Liu, J-G and Pego, RL},
   Title = {Coagulation–Fragmentation Model for Animal Group-Size
             Statistics},
   Journal = {Journal of Nonlinear Science},
   Volume = {27},
   Number = {2},
   Pages = {379-424},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1007/s00332-016-9336-3},
   Doi = {10.1007/s00332-016-9336-3},
   Key = {fds325700}
}

@article{fds327636,
   Author = {Huang, H and Liu, J-G},
   Title = {Error estimate of a random particle blob method for the
             Keller-Segel equation},
   Journal = {Mathematics of Computation},
   Volume = {86},
   Number = {308},
   Pages = {2719-2744},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1090/mcom/3174},
   Doi = {10.1090/mcom/3174},
   Key = {fds327636}
}

@article{fds325701,
   Author = {Liu, J-G and Wang, J},
   Title = {Global existence for a thin film equation with subcritical
             mass},
   Journal = {Discrete and Continuous Dynamical Systems Series
             B},
   Volume = {22},
   Number = {4},
   Pages = {1461-1492},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.3934/dcdsb.2017070},
   Doi = {10.3934/dcdsb.2017070},
   Key = {fds325701}
}

@article{fds329524,
   Author = {Gao, Y and Liu, J-G and Lu, J},
   Title = {Weak Solution of a Continuum Model For Vicinal Surface in
             The Attachment-Detachment-Limited Regime},
   Journal = {Siam Journal on Mathematical Analysis},
   Volume = {49},
   Number = {3},
   Pages = {1705-1731},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1094543},
   Doi = {10.1137/16M1094543},
   Key = {fds329524}
}

@article{fds331396,
   Author = {Liu, J-G and Wang, J},
   Title = {A generalized Sz. Nagy inequality in higher dimensions and
             the critical thin film equation},
   Journal = {Nonlinearity},
   Volume = {30},
   Number = {1},
   Pages = {35-60},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1088/0951-7715/30/1/35},
   Doi = {10.1088/0951-7715/30/1/35},
   Key = {fds331396}
}

@article{fds323838,
   Author = {Degond, P and Liu, J-G and Merino-Aceituno, S and Tardiveau,
             T},
   Title = {Continuum dynamics of the intention field under weakly
             cohesive social interaction},
   Journal = {Mathematical Models & Methods in Applied
             Sciences},
   Volume = {27},
   Number = {01},
   Pages = {159-182},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1142/S021820251740005X},
   Doi = {10.1142/S021820251740005X},
   Key = {fds323838}
}

@article{fds329525,
   Author = {Gao, Y and Liu, J-G},
   Title = {Global Convergence of a Sticky Particle Method for the
             Modified Camassa--Holm Equation},
   Journal = {Siam Journal on Mathematical Analysis},
   Volume = {49},
   Number = {2},
   Pages = {1267-1294},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1102069},
   Doi = {10.1137/16M1102069},
   Key = {fds329525}
}

@article{fds330536,
   Author = {Liu, J-G and Xu, X},
   Title = {Analytical Validation of a Continuum Model for the Evolution
             of a Crystal Surface in Multiple Space Dimensions},
   Journal = {Siam Journal on Mathematical Analysis},
   Volume = {49},
   Number = {3},
   Pages = {2220-2245},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1098474},
   Doi = {10.1137/16M1098474},
   Key = {fds330536}
}

@article{fds338528,
   Author = {Gao, Y and Ji, H and Liu, J-G and P. Witelski and T},
   Title = {A vicinal surface model for epitaxial growth with
             logarithmic free energy},
   Journal = {Discrete & Continuous Dynamical Systems B},
   Volume = {22},
   Number = {11},
   Pages = {1-21},
   Year = {2017},
   url = {http://dx.doi.org/10.3934/dcdsb.2018170},
   Doi = {10.3934/dcdsb.2018170},
   Key = {fds338528}
}

@article{fds329523,
   Author = {Huang, H and Liu, J-G},
   Title = {Discrete-in-time random particle blob method for the
             Keller–Segel equation and convergence analysis},
   Journal = {Communications in Mathematical Sciences},
   Volume = {15},
   Number = {7},
   Pages = {1821-1842},
   Year = {2017},
   url = {http://dx.doi.org/10.4310/CMS.2017.v15.n7.a2},
   Abstract = {© 2017 International Press. We establish an error estimate
             of a discrete-in-time random particle blob method for the
             Keller{Segel (KS) equation in ℝ d (d≥2). With a blob
             size ε=N -1/d(d+1) log(N), we prove the convergence rate
             between the solution to the KS equation and the empirical
             measure of the random particle method under L 2 norm in
             probability, where N is the number of the
             particles.},
   Doi = {10.4310/CMS.2017.v15.n7.a2},
   Key = {fds329523}
}

@article{fds330537,
   Author = {Degond, P and Herty, M and Liu, J-G},
   Title = {Mean-field games and model predictive control},
   Journal = {Communications in Mathematical Sciences},
   Volume = {15},
   Number = {5},
   Pages = {1403-1422},
   Year = {2017},
   url = {http://dx.doi.org/10.4310/CMS.2017.v15.n5.a9},
   Doi = {10.4310/CMS.2017.v15.n5.a9},
   Key = {fds330537}
}

@article{fds333567,
   Author = {Li, L and Liu, J-G},
   Title = {A note on deconvolution with completely monotone sequences
             and discrete fractional calculus},
   Journal = {Quarterly of Applied Mathematics},
   Pages = {1-1},
   Year = {2017},
   url = {http://dx.doi.org/10.1090/qam/1479},
   Doi = {10.1090/qam/1479},
   Key = {fds333567}
}


%% Lu, Jianfeng   
@article{fds337144,
   Author = {Cao, Y and Lu, J},
   Title = {Stochastic dynamical low-rank approximation
             method},
   Journal = {Journal of Computational Physics},
   Volume = {372},
   Pages = {564-586},
   Year = {2018},
   Month = {November},
   url = {http://dx.doi.org/10.1016/j.jcp.2018.06.058},
   Abstract = {© 2018 Elsevier Inc. In this paper, we extend the dynamical
             low-rank approximation method to the space of finite signed
             measures. Under this framework, we derive stochastic
             low-rank dynamics for stochastic differential equations
             (SDEs) coming from classical stochastic dynamics or
             unraveling of Lindblad quantum master equations. We justify
             the proposed method by error analysis and also numerical
             examples for applications in solving high-dimensional SDE,
             stochastic Burgers' equation, and high-dimensional Lindblad
             equation.},
   Doi = {10.1016/j.jcp.2018.06.058},
   Key = {fds337144}
}

@article{fds337607,
   Author = {Li, X and Liu, J and Lu, J and Zhou, X},
   Title = {Moderate deviation for random elliptic PDE with small
             noise},
   Journal = {The Annals of Applied Probability},
   Volume = {28},
   Number = {5},
   Pages = {2781-2813},
   Year = {2018},
   Month = {October},
   url = {http://dx.doi.org/10.1214/17-AAP1373},
   Abstract = {© Institute of Mathematical Statistics, 2018. Partial
             differential equations with random inputs have become
             popular models to characterize physical systems with
             uncertainty coming from imprecise measurement and intrinsic
             randomness. In this paper, we perform asymptotic rare-event
             analysis for such elliptic PDEs with random inputs. In
             particular, we consider the asymptotic regime that the noise
             level converges to zero suggesting that the system
             uncertainty is low, but does exist. We develop sharp
             approximations of the probability of a large class of rare
             events.},
   Doi = {10.1214/17-AAP1373},
   Key = {fds337607}
}

@article{fds338041,
   Author = {Barthel, T and Lu, J},
   Title = {Fundamental Limitations for Measurements in Quantum
             Many-Body Systems.},
   Journal = {Physical Review Letters},
   Volume = {121},
   Number = {8},
   Pages = {080406},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1103/physrevlett.121.080406},
   Abstract = {Dynamical measurement schemes are an important tool for the
             investigation of quantum many-body systems, especially in
             the age of quantum simulation. Here, we address the question
             whether generic measurements can be implemented efficiently
             if we have access to a certain set of experimentally
             realizable measurements and can extend it through time
             evolution. For the latter, two scenarios are considered:
             (a) evolution according to unitary circuits and
             (b) evolution due to Hamiltonians that we can control in a
             time-dependent fashion. We find that the time needed to
             realize a certain measurement to a predefined accuracy
             scales in general exponentially with the system size-posing
             a fundamental limitation. The argument is based on the
             construction of ϵ-packings for manifolds of observables
             with identical spectra and a comparison of their
             cardinalities to those of ϵ-coverings for quantum circuits
             and unitary time-evolution operators. The former is related
             to the study of Grassmann manifolds.},
   Doi = {10.1103/physrevlett.121.080406},
   Key = {fds338041}
}

@article{fds332859,
   Author = {Huang, Y and Lu, J and Ming, P},
   Title = {A Concurrent Global–Local Numerical Method for Multiscale
             PDEs},
   Journal = {Journal of Scientific Computing},
   Volume = {76},
   Number = {2},
   Pages = {1188-1215},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1007/s10915-018-0662-5},
   Abstract = {© 2018 Springer Science+Business Media, LLC, part of
             Springer Nature We present a new hybrid numerical method for
             multiscale partial differential equations, which
             simultaneously captures the global macroscopic information
             and resolves the local microscopic events over regions of
             relatively small size. The method couples concurrently the
             microscopic coefficients in the region of interest with the
             homogenized coefficients elsewhere. The cost of the method
             is comparable to the heterogeneous multiscale method, while
             being able to recover microscopic information of the
             solution. The convergence of the method is proved for
             problems with bounded and measurable coefficients, while the
             rate of convergence is established for problems with rapidly
             oscillating periodic or almost-periodic coefficients.
             Numerical results are reported to show the efficiency and
             accuracy of the proposed method.},
   Doi = {10.1007/s10915-018-0662-5},
   Key = {fds332859}
}

@article{fds337608,
   Author = {You, Z and Li, L and Lu, J and Ge, H},
   Title = {Integrated tempering enhanced sampling method as the
             infinite switching limit of simulated tempering.},
   Journal = {The Journal of Chemical Physics},
   Volume = {149},
   Number = {8},
   Pages = {084114},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1063/1.5045369},
   Abstract = {A fast and accurate sampling method is in high demand, in
             order to bridge the large gaps between molecular dynamic
             simulations and experimental observations. Recently, an
             integrated tempering enhanced sampling (ITS) method has been
             proposed and successfully applied to various biophysical
             examples, significantly accelerating conformational
             sampling. The mathematical validation for its effectiveness
             has not been elucidated yet. Here we show that the
             integrated tempering enhanced sampling method can be viewed
             as a reformulation of the infinite switching limit of the
             simulated tempering method over a mixed potential. Moreover,
             we demonstrate that the efficiency of simulated tempering
             molecular dynamics improves as the frequency of switching
             between the temperatures is increased, based on the large
             deviation principle of empirical distributions. Our theory
             provides the theoretical justification of the advantage of
             ITS. Finally, we illustrate the utility of the infinite
             switching simulated tempering method through several
             numerical examples.},
   Doi = {10.1063/1.5045369},
   Key = {fds337608}
}

@article{fds332860,
   Author = {Lu, J and Zhou, Z},
   Title = {Accelerated sampling by infinite swapping of path integral
             molecular dynamics with surface hopping.},
   Journal = {The Journal of Chemical Physics},
   Volume = {148},
   Number = {6},
   Pages = {064110},
   Year = {2018},
   Month = {February},
   url = {http://dx.doi.org/10.1063/1.5005024},
   Abstract = {To accelerate the thermal equilibrium sampling of
             multi-level quantum systems, the infinite swapping limit of
             a recently proposed multi-level ring polymer representation
             is investigated. In the infinite swapping limit, the ring
             polymer evolves according to an averaged Hamiltonian with
             respect to all possible surface index configurations of the
             ring polymer and thus connects the surface hopping approach
             to the mean-field path-integral molecular dynamics. A
             multiscale integrator for the infinite swapping limit is
             also proposed to enable efficient sampling based on the
             limiting dynamics. Numerical results demonstrate the huge
             improvement of sampling efficiency of the infinite swapping
             compared with the direct simulation of path-integral
             molecular dynamics with surface hopping.},
   Doi = {10.1063/1.5005024},
   Key = {fds332860}
}

@article{fds336984,
   Author = {Cai, Z and Lu, J},
   Title = {A Quantum Kinetic Monte Carlo Method for Quantum Many-Body
             Spin Dynamics},
   Journal = {Siam Journal on Scientific Computing},
   Volume = {40},
   Number = {3},
   Pages = {B706-B722},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1137/17M1145446},
   Doi = {10.1137/17M1145446},
   Key = {fds336984}
}

@article{fds339290,
   Author = {Lu, J and Yang, H},
   Title = {Phase-space sketching for crystal image analysis based on
             synchrosqueezed transforms},
   Journal = {Siam Journal on Imaging Sciences},
   Volume = {11},
   Number = {3},
   Pages = {1954-1978},
   Publisher = {SIAM PUBLICATIONS},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1137/17M1129441},
   Abstract = {© 2018 Society for Industrial and Applied Mathematics.
             Recent developments of imaging techniques enable researchers
             to visualize materials at atomic resolution to better
             understand the microscopic structures of materials. This
             paper aims at automatic and quantitative characterization of
             potentially complicated microscopic crystal images,
             providing feedback to tweak theories and improve synthesis
             in materials science. As such, an efficient phase-space
             sketching method is proposed to encode microscopic crystal
             images in a translation, rotation, illumination, and scale
             invariant representation, which is also stable with respect
             to small deformations. Based on the phase-space sketching,
             we generalize our previous analysis framework for crystal
             images with simple structures to those with complicated
             geometry.},
   Doi = {10.1137/17M1129441},
   Key = {fds339290}
}

@article{fds339744,
   Author = {Delgadillo, R and Lu, J and Yang, X},
   Title = {Frozen Gaussian approximation for high frequency wave
             propagation in periodic media},
   Journal = {Asymptotic Analysis},
   Volume = {110},
   Number = {3-4},
   Pages = {113-135},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.3233/ASY-181479},
   Abstract = {© 2018 - IOS Press and the authors. All rights reserved.
             Propagation of high-frequency wave in periodic media is a
             challenging problem due to the existence of multiscale
             characterized by short wavelength, small lattice constant
             and large physical domain size. Conventional computational
             methods lead to extremely expensive costs, especially in
             high dimensions. In this paper, based on Bloch decomposition
             and asymptotic analysis in the phase space, we derive the
             frozen Gaussian approximation for high-frequency wave
             propagation in periodic media and establish its converge to
             the true solution. The formulation leads to efficient
             numerical algorithms, which are presented in a companion
             paper [SIAM J. Sci. Comput. 38 (2016), A2440-A2463].},
   Doi = {10.3233/ASY-181479},
   Key = {fds339744}
}

@article{fds329344,
   Author = {Yu, VW-Z and Corsetti, F and García, A and Huhn, WP and Jacquelin, M and Jia, W and Lange, B and Lin, L and Lu, J and Mi, W and Seifitokaldani, A and Vázquez-Mayagoitia, Á and Yang, C and Yang, H and Blum,
             V},
   Title = {ELSI: A unified software interface for Kohn–Sham
             electronic structure solvers},
   Journal = {Computer Physics Communications},
   Volume = {222},
   Pages = {267-285},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1016/j.cpc.2017.09.007},
   Doi = {10.1016/j.cpc.2017.09.007},
   Key = {fds329344}
}

@article{fds335540,
   Author = {Du, Q and Li, XH and Lu, J and Tian, X},
   Title = {A Quasi-nonlocal Coupling Method for Nonlocal and Local
             Diffusion Models},
   Journal = {Siam Journal on Numerical Analysis},
   Volume = {56},
   Number = {3},
   Pages = {1386-1404},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1137/17M1124012},
   Doi = {10.1137/17M1124012},
   Key = {fds335540}
}

@article{fds332861,
   Author = {Dai, S and Li, B and Lu, J},
   Title = {Convergence of Phase-Field Free Energy and Boundary Force
             for Molecular Solvation},
   Journal = {Archive for Rational Mechanics and Analysis},
   Volume = {227},
   Number = {1},
   Pages = {105-147},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1007/s00205-017-1158-4},
   Doi = {10.1007/s00205-017-1158-4},
   Key = {fds332861}
}

@article{fds339637,
   Author = {Cai, Z and Lu, J},
   Title = {A surface hopping Gaussian beam method for high-dimensional
             transport systems},
   Journal = {Siam Journal on Scientific Computing},
   Volume = {40},
   Number = {5},
   Pages = {B1277-B1301},
   Publisher = {SIAM PUBLICATIONS},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1137/17M1121299},
   Abstract = {© 2018 Society for Industrial and Applied Mathematics. We
             consider a set of linear hyperbolic equations coupled by a
             linear source term and introduce a surface hopping Gaussian
             beam method as its numerical solver. The Gaussian beam part
             is basically classic, while the surface hopping part is
             derived from the equations. The whole algorithm shows high
             efficiency and good parallelizability. An application on the
             quantum-classical Liouville equations is presented to show
             its potential use in practice.},
   Doi = {10.1137/17M1121299},
   Key = {fds339637}
}

@article{fds335541,
   Author = {Zhu, W and Qiu, Q and Wang, B and Lu, J and Sapiro, G and Daubechies,
             I},
   Title = {Stop memorizing: A data-dependent regularization framework
             for intrinsic pattern learning.},
   Journal = {Corr},
   Volume = {abs/1805.07291},
   Year = {2018},
   Key = {fds335541}
}

@article{fds329343,
   Author = {Lu, J and Thicke, K},
   Title = {Cubic scaling algorithms for RPA correlation using
             interpolative separable density fitting},
   Journal = {Journal of Computational Physics},
   Volume = {351},
   Pages = {187-202},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1016/j.jcp.2017.09.012},
   Doi = {10.1016/j.jcp.2017.09.012},
   Key = {fds329343}
}

@article{fds332172,
   Author = {Cao, Y and Lu, J},
   Title = {Lindblad equation and its semiclassical limit of the
             Anderson-Holstein model},
   Journal = {Journal of Mathematical Physics},
   Volume = {58},
   Number = {12},
   Pages = {122105-122105},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1063/1.4993431},
   Abstract = {© 2017 Author(s). For multi-level open quantum systems, the
             interaction between different levels could pose a challenge
             to understand the quantum system both analytically and
             numerically. In this work, we study the approximation of the
             dynamics of the Anderson-Holstein model, as a model of the
             multi-level open quantum system, by Redfield and Lindblad
             equations. Both equations have a desirable property that if
             the density operators for different levels are diagonal
             initially, they remain to be diagonal for any time. Thanks
             to this nice property, the semiclassical limit of both
             Redfield and Lindblad equations could be derived explicitly;
             the resulting classical master equations share similar
             structures of transport and hopping terms. The Redfield and
             Lindblad equations are also compared from the angle of time
             dependent perturbation theory.},
   Doi = {10.1063/1.4993431},
   Key = {fds332172}
}

@article{fds337014,
   Author = {Lu, J and Zhou, Z},
   Title = {Frozen Gaussian approximation with surface hopping for mixed
             quantum-classical dynamics: A mathematical justification of
             fewest switches surface hopping algorithms},
   Journal = {Mathematics of Computation},
   Volume = {87},
   Number = {313},
   Pages = {2189-2232},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1090/mcom/3310},
   Doi = {10.1090/mcom/3310},
   Key = {fds337014}
}

@article{fds328894,
   Author = {Li, L and Liu, J-G and Lu, J},
   Title = {Fractional Stochastic Differential Equations Satisfying
             Fluctuation-Dissipation Theorem},
   Journal = {Journal of Statistical Physics},
   Volume = {169},
   Number = {2},
   Pages = {316-339},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1007/s10955-017-1866-z},
   Abstract = {© 2017 Springer Science+Business Media, LLC We propose in
             this work a fractional stochastic differential equation
             (FSDE) model consistent with the over-damped limit of the
             generalized Langevin equation model. As a result of the
             ‘fluctuation-dissipation theorem’, the differential
             equations driven by fractional Brownian noise to model
             memory effects should be paired with Caputo derivatives, and
             this FSDE model should be understood in an integral form. We
             establish the existence of strong solutions for such
             equations and discuss the ergodicity and convergence to
             Gibbs measure. In the linear forcing regime, we show
             rigorously the algebraic convergence to Gibbs measure when
             the ‘fluctuation-dissipation theorem’ is satisfied, and
             this verifies that satisfying ‘fluctuation-dissipation
             theorem’ indeed leads to the correct physical behavior. We
             further discuss possible approaches to analyze the
             ergodicity and convergence to Gibbs measure in the nonlinear
             forcing regime, while leave the rigorous analysis for future
             works. The FSDE model proposed is suitable for systems in
             contact with heat bath with power-law kernel and
             subdiffusion behaviors.},
   Doi = {10.1007/s10955-017-1866-z},
   Key = {fds328894}
}

@article{fds333283,
   Author = {Li, Q and Lu, J and Sun, W},
   Title = {A convergent method for linear half-space kinetic
             equations},
   Journal = {ESAIM. Mathematical modelling and numerical analysis =
             ESAIM. Modelisation mathematique et analyse numerique :
             M=2AN},
   Volume = {51},
   Number = {5},
   Pages = {1583-1615},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1051/m2an/2016076},
   Doi = {10.1051/m2an/2016076},
   Key = {fds333283}
}

@article{fds328895,
   Author = {Lu, J and Steinerberger, S},
   Title = {A variation on the Donsker-Varadhan inequality for the
             principal eigenvalue.},
   Journal = {Proceedings. Mathematical, Physical, and Engineering
             Sciences},
   Volume = {473},
   Number = {2204},
   Pages = {20160877},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1098/rspa.2016.0877},
   Abstract = {The purpose of this short paper is to give a variation on
             the classical Donsker-Varadhan inequality, which bounds the
             first eigenvalue of a second-order elliptic operator on a
             bounded domain Ω by the largest mean first exit time of the
             associated drift-diffusion process via [Formula: see
             text]Instead of looking at the mean of the first exit time,
             we study quantiles: let [Formula: see text] be the smallest
             time t such that the likelihood of exiting within that time
             is p, then [Formula: see text]Moreover, as [Formula: see
             text], this lower bound converges to λ1.},
   Doi = {10.1098/rspa.2016.0877},
   Key = {fds328895}
}

@article{fds325888,
   Author = {Lu, J and Yang, H},
   Title = {A cubic scaling algorithm for excited states calculations in
             particle–particle random phase approximation},
   Journal = {Journal of Computational Physics},
   Volume = {340},
   Pages = {297-308},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1016/j.jcp.2017.03.055},
   Doi = {10.1016/j.jcp.2017.03.055},
   Key = {fds325888}
}

@article{fds326080,
   Author = {Gao, Y and Liu, J-G and Lu, J},
   Title = {Continuum Limit of a Mesoscopic Model with Elasticity of
             Step Motion on Vicinal Surfaces},
   Journal = {Journal of Nonlinear Science},
   Volume = {27},
   Number = {3},
   Pages = {873-926},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1007/s00332-016-9354-1},
   Doi = {10.1007/s00332-016-9354-1},
   Key = {fds326080}
}

@article{fds326484,
   Author = {Li, C and Lu, J and Yang, W},
   Title = {On extending Kohn-Sham density functionals to systems with
             fractional number of electrons.},
   Journal = {The Journal of Chemical Physics},
   Volume = {146},
   Number = {21},
   Pages = {214109},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1063/1.4982951},
   Abstract = {We analyze four ways of formulating the Kohn-Sham (KS)
             density functionals with a fractional number of electrons,
             through extending the constrained search space from the
             Kohn-Sham and the generalized Kohn-Sham (GKS)
             non-interacting v-representable density domain for integer
             systems to four different sets of densities for fractional
             systems. In particular, these density sets are (I) ensemble
             interacting N-representable densities, (II) ensemble
             non-interacting N-representable densities, (III)
             non-interacting densities by the Janak construction, and
             (IV) non-interacting densities whose composing orbitals
             satisfy the Aufbau occupation principle. By proving the
             equivalence of the underlying first order reduced density
             matrices associated with these densities, we show that sets
             (I), (II), and (III) are equivalent, and all reduce to the
             Janak construction. Moreover, for functionals with the
             ensemble v-representable assumption at the minimizer, (III)
             reduces to (IV) and thus justifies the previous use of the
             Aufbau protocol within the (G)KS framework in the study of
             the ground state of fractional electron systems, as defined
             in the grand canonical ensemble at zero temperature. By
             further analyzing the Aufbau solution for different density
             functional approximations (DFAs) in the (G)KS scheme, we
             rigorously prove that there can be one and only one
             fractional occupation for the Hartree Fock functional, while
             there can be multiple fractional occupations for general
             DFAs in the presence of degeneracy. This has been confirmed
             by numerical calculations using the local density
             approximation as a representative of general DFAs. This work
             thus clarifies important issues on density functional theory
             calculations for fractional electron systems.},
   Doi = {10.1063/1.4982951},
   Key = {fds326484}
}

@article{fds324707,
   Author = {Lu, J and Thicke, K},
   Title = {Orbital minimization method with ℓ 1 regularization},
   Journal = {Journal of Computational Physics},
   Volume = {336},
   Pages = {87-103},
   Year = {2017},
   Month = {May},
   url = {http://dx.doi.org/10.1016/j.jcp.2017.02.005},
   Doi = {10.1016/j.jcp.2017.02.005},
   Key = {fds324707}
}

@article{fds339405,
   Author = {Huang, Y and Lu, J and Ming, P},
   Title = {A Hybrid Global-local Numerical Method for Multiscale
             PDEs},
   Year = {2017},
   Month = {April},
   Abstract = {We present a new hybrid numerical method for multiscale
             partial differential equations, which simultaneously
             captures both the global macroscopic information and
             resolves the local microscopic events. The convergence of
             the proposed method is proved for problems with bounded and
             measurable coefficient, while the rate of convergence is
             established for problems with rapidly oscillating periodic
             or almost-periodic coefficients. Numerical results are
             reported to show the efficiency and accuracy of the proposed
             method.},
   Key = {fds339405}
}

@article{fds339404,
   Author = {Li, L and Liu, J-G and Lu, J},
   Title = {Fractional stochastic differential equations satisfying
             fluctuation-dissipation theorem},
   Year = {2017},
   Month = {April},
   Abstract = {We consider in this work stochastic differential equation
             (SDE) model for particles in contact with a heat bath when
             the memory effects are non-negligible. As a result of the
             fluctuation-dissipation theorem, the differential equations
             driven by fractional Brownian noise to model memory effects
             should be paired with Caputo derivatives and based on this
             we consider fractional stochastic differential equations
             (FSDEs), which should be understood in an integral form. We
             establish the existence of strong solutions for such
             equations. In the linear forcing regime, we compute the
             solutions explicitly and analyze the asymptotic behavior,
             through which we verify that satisfying fluctuation-dissipation
             indeed leads to the correct physical behavior. We further
             discuss possible extensions to nonlinear forcing regime,
             while leave the rigorous analysis for future
             works.},
   Key = {fds339404}
}

@article{fds326081,
   Author = {Lu, J and Zhou, Z},
   Title = {Path integral molecular dynamics with surface hopping for
             thermal equilibrium sampling of nonadiabatic
             systems.},
   Journal = {The Journal of Chemical Physics},
   Volume = {146},
   Number = {15},
   Pages = {154110},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1063/1.4981021},
   Abstract = {In this work, a novel ring polymer representation for a
             multi-level quantum system is proposed for thermal average
             calculations. The proposed representation keeps the
             discreteness of the electronic states: besides position and
             momentum, each bead in the ring polymer is also
             characterized by a surface index indicating the electronic
             energy surface. A path integral molecular dynamics with
             surface hopping (PIMD-SH) dynamics is also developed to
             sample the equilibrium distribution of the ring polymer
             configurational space. The PIMD-SH sampling method is
             validated theoretically and by numerical
             examples.},
   Doi = {10.1063/1.4981021},
   Key = {fds326081}
}

@article{fds325889,
   Author = {Watson, AB and Lu, J and Weinstein, MI},
   Title = {Wavepackets in inhomogeneous periodic media: Effective
             particle-field dynamics and Berry curvature},
   Journal = {Journal of Mathematical Physics},
   Volume = {58},
   Number = {2},
   Pages = {021503-021503},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1063/1.4976200},
   Doi = {10.1063/1.4976200},
   Key = {fds325889}
}

@article{fds320926,
   Author = {Niu, X and Luo, T and Lu, J and Xiang, Y},
   Title = {Dislocation climb models from atomistic scheme to
             dislocation dynamics},
   Journal = {Journal of the Mechanics and Physics of Solids},
   Volume = {99},
   Pages = {242-258},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1016/j.jmps.2016.11.012},
   Doi = {10.1016/j.jmps.2016.11.012},
   Key = {fds320926}
}

@article{fds330519,
   Author = {Li, XH and Lu, J},
   Title = {Quasi-nonlocal Coupling of Nonlocal Diffusions},
   Journal = {Siam Journal on Numerical Analysis},
   Volume = {55},
   Number = {5},
   Pages = {2394-2415},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1086443},
   Doi = {10.1137/16M1086443},
   Key = {fds330519}
}

@article{fds325890,
   Author = {Lu, J and Yang, H},
   Title = {Preconditioning Orbital Minimization Method for Planewave
             Discretization},
   Journal = {Multiscale Modeling & Simulation},
   Volume = {15},
   Number = {1},
   Pages = {254-273},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1068670},
   Doi = {10.1137/16M1068670},
   Key = {fds325890}
}

@article{fds333284,
   Author = {Lin, L and Lu, J and Vanden-Eijnden, E},
   Title = {A Mathematical Theory of Optimal Milestoning (with a Detour
             via Exact Milestoning)},
   Journal = {Communications on Pure and Applied Mathematics},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1002/cpa.21725},
   Abstract = {© 2017 Wiley Periodicals, Inc. Milestoning is a
             computational procedure that reduces the dynamics of complex
             systems to memoryless jumps between intermediates, or
             milestones, and only retains some information about the
             probability of these jumps and the time lags between them.
             Here we analyze a variant of this procedure, termed optimal
             milestoning, which relies on a specific choice of milestones
             to capture exactly some kinetic features of the original
             dynamical system. In particular, we prove that optimal
             milestoning permits the exact calculation of the mean first
             passage times (MFPT) between any two milestones. In so
             doing, we also analyze another variant of the method, called
             exact milestoning, which also permits the exact calculation
             of certain MFPTs, but at the price of retaining more
             information about the original system's dynamics. Finally,
             we discuss importance sampling strategies based on optimal
             and exact milestoning that can be used to bypass the
             simulation of the original system when estimating the
             statistical quantities used in these methods.},
   Doi = {10.1002/cpa.21725},
   Key = {fds333284}
}

@article{fds323661,
   Author = {Li, Q and Lu, J and Sun, W},
   Title = {Validity and Regularization of Classical Half-Space
             Equations},
   Journal = {Journal of Statistical Physics},
   Volume = {166},
   Number = {2},
   Pages = {398-433},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1007/s10955-016-1688-4},
   Doi = {10.1007/s10955-016-1688-4},
   Key = {fds323661}
}

@article{fds332173,
   Author = {Li, Q and Lu, J},
   Title = {An asymptotic preserving method for transport equations with
             oscillatory scattering coefficients},
   Journal = {Multiscale Modeling & Simulation},
   Volume = {15},
   Number = {4},
   Pages = {1694-1718},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M109212X},
   Abstract = {© 2017 Society for Industrial and Applied Mathematics. We
             design a numerical scheme for transport equations with
             oscillatory periodic scattering coefficients. The scheme is
             asymptotic preserving in the diffusion limit as the Knudsen
             number goes to zero. It also captures the homogenization
             limit as the length scale of the scattering coefficient goes
             to zero. The proposed method is based on the construction of
             multiscale finite element basis and a Galerkin projection
             based on the even-odd decomposition. The method is analyzed
             in the asymptotic regime, as well as validated
             numerically.},
   Doi = {10.1137/16M109212X},
   Key = {fds332173}
}

@article{fds327371,
   Author = {Gao, Y and Liu, J-G and Lu, J},
   Title = {Weak Solution of a Continuum Model For Vicinal Surface in
             The Attachment-Detachment-Limited Regime},
   Journal = {Siam Journal on Mathematical Analysis},
   Volume = {49},
   Number = {3},
   Pages = {1705-1731},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1094543},
   Abstract = {© 2017 Society for Industrial and Applied Mathematics. We
             study in this work a continuum model derived from a
             one-dimensional attachmentdetachment-limited type step flow
             on a vicinal surface, u t = -u 2 (u 3 ) hhhh , where u,
             considered as a function of step height h, is the step slope
             of the surface. We formulate a notion of a weak solution to
             this continuum model and prove the existence of a global
             weak solution, which is positive almost everywhere. We also
             study the long time behavior of the weak solution and prove
             it converges to a constant solution as time goes to
             infinity. The space-time Hölder continuity of the weak
             solution is also discussed as a byproduct.},
   Doi = {10.1137/16M1094543},
   Key = {fds327371}
}

@article{fds325467,
   Author = {Cornelis, B and Yang, H and Goodfriend, A and Ocon, N and Lu, J and Daubechies, I},
   Title = {Removal of Canvas Patterns in Digital Acquisitions of
             Paintings.},
   Journal = {Ieee Transactions on Image Processing : a Publication of the
             Ieee Signal Processing Society},
   Volume = {26},
   Number = {1},
   Pages = {160-171},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1109/tip.2016.2621413},
   Abstract = {We address the removal of canvas artifacts from
             high-resolution digital photographs and X-ray images of
             paintings on canvas. Both imaging modalities are common
             investigative tools in art history and art conservation.
             Canvas artifacts manifest themselves very differently
             according to the acquisition modality; they can hamper the
             visual reading of the painting by art experts, for instance,
             in preparing a restoration campaign. Computer-aided canvas
             removal is desirable for restorers when the painting on
             canvas they are preparing to restore has acquired over the
             years a much more salient texture. We propose a new
             algorithm that combines a cartoon-texture decomposition
             method with adaptive multiscale thresholding in the
             frequency domain to isolate and suppress the canvas
             components. To illustrate the strength of the proposed
             method, we provide various examples, for acquisitions in
             both imaging modalities, for paintings with different types
             of canvas and from different periods. The proposed algorithm
             outperforms previous methods proposed for visual photographs
             such as morphological component analysis and Wiener
             filtering and it also works for the digital removal of
             canvas artifacts in X-ray images.},
   Doi = {10.1109/tip.2016.2621413},
   Key = {fds325467}
}


%% Lu, Yulong   
@article{fds328558,
   Author = {Lu, Y and Stuart, A and Weber, H},
   Title = {Gaussian Approximations for Transition Paths in Brownian
             Dynamics},
   Journal = {Siam Journal on Mathematical Analysis},
   Volume = {49},
   Number = {4},
   Pages = {3005-3047},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1071845},
   Doi = {10.1137/16M1071845},
   Key = {fds328558}
}


%% Ma, Ding   
@article{fds331902,
   Author = {D. Ma},
   Title = {Period polynomial relations of binomial coefficients and
             binomial realization of formal double zeta
             space},
   Journal = {International Journal of Number Theory},
   Volume = {13},
   Number = {03},
   Pages = {761-774},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1142/S1793042117500403},
   Keywords = {Period polynomial formal double zeta space binomial
             coefficient},
   Abstract = {In this paper, we give a realization of the formal double
             zeta space by using binomial coefficients. Along with the
             results in [Period polynomial relations between formal
             double zeta values of odd weight, Math. Ann. 365 (2016)
             345–362], this gives us two families of period polynomial
             relations among binomial coefficients. We also give another
             family of period polynomial relations among binomial
             coefficients which cannot be obtained from our binomial
             realization. At the end, some higher depth observation is
             provided.},
   Doi = {10.1142/S1793042117500403},
   Key = {fds331902}
}


%% Maggioni, Mauro   
@article{fds337334,
   Author = {Escande, P and Debarnot, V and Maggioni, M and Mangeat, T and Weiss,
             P},
   Title = {Learning and exploiting physics of degradations},
   Journal = {Optics Infobase Conference Papers},
   Volume = {Part F105-MATH 2018},
   Year = {2018},
   Month = {January},
   ISBN = {9781557528209},
   url = {http://dx.doi.org/10.1364/MATH.2018.MTu2D.4},
   Abstract = {© 2018 The Author(s). Even though physics of degradations
             of an acquisition system might be complex, it often relies
             on a small number of parameters. We present a methodology to
             learn this physics and exploit it for restoration
             purposes.},
   Doi = {10.1364/MATH.2018.MTu2D.4},
   Key = {fds337334}
}

@article{fds337145,
   Author = {Murphy, JM and Maggioni, M},
   Title = {Diffusion geometric methods for fusion of remotely sensed
             data},
   Journal = {Smart Structures and Materials 2005: Active Materials:
             Behavior and Mechanics},
   Volume = {10644},
   Year = {2018},
   Month = {January},
   ISBN = {9781510617995},
   url = {http://dx.doi.org/10.1117/12.2305274},
   Abstract = {© COPYRIGHT SPIE. Downloading of the abstract is permitted
             for personal use only. We propose a novel unsupervised
             learning algorithm that makes use of image fusion to
             efficiently cluster remote sensing data. Exploiting
             nonlinear structures in multimodal data, we devise a
             clustering algorithm based on a random walk in a fused
             feature space. Constructing the random walk on the fused
             space enforces that pixels are considered close only if they
             are close in both sensing modalities. The structure learned
             by this random walk is combined with density estimation to
             label all pixels. Spatial information may also be used to
             regularize the resulting clusterings. We compare the
             proposed method with several spectral methods for image
             fusion on both synthetic and real data.},
   Doi = {10.1117/12.2305274},
   Key = {fds337145}
}

@article{fds339291,
   Author = {Murphy, JM and Maggioni, M},
   Title = {Unsupervised Clustering and Active Learning of Hyperspectral
             Images With Nonlinear Diffusion},
   Journal = {Ieee Transactions on Geoscience and Remote
             Sensing},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1109/TGRS.2018.2869723},
   Abstract = {IEEE The problem of unsupervised learning and segmentation
             of hyperspectral images is a significant challenge in remote
             sensing. The high dimensionality of hyperspectral data,
             presence of substantial noise, and overlap of classes all
             contribute to the difficulty of automatically clustering and
             segmenting hyperspectral images. We propose an unsupervised
             learning technique called spectral-spatial diffusion
             learning (DLSS) that combines a geometric estimation of
             class modes with a diffusion-inspired labeling that
             incorporates both spectral and spatial information. The mode
             estimation incorporates the geometry of the hyperspectral
             data by using diffusion distance to promote learning a
             unique mode from each class. These class modes are then used
             to label all the points by a joint spectral-spatial
             nonlinear diffusion process. A related variation of DLSS is
             also discussed, which enables active learning by requesting
             labels for a very small number of well-chosen pixels,
             dramatically boosting overall clustering results. Extensive
             experimental analysis demonstrates the efficacy of the
             proposed methods against benchmark and state-of-the-art
             hyperspectral analysis techniques on a variety of real data
             sets, their robustness to choices of parameters, and their
             low computational complexity.},
   Doi = {10.1109/TGRS.2018.2869723},
   Key = {fds339291}
}

@article{fds320928,
   Author = {Little, AV and Maggioni, M and Rosasco, L},
   Title = {Multiscale geometric methods for data sets I: Multiscale
             SVD, noise and curvature},
   Journal = {Applied and Computational Harmonic Analysis},
   Volume = {43},
   Number = {3},
   Pages = {504-567},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1016/j.acha.2015.09.009},
   Doi = {10.1016/j.acha.2015.09.009},
   Key = {fds320928}
}

@article{fds331595,
   Author = {Wang, YG and Maggioni, M and Chen, G},
   Title = {Enhanced detection of chemical plumes in hyperspectral
             images and movies throughimproved backgroundmodeling},
   Journal = {Proceedings of Hyperspectral Image and Signal Processing:
             Evolution in Remote Sensing},
   Volume = {2015-June},
   Year = {2017},
   Month = {October},
   ISBN = {9781467390156},
   url = {http://dx.doi.org/10.1109/WHISPERS.2015.8075369},
   Abstract = {© 2015 IEEE. We extend recent work that models the
             background in hyperspectral images by a single distribution
             (Gaussian or subspace) to use a mixture of such
             distributions. This seems to better capture the complexity
             of the background, which often consists of heterogeneous
             regions (e.g., sky, mountain and ground). We derive mixture
             versions of the previous estimators and apply them to
             benchmark data sets for detecting chemical plumes of known
             chemicals in hyperspectral images and movies. Our
             experiments show that the mixture background models
             consistently outperform their counterparts with a single
             distribution.},
   Doi = {10.1109/WHISPERS.2015.8075369},
   Key = {fds331595}
}

@article{fds329467,
   Author = {Gerber, S and Maggioni, M},
   Title = {Multiscale strategies for computing optimal
             transport},
   Journal = {Journal of Machine Learning Research},
   Volume = {18},
   Pages = {1-32},
   Year = {2017},
   Month = {August},
   Abstract = {©2017 Samuel Gerber and Mauro Maggioni. This paper presents
             a multiscale approach to efficiently compute approximate
             optimal transport plans between point sets. It is
             particularly well-suited for point sets that are in
             high-dimensions, but are close to being intrinsically
             low-dimensional. The approach is based on an adaptive
             multiscale decomposition of the point sets. The multiscale
             decomposition yields a sequence of optimal transport
             problems, that are solved in a top-to-bottom fashion from
             the coarsest to the finest scale. We provide numerical
             evidence that this multiscale approach scales approximately
             linearly, in time and memory, in the number of nodes,
             instead of quadratically or worse for a direct solution.
             Empirically, the multiscale approach results in less than
             one percent relative error in the objective function.
             Furthermore, the multiscale plans constructed are of
             interest by themselves as they may be used to introduce
             novel features and notions of distances between point sets.
             An analysis of sets of brain MRI based on optimal transport
             distances illustrates the effectiveness of the proposed
             method on a real world data set. The application
             demonstrates that multiscale optimal transport distances
             have the potential to improve on state-of-the-art metrics
             currently used in computational anatomy.},
   Key = {fds329467}
}

@article{fds325965,
   Author = {Bongini, M and Fornasier, M and Hansen, M and Maggioni,
             M},
   Title = {Inferring interaction rules from observations of evolutive
             systems I: The variational approach},
   Journal = {Mathematical Models & Methods in Applied
             Sciences},
   Volume = {27},
   Number = {05},
   Pages = {909-951},
   Year = {2017},
   Month = {May},
   url = {http://dx.doi.org/10.1142/S0218202517500208},
   Doi = {10.1142/S0218202517500208},
   Key = {fds325965}
}

@article{fds328806,
   Author = {Tomita, TM and Maggioni, M and Vogelstein, JT},
   Title = {ROFLMAO: Robust oblique forests with linear MAtrix
             operations},
   Journal = {Proceedings of the 17th SIAM International Conference on
             Data Mining, SDM 2017},
   Pages = {498-506},
   Year = {2017},
   Month = {January},
   ISBN = {9781611974874},
   Abstract = {Copyright © by SIAM. Random Forest (RF) remains one of the
             most widely used general purpose classification methods. Two
             recent largescale empirical studies demonstrated it to be
             the best overall classification method among a variety of
             methods evaluated. One of its main limitations, however, is
             that it is restricted to only axis-aligned recursive
             partitions of the feature space. Consequently, RF is
             particularly sensitive to the orientation of the data.
             Several studies have proposed "oblique" decision forest
             methods to address this limitation. However, these methods
             either have a time and space complexity significantly
             greater than RF, are sensitive to unit and scale, or
             empirically do not perform as well as RF on real data. One
             promising oblique method that was proposed alongside the
             canonical RF method, called Forest-RC (F-RC), has not
             received as much attention by the community. Despite it
             being just as old as RF, virtually no studies exist
             investigating its theoretical or empirical performance. In
             this work, we demonstrate that F-RC empirically outperforms
             RF and another recently proposed oblique method called
             Random Rotation Random Forest, while approximately
             maintaining the same computational complexity. Furthermore,
             a variant of F-RC which rank transforms the data prior to
             learning is especially invariant to affine transformations
             and robust to data corruption. Open source code is
             available.},
   Key = {fds328806}
}

@article{fds325966,
   Author = {Crosskey, M and Maggioni, M},
   Title = {ATLAS: A Geometric Approach to Learning High-Dimensional
             Stochastic Systems Near Manifolds},
   Journal = {Multiscale Modeling & Simulation},
   Volume = {15},
   Number = {1},
   Pages = {110-156},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/140970951},
   Doi = {10.1137/140970951},
   Key = {fds325966}
}

@inproceedings{MM:EEG,
   Author = {E Causevic and R~R Coifman and R Isenhart and A Jacquin and E~R John and M Maggioni and L~S Prichep and F~J
             Warner},
   Title = {{QEEG}-based classification with wavelet packets and
             microstate features for triage applications in the
             {ER}},
   Year = {2005},
   Key = {MM:EEG}
}

@misc{PathNIH2004,
   Author = {GL Davis and Mauro Maggioni and FJ Warner and FB Geshwind and AC Coppi and RA DeVerse and RR Coifman},
   Title = {Hyper-spectral Analysis of normal and malignant colon tissue
             microarray sections using a novel DMD system},
   Year = {2004},
   Key = {PathNIH2004}
}

@techreport{CMTech,
   Author = {Ronald R Coifman and Mauro Maggioni},
   Title = {Multiresolution Analysis associated to diffusion semigroups:
             construction and fast algorithms},
   Number = {YALE/DCS/TR-1289},
   Organization = {Dept. Comp. Sci., Yale University},
   Institution = {Dept. Comp. Sci., Yale University},
   Year = {2004},
   Key = {CMTech}
}


%% Malen, Greg   
@article{fds335543,
   Author = {Malen, G},
   Title = {Homomorphism complexes and -cores},
   Journal = {Discrete Mathematics},
   Volume = {341},
   Number = {9},
   Pages = {2567-2574},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1016/j.disc.2018.06.014},
   Doi = {10.1016/j.disc.2018.06.014},
   Key = {fds335543}
}


%% Mattingly, Jonathan C.   
@article{fds328807,
   Author = {Herschlag, G and Ravier, R and Mattingly, JC},
   Title = {Evaluating Partisan Gerrymandering in Wisconsin},
   Year = {2017},
   Month = {September},
   Abstract = {We examine the extent of gerrymandering for the 2010 General
             Assembly district map of Wisconsin. We find that there is
             substantial variability in the election outcome depending on
             what maps are used. We also found robust evidence that the
             district maps are highly gerrymandered and that this
             gerrymandering likely altered the partisan make up of the
             Wisconsin General Assembly in some elections. Compared to
             the distribution of possible redistricting plans for the
             General Assembly, Wisconsin's chosen plan is an outlier in
             that it yields results that are highly skewed to the
             Republicans when the statewide proportion of Democratic
             votes comprises more than 50-52% of the overall vote (with
             the precise threshold depending on the election considered).
             Wisconsin's plan acts to preserve the Republican majority by
             providing extra Republican seats even when the Democratic
             vote increases into the range when the balance of power
             would shift for the vast majority of redistricting
             plans.},
   Key = {fds328807}
}

@article{fds328808,
   Author = {Bakhtin, Y and Hurth, T and Lawley, SD and Mattingly,
             JC},
   Title = {Smooth invariant densities for random switching on the
             torus},
   Volume = {31},
   Number = {4},
   Pages = {1331-1350},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1088/1361-6544/aaa04f},
   Abstract = {We consider a random dynamical system obtained by switching
             between the flows generated by two smooth vector fields on
             the 2d-torus, with the random switchings happening according
             to a Poisson process. Assuming that the driving vector
             fields are transversal to each other at all points of the
             torus and that each of them allows for a smooth invariant
             density and no periodic orbits, we prove that the switched
             system also has a smooth invariant density, for every
             switching rate. Our approach is based on an integration by
             parts formula inspired by techniques from Malliavin
             calculus.},
   Doi = {10.1088/1361-6544/aaa04f},
   Key = {fds328808}
}

@article{fds328809,
   Author = {Johndrow, JE and Mattingly, JC},
   Title = {Coupling and Decoupling to bound an approximating Markov
             Chain},
   Year = {2017},
   Month = {July},
   Abstract = {This simple note lays out a few observations which are well
             known in many ways but may not have been said in quite this
             way before. The basic idea is that when comparing two
             different Markov chains it is useful to couple them is such
             a way that they agree as often as possible. We construct
             such a coupling and analyze it by a simple dominating chain
             which registers if the two processes agree or disagree. We
             find that this imagery is useful when thinking about such
             problems. We are particularly interested in comparing the
             invariant measures and long time averages of the processes.
             However, since the paths agree for long runs, it also
             provides estimates on various stopping times such as hitting
             or exit times. We also show that certain bounds are tight.
             Finally, we provide a simple application to a Markov Chain
             Monte Carlo algorithm and show numerically that the results
             of the paper show a good level of approximation at
             considerable speed up by using an approximating chain rather
             than the original sampling chain.},
   Key = {fds328809}
}

@article{fds328810,
   Author = {Glatt-Holtz, NE and Herzog, DP and Mattingly, JC},
   Title = {Scaling and Saturation in Infinite-Dimensional Control
             Problems with Applications to Stochastic Partial
             Differential Equations},
   Journal = {Annals of Pde},
   Year = {2017},
   Month = {June},
   Abstract = {We establish the dual notions of scaling and saturation from
             geometric control theory in an infinite-dimensional setting.
             This generalization is applied to the low-mode control
             problem in a number of concrete nonlinear partial
             differential equations. We also develop applications
             concerning associated classes of stochastic partial
             differential equations (SPDEs). In particular, we study the
             support properties of probability laws corresponding to
             these SPDEs as well as provide applications concerning the
             ergodic and mixing properties of invariant measures for
             these stochastic systems.},
   Key = {fds328810}
}

@article{fds300245,
   Author = {Glatt-Holtz, N and Mattingly, JC and Richards,
             G},
   Title = {On Unique Ergodicity in Nonlinear Stochastic Partial
             Differential Equations},
   Journal = {Journal of Statistical Physics},
   Volume = {166},
   Number = {3-4},
   Pages = {618-649},
   Year = {2017},
   Month = {February},
   url = {http://arxiv.org/abs/1512.04126v1},
   Abstract = {We illustrate how the notion of asymptotic coupling provides
             a flexible and intuitive framework for proving the
             uniqueness of invariant measures for a variety of stochastic
             partial differential equations whose deterministic
             counterpart possesses a finite number of determining modes.
             Examples exhibiting parabolic and hyperbolic structure are
             studied in detail. In the later situation we also present a
             simple framework for establishing the existence of invariant
             measures when the usual approach relying on the
             Krylov-Bogolyubov procedure and compactness
             fails.},
   Doi = {10.1007/s10955-016-1605-x},
   Key = {fds300245}
}


%% Miller, Ezra   
@article{fds339830,
   Author = {Katthän, L and Michałek, M and Miller, E},
   Title = {When is a Polynomial Ideal Binomial After an Ambient
             Automorphism?},
   Journal = {Foundations of Computational Mathematics},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1007/s10208-018-9405-0},
   Abstract = {© 2018, The Author(s). Can an ideal I in a polynomial ring
             k[x] over a field be moved by a change of coordinates into a
             position where it is generated by binomials xA- λxb with
             λ∈ k, or by unital binomials (i.e., with λ= 0 or 1)?
             Can a variety be moved into a position where it is toric? By
             fibering the G-translates of I over an algebraic group G
             acting on affine space, these problems are special cases of
             questions about a family I of ideals over an arbitrary
             base B. The main results in this general setting are
             algorithms to find the locus of points in B over which the
             fiber of Iis contained in the fiber of a second
             family I′ of ideals over B;defines a variety of
             dimension at least d;is generated by binomials; oris
             generated by unital binomials. A faster containment
             algorithm is also presented when the fibers of I are prime.
             The big-fiber algorithm is probabilistic but likely faster
             than known deterministic ones. Applications include the
             setting where a second group T acts on affine space, in
             addition to G, in which case algorithms compute the set of
             G-translates of Iwhose stabilizer subgroups in T have
             maximal dimension; orthat admit a faithful multigrading
             by Zr of maximal rank r. Even with no ambient group action
             given, the final application is an algorithm todecide
             whether a normal projective variety is abstractly toric. All
             of these loci in B and subsets of G are
             constructible.},
   Doi = {10.1007/s10208-018-9405-0},
   Key = {fds339830}
}


%% Motta, Francis C.   
@article{fds329938,
   Author = {Motta, FC},
   Title = {Topological Data Analysis: Developments and
             Applications},
   Pages = {369-391},
   Booktitle = {Advances in Nonlinear Geosciences},
   Publisher = {Springer},
   Editor = {Tsonis, A},
   Year = {2017},
   Month = {November},
   ISBN = {3319588958},
   Abstract = {Topological Data Analysis (TDA) and its mainstay
             computational device, persistent homology (PH), has
             established a strong track record of providing researchers
             across the data-driven sciences with new insights and
             methodologies by characterizing low-dimensional geometric
             structures in high-dimensional data. When combined with
             machine learning (ML) methods, PH is valued as a
             discriminating-feature extraction tool. This work highlights
             many of the recent successes at the intersection of TDA and
             ML, introduces some of the foundational mathematics
             underpinning TDA, and summarizes the efforts to strengthen
             the bridge between TDA and ML. Thus, this document is a
             launching point for experimentalists and theoreticians to
             consider what can be learned from the shape of their
             data.},
   Key = {fds329938}
}

@article{fds329101,
   Author = {Cho, C-Y and Motta, FC and Kelliher, CM and Deckard, A and Haase,
             SB},
   Title = {Reconciling conflicting models for global control of
             cell-cycle transcription.},
   Journal = {Cell Cycle},
   Volume = {16},
   Number = {20},
   Pages = {1965-1978},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1080/15384101.2017.1367073},
   Abstract = {Models for the control of global cell-cycle transcription
             have advanced from a CDK-APC/C oscillator, a transcription
             factor (TF) network, to coupled CDK-APC/C and TF networks.
             Nonetheless, current models were challenged by a recent
             study that concluded that the cell-cycle transcriptional
             program is primarily controlled by a CDK-APC/C oscillator in
             budding yeast. Here we report an analysis of the
             transcriptome dynamics in cyclin mutant cells that were not
             queried in the previous study. We find that B-cyclin
             oscillation is not essential for control of phase-specific
             transcription. Using a mathematical model, we demonstrate
             that the function of network TFs can be retained in the face
             of significant reductions in transcript levels. Finally, we
             show that cells arrested at mitotic exit with
             non-oscillating levels of B-cyclins continue to cycle
             transcriptionally. Taken together, these findings support a
             critical role of a TF network and a requirement for CDK
             activities that need not be periodic.},
   Doi = {10.1080/15384101.2017.1367073},
   Key = {fds329101}
}

@article{fds329102,
   Author = {Burris, CS and Motta, FC and Shipman, PD},
   Title = {An Unoriented Variation on de Bruijn Sequences},
   Journal = {Graphs and Combinatorics},
   Volume = {33},
   Number = {4},
   Pages = {845-858},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1007/s00373-017-1793-4},
   Doi = {10.1007/s00373-017-1793-4},
   Key = {fds329102}
}


%% Mukherjee, Sayan   
@article{fds339843,
   Author = {Silverman, JD and Durand, HK and Bloom, RJ and Mukherjee, S and David,
             LA},
   Title = {Dynamic linear models guide design and analysis of
             microbiota studies within artificial human
             guts.},
   Journal = {Microbiome},
   Volume = {6},
   Number = {1},
   Pages = {202},
   Year = {2018},
   Month = {November},
   url = {http://dx.doi.org/10.1186/s40168-018-0584-3},
   Abstract = {BACKGROUND:Artificial gut models provide unique
             opportunities to study human-associated microbiota.
             Outstanding questions for these models' fundamental biology
             include the timescales on which microbiota vary and the
             factors that drive such change. Answering these questions
             though requires overcoming analytical obstacles like
             estimating the effects of technical variation on observed
             microbiota dynamics, as well as the lack of appropriate
             benchmark datasets. RESULTS:To address these obstacles, we
             created a modeling framework based on multinomial
             logistic-normal dynamic linear models (MALLARDs) and
             performed dense longitudinal sampling of four replicate
             artificial human guts over the course of 1 month. The
             resulting analyses revealed how the ratio of biological
             variation to technical variation from sample processing
             depends on sampling frequency. In particular, we find that
             at hourly sampling frequencies, 76% of observed variation
             could be ascribed to technical sources, which could also
             skew the observed covariation between taxa. We also found
             that the artificial guts demonstrated replicable
             trajectories even after a recovery from a transient feed
             disruption. Additionally, we observed irregular sub-daily
             oscillatory dynamics associated with the bacterial family
             Enterobacteriaceae within all four replicate vessels.
             CONCLUSIONS:Our analyses suggest that, beyond variation due
             to sequence counting, technical variation from sample
             processing can obscure temporal variation from biological
             sources in artificial gut studies. Our analyses also
             supported hypotheses that human gut microbiota fluctuates on
             sub-daily timescales in the absence of a host and that
             microbiota can follow replicable trajectories in the
             presence of environmental driving forces. Finally, multiple
             aspects of our approach are generalizable and could
             ultimately be used to facilitate the design and analysis of
             longitudinal microbiota studies in vivo.},
   Doi = {10.1186/s40168-018-0584-3},
   Key = {fds339843}
}

@article{fds338059,
   Author = {Barish, S and Nuss, S and Strunilin, I and Bao, S and Mukherjee, S and Jones, CD and Volkan, PC},
   Title = {Combinations of DIPs and Dprs control organization of
             olfactory receptor neuron terminals in Drosophila.},
   Journal = {Plos Genetics},
   Volume = {14},
   Number = {8},
   Pages = {e1007560},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1371/journal.pgen.1007560},
   Abstract = {In Drosophila, 50 classes of olfactory receptor neurons
             (ORNs) connect to 50 class-specific and uniquely positioned
             glomeruli in the antennal lobe. Despite the identification
             of cell surface receptors regulating axon guidance, how ORN
             axons sort to form 50 stereotypical glomeruli remains
             unclear. Here we show that the heterophilic cell adhesion
             proteins, DIPs and Dprs, are expressed in ORNs during
             glomerular formation. Many ORN classes express a unique
             combination of DIPs/dprs, with neurons of the same class
             expressing interacting partners, suggesting a role in
             class-specific self-adhesion between ORN axons. Analysis of
             DIP/Dpr expression revealed that ORNs that target
             neighboring glomeruli have different combinations, and ORNs
             with very similar DIP/Dpr combinations can project to
             distant glomeruli in the antennal lobe. DIP/Dpr profiles are
             dynamic during development and correlate with sensilla type
             lineage for some ORN classes. Perturbations of DIP/dpr gene
             function result in local projection defects of ORN axons and
             glomerular positioning, without altering correct matching of
             ORNs with their target neurons. Our results suggest that
             context-dependent differential adhesion through DIP/Dpr
             combinations regulate self-adhesion and sort ORN axons into
             uniquely positioned glomeruli.},
   Doi = {10.1371/journal.pgen.1007560},
   Key = {fds338059}
}

@article{fds330900,
   Author = {Singleton, KR and Crawford, L and Tsui, E and Manchester, HE and Maertens, O and Liu, X and Liberti, MV and Magpusao, AN and Stein, EM and Tingley, JP and Frederick, DT and Boland, GM and Flaherty, KT and McCall, SJ and Krepler, C and Sproesser, K and Herlyn, M and Adams, DJ and Locasale, JW and Cichowski, K and Mukherjee, S and Wood,
             KC},
   Title = {Melanoma Therapeutic Strategies that Select against
             Resistance by Exploiting MYC-Driven Evolutionary
             Convergence.},
   Journal = {Cell Reports},
   Volume = {21},
   Number = {10},
   Pages = {2796-2812},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1016/j.celrep.2017.11.022},
   Abstract = {Diverse pathways drive resistance to BRAF/MEK inhibitors in
             BRAF-mutant melanoma, suggesting that durable control of
             resistance will be a challenge. By combining statistical
             modeling of genomic data from matched pre-treatment and
             post-relapse patient tumors with functional interrogation of
             >20 in vitro and in vivo resistance models, we discovered
             that major pathways of resistance converge to activate the
             transcription factor, c-MYC (MYC). MYC expression and
             pathway gene signatures were suppressed following drug
             treatment, and then rebounded during progression.
             Critically, MYC activation was necessary and sufficient for
             resistance, and suppression of MYC activity using genetic
             approaches or BET bromodomain inhibition was sufficient to
             resensitize cells and delay BRAFi resistance. Finally,
             MYC-driven, BRAFi-resistant cells are hypersensitive to the
             inhibition of MYC synthetic lethal partners, including SRC
             family and c-KIT tyrosine kinases, as well as glucose,
             glutamine, and serine metabolic pathways. These insights
             enable the design of combination therapies that select
             against resistance evolution.},
   Doi = {10.1016/j.celrep.2017.11.022},
   Key = {fds330900}
}

@article{fds332761,
   Author = {Darnell, G and Georgiev, S and Mukherjee, S and Engelhardt,
             BE},
   Title = {Adaptive randomized dimension reduction on massive
             data},
   Journal = {Journal of machine learning research : JMLR},
   Volume = {18},
   Year = {2017},
   Month = {November},
   Abstract = {© 2017 Gregory Darnell, Stoyan Georgiev, Sayan Mukherjee,
             Barbara E Engelhardt. The scalability of statistical
             estimators is of increasing importance in modern
             applications. One approach to implementing scalable
             algorithms is to compress data into a low dimensional latent
             space using dimension reduction methods. In this paper, we
             develop an approach for dimension reduction that exploits
             the assumption of low rank structure in high dimensional
             data to gain both computational and statistical advantages.
             We adapt recent randomized low-rank approximation algorithms
             to provide an efficient solution to principal component
             analysis (PCA), and we use this efficient solver to improve
             estimation in large-scale linear mixed models (LMM) for
             association mapping in statistical genomics. A key
             observation in this paper is that randomization serves a
             dual role, improving both computational and statistical
             performance by implicitly regularizing the covariance matrix
             estimate of the random effect in an LMM. These statistical
             and computational advantages are highlighted in our
             experiments on simulated data and large-scale genomic
             studies.},
   Key = {fds332761}
}

@article{fds330010,
   Author = {Gao, T and Yapuncich, GS and Daubechies, I and Mukherjee, S and Boyer,
             DM},
   Title = {Development and Assessment of Fully Automated and Globally
             Transitive Geometric Morphometric Methods, With Application
             to a Biological Comparative Dataset With High Interspecific
             Variation.},
   Journal = {The Anatomical Record : Advances in Integrative Anatomy and
             Evolutionary Biology},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1002/ar.23700},
   Abstract = {Automated geometric morphometric methods are promising tools
             for shape analysis in comparative biology, improving
             researchers' abilities to quantify variation extensively (by
             permitting more specimens to be analyzed) and intensively
             (by characterizing shapes with greater fidelity). Although
             use of these methods has increased, published automated
             methods have some notable limitations: pairwise
             correspondences are frequently inaccurate and pairwise
             mappings are not globally consistent (i.e., they lack
             transitivity across the full sample). Here, we reassess the
             accuracy of published automated methods-cPDist (Boyer et al.
             Proc Nat Acad Sci 108 (2011) 18221-18226) and auto3Dgm
             (Boyer et al.: Anat Rec 298 (2015a) 249-276)-and evaluate
             several modifications to these methods. We show that a
             substantial percentage of alignments and pairwise maps
             between specimens of dissimilar geometries were inaccurate
             in the study of Boyer et al. (Proc Nat Acad Sci 108 (2011)
             18221-18226), despite a taxonomically partitioned variance
             structure of continuous Procrustes distances. We show these
             inaccuracies are remedied using a globally informed
             methodology within a collection of shapes, rather than
             relying on pairwise comparisons (c.f. Boyer et al.: Anat Rec
             298 (2015a) 249-276). Unfortunately, while global
             information generally enhances maps between dissimilar
             objects, it can degrade the quality of correspondences
             between similar objects due to the accumulation of numerical
             error. We explore a number of approaches to mitigate this
             degradation, quantify their performance, and compare the
             generated pairwise maps (and the shape space characterized
             by these maps) to a "ground truth" obtained from landmarks
             manually collected by geometric morphometricians. Novel
             methods both improve the quality of the pairwise
             correspondences relative to cPDist and achieve a taxonomic
             distinctiveness comparable to auto3Dgm. Anat Rec, 2017. ©
             2017 Wiley Periodicals, Inc.},
   Doi = {10.1002/ar.23700},
   Key = {fds330010}
}

@article{fds335806,
   Author = {Crawford, L and Wood, KC and Zhou, X and Mukherjee,
             S},
   Title = {Bayesian Approximate Kernel Regression With Variable
             Selection},
   Journal = {Journal of the American Statistical Association},
   Pages = {1-12},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1080/01621459.2017.1361830},
   Doi = {10.1080/01621459.2017.1361830},
   Key = {fds335806}
}

@article{fds323270,
   Author = {Bobrowski, O and Mukherjee, S and Taylor, JE},
   Title = {Topological consistency via kernel estimation},
   Journal = {Bernoulli : official journal of the Bernoulli Society for
             Mathematical Statistics and Probability},
   Volume = {23},
   Number = {1},
   Pages = {288-328},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.3150/15-BEJ744},
   Doi = {10.3150/15-BEJ744},
   Key = {fds323270}
}

@article{fds335807,
   Author = {Tan, Z and Mukherjee, S},
   Title = {Partitioned tensor factorizations for learning mixed
             membership models},
   Journal = {34th International Conference on Machine Learning, Icml
             2017},
   Volume = {7},
   Pages = {5156-5165},
   Year = {2017},
   Month = {January},
   ISBN = {9781510855144},
   Abstract = {Copyright © 2017 by the authors. We present an efficient
             algorithm for learning mixed membership models when the
             number of variables p is much larger than the number of
             hidden components k. This algorithm reduces the
             computational complexity of state-of-the-art tensor methods,
             which require decomposing an O (p3) tensor, to factorizing O
             (p/k) sub-tensors each of size O (k3). In addition, we
             address the issue of negative entries in the empirical
             method of moments based estimators. We provide sufficient
             conditions under which our approach has provable guarantees.
             Our approach obtains competitive empirical results on both
             simulated and real data.},
   Key = {fds335807}
}


%% Nagy, Akos   
@article{fds331513,
   Author = {Nagy, Á},
   Title = {The Berry Connection of the Ginzburg–Landau
             Vortices},
   Journal = {Communications in Mathematical Physics},
   Volume = {350},
   Number = {1},
   Pages = {105-128},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1007/s00220-016-2701-0},
   Doi = {10.1007/s00220-016-2701-0},
   Key = {fds331513}
}


%% Ng, Lenhard L.   
@article{fds330520,
   Author = {Ekholm, T and Ng, L and Shende, V},
   Title = {A complete knot invariant from contact homology},
   Journal = {Inventiones Mathematicae},
   Volume = {211},
   Number = {3},
   Pages = {1149-1200},
   Year = {2018},
   Month = {March},
   url = {http://dx.doi.org/10.1007/s00222-017-0761-1},
   Abstract = {© 2017, Springer-Verlag GmbH Germany. We construct an
             enhanced version of knot contact homology, and show that we
             can deduce from it the group ring of the knot group together
             with the peripheral subgroup. In particular, it completely
             determines a knot up to smooth isotopy. The enhancement
             consists of the (fully noncommutative) Legendrian contact
             homology associated to the union of the conormal torus of
             the knot and a disjoint cotangent fiber sphere, along with a
             product on a filtered part of this homology. As a corollary,
             we obtain a new, holomorphic-curve proof of a result of the
             third author that the Legendrian isotopy class of the
             conormal torus is a complete knot invariant.},
   Doi = {10.1007/s00222-017-0761-1},
   Key = {fds330520}
}

@article{fds330521,
   Author = {Cieliebak, K and Ekholm, T and Latschev, J and Ng,
             L},
   Title = {Knot contact homology, string topology, and the cord
             algebra},
   Journal = {Journal De L'Ecole Polytechnique Mathematiques},
   Volume = {4},
   Pages = {661-780},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.5802/jep.55},
   Abstract = {The conormal Lagrangian LKof a knot K in R3is the
             submanifold of the cotangent bundle T∗R3consisting of
             covectors along K that annihilate tangent vectors to K. By
             intersecting with the unit cotangent bundle S∗R3, one
             obtains the unit conormal ΛK, and the Legendrian contact
             homology of ΛKis a knot invariant of K, known as knot
             contact homology. We define a version of string topology for
             strings in R3∪ LKand prove that this is isomorphic in
             degree 0 to knot contact homology. The string topology
             perspective gives a topological derivation of the cord
             algebra (also isomorphic to degree 0 knot contact homology)
             and relates it to the knot group. Together with the
             isomorphism this gives a new proof that knot contact
             homology detects the unknot. Our techniques involve a
             detailed analysis of certain moduli spaces of holomorphic
             disks in T∗R3with boundary on R3∪ LK.},
   Doi = {10.5802/jep.55},
   Key = {fds330521}
}

@article{fds332376,
   Author = {Ng, L and Rutherford, D and Shende, V and Sivek, S},
   Title = {The cardinality of the augmentation category of a Legendrian
             link},
   Journal = {Mathematical Research Letters},
   Volume = {24},
   Number = {6},
   Pages = {1845-1874},
   Year = {2017},
   Key = {fds332376}
}


%% Nolen, James H.   
@article{fds339330,
   Author = {Cristali, I and Ranjan, V and Steinberg, J and Beckman, E and Durrett,
             R and Junge, M and Nolen, J},
   Title = {Block size in geometric(P)-biased permutations},
   Journal = {Electronic Communications in Probability},
   Volume = {23},
   Pages = {1-10},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1214/18-ECP182},
   Abstract = {© 2018, University of Washington. All rights reserved. Fix
             a probability distribution p = (p1, p2, …) on the positive
             integers. The first block in a p-biased permutation can be
             visualized in terms of raindrops that land at each positive
             integer j with probability pj. It is the first point K so
             that all sites in [1, K] are wet and all sites in (K, ∞)
             are dry. For the geometric distribution pj = p(1 − p)j−1
             we show that p log K converges in probability to an explicit
             constant as p tends to 0. Additionally, we prove that if p
             has a stretch exponential distribution, then K is infinite
             with positive probability.},
   Doi = {10.1214/18-ECP182},
   Key = {fds339330}
}

@article{fds318326,
   Author = {Nolen, J and Roquejoffre, JM and Ryzhik, L},
   Title = {Refined long-time asymptotics for Fisher-KPP
             fronts},
   Journal = {Communications in Contemporary Mathematics},
   Publisher = {World Scientific Publishing},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1142/S0219199718500724},
   Abstract = {© 2018 World Scientific Publishing Company. We study the
             one-dimensional Fisher-KPP equation, with an initial
             condition u0(x) that coincides with the step function except
             on a compact set. A well-known result of Bramson in [Maximal
             displacement of branching Brownian motion, Comm. Pure Appl.
             Math. 31 (1978) 531-581; Convergence of Solutions of the
             Kolmogorov Equation to Travelling Waves (American
             Mathematical Society, Providence, RI, 1983)] states that, as
             t → +∞, the solution converges to a traveling wave
             located at the position X(t) = 2t - (3/2)logt + x0 + o(1),
             with the shift x0 that depends on u0. Ebert and Van Saarloos
             have formally derived in [Front propagation into unstable
             states: Universal algebraic convergence towards uniformly
             translating pulled fronts, Phys. D 146 (2000) 1-99; Front
             propagation into unstable states, Phys. Rep. 386 (2003)
             29-222] a correction to the Bramson shift, arguing that X(t)
             = 2t - (3/2)logt + x0 - 3π/t + O(1/t). Here, we prove that
             this result does hold, with an error term of the size
             O(1/t1-γ), for any γ > 0. The interesting aspect of this
             asymptotics is that the coefficient in front of the 1/t-term
             does not depend on u0.},
   Doi = {10.1142/S0219199718500724},
   Key = {fds318326}
}

@article{fds316609,
   Author = {Mourrat, J-C and Nolen, J},
   Title = {Scaling limit of the corrector in stochastic
             homogenization},
   Journal = {The Annals of Applied Probability},
   Volume = {27},
   Number = {2},
   Pages = {944-959},
   Publisher = {Institute of Mathematical Statistics (IMS)},
   Year = {2017},
   Month = {April},
   ISSN = {1050-5164},
   url = {http://arxiv.org/abs/1502.07440},
   Abstract = {© Institute of Mathematical Statistics, 2017.In the
             homogenization of divergence-form equations with random
             coefficients, a central role is played by the corrector.We
             focus on a discrete space setting and on dimension 3 and
             more. Under a minor smoothness assumption on the law of the
             random coefficients, we identify the scaling limit of the
             corrector, which is akin to a Gaussian free field. This
             completes the argument started in [Ann. Probab. 44 (2016)
             3207-3233].},
   Doi = {10.1214/16-AAP1221},
   Key = {fds316609}
}

@article{fds316662,
   Author = {Nolen, J and Roquejoffre, J-M and Ryzhik, L},
   Title = {Convergence to a single wave in the Fisher-KPP
             equation},
   Journal = {Chinese Annals of Mathematics, Series B},
   Volume = {38},
   Number = {2},
   Pages = {629-646},
   Year = {2017},
   Month = {March},
   url = {http://arxiv.org/abs/1604.02994},
   Doi = {10.1007/s11401-017-1087-4},
   Key = {fds316662}
}


%% Orizaga, Saulo   
@article{fds335544,
   Author = {Glasner, K and Orizaga, S},
   Title = {Multidimensional equilibria and their stability in
             copolymer–solvent mixtures},
   Journal = {Physica D: Nonlinear Phenomena},
   Volume = {373},
   Pages = {1-12},
   Year = {2018},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.physd.2018.02.001},
   Abstract = {© 2018 Elsevier B.V. This paper discusses localized
             equilibria which arise in copolymer–solvent mixtures. A
             free boundary problem associated with the sharp-interface
             limit of a density functional model is used to identify both
             lamellar and concentric domain patterns composed of a finite
             number of layers. Stability of these morphologies is studied
             through explicit linearization of the free boundary
             evolution. For the multilayered lamellar configuration,
             transverse instability is observed for sufficiently small
             dimensionless interfacial energies. Additionally, a
             crossover between small and large wavelength instabilities
             is observed depending on whether solvent–polymer or
             monomer–monomer interfacial energy is dominant. Concentric
             domain patterns resembling multilayered micelles and
             vesicles exhibit bifurcations wherein they only exist for
             sufficiently small dimensionless interfacial energies. The
             bifurcation of large radii vesicle solutions is studied
             analytically, and a crossover from a supercritical case with
             only one solution branch to a subcritical case with two is
             observed. Linearized stability of these configurations shows
             that azimuthal perturbation may lead to instabilities as
             interfacial energy is decreased.},
   Doi = {10.1016/j.physd.2018.02.001},
   Key = {fds335544}
}

@article{fds329007,
   Author = {Orizaga, S and Riahi, DN},
   Title = {Triad resonant wave interactions in electrically charged
             jets},
   Journal = {Applied Mathematics and Mechanics},
   Volume = {38},
   Number = {8},
   Pages = {1127-1148},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1007/s10483-017-2229-9},
   Doi = {10.1007/s10483-017-2229-9},
   Key = {fds329007}
}


%% Petters, Arlie O.   
@book{fds15387,
   Author = {A. O. Petters and M. C. Werner},
   Title = {Gravitational Lensing and Black Holes},
   Publisher = {Springer, in preparation},
   Year = {2017},
   Month = {Spring},
   Key = {fds15387}
}


%% Pfister, Henry   
@article{fds336004,
   Author = {Rengaswamy, N and Calderbank, R and Pfister, HD and Kadhe,
             S},
   Title = {Synthesis of Logical Clifford Operators via Symplectic
             Geometry},
   Journal = {Ieee International Symposium on Information Theory
             Proceedings},
   Volume = {2018-June},
   Pages = {791-795},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1109/ISIT.2018.8437652},
   Abstract = {© 2018 IEEE. Quantum error-correcting codes can be used to
             protect qubits involved in quantum computation. This
             requires that logical operators acting on protected qubits
             be translated to physical operators (circuits) acting on
             physical quantum states. We propose a mathematical framework
             for synthesizing physical circuits that implement logical
             Clifford operators for stabilizer codes. Circuit synthesis
             is enabled by representing the desired physical Clifford
             operator in \mathbb{C}-{N\times N} as a 2m\times 2m binary
             sym-plectic matrix, where N=2-{m}. We show that for an
             \!\!\!\![\!\!\![\ {m, m-k}\ ]\!\!\!]\!\!\!\! stabilizer code
             every logical Clifford operator has 2-{k(k+1)/2} symplectic
             solutions, and we enumerate them efficiently using
             symplectic transvections. The desired circuits are then
             obtained by writing each of the solutions as a product of
             elementary symplectic matrices. For a given operator, our
             assembly of all of its physical realizations enables
             optimization over them with respect to a suitable metric.
             Our method of circuit synthesis can be applied to any
             stabilizer code, and this paper provides a proof of concept
             synthesis of universal Clifford gates for the well-known
             \!\!\!\![\!\!\![\ 6,4,2\ ]\!\!\!]\!\!\!\! code. Programs
             implementing our algorithms can be found at
             https://github.com/nrenga/symplectic-arxiv18a.},
   Doi = {10.1109/ISIT.2018.8437652},
   Key = {fds336004}
}

@article{fds337694,
   Author = {Hager, C and Pfister, HD},
   Title = {Deep Learning of the Nonlinear Schrödinger Equation in
             Fiber-Optic Communications},
   Journal = {Ieee International Symposium on Information Theory
             Proceedings},
   Volume = {2018-June},
   Pages = {1590-1594},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1109/ISIT.2018.8437734},
   Abstract = {© 2018 IEEE. An important problem in fiber-optic
             communications is to invert the nonlinear Schrödinger
             equation in real time to reverse the deterministic effects
             of the channel. Interestingly, the popular split-step
             Fourier method (SSFM) leads to a computation graph that is
             reminiscent of a deep neural network. This observation
             allows one to leverage tools from machine learning to reduce
             complexity. In particular, the main disadvantage of the SSFM
             is that its complexity using M steps is at least M times
             larger than a linear equalizer. This is because the linear
             SSFM operator is a dense matrix. In previous work,
             truncation methods such as frequency sampling, wavelets, or
             least-squares have been used to obtain 'cheaper' operators
             that can be implemented using filters. However, a large
             number of filter taps are typically required to limit
             truncation errors. For example, Ip and Kahn showed that for
             a 10 Gbaud signal and 2000 km optical link, a truncated SSFM
             with 25 steps would require 70-tap filters in each step and
             100 times more operations than linear equalization. We find
             that, by jointly optimizing all filters with deep learning,
             the complexity can be reduced significantly for similar
             accuracy. Using optimized 5-tap and 3-tap filters in an
             alternating fashion, one requires only around 2-6 times the
             complexity of linear equalization, depending on the
             implementation.},
   Doi = {10.1109/ISIT.2018.8437734},
   Key = {fds337694}
}

@article{fds337695,
   Author = {Santi, E and Hager, C and Pfister, HD},
   Title = {Decoding Reed-Muller Codes Using Minimum- Weight Parity
             Checks},
   Journal = {Ieee International Symposium on Information Theory
             Proceedings},
   Volume = {2018-June},
   Pages = {1296-1300},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1109/ISIT.2018.8437637},
   Abstract = {© 2018 IEEE. Reed-Muller (RM) codes exhibit good
             performance under maximum-likelihood (ML) decoding due to
             their highly-symmetric structure. In this paper, we explore
             the question of whether the code symmetry of RM codes can
             also be exploited to achieve near-ML performance in
             practice. The main idea is to apply iterative decoding to a
             highly-redundant parity-check (PC) matrix that contains only
             the minimum-weight dual codewords as rows. As examples, we
             consider the peeling decoder for the binary erasure channel,
             linear-programming and belief propagation (BP) decoding for
             the binary-input additive white Gaussian noise channel, and
             bit-flipping and BP decoding for the binary symmetric
             channel. For short block lengths, it is shown that near-ML
             performance can indeed be achieved in many cases. We also
             propose a method to tailor the PC matrix to the received
             observation by selecting only a small fraction of useful
             minimum-weight PCs before decoding begins. This allows one
             to both improve performance and significantly reduce
             complexity compared to using the full set of minimum-weight
             PCs.},
   Doi = {10.1109/ISIT.2018.8437637},
   Key = {fds337695}
}

@article{fds337696,
   Author = {Reeves, G and Pfister, HD and Dytso, A},
   Title = {Mutual Information as a Function of Matrix SNR for Linear
             Gaussian Channels},
   Journal = {Ieee International Symposium on Information Theory
             Proceedings},
   Volume = {2018-June},
   Pages = {1754-1758},
   Year = {2018},
   Month = {August},
   ISBN = {9781538647806},
   url = {http://dx.doi.org/10.1109/ISIT.2018.8437326},
   Abstract = {© 2018 IEEE. This paper focuses on the mutual information
             and minimum mean-squared error (MMSE) as a function a
             matrix-valued signal-to-noise ratio (SNR) for a linear
             Gaussian channel with arbitrary input distribution. As shown
             by Lamarca, the mutual-information is a concave function of
             a positive semidefinite matrix, which we call the matrix
             SNR. This implies that the mapping from the matrix SNR to
             the MMSE matrix is decreasing monotone. Building upon these
             functional properties, we start to construct a unifying
             framework that provides a bridge between classical
             information-theoretic inequalities, such as the entropy
             power inequality, and interpolation techniques used in
             statistical physics and random matrix theory. This framework
             provides new insight into the structure of phase transitions
             in coding theory and compressed sensing. In particular, it
             is shown that the parallel combination of linear channels
             with freely-independent matrices can be characterized
             succinctly via free convolution.},
   Doi = {10.1109/ISIT.2018.8437326},
   Key = {fds337696}
}

@article{fds336001,
   Author = {Hager, C and Pfister, HD},
   Title = {Approaching Miscorrection-Free Performance of Product Codes
             With Anchor Decoding},
   Journal = {Ieee Transactions on Communications},
   Volume = {66},
   Number = {7},
   Pages = {2797-2808},
   Year = {2018},
   Month = {July},
   url = {http://dx.doi.org/10.1109/TCOMM.2018.2816073},
   Doi = {10.1109/TCOMM.2018.2816073},
   Key = {fds336001}
}

@article{fds336002,
   Author = {Hager, C and Pfister, HD},
   Title = {Nonlinear interference mitigation via deep neural
             networks},
   Journal = {2018 Optical Fiber Communications Conference and Exposition,
             Ofc 2018 Proceedings},
   Pages = {1-3},
   Year = {2018},
   Month = {June},
   ISBN = {9781943580385},
   Abstract = {© 2018 OSA. A neural-network-based approach is presented to
             efficiently implement digital backpropagation (DBP). For a
             32×100 km fiber-optic link, the resulting 'learned' DBP
             significantly reduces the complexity compared to
             conventional DBP implementations.},
   Key = {fds336002}
}

@article{fds336003,
   Author = {Häger, C and Pfister, HD},
   Title = {Nonlinear interference mitigation via deep neural
             networks},
   Journal = {Optics Infobase Conference Papers},
   Volume = {Part F84-OFC 2018},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1364/OFC.2018.W3A.4},
   Abstract = {© OSA 2018. A neural-network-based approach is presented to
             efficiently implement digital backpropagation (DBP). For a
             32×100 km fiber-optic link, the resulting “learned“ DBP
             significantly reduces the complexity compared to
             conventional DBP implementations.},
   Doi = {10.1364/OFC.2018.W3A.4},
   Key = {fds336003}
}

@article{fds339599,
   Author = {Yoo, I and Imani, MF and Sleasman, T and Pfister, HD and Smith,
             DR},
   Title = {Enhancing Capacity of Spatial Multiplexing Systems Using
             Reconfigurable Cavity-backed Metasurface Antennas in
             Clustered MIMO Channels},
   Journal = {Ieee Transactions on Communications},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1109/TCOMM.2018.2876899},
   Abstract = {IEEE We propose a spatial multiplexing system using
             reconfigurable cavity-backed metasurface antennas. The
             metasurface antennas consist of a printed cavity with
             dynamically tunable metamaterial radiators patterned on one
             side and fed by multiple RF ports on the other side (each
             port representing one communication node), forming a shared
             aperture. By individual tuning of the radiators, the
             antennas can generate steerable, concurrent beams that can
             be adapted to the properties of multiple-input-multiple-output
             (MIMO) channels. In this paper, we present a 2 &#x00D7; 2
             MIMO system with simulated metasurface antennas as the
             transmit and receive antennas operating at 5.9 GHz. We
             demonstrate that the flexibility in beamforming supported by
             the metasurface antennas can be used to achieve low spatial
             correlation and high SNR-gain in clustered MIMO channels,
             leading to a significant improvement of the channel
             capacity. Numerical studies show 2.36-fold, 2.11-fold
             enhancements of capacity in MIMO channels with one and two
             clusters, respectively, compared with a MIMO system
             consisting of linear dipoles. The MIMO system based on the
             metasurface antennas can be low-cost, low profile, and
             low-power. The metasurface antenna thus has potential
             applications in small cell networks requiring high data rate
             under bandwidth, energy, and cost constraints.},
   Doi = {10.1109/TCOMM.2018.2876899},
   Key = {fds339599}
}

@article{fds333681,
   Author = {Häger, C and Pfister, HD},
   Title = {Miscorrection-free Decoding of Staircase
             Codes},
   Journal = {European Conference on Optical Communication,
             Ecoc},
   Volume = {2017-September},
   Pages = {1-3},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1109/ECOC.2017.8345919},
   Abstract = {© 2017 IEEE. We propose a novel decoding algorithm for
             staircase codes which reduces the effect of undetected
             component code miscorrections. The algorithm significantly
             improves performance, while retaining a low-complexity
             implementation suitable for high-speed optical transport
             networks.},
   Doi = {10.1109/ECOC.2017.8345919},
   Key = {fds333681}
}

@article{fds328986,
   Author = {Charbonneau, P and Li, YC and Pfister, HD and Yaida,
             S},
   Title = {Cycle-expansion method for the Lyapunov exponent,
             susceptibility, and higher moments.},
   Journal = {Physical Review. E},
   Volume = {96},
   Number = {3-1},
   Pages = {032129},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1103/physreve.96.032129},
   Abstract = {Lyapunov exponents characterize the chaotic nature of
             dynamical systems by quantifying the growth rate of
             uncertainty associated with the imperfect measurement of
             initial conditions. Finite-time estimates of the exponent,
             however, experience fluctuations due to both the initial
             condition and the stochastic nature of the dynamical path.
             The scale of these fluctuations is governed by the Lyapunov
             susceptibility, the finiteness of which typically provides a
             sufficient condition for the law of large numbers to apply.
             Here, we obtain a formally exact expression for this
             susceptibility in terms of the Ruelle dynamical ζ function
             for one-dimensional systems. We further show that, for
             systems governed by sequences of random matrices, the cycle
             expansion of the ζ function enables systematic computations
             of the Lyapunov susceptibility and of its higher-moment
             generalizations. The method is here applied to a class of
             dynamical models that maps to static disordered spin chains
             with interactions stretching over a varying distance and is
             tested against Monte Carlo simulations.},
   Doi = {10.1103/physreve.96.032129},
   Key = {fds328986}
}

@article{fds326795,
   Author = {Kudekar, S and Kumar, S and Mondelli, M and Pfister, HD and Sasoglu, E and Urbanke, RL},
   Title = {Reed–Muller Codes Achieve Capacity on Erasure
             Channels},
   Journal = {Ieee Transactions on Information Theory},
   Volume = {63},
   Number = {7},
   Pages = {4298-4316},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1109/TIT.2017.2673829},
   Doi = {10.1109/TIT.2017.2673829},
   Key = {fds326795}
}

@article{fds326794,
   Author = {Hager, C and Pfister, HD and Graell i Amat and A and Brannstrom,
             F},
   Title = {Density Evolution for Deterministic Generalized Product
             Codes on the Binary Erasure Channel at High
             Rates},
   Journal = {Ieee Transactions on Information Theory},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1109/TIT.2017.2689783},
   Doi = {10.1109/TIT.2017.2689783},
   Key = {fds326794}
}

@article{fds324463,
   Author = {Sabag, O and Permuter, HH and Pfister, HD},
   Title = {A Single-Letter Upper Bound on the Feedback Capacity of
             Unifilar Finite-State Channels},
   Journal = {Ieee Transactions on Information Theory},
   Volume = {63},
   Number = {3},
   Pages = {1392-1409},
   Year = {2017},
   Month = {March},
   url = {http://dx.doi.org/10.1109/TIT.2016.2636851},
   Abstract = {© 1963-2012 IEEE.An upper bound on the feedback capacity of
             unifilar finite-state channels (FSCs) is derived. A new
             technique, called the Q-context mapping, is based on a
             construction of a directed graph that is used for a
             sequential quantization of the receiver's output sequences
             to a finite set of contexts. For any choice of Q-graph, the
             feedback capacity is bounded by a single-letter expression,
             Cfb ≤ sup I (X, S; Y|Q), where the supremum is over p(x|s,
             q) and the distribution of (S, Q) is their stationary
             distribution. It is shown that the bound is tight for all
             unifilar FSCs, where feedback capacity is known: channels
             where the state is a function of the outputs, the trapdoor
             channel, Ising channels, the no-consecutive-ones
             input-constrained erasure channel, and the memoryless
             channel. Its efficiency is also demonstrated by deriving a
             new capacity result for the dicode erasure channel; the
             upper bound is obtained directly from the above-mentioned
             expression and its tightness is concluded with a general
             sufficient condition on the optimality of the upper bound.
             This sufficient condition is based on a fixed point
             principle of the BCJR equation and, indeed, formulated as a
             simple lower bound on feedback capacity of unifilar FSCs for
             arbitrary Q-graphs. This upper bound indicates that a
             single-letter expression might exist for the capacity of
             finite-state channels with or without feedback based on a
             construction of auxiliary random variable with specified
             structure, such as the Q-graph, and not with i.i.d
             distribution. The upper bound also serves as a non-trivial
             bound on the capacity of channels without feedback, a
             problem that is still open.},
   Doi = {10.1109/TIT.2016.2636851},
   Key = {fds324463}
}

@article{fds325508,
   Author = {Sabag, O and Permuter, HH and Pfister, HD},
   Title = {Single-letter bounds on the feedback capacity of unifilar
             finite-state channels},
   Journal = {2016 IEEE International Conference on the Science of
             Electrical Engineering, ICSEE 2016},
   Year = {2017},
   Month = {January},
   ISBN = {9781509021529},
   url = {http://dx.doi.org/10.1109/ICSEE.2016.7806200},
   Abstract = {© 2016 IEEE. Upper and lower bounds on the feedback
             capacity of unifilar finite-state channels (FSCs) are
             derived. The upper bound is derived using a new technique,
             called the Q-contexts, which is based on a construction of a
             directed graph that is used to quantize recursively the
             receiver's output sequences to a finite set of contexts. For
             any choice of Q-graph, the feedback capacity is bounded by a
             single-letter expression, C fb ≤ sup I (X, S; Y |Q), where
             the supremum is over P x|s,q and the distribution of (S, Q)
             is their stationary distribution. The bound is tight for all
             unifilar FSCs where feedback capacity is known: channels
             where the state is a function of the outputs, the trapdoor
             channel, Ising channels, the no-consecutive-ones
             input-constrained erasure channel and for the memoryless
             channel. The upper bound indicates that a single-letter
             expression might exist for the capacity of finite-state
             channels with or without feedback which are based on a
             construction of auxiliary random variable with memory, such
             as Q-graph, and not with i.i.d distribution. The lower bound
             provides a sufficient condition for the optimality of the
             upper bound, however, it is formulated such that independent
             lower bounds on feedback capacity may be calculated. The
             efficiency of these bounds is demonstrated by deriving a new
             capacity result for the dicode erasure channel (DEC). The
             upper bound also serves as a non-trivial bound on the
             capacity of channels without feedback, a problem that is
             still open.},
   Doi = {10.1109/ICSEE.2016.7806200},
   Key = {fds325508}
}

@article{fds327403,
   Author = {Jian, Y-Y and Pfister, HD and Narayanan, KR},
   Title = {Approaching Capacity at High Rates with Iterative
             Hard-Decision Decoding},
   Journal = {Ieee Transactions on Information Theory},
   Pages = {1-1},
   Year = {2017},
   url = {http://dx.doi.org/10.1109/TIT.2017.2717838},
   Doi = {10.1109/TIT.2017.2717838},
   Key = {fds327403}
}


%% Pierce, Lillian B.   
@article{fds331376,
   Author = {Pierce, LB and Yung, PL},
   Title = {A polynomial Carleson operator along the
             paraboloid},
   Journal = {Revista Matemática Iberoamericana},
   Publisher = {European Mathematical Society},
   Year = {2018},
   Key = {fds331376}
}

@article{fds328917,
   Author = {Carneiro, E and Madrid, J and Pierce, LB},
   Title = {Endpoint Sobolev and BV continuity for maximal
             operators},
   Journal = {Journal of Functional Analysis},
   Volume = {273},
   Number = {10},
   Pages = {3262-3294},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1016/j.jfa.2017.08.012},
   Doi = {10.1016/j.jfa.2017.08.012},
   Key = {fds328917}
}

@article{fds328811,
   Author = {Heath-Brown, DR and Pierce, LB},
   Title = {Averages and moments associated to class numbers of
             imaginary quadratic fields},
   Journal = {Compositio Mathematica},
   Volume = {153},
   Number = {11},
   Pages = {2287-2309},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1112/S0010437X1700728X},
   Doi = {10.1112/S0010437X1700728X},
   Key = {fds328811}
}

@article{fds330204,
   Author = {Pierce, LB},
   Title = {The Vinogradov Mean Value Theorem [after Wooley, and
             Bourgain, Demeter and Guth]},
   Journal = {Astérisque},
   Publisher = {Centre National de la Recherche Scientifique},
   Year = {2017},
   Month = {July},
   Abstract = {This is the expository essay that accompanies my Bourbaki
             Seminar on 17 June 2017 on the landmark proof of the
             Vinogradov Mean Value Theorem, and the two approaches
             developed in the work of Wooley and of Bourgain, Demeter and
             Guth.},
   Key = {fds330204}
}

@article{fds320389,
   Author = {Heath-Brown, DR and Pierce, LB},
   Title = {Simultaneous integer values of pairs of quadratic
             forms},
   Journal = {Journal Fur Die Reine Und Angewandte Mathematik},
   Volume = {2017},
   Number = {727},
   Pages = {85-143},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1515/crelle-2014-0112},
   Abstract = {We prove that a pair of integral quadratic forms in five or
             more variables will simultaneously represent "almost all"
             pairs of integers that satisfy the necessary local
             conditions, provided that the forms satisfy a suitable
             nonsingularity condition. In particular such forms
             simultaneously attain prime values if the obvious local
             conditions hold. The proof uses the circle method, and in
             particular pioneers a two-dimensional version of a
             Kloosterman refinement.},
   Doi = {10.1515/crelle-2014-0112},
   Key = {fds320389}
}

@article{fds330203,
   Author = {Pierce, LB and Turnage-Butterbaugh, CL and Wood,
             MM},
   Title = {An effective Chebotarev density theorem for families of
             number fields, with an application to $\ell$-torsion in
             class groups},
   Journal = {(Submitted)},
   Year = {2017},
   Abstract = {An effective Chebotarev density theorem for a fixed normal
             extension $L/\mathbb{Q}$ provides an asymptotic, with an
             explicit error term, for the number of primes of bounded
             size with a prescribed splitting type in $L$. In many
             applications one is most interested in the case where the
             primes are small (with respect to the absolute discriminant
             of $L$); this is well-known to be closely related to the
             Generalized Riemann Hypothesis for the Dedekind zeta
             function of $L$. In this work we prove a new effective
             Chebotarev density theorem, independent of GRH, that
             improves the previously known unconditional error term and
             allows primes to be taken quite small (certainly as small as
             an arbitrarily small power of the discriminant of $L$); this
             theorem holds for the Galois closures of "almost all" number
             fields that lie in an appropriate family of field
             extensions. Such a family has fixed degree, fixed Galois
             group of the Galois closure, and in certain cases a
             ramification restriction on all tamely ramified primes in
             each field; examples include totally ramified cyclic fields,
             degree $n$ $S_n$-fields with square-free discriminant, and
             degree $n$ $A_n$-fields. In all cases, our work is
             independent of GRH; in some cases we assume the strong Artin
             conjecture or hypotheses on counting number fields. The new
             effective Chebotarev theorem is expected to have many
             applications, of which we demonstrate two. First we prove
             (for all integers $\ell \geq 1$) nontrivial bounds for
             $\ell$-torsion in the class groups of "almost all" fields in
             the families of fields we consider. This provides the first
             nontrivial upper bounds for $\ell$-torsion, for all integers
             $\ell \geq 1$, applicable to infinite families of fields of
             arbitrarily large degree. Second, in answer to a question of
             Ruppert, we prove that within each family, "almost all"
             fields have a small generator.},
   Key = {fds330203}
}

@article{fds320661,
   Author = {Guo, S and Pierce, LB and Roos, J and Yung, P},
   Title = {Polynomial Carleson operators along monomial curves in the
             plane},
   Journal = {Journal of Geometric Analysis},
   Publisher = {Springer Verlag},
   Year = {2017},
   Abstract = {We prove $L^p$ bounds for partial polynomial Carleson
             operators along monomial curves $(t,t^m)$ in the plane
             $\mathbb{R}^2$ with a phase polynomial consisting of a
             single monomial. These operators are "partial" in the sense
             that we consider linearizing stopping-time functions that
             depend on only one of the two ambient variables. A
             motivation for studying these partial operators is the
             curious feature that, despite their apparent limitations,
             for certain combinations of curve and phase, $L^2$ bounds
             for partial operators along curves imply the full strength
             of the $L^2$ bound for a one-dimensional Carleson operator,
             and for a quadratic Carleson operator. Our methods, which
             can at present only treat certain combinations of curves and
             phases, in some cases adapt a $TT^*$ method to treat phases
             involving fractional monomials, and in other cases use a
             known vector-valued variant of the Carleson-Hunt
             theorem.},
   Key = {fds320661}
}

@article{fds320660,
   Author = {Ellenberg, J and Pierce, LB and Wood, MM},
   Title = {On ℓ-torsion in class groups of number
             fields},
   Journal = {Algebra & Number Theory},
   Volume = {11},
   Number = {8},
   Pages = {1739-1778},
   Year = {2017},
   url = {http://dx.doi.org/10.2140/ant.2017.11.1739},
   Abstract = {© 2017 Mathematical Sciences Publishers. For each integer
             ℓ ≥ 1, we prove an unconditional upper bound on the size
             of the ℓ-torsion subgroup of the class group, which holds
             for all but a zerodensity set of field extensions of Q of
             degree d, for any fixed d ε {2; 3; 4; 5} (with the
             additional restriction in the case d D 4 that the field be
             non-D 4 ). For sufficiently large ℓ (specified
             explicitly), these results are as strong as a previously
             known bound that is conditional on GRH. As part of our
             argument, we develop a probabilistic “Chebyshev sieve,”
             and give uniform, power-saving error terms for the
             asymptotics of quartic (non-D 4 ) and quintic fields with
             chosen splitting types at a finite set of
             primes.},
   Doi = {10.2140/ant.2017.11.1739},
   Key = {fds320660}
}


%% Plesser, M. Ronen   
@article{fds338044,
   Author = {Bertolini, M and Plesser, MR},
   Title = {(0,2) hybrid models},
   Journal = {Journal of High Energy Physics},
   Volume = {2018},
   Number = {9},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1007/JHEP09(2018)067},
   Abstract = {© 2018, The Author(s). We introduce a class of (0,2)
             superconformal field theories based on hybrid geometries,
             generalizing various known constructions. We develop
             techniques for the computation of the complete massless
             spectrum when the theory can be interpreted as determining a
             perturbative heterotic string compactification. We provide
             evidence for surprising properties regarding RG flows and IR
             accidental symmetries in (0,2) hybrid CFTs. We also study
             the conditions for embedding a hybrid theory in a particular
             class of gauged linear sigma models. This perspective
             suggests that our construction generates models which cannot
             be realized or analyzed by previously known
             methods.},
   Doi = {10.1007/JHEP09(2018)067},
   Key = {fds338044}
}

@article{fds325481,
   Author = {Jockers, H and Katz, S and Morrison, DR and Plesser,
             MR},
   Title = {SU(N) Transitions in M-Theory on Calabi–Yau Fourfolds and
             Background Fluxes},
   Journal = {Communications in Mathematical Physics},
   Volume = {351},
   Number = {2},
   Pages = {837-871},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1007/s00220-016-2741-5},
   Doi = {10.1007/s00220-016-2741-5},
   Key = {fds325481}
}


%% Pollack, Aaron   
@article{fds330522,
   Author = {Pollack, A},
   Title = {The spin -function on for Siegel modular
             forms},
   Journal = {Compositio Mathematica},
   Volume = {153},
   Number = {07},
   Pages = {1391-1432},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1112/S0010437X17007114},
   Doi = {10.1112/S0010437X17007114},
   Key = {fds330522}
}

@article{fds330523,
   Author = {Pollack, A and Shah, S},
   Title = {On the Rankin–Selberg integral of Kohnen and
             Skoruppa},
   Journal = {Mathematical Research Letters},
   Volume = {24},
   Number = {1},
   Pages = {173-222},
   Year = {2017},
   url = {http://dx.doi.org/10.4310/MRL.2017.v24.n1.a8},
   Doi = {10.4310/MRL.2017.v24.n1.a8},
   Key = {fds330523}
}


%% Randles, Amanda   
@article{fds339595,
   Author = {Gounley, J and Draeger, EW and Oppelstrup, T and Krauss, WD and Gunnels,
             JA and Chaudhury, R and Nair, P and Frakes, D and Leopold, JA and Randles,
             A},
   Title = {Computing the ankle-brachial index with parallel
             computational fluid dynamics.},
   Journal = {Journal of Biomechanics},
   Year = {2018},
   Month = {October},
   url = {http://dx.doi.org/10.1016/j.jbiomech.2018.10.007},
   Abstract = {The ankle-brachial index (ABI), a ratio of arterial blood
             pressure in the ankles and upper arms, is used to diagnose
             and monitor circulatory conditions such as coarctation of
             the aorta and peripheral artery disease. Computational
             simulations of the ABI can potentially determine the
             parameters that produce an ABI indicative of ischemia or
             other abnormalities in blood flow. However, 0- and 1-D
             computational methods are limited in describing a 3-D
             patient-derived geometry. Thus, we present a massively
             parallel framework for computational fluid dynamics (CFD)
             simulations in the full arterial system. Using the lattice
             Boltzmann method to solve the Navier-Stokes equations, we
             employ highly parallelized and scalable methods to generate
             the simulation domain and efficiently distribute the
             computational load among processors. For the first time, we
             compute an ABI with 3-D CFD. In this proof-of-concept study,
             we investigate the dependence of ABI on the presence of
             stenoses, or narrowed regions of the arteries, by directly
             modifying the arterial geometry. As a result, our framework
             enables the computation a hemodynamic factor characterizing
             flow at the scale of the full arterial system, in a manner
             that is extensible to patient-specific imaging data and
             holds potential for treatment planning.},
   Doi = {10.1016/j.jbiomech.2018.10.007},
   Key = {fds339595}
}

@article{fds339258,
   Author = {Hegele, LA and Scagliarini, A and Sbragaglia, M and Mattila, KK and Philippi, PC and Puleri, DF and Gounley, J and Randles,
             A},
   Title = {High-Reynolds-number turbulent cavity flow using the lattice
             Boltzmann method},
   Journal = {Physical Review. E},
   Volume = {98},
   Number = {4},
   Year = {2018},
   Month = {October},
   url = {http://dx.doi.org/10.1103/PhysRevE.98.043302},
   Abstract = {© 2018 American Physical Society. We present a boundary
             condition scheme for the lattice Boltzmann method that has
             significantly improved stability for modeling turbulent
             flows while maintaining excellent parallel scalability.
             Simulations of a three-dimensional lid-driven cavity flow
             are found to be stable up to the unprecedented Reynolds
             number Re=5×104 for this setup. Excellent agreement with
             energy balance equations, computational and experimental
             results are shown. We quantify rises in the production of
             turbulence and turbulent drag, and determine peak locations
             of turbulent production.},
   Doi = {10.1103/PhysRevE.98.043302},
   Key = {fds339258}
}

@article{fds337736,
   Author = {Herschlag, G and Lee, S and Vetter, JS and Randles,
             A},
   Title = {GPU data access on complex geometries for D3Q19 lattice
             boltzmann method},
   Journal = {Proceedings 2018 Ieee 32nd International Parallel and
             Distributed Processing Symposium, Ipdps 2018},
   Pages = {825-834},
   Year = {2018},
   Month = {August},
   ISBN = {9781538643686},
   url = {http://dx.doi.org/10.1109/IPDPS.2018.00092},
   Abstract = {© 2018 IEEE. GPU performance of the lattice Boltzmann
             method (LBM) depends heavily on memory access patterns. When
             LBM is advanced with GPUS on complex computational domains,
             geometric data is typically accessed indirectly, and lattice
             data is typically accessed lexicographically in the
             Structure of Array (SoA) layout. Although there are a
             variety of existing access patterns beyond the typical
             choices, no study has yet examined the relative efficacy
             between them. Here, we compare a suite of memory access
             schemes via empirical testing and performance modeling. We
             find strong evidence that semi-direct addressing is the
             superior addressing scheme for the majority of cases
             examined: Semi-direct addressing increases computational
             speed and often reduces memory consumption. For lattice
             layout, we find that the Collected Structure of Arrays
             (CSoA) layout outperforms the SoA layout. When compared to
             state-of-The-Art practices, our recommended addressing
             modifications lead to performance gains between 10-40%
             across different complex geometries, fluid volume fractions,
             and resolutions. The modifications also lead to a decrease
             in memory consumption by as much as 17%. Having discovered
             these improvements, we examine a highly resolved arterial
             geometry on a leadership class system. On this system we
             present the first near-optimal strong results for LBM with
             arterial geometries run on GPUS. We also demonstrate that
             the above recommendations remain valid for large scale, many
             device simulations, which leads to an increased
             computational speed and average memory usage reductions. To
             understand these observations, we employ performance
             modeling which reveals that semi-direct methods outperform
             indirect methods due to a reduced number of total
             loads/stores in memory, and that CSoA outperforms SoA and
             bundling due to improved caching behavior.},
   Doi = {10.1109/IPDPS.2018.00092},
   Key = {fds337736}
}

@article{fds333543,
   Author = {Rafat, M and Stone, HA and Auguste, DT and Dabagh, M and Randles, A and Heller, M and Rabinov, JD},
   Title = {Impact of diversity of morphological characteristics and
             Reynolds number on local hemodynamics in basilar
             aneurysms},
   Journal = {Aiche Journal},
   Volume = {64},
   Number = {7},
   Pages = {2792-2802},
   Year = {2018},
   Month = {July},
   url = {http://dx.doi.org/10.1002/aic.16091},
   Abstract = {© 2018 American Institute of Chemical Engineers.
             Morphological and hemodynamic parameters have been suggested
             to affect the rupture of cerebral aneurysms, but detailed
             mechanisms of rupture are poorly understood. The purpose of
             our study is to determine criteria for predicting the risk
             of aneurysm rupture, which is critical for improved patient
             management. Existing aneurysm hemodynamics studies generally
             evaluate limited geometries or Reynolds numbers (Re), which
             are difficult to apply to a wide range of patient-specific
             cases. Association between hemodynamic characteristics and
             morphology is focused. Several two-dimensional (2D) and
             three-dimensional (3D) idealized and physiological
             geometries is assessed to characterize the hemodynamic
             landscape between flow patterns. The impact of morphology on
             velocity and wall shear stress (WSS) profiles were
             evaluated. Slight changes in aneurysm geometry is found or
             Re result in significant changes in the hemodynamic and WSS
             profiles. Our systematic mapping and nondimensional analysis
             qualitatively identify hemodynamic conditions that may
             predispose aneurysms to rupture.},
   Doi = {10.1002/aic.16091},
   Key = {fds333543}
}

@article{fds337027,
   Author = {Gounley, J and Vardhan, M and Randles, A},
   Title = {A framework for comparing vascular hemodynamics at different
             points in time},
   Journal = {Computer Physics Communications},
   Year = {2018},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.cpc.2018.05.014},
   Doi = {10.1016/j.cpc.2018.05.014},
   Key = {fds337027}
}

@article{fds329286,
   Author = {Randles, A and Frakes, DH and Leopold, JA},
   Title = {Computational Fluid Dynamics and Additive Manufacturing to
             Diagnose and Treat Cardiovascular Disease.},
   Journal = {Trends in Biotechnology},
   Volume = {35},
   Number = {11},
   Pages = {1049-1061},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1016/j.tibtech.2017.08.008},
   Abstract = {Noninvasive engineering models are now being used for
             diagnosing and planning the treatment of cardiovascular
             disease. Techniques in computational modeling and additive
             manufacturing have matured concurrently, and results from
             simulations can inform and enable the design and
             optimization of therapeutic devices and treatment
             strategies. The emerging synergy between large-scale
             simulations and 3D printing is having a two-fold benefit:
             first, 3D printing can be used to validate the complex
             simulations, and second, the flow models can be used to
             improve treatment planning for cardiovascular disease. In
             this review, we summarize and discuss recent methods and
             findings for leveraging advances in both additive
             manufacturing and patient-specific computational modeling,
             with an emphasis on new directions in these fields and
             remaining open questions.},
   Doi = {10.1016/j.tibtech.2017.08.008},
   Key = {fds329286}
}

@article{fds328038,
   Author = {Gounley, J and Vardhan, M and Randles, A},
   Title = {A computational framework to assess the influence of changes
             in vascular geometry on blood flow},
   Journal = {PASC 2017 - Proceedings of the Platform for Advanced
             Scientific Computing Conference},
   Year = {2017},
   Month = {June},
   ISBN = {9781450350624},
   url = {http://dx.doi.org/10.1145/3093172.3093227},
   Abstract = {© 2017 Association for Computing Machinery. Many vascular
             abnormalities, such as aneurysms or stenoses, develop
             gradually over time. In the early stages of their
             development, they require monitoring but do not pose
             sufficient risk to the patient for a clinician to recommend
             invasive treatment. With a better understanding of the
             interplay between hemodynamic factors and changes in blood
             vessel geometry, there is an opportunity to improve clinical
             care by earlier identification of aneurysms or stenoses with
             significant potential for further development. Computational
             fluid dynamics has shown great promise for investigating
             this interplay and identifying the associated underlying
             mechanisms, by using patient-derived geometries and
             modifying them to represent potential evolution of the
             vascular disease. However, a general, extensible framework
             for comparing simulation results from different vascular
             geometries in a direct, quantitative manner does not
             currently exist. As a first step toward the development of
             such a framework, we present a method for quantifying the
             relationship between changes in vascular geometry and
             hemodynamic factors, such as wall shear stress. We apply
             this framework to study the correlation between wall shear
             stress and geometric changes in two opposite settings: When
             flow properties are associated with consequent changes in
             the vascular geometry, as in a thoracic aortic aneurysm, and
             when geometric changes alter the flow, as in a worsening
             aortic stenosis.},
   Doi = {10.1145/3093172.3093227},
   Key = {fds328038}
}

@article{fds326715,
   Author = {Dabagh, M and Jalali, P and Butler, PJ and Randles, A and Tarbell,
             JM},
   Title = {Mechanotransmission in endothelial cells subjected to
             oscillatory and multi-directional shear flow.},
   Journal = {Journal of the Royal Society, Interface},
   Volume = {14},
   Number = {130},
   Year = {2017},
   Month = {May},
   url = {http://dx.doi.org/10.1098/rsif.2017.0185},
   Abstract = {Local haemodynamics are linked to the non-uniform
             distribution of atherosclerosic lesions in arteries. Low and
             oscillatory (reversing in the axial flow direction) wall
             shear stress (WSS) induce inflammatory responses in
             endothelial cells (ECs) mediating disease localization. The
             objective of this study is to investigate computationally
             how the flow direction (reflected in WSS variation on the EC
             surface over time) influences the forces experienced by
             structural components of ECs that are believed to play
             important roles in mechanotransduction. A three-dimensional,
             multi-scale, multi-component, viscoelastic model of focally
             adhered ECs is developed, in which oscillatory WSS
             (reversing or non-reversing) parallel to the principal flow
             direction, or multi-directional oscillatory WSS with
             reversing axial and transverse components are applied over
             the EC surface. The computational model includes the
             glycocalyx layer, actin cortical layer, nucleus,
             cytoskeleton, focal adhesions (FAs), stress fibres and
             adherens junctions (ADJs). We show the distinct effects of
             atherogenic flow profiles (reversing unidirectional flow and
             reversing multi-directional flow) on subcellular structures
             relative to non-atherogenic flow (non-reversing flow).
             Reversing flow lowers stresses and strains due to
             viscoelastic effects, and multi-directional flow alters
             stress on the ADJs perpendicular to the axial flow
             direction. The simulations predict forces on integrins, ADJ
             filaments and other substructures in the range that activate
             mechanotransduction.},
   Doi = {10.1098/rsif.2017.0185},
   Key = {fds326715}
}

@article{fds328446,
   Author = {Gounley, J and Draeger, EW and Randles, A},
   Title = {Numerical simulation of a compound capsule in a constricted
             microchannel.},
   Journal = {Procedia Computer Science},
   Volume = {108},
   Pages = {175-184},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1016/j.procs.2017.05.209},
   Abstract = {Simulations of the passage of eukaryotic cells through a
             constricted channel aid in studying the properties of cancer
             cells and their transport in the bloodstream. Compound
             capsules, which explicitly model the outer cell membrane and
             nuclear lamina, have the potential to improve computational
             model fidelity. However, general simulations of compound
             capsules transiting a constricted microchannel have not been
             conducted and the influence of the compound capsule model on
             computational performance is not well known. In this study,
             we extend a parallel hemodynamics application to simulate
             the fluid-structure interaction between compound capsules
             and fluid. With this framework, we compare the deformation
             of simple and compound capsules in constricted
             microchannels, and explore how deformation depends on the
             capillary number and on the volume fraction of the inner
             membrane. The computational framework's parallel performance
             in this setting is evaluated and future development lessons
             are discussed.},
   Doi = {10.1016/j.procs.2017.05.209},
   Key = {fds328446}
}

@article{fds326839,
   Author = {Laurence, TA and Ly, S and Fong, E and Shusteff, M and Randles, A and Gounley, J and Draeger, E},
   Title = {Using stroboscopic flow imaging to validate large-scale
             computational fluid dynamics simulations},
   Journal = {Progress in Biomedical Optics and Imaging Proceedings of
             Spie},
   Volume = {10076},
   Year = {2017},
   Month = {January},
   ISBN = {9781510605930},
   url = {http://dx.doi.org/10.1117/12.2253319},
   Abstract = {Copyright © 2017 SPIE. The utility and accuracy of
             computational modeling often requires direct validation
             against experimental measurements. The work presented here
             is motivated by taking a combined experimental and
             computational approach to determine the ability of
             large-scale computational fluid dynamics (CFD) simulations
             to understand and predict the dynamics of circulating tumor
             cells in clinically relevant environments. We use
             stroboscopic light sheet fluorescence imaging to track the
             paths and measure the velocities of fluorescent microspheres
             throughout a human aorta model. Performed over complex
             physiologicallyrealistic 3D geometries, large data sets are
             acquired with microscopic resolution over macroscopic
             distances.},
   Doi = {10.1117/12.2253319},
   Key = {fds326839}
}


%% Reed, Michael C.   
@article{fds339491,
   Author = {Nijhout, HF and Best, JA and Reed, MC},
   Title = {Systems biology of robustness and homeostatic
             mechanisms.},
   Journal = {Wiley Interdisciplinary Reviews. Systems Biology and
             Medicine},
   Pages = {e1440},
   Year = {2018},
   Month = {October},
   url = {http://dx.doi.org/10.1002/wsbm.1440},
   Abstract = {All organisms are subject to large amounts of genetic and
             environmental variation and have evolved mechanisms that
             allow them to function well in spite of these challenges.
             This property is generally referred to as robustness. We
             start with the premise that phenotypes arise from dynamical
             systems and are therefore system properties. Phenotypes
             occur at all levels of the biological organizational
             hierarchy, from gene products, to biochemical pathways, to
             cells, tissues, organs, appendages, and whole bodies.
             Phenotypes at all these levels are subject to environmental
             and genetic challenges against which their form and function
             need to be protected. The mechanisms that can produce
             robustness are diverse and several different kinds often
             operate simultaneously. We focus, in particular, on
             homeostatic mechanisms that dynamically maintain form and
             function against varying environmental and genetic factors.
             Understanding how homeostatic mechanisms operate, how they
             reach their set point, and the nature of the set point pose
             difficult challenges. In developmental systems, homeostatic
             mechanisms make the progression of morphogenesis relatively
             insensitive to genetic and environmental variation so that
             the outcomes vary little, even in the presence of severe
             mutational and environmental stress. Accordingly,
             developmental systems give the appearance of being
             goal-oriented, but how the target phenotype is encoded is
             not known. We discuss why and how individual variation poses
             challenges for mathematical modeling of biological systems,
             and conclude with an explanation of how system population
             models are a useful method for incorporating individual
             variation into deterministic ordinary differential equation
             (ODE) models. This article is categorized under: Models of
             Systems Properties and Processes > Mechanistic Models
             Physiology > Mammalian Physiology in Health and Disease
             Physiology > Organismal Responses to Environment Biological
             Mechanisms > Regulatory Biology.},
   Doi = {10.1002/wsbm.1440},
   Key = {fds339491}
}

@article{fds339359,
   Author = {Sadre-Marandi, F and Dahdoul, T and Reed, MC and Nijhout,
             HF},
   Title = {Sex differences in hepatic one-carbon metabolism.},
   Journal = {Bmc Systems Biology},
   Volume = {12},
   Number = {1},
   Pages = {89},
   Year = {2018},
   Month = {October},
   url = {http://dx.doi.org/10.1186/s12918-018-0621-7},
   Abstract = {BACKGROUND:There are large differences between men and women
             of child-bearing age in the expression level of 5 key
             enzymes in one-carbon metabolism almost certainly caused by
             the sex hormones. These male-female differences in
             one-carbon metabolism are greatly accentuated during
             pregnancy. Thus, understanding the origin and consequences
             of sex differences in one-carbon metabolism is important for
             precision medicine. RESULTS:We have created a mathematical
             model of hepatic one-carbon metabolism based on the
             underlying physiology and biochemistry. We use the model to
             investigate the consequences of sex differences in gene
             expression. We give a mechanistic understanding of observed
             concentration differences in one-carbon metabolism and
             explain why women have lower S-andenosylmethionine, lower
             homocysteine, and higher choline and betaine. We give a new
             explanation of the well known phenomenon that folate
             supplementation lowers homocysteine and we show how to use
             the model to investigate the effects of vitamin
             deficiencies, gene polymorphisms, and nutrient input
             changes. CONCLUSIONS:Our model of hepatic one-carbon
             metabolism is a useful platform for investigating the
             mechanistic reasons that underlie known associations between
             metabolites. In particular, we explain how gene expression
             differences lead to metabolic differences between males and
             females.},
   Doi = {10.1186/s12918-018-0621-7},
   Key = {fds339359}
}

@article{fds337146,
   Author = {West, A and Best, J and Abdalla, A and Nijhout, F and Reed, M and Hashemi,
             P},
   Title = {Voltammetric evidence for discrete serotonin circuits,
             linked to specific reuptake domains, in the mouse medial
             prefrontal cortex.},
   Journal = {Neurochemistry International},
   Year = {2018},
   Month = {July},
   url = {http://dx.doi.org/10.1016/j.neuint.2018.07.004},
   Abstract = {The medial prefrontal cortex (mPFC) is an important brain
             region, that controls a variety of behavioral and functional
             outputs. As an important step in characterizing mPFC
             functionality, in this paper we focus on chemically defining
             serotonin transmission in this area. We apply cutting-edge
             analytical methods, fast-scan cyclic voltammetry (FSCV) and
             fast-scan controlled adsorption cyclic voltammetry (FSCAV),
             pioneered in our laboratory, for the first real-time in vivo
             analysis of serotonin in the mPFC. In prior in vivo work in
             the substantia nigra, pars reticulata, we found that our
             sub-second measurements of a single evoked serotonin release
             were subject to two clearance mechanisms. These mechanisms
             were readily modeled via Uptake 1, mediated by the serotonin
             transporters (SERTs), and Uptake 2, mediated by monoamine
             transporters (dopamine transporters (DATs), norepinephrine
             transporters (NETs), and organic cation transporters
             (OCTs)). Here in the mPFC, for the first time to our
             knowledge, we observe two release events in response to a
             single stimulation of the medial forebrain bundle (MFB). Of
             particular note is that each response is tied to a discrete
             reuptake profile comprising both Uptake 1 and 2. We
             hypothesize that two distinct populations of serotonin axons
             traverse the MFB and terminate in different domains with
             specific reuptake profiles. We test and confirm this
             hypothesis using a multifaceted pharmacological,
             histological and mathematical approach. We thus present
             evidence for a highly elaborate biochemical organization
             that regulates serotonin chemistry in the mPFC. This
             knowledge provides a solid foundation on which to base
             future studies of the involvement of the mPFC in brain
             function and behavior.},
   Doi = {10.1016/j.neuint.2018.07.004},
   Key = {fds337146}
}

@article{fds333668,
   Author = {Duncan, W and Best, J and Golubitsky, M and Nijhout, HF and Reed,
             M},
   Title = {Homeostasis despite instability.},
   Journal = {Mathematical Biosciences},
   Volume = {300},
   Pages = {130-137},
   Year = {2018},
   Month = {March},
   url = {http://dx.doi.org/10.1016/j.mbs.2018.03.025},
   Abstract = {We have shown previously that different homeostatic
             mechanisms in biochemistry create input-output curves with a
             "chair" shape. At equilibrium, for intermediate values of a
             parameter (often an input), a variable, Z, changes very
             little (the homeostatic plateau), but for low and high
             values of the parameter, Z changes rapidly (escape from
             homeostasis). In all cases previously studied, the steady
             state was stable for each value of the input parameter. Here
             we show that, for the feedback inhibition motif, stability
             may be lost through a Hopf bifurcation on the homeostatic
             plateau and then regained by another Hopf bifurcation. If
             the limit cycle oscillations are relatively small in the
             unstable interval, then the variable Z maintains homeostasis
             despite the instability. We show that the existence of an
             input interval in which there are oscillations, the length
             of the interval, and the size of the oscillations depend in
             interesting and complicated ways on the properties of the
             inhibition function, f, the length of the chain, and the
             size of a leakage parameter.},
   Doi = {10.1016/j.mbs.2018.03.025},
   Key = {fds333668}
}

@article{fds333703,
   Author = {Suppiramaniam, V and Bloemer, J and Reed, M and Bhattacharya,
             S},
   Title = {Neurotransmitter Receptors},
   Volume = {6-15},
   Pages = {174-201},
   Booktitle = {Comprehensive Toxicology: Third Edition},
   Year = {2017},
   Month = {December},
   ISBN = {9780081006122},
   url = {http://dx.doi.org/10.1016/B978-0-12-801238-3.65382-5},
   Abstract = {© 2018 Elsevier Ltd All rights reserved. Neurotransmitter
             receptors play a vital role in the normal functioning of the
             nervous system. Controlled modulation of neurotransmitter
             receptors is critical for proper signaling between nerve
             cells and effector organs. Factors that disrupt normal
             neurotransmitter signaling can alter the homeostasis of the
             cells or tissues, leading to adverse effects. The release of
             neurotransmitters at the presynaptic neuron and the
             subsequent activation of postsynaptic receptors lead to
             stimulation or inhibition of neuronal transmission. The
             excitatory neurotransmission involves depolarization of the
             postsynaptic neuron or cell due to a decrease in the
             polarity of the cells by the influx of cations such as
             sodium ions. The excitatory neurotransmission is mainly
             carried out by glutamate receptors in the mammalian nervous
             system. The inhibitory neurotransmission is due to
             hyperpolarization of the cells by either influx of anions
             such as chloride ions or efflux of cations such as potassium
             ions. The GABA and glycine receptors serve as major
             inhibitory neurotransmitter receptors. Toxins and toxicants
             can interfere with neuronal transmission by directly binding
             receptors and modulating their function or by altering
             transmitter synthesis, release, and reuptake mechanisms.
             Therefore, neurotoxins can impair neuronal transmission at
             the synapse by either presynaptic modulation or postsynaptic
             modifications. Due to the intricate network of the nervous
             system, impairment of the receptor functions in the synapse
             can lead to regional network dysfunction, eventually
             resulting in adverse cellular effects and behavioral
             deficits. Therefore, a thorough knowledge of
             neurotransmitter receptor modulation by toxins and toxicants
             is essential for future development of therapies against
             adverse effects of these neurotoxic substances.},
   Doi = {10.1016/B978-0-12-801238-3.65382-5},
   Key = {fds333703}
}

@article{fds331377,
   Author = {Best, J and Nijhout, HF and Samaranayake, S and Hashemi, P and Reed,
             M},
   Title = {A mathematical model for histamine synthesis, release, and
             control in varicosities.},
   Journal = {Theoretical Biology & Medical Modelling},
   Volume = {14},
   Number = {1},
   Pages = {24},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1186/s12976-017-0070-9},
   Abstract = {Histamine (HA), a small molecule that is synthesized from
             the amino acid histidine, plays an important role in the
             immune system where it is associated with allergies,
             inflammation, and T-cell regulation. In the brain, histamine
             is stored in mast cells and other non-neuronal cells and
             also acts as a neurotransmitter. The histamine neuron cell
             bodies are in the tuberomammillary (TM) nucleus of the
             hypothalamus and these neurons send projections throughout
             the central nervous system (CNS), in particular to the
             cerebral cortex, amygdala, basal ganglia, hippocampus,
             thalamus, retina, and spinal cord. HA neurons make few
             synapses, but release HA from the cell bodies and from
             varicosities when the neurons fire. Thus the HA neural
             system seems to modulate and control the HA concentration in
             projection regions. It is known that high HA levels in the
             extracellular space inhibit serotonin release, so HA may
             play a role in the etiology of depression.We compare model
             predictions to classical physiological experiments on HA
             half-life, the concentration of brain HA after histidine
             loading, and brain HA after histidine is dramatically
             increased or decreased in the diet. The model predictions
             are also consistent with in vivo experiments in which
             extracellular HA is measured, using Fast Scan Cyclic
             Voltammetry, in the premammillary nucleus (PM) after a 2 s
             antidromic stimulation of the TM, both without and in the
             presence of the H 3 autoreceptor antagonist thioperamide. We
             show that the model predicts well the temporal behavior of
             HA in the extracellular space over 30 s in both
             experiments.Our ability to measure in vivo histamine
             dynamics in the extracellular space after stimulation
             presents a real opportunity to understand brain function and
             control. The observed extracellular dynamics depends on
             synthesis, storage, neuronal firing, release, reuptake,
             glial cells, and control by autoreceptors, as well as the
             behavioral state of the animal (for example, depression) or
             the presence of neuroinflammation. In this complicated
             situation, the mathematical model will be useful for
             interpreting data and conducting in silico experiments to
             understand causal mechanisms. And, better understanding can
             suggest new therapeutic drug targets.},
   Doi = {10.1186/s12976-017-0070-9},
   Key = {fds331377}
}

@article{fds329014,
   Author = {Reed, M and Best, J and Golubitsky, M and Stewart, I and Nijhout,
             HF},
   Title = {Analysis of Homeostatic Mechanisms in Biochemical
             Networks.},
   Journal = {Bulletin of Mathematical Biology},
   Volume = {79},
   Number = {11},
   Pages = {2534-2557},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1007/s11538-017-0340-z},
   Abstract = {Cell metabolism is an extremely complicated dynamical system
             that maintains important cellular functions despite large
             changes in inputs. This "homeostasis" does not mean that the
             dynamical system is rigid and fixed. Typically, large
             changes in external variables cause large changes in some
             internal variables so that, through various regulatory
             mechanisms, certain other internal variables (concentrations
             or velocities) remain approximately constant over a finite
             range of inputs. Outside that range, the mechanisms cease to
             function and concentrations change rapidly with changes in
             inputs. In this paper we analyze four different common
             biochemical homeostatic mechanisms: feedforward excitation,
             feedback inhibition, kinetic homeostasis, and parallel
             inhibition. We show that all four mechanisms can occur in a
             single biological network, using folate and methionine
             metabolism as an example. Golubitsky and Stewart have
             proposed a method to find homeostatic nodes in networks. We
             show that their method works for two of these mechanisms but
             not the other two. We discuss the many interesting
             mathematical and biological questions that emerge from this
             analysis, and we explain why understanding homeostatic
             control is crucial for precision medicine.},
   Doi = {10.1007/s11538-017-0340-z},
   Key = {fds329014}
}

@article{fds330703,
   Author = {Nijhout, HF and Sadre-Marandi, F and Best, J and Reed,
             MC},
   Title = {Systems Biology of Phenotypic Robustness and
             Plasticity.},
   Journal = {Integrative and Comparative Biology},
   Volume = {57},
   Number = {2},
   Pages = {171-184},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1093/icb/icx076},
   Abstract = {Gene regulatory networks, cellular biochemistry, tissue
             function, and whole body physiology are imbued with myriad
             overlapping and interacting homeostatic mechanisms that
             ensure that many phenotypes are robust to genetic and
             environmental variation. Animals also often have plastic
             responses to environmental variables, which means that many
             different phenotypes can correspond to a single genotype.
             Since natural selection acts on phenotypes, this raises the
             question of how selection can act on the genome if genotypes
             are decoupled from phenotypes by robustness and plasticity
             mechanisms. The answer can be found in the systems biology
             of the homeostatic mechanisms themselves. First, all such
             mechanisms operate over a limited range and outside that
             range the controlled variable changes rapidly allowing
             natural selection to act. Second, mutations and
             environmental stressors can disrupt homeostatic mechanisms,
             exposing cryptic genetic variation and allowing natural
             selection to act. We illustrate these ideas by examining the
             systems biology of four specific examples. We show how it is
             possible to analyze and visualize the roles of specific
             genes and specific polymorphisms in robustness in the
             context of large and realistic nonlinear systems. We also
             describe a new method, system population models, that allows
             one to connect causal dynamics to the variable outcomes that
             one sees in biological populations with large
             variation.},
   Doi = {10.1093/icb/icx076},
   Key = {fds330703}
}

@article{fds320463,
   Author = {Reed, MC and Best, J and Nijhout, HF},
   Title = {Mathematical models of neuromodulation and implications for
             neurology and psychiatry},
   Editor = {Erdi, P and Battacharya, B and Cochran, A},
   Year = {2017},
   Key = {fds320463}
}

@article{fds320468,
   Author = {Reed, MC and Lawley, S and Nijhout, HF},
   Title = {Spiracular fluttering increases oxygen uptake},
   Year = {2017},
   Key = {fds320468}
}

@article{fds321770,
   Author = {Reed, MC and Best, J and Nijhout, HF},
   Title = {Mathematical models of neuromodulation and implications for
             neurology and psychiatry},
   Booktitle = {Computational Neurology and Psychiatry},
   Publisher = {SPRINGER},
   Editor = {Erdi, P and Bhattacharya, B and Cochran, A},
   Year = {2017},
   Key = {fds321770}
}

@article{fds330704,
   Author = {Thanacoody, HKR and Nijhout, HF and Reed, MC and Thomas,
             S},
   Title = {Mathematical modeling of the effect of different intravenous
             acetylcysteine regimens on hepatic glutathione regeneration
             and hepatocyte death following simulated acetaminophen
             overdose},
   Journal = {Clinical Toxicology (Philadelphia, Pa.)},
   Volume = {55},
   Number = {7},
   Pages = {753-753},
   Year = {2017},
   Key = {fds330704}
}

@article{fds330705,
   Author = {Thanacoody, HKR and Nijhout, HF and Reed, MC and Thomas,
             S},
   Title = {Mathematical modeling of the effect of late administration
             of a novel acetylcysteine regimen based on the SNAP trial on
             hepatic glutathione regeneration and hepatocyte death
             following simulated acetaminophen overdose},
   Journal = {Clinical Toxicology (Philadelphia, Pa.)},
   Volume = {55},
   Number = {7},
   Pages = {753-754},
   Year = {2017},
   Key = {fds330705}
}


%% Robles, Colleen M   
@article{fds328918,
   Author = {Robles, C},
   Title = {Characterization of Calabi–Yau variations of Hodge
             structure over tube domains by characteristic
             forms},
   Journal = {Mathematische Annalen},
   Pages = {1-25},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1007/s00208-017-1594-3},
   Abstract = {© 2017 Springer-Verlag GmbH Deutschland Sheng and Zuo’s
             characteristic forms are invariants of a variation of Hodge
             structure. We show that they characterize Gross’s
             canonical variations of Hodge structure of Calabi–Yau type
             over (Hermitian symmetric) tube domains.},
   Doi = {10.1007/s00208-017-1594-3},
   Key = {fds328918}
}

@article{fds326604,
   Author = {Kerr, M and Robles, C},
   Title = {Variations of Hodge structure and orbits in flag
             varieties},
   Journal = {Advances in Mathematics},
   Volume = {315},
   Pages = {27-87},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1016/j.aim.2017.05.013},
   Abstract = {© 2017 Elsevier Inc.Period domains, the classifying spaces
             for (pure, polarized) Hodge structures, and more generally
             Mumford–Tate domains, arise as open GR-orbits in flag
             varieties G/P. We investigate Hodge-theoretic aspects of the
             geometry and representation theory associated with these
             flag varieties. In particular, we relate the
             Griffiths–Yukawa coupling to the variety of lines on G/P
             (under a minimal homogeneous embedding), construct a large
             class of polarized GR-orbits in G/P, and compute the
             associated Hodge-theoretic boundary components. An emphasis
             is placed throughout on adjoint flag varieties and the
             corresponding families of Hodge structures of levels two and
             four.},
   Doi = {10.1016/j.aim.2017.05.013},
   Key = {fds326604}
}

@article{fds327152,
   Author = {Kerr, M and Robles, C},
   Title = {Classification of smooth horizontal Schubert
             varieties},
   Journal = {European Journal of Mathematics},
   Volume = {3},
   Number = {2},
   Pages = {289-310},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1007/s40879-017-0140-x},
   Doi = {10.1007/s40879-017-0140-x},
   Key = {fds327152}
}


%% Rudin, Cynthia D.   
@article{fds339230,
   Author = {Rudin, C and Ertekin, Ş},
   Title = {Learning customized and optimized lists of rules with
             mathematical programming},
   Journal = {Mathematical Programming Computation},
   Volume = {10},
   Number = {4},
   Pages = {659-702},
   Year = {2018},
   Month = {December},
   url = {http://dx.doi.org/10.1007/s12532-018-0143-8},
   Abstract = {© 2018, Springer-Verlag GmbH Germany, part of Springer
             Nature and The Mathematical Programming Society. We
             introduce a mathematical programming approach to building
             rule lists, which are a type of interpretable, nonlinear,
             and logical machine learning classifier involving IF-THEN
             rules. Unlike traditional decision tree algorithms like CART
             and C5.0, this method does not use greedy splitting and
             pruning. Instead, it aims to fully optimize a combination of
             accuracy and sparsity, obeying user-defined constraints.
             This method is useful for producing non-black-box predictive
             models, and has the benefit of a clear user-defined tradeoff
             between training accuracy and sparsity. The flexible
             framework of mathematical programming allows users to create
             customized models with a provable guarantee of optimality.
             The software reviewed as part of this submission was given
             the DOI (Digital Object Identifier) https://doi.org/10.5281/zenodo.1344142.},
   Doi = {10.1007/s12532-018-0143-8},
   Key = {fds339230}
}

@article{fds339633,
   Author = {Rudin, C and Ustunb, B},
   Title = {Optimized scoring systems: Toward trust in machine learning
             for healthcare and criminal justice},
   Journal = {Interfaces},
   Volume = {48},
   Number = {5},
   Pages = {449-466},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1287/inte.2018.0957},
   Abstract = {© 2018 INFORMS. Abstract. Questions of trust in
             machine-learning models are becoming increasingly important
             as these tools are starting to be used widely for
             high-stakes decisions in medicine and criminal justice.
             Transparency of models is a key aspect affecting trust. This
             paper reveals that there is new technology to build
             transparent machine-learning models that are often as
             accurate as black-box machine-learning models. These methods
             have already had an impact in medicine and criminal justice.
             This work calls into question the overall need for black-box
             models in these applications. Copyright:},
   Doi = {10.1287/inte.2018.0957},
   Key = {fds339633}
}

@article{fds332384,
   Author = {Vu, M-AT and Adalı, T and Ba, D and Buzsáki, G and Carlson, D and Heller,
             K and Liston, C and Rudin, C and Sohal, VS and Widge, AS and Mayberg, HS and Sapiro, G and Dzirasa, K},
   Title = {A Shared Vision for Machine Learning in Neuroscience.},
   Journal = {The Journal of Neuroscience : the Official Journal of the
             Society for Neuroscience},
   Volume = {38},
   Number = {7},
   Pages = {1601-1607},
   Year = {2018},
   Month = {February},
   url = {http://dx.doi.org/10.1523/jneurosci.0508-17.2018},
   Abstract = {With ever-increasing advancements in technology,
             neuroscientists are able to collect data in greater volumes
             and with finer resolution. The bottleneck in understanding
             how the brain works is consequently shifting away from the
             amount and type of data we can collect and toward what we
             actually do with the data. There has been a growing interest
             in leveraging this vast volume of data across levels of
             analysis, measurement techniques, and experimental paradigms
             to gain more insight into brain function. Such efforts are
             visible at an international scale, with the emergence of big
             data neuroscience initiatives, such as the BRAIN initiative
             (Bargmann et al., 2014), the Human Brain Project, the Human
             Connectome Project, and the National Institute of Mental
             Health's Research Domain Criteria initiative. With these
             large-scale projects, much thought has been given to
             data-sharing across groups (Poldrack and Gorgolewski, 2014;
             Sejnowski et al., 2014); however, even with such
             data-sharing initiatives, funding mechanisms, and
             infrastructure, there still exists the challenge of how to
             cohesively integrate all the data. At multiple stages and
             levels of neuroscience investigation, machine learning holds
             great promise as an addition to the arsenal of analysis
             tools for discovering how the brain works.},
   Doi = {10.1523/jneurosci.0508-17.2018},
   Key = {fds332384}
}

@article{fds338419,
   Author = {Angelino, E and Larus-Stone, N and Alabi, D and Seltzer, M and Rudin,
             C},
   Title = {Learning certifiably optimal rule lists for categorical
             data},
   Journal = {Journal of Machine Learning Research},
   Volume = {18},
   Pages = {1-78},
   Year = {2018},
   Month = {January},
   Abstract = {© 2018 Elaine Angelino, Nicholas Larus-Stone, Daniel Alabi,
             Margo Seltzer, and Cynthia Rudin. We present the design and
             implementation of a custom discrete optimization technique
             for building rule lists over a categorical feature space.
             Our algorithm produces rule lists with optimal training
             performance, according to the regularized empirical risk,
             with a certificate of optimality. By leveraging algorithmic
             bounds, efficient data structures, and computational reuse,
             we achieve several orders of magnitude speedup in time and a
             massive reduction of memory consumption. We demonstrate that
             our approach produces optimal rule lists on practical
             problems in seconds. Our results indicate that it is
             possible to construct optimal sparse rule lists that are
             approximately as accurate as the COMPAS proprietary risk
             prediction tool on data from Broward County, Florida, but
             that are completely interpretable. This framework is a novel
             alternative to CART and other decision tree methods for
             interpretable modeling.},
   Key = {fds338419}
}

@article{fds331943,
   Author = {Struck, AF and Ustun, B and Ruiz, AR and Lee, JW and LaRoche, SM and Hirsch, LJ and Gilmore, EJ and Vlachy, J and Haider, HA and Rudin, C and Westover, MB},
   Title = {Association of an Electroencephalography-Based Risk Score
             With Seizure Probability in Hospitalized
             Patients.},
   Journal = {Jama Neurology},
   Volume = {74},
   Number = {12},
   Pages = {1419-1424},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1001/jamaneurol.2017.2459},
   Abstract = {Importance:Continuous electroencephalography (EEG) use in
             critically ill patients is expanding. There is no validated
             method to combine risk factors and guide clinicians in
             assessing seizure risk. Objective:To use seizure risk
             factors from EEG and clinical history to create a simple
             scoring system associated with the probability of seizures
             in patients with acute illness. Design, Setting, and
             Participants:We used a prospective multicenter (Emory
             University Hospital, Brigham and Women's Hospital, and Yale
             University Hospital) database containing clinical and
             electrographic variables on 5427 continuous EEG sessions
             from eligible patients if they had continuous EEG for
             clinical indications, excluding epilepsy monitoring unit
             admissions. We created a scoring system model to estimate
             seizure risk in acutely ill patients undergoing continuous
             EEG. The model was built using a new machine learning method
             (RiskSLIM) that is designed to produce accurate,
             risk-calibrated scoring systems with a limited number of
             variables and small integer weights. We validated the
             accuracy and risk calibration of our model using
             cross-validation and compared its performance with models
             built with state-of-the-art logistic regression methods. The
             database was developed by the Critical Care EEG Research
             Consortium and used data collected over 3 years. The EEG
             variables were interpreted using standardized terminology by
             certified reviewers. Exposures:All patients had more than 6
             hours of uninterrupted EEG recordings. Main Outcomes and
             Measures:The main outcome was the average risk calibration
             error. Results:There were 5427 continuous EEGs performed on
             4772 participants (2868 men, 49.9%; median age, 61 years)
             performed at 3 institutions, without further demographic
             stratification. Our final model, 2HELPS2B, had an area under
             the curve of 0.819 and average calibration error of 2.7%
             (95% CI, 2.0%-3.6%). It included 6 variables with the
             following point assignments: (1) brief (ictal) rhythmic
             discharges (B[I]RDs) (2 points); (2) presence of lateralized
             periodic discharges, lateralized rhythmic delta activity, or
             bilateral independent periodic discharges (1 point); (3)
             prior seizure (1 point); (4) sporadic epileptiform
             discharges (1 point); (5) frequency greater than 2.0 Hz for
             any periodic or rhythmic pattern (1 point); and (6) presence
             of "plus" features (superimposed, rhythmic, sharp, or fast
             activity) (1 point). The probable seizure risk of each score
             was 5% for a score of 0, 12% for a score of 1, 27% for a
             score of 2, 50% for a score of 3, 73% for a score of 4, 88%
             for a score of 5, and greater than 95% for a score of 6 or
             7. Conclusions and Relevance:The 2HELPS2B model is a quick
             accurate tool to aid clinical judgment of the risk of
             seizures in critically ill patients.},
   Doi = {10.1001/jamaneurol.2017.2459},
   Key = {fds331943}
}

@article{fds330620,
   Author = {Ustun, B and Rudin, C},
   Title = {Optimized risk scores},
   Journal = {Proceedings of the ACM SIGKDD International Conference on
             Knowledge Discovery and Data Mining},
   Volume = {Part F129685},
   Pages = {1125-1134},
   Year = {2017},
   Month = {August},
   ISBN = {9781450348874},
   url = {http://dx.doi.org/10.1145/3097983.3098161},
   Abstract = {© 2017 Copyright held by the owner/author(s). Risk scores
             are simple classification models that let users quickly
             assess risk by adding, subtracting, and multiplying a few
             small numbers. Such models are widely used in healthcare and
             criminal justice, but are often built ad hoc. In this paper,
             we present a principled approach to learn risk scores that
             are fully optimized for feature selection, integer
             coefficients, and operational constraints. We formulate the
             risk score problem as a mixed integer nonlinear program, and
             present a new cutting plane algorithm to efficiently recover
             its optimal solution. Our approach can fit optimized risk
             scores in a way that scales linearly with the sample size of
             a dataset, provides a proof of optimality, and obeys complex
             constraints without parameter tuning. We illustrate these
             benefits through an extensive set of numerical experiments,
             and an application where we build a customized risk score
             for ICU seizure prediction.},
   Doi = {10.1145/3097983.3098161},
   Key = {fds330620}
}

@article{fds330621,
   Author = {Angelino, E and Larus-Stone, N and Alabi, D and Seltzer, M and Rudin,
             C},
   Title = {Learning certifiably optimal rule lists},
   Journal = {Proceedings of the Acm Sigkdd International Conference on
             Knowledge Discovery and Data Mining},
   Volume = {Part F129685},
   Pages = {35-44},
   Year = {2017},
   Month = {August},
   ISBN = {9781450348874},
   url = {http://dx.doi.org/10.1145/3097983.3098047},
   Abstract = {© 2017 Copyright held by the owner/author(s). We present
             the design and implementation of a custom discrete
             optimization technique for building rule lists over a
             categorical feature space. Our algorithm provides the
             optimal solution, with a certificate of optimality. By
             leveraging algorithmic bounds, efficient data structures,
             and computational reuse, we achieve several orders of
             magnitude speedup in time and a massive reduction of memory
             consumption. We demonstrate that our approach produces
             optimal rule lists on practical problems in seconds. This
             framework is a novel alternative to CART and other decision
             tree methods.},
   Doi = {10.1145/3097983.3098047},
   Key = {fds330621}
}

@article{fds330622,
   Author = {Wang, T and Rudin, C and Doshi-Velez, F and Liu, Y and Klampfl, E and MacNeille, P},
   Title = {A Bayesian framework for learning rule sets for
             interpretable classification},
   Journal = {Journal of Machine Learning Research},
   Volume = {18},
   Pages = {1-37},
   Year = {2017},
   Month = {August},
   Abstract = {©2017 Tong Wang, Cynthia Rudin, Finale Doshi-Velez, Yimin
             Liu, Erica Klampfl, and Perry MacNeille. We present a
             machine learning algorithm for building classifiers that are
             comprised of a small number of short rules. These are
             restricted disjunctive normal form models. An example of a
             classifier of this form is as follows: If X satisfies
             (condition A AND condition B) OR (condition C) OR · · · ,
             then Y = 1. Models of this form have the advantage of being
             interpretable to human experts since they produce a set of
             rules that concisely describe a specific class. We present
             two probabilistic models with prior parameters that the user
             can set to encourage the model to have a desired size and
             shape, to conform with a domain-specific definition of
             interpretability. We provide a scalable MAP inference
             approach and develop theoretical bounds to reduce
             computation by iteratively pruning the search space. We
             apply our method (Bayesian Rule Sets – BRS) to
             characterize and predict user behavior with respect to
             in-vehicle context-aware personalized recommender systems.
             Our method has a major advantage over classical associative
             classification methods and decision trees in that it does
             not greedily grow the model.},
   Key = {fds330622}
}

@article{fds330623,
   Author = {Letham, B and Letham, PA and Rudin, C and Browne,
             EP},
   Title = {Erratum: "Prediction uncertainty and optimal experimental
             design for learning dynamical systems" [Chaos 26, 063110
             (2016)].},
   Journal = {Chaos (Woodbury, N.Y.)},
   Volume = {27},
   Number = {6},
   Pages = {069901},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1063/1.4986799},
   Doi = {10.1063/1.4986799},
   Key = {fds330623}
}

@article{fds330624,
   Author = {Zeng, J and Ustun, B and Rudin, C},
   Title = {Interpretable classification models for recidivism
             prediction},
   Journal = {Journal of the Royal Statistical Society: Series a
             (Statistics in Society)},
   Volume = {180},
   Number = {3},
   Pages = {689-722},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1111/rssa.12227},
   Doi = {10.1111/rssa.12227},
   Key = {fds330624}
}

@article{fds330625,
   Author = {Ustun, B and Adler, LA and Rudin, C and Faraone, SV and Spencer, TJ and Berglund, P and Gruber, MJ and Kessler, RC},
   Title = {The World Health Organization Adult Attention-Deficit/Hyperactivity
             Disorder Self-Report Screening Scale for
             DSM-5.},
   Journal = {Jama Psychiatry},
   Volume = {74},
   Number = {5},
   Pages = {520-526},
   Year = {2017},
   Month = {May},
   url = {http://dx.doi.org/10.1001/jamapsychiatry.2017.0298},
   Abstract = {Importance:Recognition that adult attention-deficit/hyperactivity
             disorder (ADHD) is common, seriously impairing, and usually
             undiagnosed has led to the development of adult ADHD
             screening scales for use in community, workplace, and
             primary care settings. However, these scales are all
             calibrated to DSM-IV criteria, which are narrower than the
             recently developed DSM-5 criteria. Objectives:To update for
             DSM-5 criteria and improve the operating characteristics of
             the widely used World Health Organization Adult ADHD
             Self-Report Scale (ASRS) for screening. Design, Setting, and
             Participants:Probability subsamples of participants in 2
             general population surveys (2001-2003 household survey
             [n = 119] and 2004-2005 managed care subscriber survey
             [n = 218]) who completed the full 29-question
             self-report ASRS, with both subsamples over-sampling
             ASRS-screened positives, were blindly administered a
             semistructured research diagnostic interview for DSM-5 adult
             ADHD. In 2016, the Risk-Calibrated Supersparse Linear
             Integer Model, a novel machine-learning algorithm designed
             to create screening scales with optimal integer weights and
             limited numbers of screening questions, was applied to the
             pooled data to create a DSM-5 version of the ASRS screening
             scale. The accuracy of the new scale was then confirmed in
             an independent 2011-2012 clinical sample of patients seeking
             evaluation at the New York University Langone Medical Center
             Adult ADHD Program (NYU Langone) and 2015-2016 primary care
             controls (n = 300). Data analysis was conducted from
             April 4, 2016, to September 22, 2016. Main Outcomes and
             Measures:The sensitivity, specificity, area under the curve
             (AUC), and positive predictive value (PPV) of the revised
             ASRS. Results:Of the total 637 participants, 44 (37.0%)
             household survey respondents, 51 (23.4%) managed care
             respondents, and 173 (57.7%) NYU Langone respondents met
             DSM-5 criteria for adult ADHD in the semistructured
             diagnostic interview. Of the respondents who met DSM-5
             criteria for adult ADHD, 123 were male (45.9%); mean (SD)
             age was 33.1 (11.4) years. A 6-question screening scale was
             found to be optimal in distinguishing cases from noncases in
             the first 2 samples. Operating characteristics were
             excellent at the diagnostic threshold in the weighted (to
             the 8.2% DSM-5/Adult ADHD Clinical Diagnostic Scale
             population prevalence) data (sensitivity, 91.4%;
             specificity, 96.0%; AUC, 0.94; PPV, 67.3%). Operating
             characteristics were similar despite a much higher
             prevalence (57.7%) when the scale was applied to the NYU
             Langone clinical sample (sensitivity, 91.9%; specificity,
             74.0%; AUC, 0.83; PPV, 82.8%). Conclusions and Relevance:The
             new ADHD screening scale is short, easily scored, detects
             the vast majority of general population cases at a threshold
             that also has high specificity and PPV, and could be used as
             a screening tool in specialty treatment settings.},
   Doi = {10.1001/jamapsychiatry.2017.0298},
   Key = {fds330625}
}

@article{fds330626,
   Author = {Wang, T and Rudin, C and Velez-Doshi, F and Liu, Y and Klampfl, E and Macneille, P},
   Title = {Bayesian rule sets for interpretable classification},
   Journal = {Proceedings Ieee International Conference on Data Mining,
             Icdm},
   Pages = {1269-1274},
   Year = {2017},
   Month = {January},
   ISBN = {9781509054725},
   url = {http://dx.doi.org/10.1109/ICDM.2016.130},
   Abstract = {© 2016 IEEE. A Rule Set model consists of a small number of
             short rules for interpretable classification, where an
             instance is classified as positive if it satisfies at least
             one of the rules. The rule set provides reasons for
             predictions, and also descriptions of a particular class. We
             present a Bayesian framework for learning Rule Set models,
             with prior parameters that the user can set to encourage the
             model to have a desired size and shape in order to conform
             with a domain-specific definition of interpretability. We
             use an efficient inference approach for searching for the
             MAP solution and provide theoretical bounds to reduce
             computation. We apply Rule Set models to ten UCI data sets
             and compare the performance with other interpretable and
             non-interpretable models.},
   Doi = {10.1109/ICDM.2016.130},
   Key = {fds330626}
}

@article{fds336348,
   Author = {Yang, H and Rudin, C and Seltzer, M},
   Title = {Scalable Bayesian rule lists},
   Journal = {34th International Conference on Machine Learning, Icml
             2017},
   Volume = {8},
   Pages = {5971-5980},
   Year = {2017},
   Month = {January},
   ISBN = {9781510855144},
   Abstract = {© Copyright 2017 by the authors(s). We present an algorithm
             for building probabilistic rule lists that is two orders of
             magnitude faster than previous work. Rule list algorithms
             are competitors for decision tree algorithms. They are
             associative classifiers, in that they are built from
             pre-mined association rules. They have a logical structure
             that is a sequence of IF-THEN rules, identical to a decision
             list or one-sided decision tree. Instead of using greedy
             splitting and pruning like decision tree algorithms, we aim
             to fully optimize over rule lists, striking a practical
             balance between accuracy, inter-pretability, and
             computational speed. The algorithm presented here uses a
             mixture of theoretical bounds (tight enough to have
             practical implications as a screening or bounding
             procedure), computational reuse, and highly tuned language
             libraries to achieve computational efficiency. Currently,
             for many practical problems, this method achieves better
             accuracy and sparsity than decision trees, with practical
             running times. The predictions in each leaf are
             probabilistic.},
   Key = {fds336348}
}


%% Ryser, Marc D.   
@article{fds339945,
   Author = {Ryser, MD and Yu, M and Grady, W and Siegmund, K and Shibata,
             D},
   Title = {Epigenetic Heterogeneity in Human Colorectal Tumors Reveals
             Preferential Conservation And Evidence of Immune
             Surveillance.},
   Journal = {Scientific Reports},
   Volume = {8},
   Number = {1},
   Pages = {17292},
   Year = {2018},
   Month = {November},
   url = {http://dx.doi.org/10.1038/s41598-018-35621-y},
   Abstract = {Genomic intratumoral heterogeneity (ITH) is common in
             cancers, but the extent of phenotypic ITH is uncertain
             because most subclonal mutations are passengers. Since tumor
             phenotypes are largely driven by epigenetics, methylomic
             analyses can provide insights into phenotypic ITH. Following
             this principle, we determined the extent of epigenetic ITH
             in 16 human colorectal tumors by comparing the methylomes
             from spatially separated regions in each tumor. Methylomes
             from opposite tumor sides were similar (Pearson correlation
             >0.95) with little evidence of ITH or stepwise selection
             during growth, suggesting that the epigenome of a sampled
             tumor largely reflects that of its founder cell. Epigenetic
             conservation was functional, with higher conservation at
             promoters and expressed genes compared to non-coding
             regions. Despite epigenomic conservation, RNA expression
             varied between individual tumor glands, indicating continued
             adaption during growth. Because many promoters and enhancers
             were unmethylated, continued adaptation may be due to
             phenotypic plasticity. Gene enrichment analyses identified
             that interferon signaling and antigen-processing and
             presenting pathways were strongly conserved during tumor
             growth, suggesting a mechanism for immune evasion. In
             summary, our findings suggest that epigenomes are
             preferentially conserved during tumor growth and that early
             tumor cells are poised for rapid growth, phenotypic
             adaptation, and immune evasion.},
   Doi = {10.1038/s41598-018-35621-y},
   Key = {fds339945}
}

@article{fds339494,
   Author = {Ryser, MD and Gulati, R and Eisenberg, MC and Shen, Y and Hwang, ES and Etzioni, RB},
   Title = {Identification of the Fraction of Indolent Tumors and
             Associated Overdiagnosis in Breast Cancer Screening
             Trials.},
   Journal = {American Journal of Epidemiology},
   Year = {2018},
   Month = {October},
   url = {http://dx.doi.org/10.1093/aje/kwy214},
   Abstract = {It is generally accepted that some screen-detected breast
             cancers are overdiagnosed and would not progress to
             symptomatic cancer if left untreated. However, precise
             estimates of the fraction of non-progressive cancers remain
             elusive. In recognition of the weaknesses of overdiagnosis
             estimation methods based on excess incidence, there is a
             need for model-based approaches that accommodate
             non-progressive lesions. Here, we present an in-depth
             analysis of a generalized breast cancer natural history
             model that allows for a mixture of progressive and indolent
             lesions. We provide a formal proof of global structural
             identifiability of the model and use simulation to identify
             conditions that allow for parameter estimates that are
             sufficiently precise and practically actionable. We show
             that clinical follow-up after the last screen can play a
             critical role in ensuring adequately precise identification
             of the fraction of indolent cancers in a stop-screen trial
             design, and we demonstrate that model misspecification can
             lead to substantially biased mean sojourn time estimates.
             Finally, we illustrate our findings on the example of the
             Canadian National Breast Screening Study-2 and show that the
             fraction of indolent cancers is not precisely identifiable.
             Our findings provide the foundation for extended models that
             account for both in situ and invasive lesions.},
   Doi = {10.1093/aje/kwy214},
   Key = {fds339494}
}

@article{fds338377,
   Author = {Ryser, MD and Min, B-H and Siegmund, KD and Shibata,
             D},
   Title = {Spatial mutation patterns as markers of early colorectal
             tumor cell mobility.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {115},
   Number = {22},
   Pages = {5774-5779},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1073/pnas.1716552115},
   Abstract = {A growing body of evidence suggests that a subset of human
             cancers grows as single clonal expansions. In such a nearly
             neutral evolution scenario, it is possible to infer the
             early ancestral tree of a full-grown tumor. We hypothesized
             that early tree reconstruction can provide insights into the
             mobility phenotypes of tumor cells during their first few
             cell divisions. We explored this hypothesis by means of a
             computational multiscale model of tumor expansion
             incorporating the glandular structure of colorectal tumors.
             After calibrating the model to multiregional and single
             gland data from 19 human colorectal tumors using approximate
             Bayesian computation, we examined the role of early tumor
             cell mobility in shaping the private mutation patterns of
             the final tumor. The simulations showed that early cell
             mixing in the first tumor gland can result in
             side-variegated patterns where the same private mutations
             could be detected on opposite tumor sides. In contrast,
             absence of early mixing led to nonvariegated, sectional
             mutation patterns. These results suggest that the patterns
             of detectable private mutations in colorectal tumors may be
             a marker of early cell movement and hence the invasive and
             metastatic potential of the tumor at the start of the
             growth. In alignment with our hypothesis, we found evidence
             of early abnormal cell movement in 9 of 15 invasive
             colorectal carcinomas ("born to be bad"), but in none of 4
             benign adenomas. If validated with a larger dataset, the
             private mutation patterns may be used for outcome prediction
             among screen-detected lesions with unknown invasive
             potential.},
   Doi = {10.1073/pnas.1716552115},
   Key = {fds338377}
}

@article{fds339495,
   Title = {Role of Preoperative Variables in Reducing the Rate of
             Occult Invasive Disease for Women Considering Active
             Surveillance for Ductal Carcinoma In Situ.},
   Journal = {Jama Surgery},
   Volume = {153},
   Number = {3},
   Pages = {290-291},
   Year = {2018},
   Month = {March},
   url = {http://dx.doi.org/10.1001/jamasurg.2017.5566},
   Doi = {10.1001/jamasurg.2017.5566},
   Key = {fds339495}
}

@article{fds339496,
   Author = {Ryser, MD and Horton, JK and Hwang, ES},
   Title = {How Low Can We Go-and Should We? Risk Reduction for
             Minimal-Volume DCIS.},
   Journal = {Annals of Surgical Oncology},
   Volume = {25},
   Number = {2},
   Pages = {354-355},
   Year = {2018},
   Month = {February},
   url = {http://dx.doi.org/10.1245/s10434-017-6128-4},
   Doi = {10.1245/s10434-017-6128-4},
   Key = {fds339496}
}

@article{fds339497,
   Author = {Ryser, MD and Weaver, DL and Marks, JR and Hyslop, T and Hwang,
             ES},
   Title = {Quantifying the natural history and overtreatment rate of
             ductal carcinoma in situ},
   Journal = {Cancer Research},
   Volume = {78},
   Number = {4},
   Year = {2018},
   Month = {February},
   Key = {fds339497}
}

@article{fds339498,
   Author = {Shen, Y and Dong, W and Gulati, R and Ryser, MD and Etzioni,
             R},
   Title = {Estimating the frequency of indolent breast cancer in
             screening trials.},
   Journal = {Statistical Methods in Medical Research},
   Pages = {962280217754232},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1177/0962280217754232},
   Abstract = {Cancer screening can detect cancer that would not have been
             detected in a patient's lifetime without screening. Standard
             methods for analyzing screening data do not explicitly
             account for the possibility that a fraction of tumors may
             remain latent indefinitely. We extend these methods by
             representing cancers as a mixture of those that progress to
             symptoms (progressive) and those that remain latent
             (indolent). Given sensitivity of the screening test, we
             derive likelihood expressions to simultaneously estimate (1)
             the rate of onset of preclinical cancer, (2) the average
             preclinical duration of progressive cancers, and (3) the
             fraction of preclinical cancers that are indolent.
             Simulations demonstrate satisfactory performance of the
             estimation approach to identify model parameters subject to
             precise specifications of input parameters and adequate
             numbers of interval cancers. In application to four breast
             cancer screening trials, the estimated indolent fraction
             among preclinical cancers varies between 2% and 35% when
             assuming 80% test sensitivity and varying specifications for
             the earliest time that participants could plausibly have
             developed cancer. We conclude that standard methods for
             analyzing screening data can be extended to allow some
             indolent cancers, but accurate estimation depends on
             correctly specifying key inputs that may be difficult to
             determine precisely in practice.},
   Doi = {10.1177/0962280217754232},
   Key = {fds339498}
}

@article{fds339499,
   Author = {Grimm, LJ and Ryser, MD and Partridge, AH and Thompson, AM and Thomas,
             JS and Wesseling, J and Hwang, ES},
   Title = {Surgical Upstaging Rates for Vacuum Assisted Biopsy Proven
             DCIS: Implications for Active Surveillance
             Trials.},
   Journal = {Annals of Surgical Oncology},
   Volume = {24},
   Number = {12},
   Pages = {3534-3540},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1245/s10434-017-6018-9},
   Abstract = {This study was designed to determine invasive cancer
             upstaging rates at surgical excision following
             vacuum-assisted biopsy of ductal carcinoma in situ (DCIS)
             among women meeting eligibility for active surveillance
             trials.Patients with vacuum-assisted, biopsy-proven DCIS at
             a single center from 2008 to 2015 were retrospectively
             reviewed. Imaging and pathology reports were interrogated
             for the imaging appearance, tumor grade, hormone receptor
             status, and presence of comedonecrosis. Subsequent surgical
             reports were reviewed for upstaging to invasive disease.
             Cases were classified by eligibility criteria for the COMET,
             LORIS, and LORD DCIS active surveillance trials.Of 307 DCIS
             diagnoses, 15 (5%) were low, 95 (31%) intermediate, and 197
             (64%) high nuclear grade. The overall upstage rate to
             invasive disease was 17% (53/307). Eighty-one patients were
             eligible for the COMET Trial, 74 for the LORIS trial, and 10
             for the LORD Trial, although LORIS trial eligibility also
             included real-time, multiple central pathology review,
             including elements not routinely reported. The upstaging
             rates to invasive disease were 6% (5/81), 7% (5/74), and 10%
             (1/10) for the COMET, LORIS, and LORD trials, respectively.
             Among upstaged cancers (n = 5), four tumors were Stage IA
             invasive ductal carcinoma and one was Stage IIA invasive
             lobular carcinoma; all were node-negative.DCIS upstaging
             rates in women eligible for active surveillance trials are
             low (6-10%), and in this series, all those with invasive
             disease were early-stage, node-negative. The careful patient
             selection for DCIS active surveillance trials has a low risk
             of missing occult invasive cancer and additional studies
             will determine clinical outcomes.},
   Doi = {10.1245/s10434-017-6018-9},
   Key = {fds339499}
}

@article{fds339500,
   Author = {Cao, Y and Feng, Y and Ryser, MD and Zhu, K and Herschlag, G and Cao, C and Marusak, K and Zauscher, S and You, L},
   Title = {Programmable assembly of pressure sensors using
             pattern-forming bacteria.},
   Journal = {Nature Biotechnology},
   Volume = {35},
   Number = {11},
   Pages = {1087-1093},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1038/nbt.3978},
   Abstract = {Biological systems can generate microstructured materials
             that combine organic and inorganic components and possess
             diverse physical and chemical properties. However, these
             natural processes in materials fabrication are not readily
             programmable. Here, we use a synthetic-biology approach to
             assemble patterned materials. We demonstrate programmable
             fabrication of three-dimensional (3D) materials by printing
             engineered self-patterning bacteria on permeable membranes
             that serve as a structural scaffold. Application of gold
             nanoparticles to the colonies creates hybrid
             organic-inorganic dome structures. The dynamics of the dome
             structures' response to pressure is determined by their
             geometry (colony size, dome height, and pattern), which is
             easily modified by varying the properties of the membrane
             (e.g., pore size and hydrophobicity). We generate resettable
             pressure sensors that process signals in response to varying
             pressure intensity and duration.},
   Doi = {10.1038/nbt.3978},
   Key = {fds339500}
}

@article{fds339501,
   Author = {Ryser, MD and Rositch, A and Gravitt, PE},
   Title = {Modeling of US Human Papillomavirus (HPV) Seroprevalence by
             Age and Sexual Behavior Indicates an Increasing Trend of HPV
             Infection Following the Sexual Revolution.},
   Journal = {The Journal of Infectious Diseases},
   Volume = {216},
   Number = {5},
   Pages = {604-611},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1093/infdis/jix333},
   Abstract = {The United States has experienced an increase in the
             incidence of human papillomavirus (HPV)-related cancers that
             are not screen-detectable. It has been hypothesized, but not
             directly demonstrated, that this is due to increasing HPV
             prevalence in the unvaccinated population.Female
             self-reported numbers of lifetime sex partners and HPV
             serology from the National Health and Nutrition Examination
             Survey (NHANES) were used to develop mathematical models of
             sexual partner acquisition and antibody dynamics. Modeled
             trends in sexual behaviors were compared to incidence data
             for cervical adenocarcinoma, oropharyngeal cancer, and anal
             cancer.The age-specific HPV seroprevalence data were best
             explained by a partner acquisition model that explicitly
             accounted for cohort-dependent changes in sexual behavior.
             Estimates of the mean time to loss of natural antibodies
             varied by model, ranging from 49 to 145 years. Inferred
             trends in sexual behavior over the past decades paralleled
             the increasing incidence of HPV-related cancers in the
             United States.The findings suggest that lower HPV
             seroprevalence in older US women primarily reflects
             cohort-specific differences in sexual behaviors, and is only
             marginally attributable to immune waning with age. Our
             results emphasize the importance of continuing surveillance
             of sexual behaviors, alongside vaccine status, to predict
             future disease burden.},
   Doi = {10.1093/infdis/jix333},
   Key = {fds339501}
}

@article{fds339502,
   Author = {Ryser, MD and Gravitt, PE and Myers, ER},
   Title = {Mechanistic mathematical models: An underused platform for
             HPV research.},
   Journal = {Papillomavirus research},
   Volume = {3},
   Pages = {46-49},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.pvr.2017.01.004},
   Abstract = {Health economic modeling has become an invaluable
             methodology for the design and evaluation of clinical and
             public health interventions against the human papillomavirus
             (HPV) and associated diseases. At the same time, relatively
             little attention has been paid to a different yet
             complementary class of models, namely that of mechanistic
             mathematical models. The primary focus of mechanistic
             mathematical models is to better understand the intricate
             biologic mechanisms and dynamics of disease. Inspired by a
             long and successful history of mechanistic modeling in other
             biomedical fields, we highlight several areas of HPV
             research where mechanistic models have the potential to
             advance the field. We argue that by building quantitative
             bridges between biologic mechanism and population level
             data, mechanistic mathematical models provide a unique
             platform to enable collaborations between experimentalists
             who collect data at different physical scales of the HPV
             infection process. Through such collaborations, mechanistic
             mathematical models can accelerate and enhance the
             investigation of HPV and related diseases.},
   Doi = {10.1016/j.pvr.2017.01.004},
   Key = {fds339502}
}

@article{fds339503,
   Author = {Storey, K and Ryser, MD and Leder, K and Foo, J},
   Title = {Spatial Measures of Genetic Heterogeneity During
             Carcinogenesis.},
   Journal = {Bulletin of Mathematical Biology},
   Volume = {79},
   Number = {2},
   Pages = {237-276},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1007/s11538-016-0234-5},
   Abstract = {In this work we explore the temporal dynamics of spatial
             heterogeneity during the process of tumorigenesis from
             healthy tissue. We utilize a spatial stochastic model of
             mutation accumulation and clonal expansion in a structured
             tissue to describe this process. Under a two-step
             tumorigenesis model, we first derive estimates of a
             non-spatial measure of diversity: Simpson's Index, which is
             the probability that two individuals sampled at random from
             the population are identical, in the premalignant
             population. We next analyze two new measures of spatial
             population heterogeneity. In particular we study the typical
             length scale of genetic heterogeneity during the
             carcinogenesis process and estimate the extent of a
             surrounding premalignant clone given a clinical observation
             of a premalignant point biopsy. This evolutionary framework
             contributes to a growing literature focused on developing a
             better understanding of the spatial population dynamics of
             cancer initiation and progression.},
   Doi = {10.1007/s11538-016-0234-5},
   Key = {fds339503}
}


%% Saper, Leslie   
@article{fds320773,
   Author = {Saper, L},
   Title = {ℒ-modules and micro-support},
   Journal = {to appear in Annals of Mathematics},
   Year = {2018},
   Key = {fds320773}
}

@article{fds320662,
   Author = {Saper, L},
   Title = {Perverse sheaves and the reductive Borel-Serre
             compactification},
   Volume = {39},
   Pages = {555-581},
   Booktitle = {Hodge Theory and L²-analysis},
   Publisher = {International Press},
   Editor = {Ji, L},
   Year = {2017},
   Abstract = {We briefly introduce the theory of perverse sheaves with
             special attention to the topological situation where strata
             can have odd dimension. This is part of a project to use
             perverse sheaves on the topological reductive Borel-Serre
             compactification of a Hermitian locally symmetric space as a
             tool to study perverse sheaves on the Baily-Borel
             compactification, a projective algebraic variety. We sketch
             why the decomposition theorem holds for the natural map
             between the reductive Borel-Serre and the Baily-Borel
             compactifications. We demonstrate how to calculate
             extensions of simple perverse sheaves on the reductive
             Borel-Serre compactification and illustrate with the example
             of Sp(4,R).},
   Key = {fds320662}
}


%% Sapiro, Guillermo   
@article{fds339768,
   Author = {Dawson, G and Campbell, K and Hashemi, J and Lippmann, SJ and Smith, V and Carpenter, K and Egger, H and Espinosa, S and Vermeer, S and Baker, J and Sapiro, G},
   Title = {Atypical postural control can be detected via computer
             vision analysis in toddlers with autism spectrum
             disorder.},
   Journal = {Scientific Reports},
   Volume = {8},
   Number = {1},
   Pages = {17008},
   Year = {2018},
   Month = {November},
   url = {http://dx.doi.org/10.1038/s41598-018-35215-8},
   Abstract = {Evidence suggests that differences in motor function are an
             early feature of autism spectrum disorder (ASD). One aspect
             of motor ability that develops during childhood is postural
             control, reflected in the ability to maintain a steady head
             and body position without excessive sway. Observational
             studies have documented differences in postural control in
             older children with ASD. The present study used computer
             vision analysis to assess midline head postural control, as
             reflected in the rate of spontaneous head movements during
             states of active attention, in 104 toddlers between 16-31
             months of age (Mean = 22 months), 22 of whom were
             diagnosed with ASD. Time-series data revealed robust group
             differences in the rate of head movements while the toddlers
             watched movies depicting social and nonsocial stimuli.
             Toddlers with ASD exhibited a significantly higher rate of
             head movement as compared to non-ASD toddlers, suggesting
             difficulties in maintaining midline position of the head
             while engaging attentional systems. The use of digital
             phenotyping approaches, such as computer vision analysis, to
             quantify variation in early motor behaviors will allow for
             more precise, objective, and quantitative characterization
             of early motor signatures and potentially provide new
             automated methods for early autism risk identification.},
   Doi = {10.1038/s41598-018-35215-8},
   Key = {fds339768}
}

@article{fds339597,
   Author = {Kim, J and Duchin, Y and Shamir, RR and Patriat, R and Vitek, J and Harel,
             N and Sapiro, G},
   Title = {Automatic localization of the subthalamic nucleus on
             patient-specific clinical MRI by incorporating 7 T MRI and
             machine learning: Application in deep brain
             stimulation.},
   Journal = {Human Brain Mapping},
   Year = {2018},
   Month = {October},
   url = {http://dx.doi.org/10.1002/hbm.24404},
   Abstract = {Deep brain stimulation (DBS) of the subthalamic nucleus
             (STN) has shown clinical potential for relieving the motor
             symptoms of advanced Parkinson's disease. While accurate
             localization of the STN is critical for consistent
             across-patients effective DBS, clear visualization of the
             STN under standard clinical MR protocols is still
             challenging. Therefore, intraoperative microelectrode
             recordings (MER) are incorporated to accurately localize the
             STN. However, MER require significant neurosurgical
             expertise and lengthen the surgery time. Recent advances in
             7 T MR technology facilitate the ability to clearly
             visualize the STN. The vast majority of centers, however,
             still do not have 7 T MRI systems, and fewer have the
             ability to collect and analyze the data. This work
             introduces an automatic STN localization framework based on
             standard clinical MRIs without additional cost in the
             current DBS planning protocol. Our approach benefits from a
             large database of 7 T MRI and its clinical MRI pairs. We
             first model in the 7 T database, using efficient machine
             learning algorithms, the spatial and geometric dependency
             between the STN and its adjacent structures (predictors).
             Given a standard clinical MRI, our method automatically
             computes the predictors and uses the learned information to
             predict the patient-specific STN. We validate our proposed
             method on clinical T2 W MRI of 80 subjects, comparing with
             experts-segmented STNs from the corresponding 7 T MRI pairs.
             The experimental results show that our framework provides
             more accurate and robust patient-specific STN localization
             than using state-of-the-art atlases. We also demonstrate the
             clinical feasibility of the proposed technique assessing the
             post-operative electrode active contact locations.},
   Doi = {10.1002/hbm.24404},
   Key = {fds339597}
}

@article{fds339259,
   Author = {Aguerrebere, C and Delbracio, M and Bartesaghi, A and Sapiro,
             G},
   Title = {A Practical Guide to Multi-Image Alignment},
   Journal = {2015 Ieee International Conference on Acoustics, Speech, and
             Signal Processing (Icassp)},
   Volume = {2018-April},
   Pages = {1927-1931},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1109/ICASSP.2018.8461588},
   Abstract = {© 2018 IEEE. Multi-image alignment, bringing a group of
             images into common register, is an ubiquitous problem and
             the first step of many applications in a wide variety of
             domains. As a result, a great amount of effort is being
             invested in developing efficient multi-image alignment
             algorithms. Little has been done, however, to answer
             fundamental practical questions such as: what is the
             comparative performance of existing methods? is there still
             room for improvement? under which conditions should one
             technique be preferred over another? does adding more images
             or prior image information improve the registration results?
             In this work, we present a thorough analysis and evaluation
             of the main multi-image alignment methods which, combined
             with theoretical limits in multi-image alignment
             performance, allows us to organize them under a common
             framework and provide practical answers to these essential
             questions.},
   Doi = {10.1109/ICASSP.2018.8461588},
   Key = {fds339259}
}

@article{fds339260,
   Author = {Ahn, HK and Qiu, Q and Bosch, E and Thompson, A and Robles, FE and Sapiro,
             G and Warren, WS and Calderbank, R},
   Title = {Classifying Pump-Probe Images of Melanocytic Lesions Using
             the WEYL Transform},
   Journal = {2015 Ieee International Conference on Acoustics, Speech, and
             Signal Processing (Icassp)},
   Volume = {2018-April},
   Pages = {4209-4213},
   Year = {2018},
   Month = {September},
   ISBN = {9781538646588},
   url = {http://dx.doi.org/10.1109/ICASSP.2018.8461298},
   Abstract = {© 2018 IEEE. Diagnosis of melanoma is fraught with
             uncertainty, and discordance rates among physicians remain
             high because of the lack of a definitive criterion.
             Motivated by this challenge, this paper first introduces the
             Patch Weyl transform (PWT), a 2-dimensional variant of the
             Weyl transform. It then presents a method for classifying
             pump-probe images of melanocytic lesions based on the PWT
             coefficients. Performance of the PWT coefficients is shown
             to be superior to classification based on baseline
             intensity, on standard descriptors such as the Histogram of
             Oriented Gradients (HOG) and Local Binary Patterns (LBP),
             and on coefficients derived from PCA and Fourier
             representations of the data.},
   Doi = {10.1109/ICASSP.2018.8461298},
   Key = {fds339260}
}

@article{fds339261,
   Author = {Giryes, R and Eldar, YC and Bronstein, AM and Sapiro,
             G},
   Title = {The Learned Inexact Project Gradient Descent
             Algorithm},
   Journal = {2015 Ieee International Conference on Acoustics, Speech, and
             Signal Processing (Icassp)},
   Volume = {2018-April},
   Pages = {6767-6771},
   Year = {2018},
   Month = {September},
   ISBN = {9781538646588},
   url = {http://dx.doi.org/10.1109/ICASSP.2018.8462136},
   Abstract = {© 2018 IEEE. Accelerating iterative algorithms for solving
             inverse problems using neural networks have become a very
             popular strategy in the recent years. In this work, we
             propose a theoretical analysis that may provide an
             explanation for its success. Our theory relies on the usage
             of inexact projections with the projected gradient descent
             (PGD) method. It is demonstrated in various problems
             including image super-resolution.},
   Doi = {10.1109/ICASSP.2018.8462136},
   Key = {fds339261}
}

@article{fds338014,
   Author = {Hashemi, J and Dawson, G and Carpenter, KLH and Campbell, K and Qiu, Q and Espinosa, S and Marsan, S and Baker, JP and Egger, HL and Sapiro,
             G},
   Title = {Computer Vision Analysis for Quantification of Autism Risk
             Behaviors},
   Journal = {Ieee Transactions on Affective Computing},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1109/TAFFC.2018.2868196},
   Abstract = {IEEE Observational behavior analysis plays a key role for
             the discovery and evaluation of risk markers for many
             neurodevelopmental disorders. Research on autism spectrum
             disorder (ASD) suggests that behavioral risk markers can be
             observed at 12 months of age, with diagnosis possible at 18
             months. To date, studies and evaluations involving
             observational analysis tend to rely heavily on clinical
             practitioners and specialists who have undergone intensive
             training to be able to reliably administer carefully
             designed behavioral-eliciting tasks, code the resulting
             behaviors, and interpret them. These methods are therefore
             extremely expensive, time-intensive, and are not easily
             scalable for large or longitudinal observational analysis.
             We developed a self-contained, closed-loop, mobile
             application with movie stimuli designed to engage the
             child&#x0027;s attention and elicit specific behavioral and
             social responses, which are recorded with the mobile
             device&#x0027;s camera and analyzed via computer vision
             algorithms. Here, in addition to presenting this paradigm,
             we validate the system to measure engagement, name-call, and
             emotional responses of toddlers with and without ASD who
             were presented with the application. Additionally, we
             demonstrate how the proposed framework can further risk
             marker research with fine-grained quantification of
             behaviors. The results suggest these objective and automatic
             methods can be considered to aid behavioral
             analysis.},
   Doi = {10.1109/TAFFC.2018.2868196},
   Key = {fds338014}
}

@article{fds335962,
   Author = {Bartesaghi, A and Aguerrebere, C and Falconieri, V and Banerjee, S and Earl, LA and Zhu, X and Grigorieff, N and Milne, JLS and Sapiro, G and Wu,
             X and Subramaniam, S},
   Title = {Atomic Resolution Cryo-EM Structure of β-Galactosidase.},
   Journal = {Structure (London, England : 1993)},
   Volume = {26},
   Number = {6},
   Pages = {848-856.e3},
   Year = {2018},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.str.2018.04.004},
   Abstract = {The advent of direct electron detectors has enabled the
             routine use of single-particle cryo-electron microscopy (EM)
             approaches to determine structures of a variety of protein
             complexes at near-atomic resolution. Here, we report the
             development of methods to account for local variations in
             defocus and beam-induced drift, and the implementation of a
             data-driven dose compensation scheme that significantly
             improves the extraction of high-resolution information
             recorded during exposure of the specimen to the electron
             beam. These advances enable determination of a cryo-EM
             density map for β-galactosidase bound to the inhibitor
             phenylethyl β-D-thiogalactopyranoside where the ordered
             regions are resolved at a level of detail seen in X-ray maps
             at ∼ 1.5 Å resolution. Using this density map in
             conjunction with constrained molecular dynamics simulations
             provides a measure of the local flexibility of the
             non-covalently bound inhibitor and offers further
             opportunities for structure-guided inhibitor
             design.},
   Doi = {10.1016/j.str.2018.04.004},
   Key = {fds335962}
}

@article{fds332366,
   Author = {Giryes, R and Eldar, YC and Bronstein, AM and Sapiro,
             G},
   Title = {Tradeoffs Between Convergence Speed and Reconstruction
             Accuracy in Inverse Problems},
   Journal = {Ieee Transactions on Signal Processing},
   Volume = {66},
   Number = {7},
   Pages = {1676-1690},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1109/TSP.2018.2791945},
   Abstract = {IEEE Solving inverse problems with iterative algorithms is
             popular, especially for large data. Due to time constraints,
             the number of possible iterations is usually limited,
             potentially limiting the achievable accuracy. Given an error
             one is willing to tolerate, an important question is whether
             it is possible to modify the original iterations to obtain
             faster convergence to a minimizer achieving the allowed
             error without increasing the computational cost of each
             iteration considerably. Relying on recent recovery
             techniques developed for settings in which the desired
             signal belongs to some low-dimensional set, we show that
             using a coarse estimate of this set may lead to a faster
             convergence at the cost of an additional error in the
             reconstruction related to the accuracy of the set
             approximation. Our theory ties to recent advances in sparse
             recovery, compressed sensing, and deep learning.
             Particularly, it may provide a possible explanation to the
             successful approximation of the l_1-minimization solution by
             neural networks with layers representing iterations, as
             practiced in the learned iterative shrinkage-thresholding
             algorithm (LISTA).},
   Doi = {10.1109/TSP.2018.2791945},
   Key = {fds332366}
}

@article{fds335963,
   Author = {Campbell, K and Carpenter, KL and Hashemi, J and Espinosa, S and Marsan,
             S and Borg, JS and Chang, Z and Qiu, Q and Vermeer, S and Adler, E and Tepper,
             M and Egger, HL and Baker, JP and Sapiro, G and Dawson,
             G},
   Title = {Computer vision analysis captures atypical attention in
             toddlers with autism.},
   Journal = {Autism},
   Pages = {1362361318766247},
   Year = {2018},
   Month = {March},
   url = {http://dx.doi.org/10.1177/1362361318766247},
   Abstract = {To demonstrate the capability of computer vision analysis to
             detect atypical orienting and attention behaviors in
             toddlers with autism spectrum disorder. One hundered and
             four toddlers of 16-31 months old (mean = 22)
             participated in this study. Twenty-two of the toddlers had
             autism spectrum disorder and 82 had typical development or
             developmental delay. Toddlers watched video stimuli on a
             tablet while the built-in camera recorded their head
             movement. Computer vision analysis measured participants'
             attention and orienting in response to name calls.
             Reliability of the computer vision analysis algorithm was
             tested against a human rater. Differences in behavior were
             analyzed between the autism spectrum disorder group and the
             comparison group. Reliability between computer vision
             analysis and human coding for orienting to name was
             excellent (intra-class coefficient 0.84, 95% confidence
             interval 0.67-0.91). Only 8% of toddlers with autism
             spectrum disorder oriented to name calling on >1 trial,
             compared to 63% of toddlers in the comparison group
             (p = 0.002). Mean latency to orient was significantly
             longer for toddlers with autism spectrum disorder (2.02 vs
             1.06 s, p = 0.04). Sensitivity for autism spectrum
             disorder of atypical orienting was 96% and specificity was
             38%. Older toddlers with autism spectrum disorder showed
             less attention to the videos overall (p = 0.03).
             Automated coding offers a reliable, quantitative method for
             detecting atypical social orienting and reduced sustained
             attention in toddlers with autism spectrum
             disorder.},
   Doi = {10.1177/1362361318766247},
   Key = {fds335963}
}

@article{fds332805,
   Author = {Vu, M-AT and Adalı, T and Ba, D and Buzsáki, G and Carlson, D and Heller,
             K and Liston, C and Rudin, C and Sohal, VS and Widge, AS and Mayberg, HS and Sapiro, G and Dzirasa, K},
   Title = {A Shared Vision for Machine Learning in Neuroscience.},
   Journal = {The Journal of Neuroscience : the Official Journal of the
             Society for Neuroscience},
   Volume = {38},
   Number = {7},
   Pages = {1601-1607},
   Year = {2018},
   Month = {February},
   url = {http://dx.doi.org/10.1523/jneurosci.0508-17.2018},
   Abstract = {With ever-increasing advancements in technology,
             neuroscientists are able to collect data in greater volumes
             and with finer resolution. The bottleneck in understanding
             how the brain works is consequently shifting away from the
             amount and type of data we can collect and toward what we
             actually do with the data. There has been a growing interest
             in leveraging this vast volume of data across levels of
             analysis, measurement techniques, and experimental paradigms
             to gain more insight into brain function. Such efforts are
             visible at an international scale, with the emergence of big
             data neuroscience initiatives, such as the BRAIN initiative
             (Bargmann et al., 2014), the Human Brain Project, the Human
             Connectome Project, and the National Institute of Mental
             Health's Research Domain Criteria initiative. With these
             large-scale projects, much thought has been given to
             data-sharing across groups (Poldrack and Gorgolewski, 2014;
             Sejnowski et al., 2014); however, even with such
             data-sharing initiatives, funding mechanisms, and
             infrastructure, there still exists the challenge of how to
             cohesively integrate all the data. At multiple stages and
             levels of neuroscience investigation, machine learning holds
             great promise as an addition to the arsenal of analysis
             tools for discovering how the brain works.},
   Doi = {10.1523/jneurosci.0508-17.2018},
   Key = {fds332805}
}

@article{fds327666,
   Author = {Pisharady, PK and Sotiropoulos, SN and Duarte-Carvajalino, JM and Sapiro, G and Lenglet, C},
   Title = {Estimation of white matter fiber parameters from compressed
             multiresolution diffusion MRI using sparse Bayesian
             learning.},
   Journal = {Neuroimage},
   Volume = {167},
   Pages = {488-503},
   Year = {2018},
   Month = {February},
   url = {http://dx.doi.org/10.1016/j.neuroimage.2017.06.052},
   Abstract = {We present a sparse Bayesian unmixing algorithm BusineX:
             Bayesian Unmixing for Sparse Inference-based Estimation of
             Fiber Crossings (X), for estimation of white matter fiber
             parameters from compressed (under-sampled) diffusion MRI
             (dMRI) data. BusineX combines compressive sensing with
             linear unmixing and introduces sparsity to the previously
             proposed multiresolution data fusion algorithm RubiX,
             resulting in a method for improved reconstruction,
             especially from data with lower number of diffusion
             gradients. We formulate the estimation of fiber parameters
             as a sparse signal recovery problem and propose a linear
             unmixing framework with sparse Bayesian learning for the
             recovery of sparse signals, the fiber orientations and
             volume fractions. The data is modeled using a parametric
             spherical deconvolution approach and represented using a
             dictionary created with the exponential decay components
             along different possible diffusion directions. Volume
             fractions of fibers along these directions define the
             dictionary weights. The proposed sparse inference, which is
             based on the dictionary representation, considers the
             sparsity of fiber populations and exploits the spatial
             redundancy in data representation, thereby facilitating
             inference from under-sampled q-space. The algorithm improves
             parameter estimation from dMRI through data-dependent local
             learning of hyperparameters, at each voxel and for each
             possible fiber orientation, that moderate the strength of
             priors governing the parameter variances. Experimental
             results on synthetic and in-vivo data show improved accuracy
             with a lower uncertainty in fiber parameter estimates.
             BusineX resolves a higher number of second and third fiber
             crossings. For under-sampled data, the algorithm is also
             shown to produce more reliable estimates.},
   Doi = {10.1016/j.neuroimage.2017.06.052},
   Key = {fds327666}
}

@article{fds335964,
   Author = {Qiu, Q and Hashemi, J and Sapiro, G},
   Title = {Intelligent synthesis driven model calibration: framework
             and face recognition application},
   Journal = {Proceedings 2017 Ieee International Conference on Computer
             Vision Workshops, Iccvw 2017},
   Volume = {2018-January},
   Pages = {2564-2572},
   Year = {2018},
   Month = {January},
   ISBN = {9781538610343},
   url = {http://dx.doi.org/10.1109/ICCVW.2017.301},
   Abstract = {© 2017 IEEE. Deep Neural Networks (DNNs) that achieve
             state-of-the-art results are still prone to suffer
             performance degradation when deployed in many real-world
             scenarios due to shifts between the training and deployment
             domains. Limited data from a given setting can be enriched
             through synthesis, then used to calibrate a pre-trained DNN
             to improve the performance in the setting. Most enrichment
             approaches try to generate as much data as possible;
             however, this blind approach is computationally expensive
             and can lead to generating redundant data. Contrary to this,
             we develop synthesis, here exemplified for faces, methods
             and propose information-driven approaches to exploit and
             optimally select face synthesis types both at training and
             testing. We show that our approaches, without re-designing a
             new DNN, lead to more efficient training and improved
             performance. We demonstrate the effectiveness of our
             approaches by calibrating a state-of-the-art DNN to two
             challenging face recognition datasets.},
   Doi = {10.1109/ICCVW.2017.301},
   Key = {fds335964}
}

@article{fds335965,
   Author = {Sokolić, J and Qiu, Q and Rodrigues, MRD and Sapiro,
             G},
   Title = {Learning to identify while failing to discriminate},
   Journal = {Proceedings 2017 Ieee International Conference on Computer
             Vision Workshops, Iccvw 2017},
   Volume = {2018-January},
   Pages = {2537-2544},
   Year = {2018},
   Month = {January},
   ISBN = {9781538610343},
   url = {http://dx.doi.org/10.1109/ICCVW.2017.298},
   Abstract = {© 2017 IEEE. Privacy and fairness are critical in computer
             vision applications, in particular when dealing with human
             identification. Achieving a universally secure, private, and
             fair systems is practically impossible as the exploitation
             of additional data can reveal private information in the
             original one. Faced with this challenge, we propose a new
             line of research, where the privacy is learned and used in a
             closed environment. The goal is to ensure that a given
             entity, trusted to infer certain information with our data,
             is blocked from inferring protected information from it. We
             design a system that learns to succeed on the positive task
             while simultaneously fail at the negative one, and
             illustrate this with challenging cases where the positive
             task (face verification) is harder than the negative one
             (gender classification). The framework opens the door to
             privacy and fairness in very important closed scenarios,
             ranging from private data accumulation companies to
             law-enforcement and hospitals.},
   Doi = {10.1109/ICCVW.2017.298},
   Key = {fds335965}
}

@article{fds339262,
   Author = {Simhal, AK and Gong, B and Trimmer, JS and Weinberg, RJ and Smith, SJ and Sapiro, G and Micheva, KD},
   Title = {A Computational Synaptic Antibody Characterization Tool for
             Array Tomography.},
   Journal = {Frontiers in Neuroanatomy},
   Volume = {12},
   Pages = {51},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.3389/fnana.2018.00051},
   Abstract = {Application-specific validation of antibodies is a critical
             prerequisite for their successful use. Here we introduce an
             automated framework for characterization and screening of
             antibodies against synaptic molecules for high-resolution
             immunofluorescence array tomography (AT). The proposed
             Synaptic Antibody Characterization Tool (SACT) is designed
             to provide an automatic, robust, flexible, and efficient
             tool for antibody characterization at scale. SACT
             automatically detects puncta of immunofluorescence labeling
             from candidate antibodies and determines whether a punctum
             belongs to a synapse. The molecular composition and size of
             the target synapses expected to contain the antigen is
             determined by the user, based on biological knowledge.
             Operationally, the presence of a synapse is defined by the
             colocalization or adjacency of the candidate antibody
             punctum to one or more reference antibody puncta. The
             outputs of SACT are automatically computed measurements such
             as target synapse density and target specificity ratio that
             reflect the sensitivity and specificity of immunolabeling
             with a given candidate antibody. These measurements provide
             an objective way to characterize and compare the performance
             of different antibodies against the same target, and can be
             used to objectively select the antibodies best suited for AT
             and potentially for other immunolabeling
             applications.},
   Doi = {10.3389/fnana.2018.00051},
   Key = {fds339262}
}

@article{fds335968,
   Author = {Bertrán, MA and Martínez, NL and Wang, Y and Dunson, D and Sapiro, G and Ringach, D},
   Title = {Active learning of cortical connectivity from two-photon
             imaging data.},
   Journal = {Plos One},
   Volume = {13},
   Number = {5},
   Pages = {e0196527},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0196527},
   Abstract = {Understanding how groups of neurons interact within a
             network is a fundamental question in system neuroscience.
             Instead of passively observing the ongoing activity of a
             network, we can typically perturb its activity, either by
             external sensory stimulation or directly via techniques such
             as two-photon optogenetics. A natural question is how to use
             such perturbations to identify the connectivity of the
             network efficiently. Here we introduce a method to infer
             sparse connectivity graphs from in-vivo, two-photon imaging
             of population activity in response to external stimuli. A
             novel aspect of the work is the introduction of a
             recommended distribution, incrementally learned from the
             data, to optimally refine the inferred network. Unlike
             existing system identification techniques, this "active
             learning" method automatically focuses its attention on key
             undiscovered areas of the network, instead of targeting
             global uncertainty indicators like parameter variance. We
             show how active learning leads to faster inference while, at
             the same time, provides confidence intervals for the network
             parameters. We present simulations on artificial small-world
             networks to validate the methods and apply the method to
             real data. Analysis of frequency of motifs recovered show
             that cortical networks are consistent with a small-world
             topology model.},
   Doi = {10.1371/journal.pone.0196527},
   Key = {fds335968}
}

@article{fds335966,
   Author = {Asiedu, MN and Simhal, A and Lam, CT and Mueller, J and Chaudhary, U and Schmitt, JW and Sapiro, G and Ramanujam, N},
   Title = {Image processing and machine learning techniques to automate
             diagnosis of Lugol's iodine cervigrams for a low-cost
             point-of-care digital colposcope},
   Journal = {Progress in Biomedical Optics and Imaging Proceedings of
             Spie},
   Volume = {10485},
   Year = {2018},
   Month = {January},
   ISBN = {9781510614550},
   url = {http://dx.doi.org/10.1117/12.2282792},
   Abstract = {Copyright © 2018 SPIE. The world health organization
             recommends visual inspection with acetic acid (VIA) and/or
             Lugol's Iodine (VILI) for cervical cancer screening in
             low-resource settings. Human interpretation of diagnostic
             indicators for visual inspection is qualitative, subjective,
             and has high inter-observer discordance, which could lead
             both to adverse outcomes for the patient and unnecessary
             follow-ups. In this work, we a simple method for automatic
             feature extraction and classification for Lugol's Iodine
             cervigrams acquired with a low-cost, miniature, digital
             colposcope. Algorithms to preprocess expert
             physician-labelled cervigrams and to extract simple but
             powerful color-based features are introduced. The features
             are used to train a support vector machine model to classify
             cervigrams based on expert physician labels. The selected
             framework achieved a sensitivity, specificity, and accuracy
             of 89.2%, 66.7% and 80.6% with majority diagnosis of the
             expert physicians in discriminating cervical intraepithelial
             neoplasia (CIN +) relative to normal tissues. The proposed
             classifier also achieved an area under the curve of 84 when
             trained with majority diagnosis of the expert physicians.
             The results suggest that utilizing simple color-based
             features may enable unbiased automation of VILI cervigrams,
             opening the door to a full system of low-cost data
             acquisition complemented with automatic interpretation.},
   Doi = {10.1117/12.2282792},
   Key = {fds335966}
}

@article{fds335967,
   Author = {Chiew, KS and Hashemi, J and Gans, LK and Lerebours, L and Clement, NJ and Vu, M-AT and Sapiro, G and Heller, NE and Adcock,
             RA},
   Title = {Motivational valence alters memory formation without
             altering exploration of a real-life spatial
             environment.},
   Journal = {Plos One},
   Volume = {13},
   Number = {3},
   Pages = {e0193506},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0193506},
   Abstract = {Volitional exploration and learning are key to adaptive
             behavior, yet their characterization remains a complex
             problem for cognitive science. Exploration has been posited
             as a mechanism by which motivation promotes memory, but this
             relationship is not well-understood, in part because novel
             stimuli that motivate exploration also reliably elicit
             changes in neuromodulatory brain systems that directly alter
             memory formation, via effects on neural plasticity. To
             deconfound interrelationships between motivation,
             exploration, and memory formation we manipulated
             motivational state prior to entering a spatial context,
             measured exploratory responses to the context and novel
             stimuli within it, and then examined motivation and
             exploration as predictors of memory outcomes. To elicit
             spontaneous exploration, we used the physical space of an
             art exhibit with affectively rich content; we expected
             motivated exploration and memory to reflect multiple
             factors, including not only motivational valence, but also
             individual differences. Motivation was manipulated via an
             introductory statement framing exhibit themes in terms of
             Promotion- or Prevention-oriented goals. Participants
             explored the exhibit while being tracked by video. They
             returned 24 hours later for recall and spatial memory tests,
             followed by measures of motivation, personality, and
             relevant attitude variables. Promotion and Prevention
             condition participants did not differ in terms of
             group-level exploration time or memory metrics, suggesting
             similar motivation to explore under both framing contexts.
             However, exploratory behavior and memory outcomes were
             significantly more closely related under Promotion than
             Prevention, indicating that Prevention framing disrupted
             expected depth-of-encoding effects. Additionally, while
             trait measures predicted exploration similarly across
             framing conditions, traits interacted with motivational
             framing context and facial affect to predict memory
             outcomes. This novel characterization of motivated learning
             implies that dissociable behavioral and biological
             mechanisms, here varying as a function of valence,
             contribute to memory outcomes in complex, real-life
             environments.},
   Doi = {10.1371/journal.pone.0193506},
   Key = {fds335967}
}

@article{fds337693,
   Author = {Duchin, Y and Shamir, RR and Patriat, R and Kim, J and Vitek, JL and Sapiro, G and Harel, N},
   Title = {Patient-specific anatomical model for deep brain stimulation
             based on 7 Tesla MRI.},
   Journal = {Plos One},
   Volume = {13},
   Number = {8},
   Pages = {e0201469},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0201469},
   Abstract = {Deep brain stimulation (DBS) requires accurate localization
             of the anatomical target structure, and the precise
             placement of the DBS electrode within it. Ultra-high field 7
             Tesla (T) MR images can be utilized to create
             patient-specific anatomical 3D models of the subthalamic
             nuclei (STN) to enhance pre-surgical DBS targeting as well
             as post-surgical visualization of the DBS lead position and
             orientation. We validated the accuracy of the 7T
             imaging-based patient-specific model of the STN and measured
             the variability of the location and dimensions across
             movement disorder patients.72 patients who underwent DBS
             surgery were scanned preoperatively on 7T MRI. Segmentations
             and 3D volume rendering of the STN were generated for all
             patients. For 21 STN-DBS cases, microelectrode recording
             (MER) was used to validate the segmentation. For 12 cases,
             we computed the correlation between the overlap of the STN
             and volume of tissue activated (VTA) and the monopolar
             review for a further validation of the model's accuracy and
             its clinical relevancy.We successfully reconstructed and
             visualized the STN in all patients. Significant variability
             was found across individuals regarding the location of the
             STN center of mass as well as its volume, length, depth and
             width. Significant correlations were found between MER and
             the 7T imaging-based model of the STN (r = 0.86) and VTA-STN
             overlap and the monopolar review outcome (r = 0.61).The
             results suggest that an accurate visualization and
             localization of a patient-specific 3D model of the STN can
             be generated based on 7T MRI. The imaging-based 7T MRI STN
             model was validated using MER and patient's clinical
             outcomes. The significant variability observed in the STN
             location and shape based on a large number of patients
             emphasizes the importance of an accurate direct
             visualization of the STN for DBS targeting. An accurate STN
             localization can facilitate postoperative stimulation
             parameters for optimized patient outcome.},
   Doi = {10.1371/journal.pone.0201469},
   Key = {fds337693}
}

@article{fds339596,
   Author = {Qiu, Q and Lezama, J and Bronstein, A and Sapiro,
             G},
   Title = {ForestHash: Semantic Hashing with Shallow Random Forests and
             Tiny Convolutional Networks},
   Journal = {Lecture Notes in Computer Science (Including Subseries
             Lecture Notes in Artificial Intelligence and Lecture Notes
             in Bioinformatics)},
   Volume = {11206 LNCS},
   Pages = {442-459},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1007/978-3-030-01216-8_27},
   Abstract = {© 2018, Springer Nature Switzerland AG. In this paper, we
             introduce a random forest semantic hashing scheme that
             embeds tiny convolutional neural networks (CNN) into shallow
             random forests. A binary hash code for a data point is
             obtained by a set of decision trees, setting ‘1’ for the
             visited tree leaf, and ‘0’ for the rest. We propose to
             first randomly group arriving classes at each tree split
             node into two groups, obtaining a significantly simplified
             two-class classification problem that can be a handled with
             a light-weight CNN weak learner. Code uniqueness is achieved
             via the random class grouping, whilst code consistency is
             achieved using a low-rank loss in the CNN weak learners that
             encourages intra-class compactness for the two random class
             groups. Finally, we introduce an information-theoretic
             approach for aggregating codes of individual trees into a
             single hash code, producing a near-optimal unique hash for
             each class. The proposed approach significantly outperforms
             state-of-the-art hashing methods for image retrieval tasks
             on large-scale public datasets, and is comparable to image
             classification methods while utilizing a more compact,
             efficient and scalable representation. This work proposes a
             principled and robust procedure to train and deploy in
             parallel an ensemble of light-weight CNNs, instead of simply
             going deeper.},
   Doi = {10.1007/978-3-030-01216-8_27},
   Key = {fds339596}
}

@article{fds335969,
   Author = {Lezama, J and Qiu, Q and Sapiro, G},
   Title = {Not afraid of the dark: NIR-VIS face recognition via
             cross-spectral hallucination and low-rank
             embedding},
   Journal = {Proceedings 30th Ieee Conference on Computer Vision and
             Pattern Recognition, Cvpr 2017},
   Volume = {2017-January},
   Pages = {6807-6816},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1109/CVPR.2017.720},
   Abstract = {© 2017 IEEE. Surveillance cameras today often capture NIR
             (near infrared) images in low-light environments. However,
             most face datasets accessible for training and verification
             are only collected in the VIS (visible light) spectrum. It
             remains a challenging problem to match NIR to VIS face
             images due to the different light spectrum. Recently,
             breakthroughs have been made for VIS face recognition by
             applying deep learning on a huge amount of labeled VIS face
             samples. The same deep learning approach cannot be simply
             applied to NIR face recognition for two main reasons: First,
             much limited NIR face images are available for training
             compared to the VIS spectrum. Second, face galleries to be
             matched are mostly available only in the VIS spectrum. In
             this paper, we propose an approach to extend the deep
             learning breakthrough for VIS face recognition to the NIR
             spectrum, without retraining the underlying deep models that
             see only VIS faces. Our approach consists of two core
             components, cross-spectral hallucination and low-rank
             embedding, to optimize respectively input and output of a
             VIS deep model for cross-spectral face recognition.
             Cross-spectral hallucination produces VIS faces from NIR
             images through a deep learning approach. Low-rank embedding
             restores a low-rank structure for faces deep features across
             both NIR and VIS spectrum. We observe that it is often
             equally effective to perform hallucination to input NIR
             images or low-rank embedding to output deep features for a
             VIS deep model for cross-spectral recognition. When
             hallucination and low-rank embedding are deployed together,
             we observe significant further improvement; we obtain
             state-of-the-art accuracy on the CASIA NIR-VIS v2.0
             benchmark, without the need at all to re-train the
             recognition system.},
   Doi = {10.1109/CVPR.2017.720},
   Key = {fds335969}
}

@article{fds335970,
   Author = {Ye, Q and Zhang, T and Ke, W and Qiu, Q and Chen, J and Sapiro, G and Zhang,
             B},
   Title = {Self-learning scene-specific pedestrian detectors using a
             progressive latent model},
   Journal = {Proceedings 30th Ieee Conference on Computer Vision and
             Pattern Recognition, Cvpr 2017},
   Volume = {2017-January},
   Pages = {2057-2066},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1109/CVPR.2017.222},
   Abstract = {© 2017 IEEE. In this paper, a self-learning approach is
             proposed towards solving scene-specific pedestrian detection
             problem without any human' annotation involved. The
             self-learning approach is deployed as progressive steps of
             object discovery, object enforcement, and label propagation.
             In the learning procedure, object locations in each frame
             are treated as latent variables that are solved with a
             progressive latent model (PLM). Compared with conventional
             latent models, the proposed PLM incorporates a spatial
             regularization term to reduce ambiguities in object
             proposals and to enforce object localization, and also a
             graph-based label propagation to discover harder instances
             in adjacent frames. With the difference of convex (DC)
             objective functions, PLM can be efficiently optimized with a
             concave-convex programming and thus guaranteeing the
             stability of self-learning. Extensive experiments
             demonstrate that even without annotation the proposed
             self-learning approach outperforms weakly supervised
             learning approaches, while achieving comparable performance
             with transfer learning and fully supervised
             approaches.},
   Doi = {10.1109/CVPR.2017.222},
   Key = {fds335970}
}

@article{fds335971,
   Author = {Su, S and Delbracio, M and Wang, J and Sapiro, G and Heidrich, W and Wang,
             O},
   Title = {Deep video deblurring for hand-held cameras},
   Journal = {Proceedings 30th Ieee Conference on Computer Vision and
             Pattern Recognition, Cvpr 2017},
   Volume = {2017-January},
   Pages = {237-246},
   Year = {2017},
   Month = {November},
   ISBN = {9781538604571},
   url = {http://dx.doi.org/10.1109/CVPR.2017.33},
   Abstract = {© 2017 IEEE. Motion blur from camera shake is a major
             problem in videos captured by hand-held devices. Unlike
             single-image deblurring, video-based approaches can take
             advantage of the abundant information that exists across
             neighboring frames. As a result the best performing methods
             rely on the alignment of nearby frames. However, aligning
             images is a computationally expensive and fragile procedure,
             and methods that aggregate information must therefore be
             able to identify which regions have been accurately aligned
             and which have not, a task that requires high level scene
             understanding. In this work, we introduce a deep learning
             solution to video deblurring, where a CNN is trained
             end-toend to learn how to accumulate information across
             frames. To train this network, we collected a dataset of
             real videos recorded with a high frame rate camera, which we
             use to generate synthetic motion blur for supervision. We
             show that the features learned from this dataset extend to
             deblurring motion blur that arises due to camera shake in a
             wide range of videos, and compare the quality of results to
             a number of other baselines.},
   Doi = {10.1109/CVPR.2017.33},
   Key = {fds335971}
}

@article{fds335972,
   Author = {Tepper, M and Sapiro, G},
   Title = {Nonnegative matrix underapproximation for robust multiple
             model fitting},
   Journal = {Proceedings 30th Ieee Conference on Computer Vision and
             Pattern Recognition, Cvpr 2017},
   Volume = {2017-January},
   Pages = {655-663},
   Year = {2017},
   Month = {November},
   ISBN = {9781538604571},
   url = {http://dx.doi.org/10.1109/CVPR.2017.77},
   Abstract = {© 2017 IEEE. In this work, we introduce a highly efficient
             algorithm to address the nonnegative matrix
             underapproximation (NMU) problem, i.e., nonnegative matrix
             factorization (NMF) with an additional underapproximation
             constraint. NMU results are interesting as, compared to
             traditional NMF, they present additional sparsity and
             part-based behavior, explaining unique data features. To
             show these features in practice, we first present an
             application to the analysis of climate data. We then present
             an NMU-based algorithm to robustly fit multiple parametric
             models to a dataset. The proposed approach delivers
             state-of-the-art results for the estimation of multiple
             fundamental matrices and homographies, outperforming other
             alternatives in the literature and exemplifying the use of
             efficient NMU computations.},
   Doi = {10.1109/CVPR.2017.77},
   Key = {fds335972}
}

@article{fds329136,
   Author = {Pisharady, PK and Sotiropoulos, SN and Sapiro, G and Lenglet,
             C},
   Title = {A Sparse Bayesian Learning Algorithm for White Matter
             Parameter Estimation from Compressed Multi-shell Diffusion
             MRI.},
   Journal = {Medical image computing and computer-assisted intervention :
             MICCAI ... International Conference on Medical Image
             Computing and Computer-Assisted Intervention},
   Volume = {10433},
   Pages = {602-610},
   Year = {2017},
   Month = {September},
   ISBN = {9783319661810},
   url = {http://dx.doi.org/10.1007/978-3-319-66182-7_69},
   Abstract = {We propose a sparse Bayesian learning algorithm for improved
             estimation of white matter fiber parameters from compressed
             (under-sampled q-space) multi-shell diffusion MRI data. The
             multi-shell data is represented in a dictionary form using a
             non-monoexponential decay model of diffusion, based on
             continuous gamma distribution of diffusivities. The fiber
             volume fractions with predefined orientations, which are the
             unknown parameters, form the dictionary weights. These
             unknown parameters are estimated with a linear un-mixing
             framework, using a sparse Bayesian learning algorithm. A
             localized learning of hyperparameters at each voxel and for
             each possible fiber orientations improves the parameter
             estimation. Our experiments using synthetic data from the
             ISBI 2012 HARDI reconstruction challenge and in-vivo data
             from the Human Connectome Project demonstrate the
             improvements.},
   Doi = {10.1007/978-3-319-66182-7_69},
   Key = {fds329136}
}

@article{fds329481,
   Author = {Sokolić, J and Giryes, R and Sapiro, G and Rodrigues,
             MRD},
   Title = {Generalization error of deep neural networks: Role of
             classification margin and data structure},
   Journal = {2017 12th International Conference on Sampling Theory and
             Applications, SampTA 2017},
   Pages = {147-151},
   Year = {2017},
   Month = {September},
   ISBN = {9781538615652},
   url = {http://dx.doi.org/10.1109/SAMPTA.2017.8024476},
   Abstract = {© 2017 IEEE. Understanding the generalization properties of
             deep learning models is critical for their successful usage
             in many applications, especially in the regimes where the
             number of training samples is limited. We study the
             generalization properties of deep neural networks (DNNs) via
             the Jacobian matrix of the network. Our analysis is general
             to arbitrary network structures, types of non-linearities
             and pooling operations. We show that bounding the spectral
             norm of the Jacobian matrix in the network reduces the
             generalization error. In addition, we tie this error to the
             invariance in the data and the network. Experiments on the
             MNIST and ImageNet datasets support these findings. This
             short paper summarizes our generalization error theorems for
             DNNs and for general invariant classifiers [1], [2]
             .},
   Doi = {10.1109/SAMPTA.2017.8024476},
   Key = {fds329481}
}

@article{fds328865,
   Author = {Sokolic, J and Giryes, R and Sapiro, G and Rodrigues,
             MRD},
   Title = {Robust Large Margin Deep Neural Networks},
   Journal = {Ieee Transactions on Signal Processing},
   Volume = {65},
   Number = {16},
   Pages = {4265-4280},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1109/TSP.2017.2708039},
   Doi = {10.1109/TSP.2017.2708039},
   Key = {fds328865}
}

@article{fds326146,
   Author = {Simhal, AK and Aguerrebere, C and Collman, F and Vogelstein, JT and Micheva, KD and Weinberg, RJ and Smith, SJ and Sapiro,
             G},
   Title = {Probabilistic fluorescence-based synapse
             detection.},
   Journal = {Plos Computational Biology},
   Volume = {13},
   Number = {4},
   Pages = {e1005493},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1371/journal.pcbi.1005493},
   Abstract = {Deeper exploration of the brain's vast synaptic networks
             will require new tools for high-throughput structural and
             molecular profiling of the diverse populations of synapses
             that compose those networks. Fluorescence microscopy (FM)
             and electron microscopy (EM) offer complementary advantages
             and disadvantages for single-synapse analysis. FM combines
             exquisite molecular discrimination capacities with high
             speed and low cost, but rigorous discrimination between
             synaptic and non-synaptic fluorescence signals is
             challenging. In contrast, EM remains the gold standard for
             reliable identification of a synapse, but offers only
             limited molecular discrimination and is slow and costly. To
             develop and test single-synapse image analysis methods, we
             have used datasets from conjugate array tomography (cAT),
             which provides voxel-conjugate FM and EM (annotated) images
             of the same individual synapses. We report a novel
             unsupervised probabilistic method for detection of synapses
             from multiplex FM (muxFM) image data, and evaluate this
             method both by comparison to EM gold standard annotated data
             and by examining its capacity to reproduce known important
             features of cortical synapse distributions. The proposed
             probabilistic model-based synapse detector accepts
             molecular-morphological synapse models as user queries, and
             delivers a volumetric map of the probability that each voxel
             represents part of a synapse. Taking human annotation of cAT
             EM data as ground truth, we show that our algorithm detects
             synapses from muxFM data alone as successfully as human
             annotators seeing only the muxFM data, and accurately
             reproduces known architectural features of cortical synapse
             distributions. This approach opens the door to data-driven
             discovery of new synapse types and their density. We suggest
             that our probabilistic synapse detector will also be useful
             for analysis of standard confocal and super-resolution FM
             images, where EM cross-validation is not
             practical.},
   Doi = {10.1371/journal.pcbi.1005493},
   Key = {fds326146}
}

@article{fds323853,
   Author = {Campbell, K and Carpenter, KLH and Espinosa, S and Hashemi, J and Qiu,
             Q and Tepper, M and Calderbank, R and Sapiro, G and Egger, HL and Baker,
             JP and Dawson, G},
   Title = {Use of a Digital Modified Checklist for Autism in Toddlers -
             Revised with Follow-up to Improve Quality of Screening for
             Autism.},
   Journal = {The Journal of Pediatrics},
   Volume = {183},
   Pages = {133-139.e1},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1016/j.jpeds.2017.01.021},
   Abstract = {OBJECTIVES:To assess changes in quality of care for children
             at risk for autism spectrum disorders (ASD) due to process
             improvement and implementation of a digital screening form.
             STUDY DESIGN:The process of screening for ASD was studied in
             an academic primary care pediatrics clinic before and after
             implementation of a digital version of the Modified
             Checklist for Autism in Toddlers - Revised with Follow-up
             with automated risk assessment. Quality metrics included
             accuracy of documentation of screening results and
             appropriate action for positive screens (secondary screening
             or referral). Participating physicians completed pre- and
             postintervention surveys to measure changes in attitudes
             toward feasibility and value of screening for ASD. Evidence
             of change was evaluated with statistical process control
             charts and χ2 tests. RESULTS:Accurate documentation in the
             electronic health record of screening results increased from
             54% to 92% (38% increase, 95% CI 14%-64%) and appropriate
             action for children screening positive increased from 25% to
             85% (60% increase, 95% CI 35%-85%). A total of 90% of
             participating physicians agreed that the transition to a
             digital screening form improved their clinical assessment of
             autism risk. CONCLUSIONS:Implementation of a tablet-based
             digital version of the Modified Checklist for Autism in
             Toddlers - Revised with Follow-up led to improved quality of
             care for children at risk for ASD and increased
             acceptability of screening for ASD. Continued efforts
             towards improving the process of screening for ASD could
             facilitate rapid, early diagnosis of ASD and advance the
             accuracy of studies of the impact of screening.},
   Doi = {10.1016/j.jpeds.2017.01.021},
   Key = {fds323853}
}

@article{fds324086,
   Author = {Chen, J and Chang, Z and Qiu, Q and Li, X and Sapiro, G and Bronstein, A and Pietikäinen, M},
   Title = {RealSense = real heart rate: Illumination invariant heart
             rate estimation from videos},
   Journal = {2016 6th International Conference on Image Processing
             Theory, Tools and Applications, IPTA 2016},
   Year = {2017},
   Month = {January},
   ISBN = {9781467389105},
   url = {http://dx.doi.org/10.1109/IPTA.2016.7820970},
   Abstract = {© 2016 IEEE. Recent studies validated the feasibility of
             estimating heart rate from human faces in RGB video.
             However, test subjects are often recorded under controlled
             conditions, as illumination variations significantly affect
             the RGB-based heart rate estimation accuracy. Intel
             newly-announced low-cost RealSense 3D (RGBD) camera is
             becoming ubiquitous in laptops and mobile devices starting
             this year, opening the door to new and more robust computer
             vision. RealSense cameras produce RGB images with extra
             depth information inferred from a latent near-infrared (NIR)
             channel. In this paper, we experimentally demonstrate, for
             the first time, that heart rate can be reliably estimated
             from RealSense near-infrared images. This enables
             illumination invariant heart rate estimation, extending the
             heart rate from video feasibility to low-light applications,
             such as night driving. With the (coming) ubiquitous presence
             of RealSense devices, the proposed method not only utilizes
             its near-infrared channel, designed originally to be hidden
             from consumers; but also exploits the associated depth
             information for improved robustness to head
             pose.},
   Doi = {10.1109/IPTA.2016.7820970},
   Key = {fds324086}
}

@article{fds326840,
   Author = {Gunalan, K and Chaturvedi, A and Howell, B and Duchin, Y and Lempka, SF and Patriat, R and Sapiro, G and Harel, N and McIntyre,
             CC},
   Title = {Creating and parameterizing patient-specific deep brain
             stimulation pathway-activation models using the hyperdirect
             pathway as an example.},
   Journal = {Plos One},
   Volume = {12},
   Number = {4},
   Pages = {e0176132},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0176132},
   Abstract = {Deep brain stimulation (DBS) is an established clinical
             therapy and computational models have played an important
             role in advancing the technology. Patient-specific DBS
             models are now common tools in both academic and industrial
             research, as well as clinical software systems. However, the
             exact methodology for creating patient-specific DBS models
             can vary substantially and important technical details are
             often missing from published reports.Provide a detailed
             description of the assembly workflow and parameterization of
             a patient-specific DBS pathway-activation model (PAM) and
             predict the response of the hyperdirect pathway to clinical
             stimulation.Integration of multiple software tools (e.g.
             COMSOL, MATLAB, FSL, NEURON, Python) enables the creation
             and visualization of a DBS PAM. An example DBS PAM was
             developed using 7T magnetic resonance imaging data from a
             single unilaterally implanted patient with Parkinson's
             disease (PD). This detailed description implements our best
             computational practices and most elaborate parameterization
             steps, as defined from over a decade of technical
             evolution.Pathway recruitment curves and strength-duration
             relationships highlight the non-linear response of axons to
             changes in the DBS parameter settings.Parameterization of
             patient-specific DBS models can be highly detailed and
             constrained, thereby providing confidence in the simulation
             predictions, but at the expense of time demanding technical
             implementation steps. DBS PAMs represent new tools for
             investigating possible correlations between brain pathway
             activation patterns and clinical symptom
             modulation.},
   Doi = {10.1371/journal.pone.0176132},
   Key = {fds326840}
}


%% Sober, Barak   
@article{fds338348,
   Author = {Shaus, A and Sober, B and Tzang, O and Ioffe, Z and Cheshnovsky, O and Finkelstein, I and Piasetzky, E},
   Title = {Raman Binary Mapping of Iron Age Ostracon in an Unknown
             Material Composition and High-Fluorescence Setting—A Proof
             of Concept},
   Journal = {Archaeometry},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1111/arcm.12419},
   Abstract = {© 2018 University of Oxford The textual evidence from
             ancient Judah is mainly limited to ostraca, ink-on-clay
             inscriptions. Their facsimiles (binary depictions) are
             indispensable for further analysis. Previous attempts at
             mechanizing the creation of facsimiles have been
             problematic. Here, we present a proof of concept of
             objective binary image acquisition, via Raman mapping. Our
             method is based on a new peak detection transform, handling
             the challenging fluorescence of the clay, and circumventing
             preparatory ink composition analysis. A sequence of binary
             mappings (signifying the peaks) is created for each
             wavelength; their legibility reflects the prominence of
             Raman lines. Applied to a biblical-period ostracon, the
             method exhibits high statistical significance.},
   Doi = {10.1111/arcm.12419},
   Key = {fds338348}
}

@article{fds338349,
   Author = {Sober, B and Levin, D},
   Title = {Computer aided restoration of handwritten character
             strokes},
   Journal = {Computer Aided Design},
   Volume = {89},
   Pages = {12-24},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1016/j.cad.2017.04.005},
   Doi = {10.1016/j.cad.2017.04.005},
   Key = {fds338349}
}

@article{fds339336,
   Author = {Shaus, A and Faigenbaum-Golovin, S and Sober, B and Turkel,
             E},
   Title = {Potential Contrast – A New Image Quality
             Measure},
   Journal = {Electronic Imaging},
   Volume = {2017},
   Number = {12},
   Pages = {52-58},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.2352/ISSN.2470-1173.2017.12.IQSP-226},
   Doi = {10.2352/ISSN.2470-1173.2017.12.IQSP-226},
   Key = {fds339336}
}

@article{fds339337,
   Author = {Shaus, A and Sober, B and Turkel, E and Piasetzky,
             E},
   Title = {Beyond the ground truth: Alternative quality measures of
             document binarizations},
   Journal = {Proceedings of International Conference on Frontiers in
             Handwriting Recognition, Icfhr},
   Pages = {495-500},
   Year = {2017},
   Month = {January},
   ISBN = {9781509009817},
   url = {http://dx.doi.org/10.1109/ICFHR.2016.0097},
   Abstract = {© 2016 IEEE. This article discusses the quality assessment
             of binary images. The customary, ground truth based
             methodology, used in the literature is shown to be
             problematic due to its subjective nature. Several previously
             suggested alternatives are surveyed and are also found to be
             inadequate in certain scenarios. A new approach, quantifying
             the adherence of a binarization to its document image is
             proposed and tested using six different measures of
             accuracy. The measures are evaluated experimentally based on
             datasets from DIBCO and H-DIBCO competitions, with respect
             to different kinds of binarization degradations.},
   Doi = {10.1109/ICFHR.2016.0097},
   Key = {fds339337}
}

@article{fds339338,
   Author = {Faigenbaum-Golovin, S and Mendel-Geberovich, A and Shaus, A and Sober, B and Cordonsky, M and Levin, D and Moinester, M and Sass, B and Turkel, E and Piasetzky, E and Finkelstein, I},
   Title = {Multispectral imaging reveals biblical-period inscription
             unnoticed for half a century.},
   Journal = {Plos One},
   Volume = {12},
   Number = {6},
   Pages = {e0178400},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0178400},
   Abstract = {Most surviving biblical period Hebrew inscriptions are
             ostraca-ink-on-clay texts. They are poorly preserved and
             once unearthed, fade rapidly. Therefore, proper and timely
             documentation of ostraca is essential. Here we show a
             striking example of a hitherto invisible text on the back
             side of an ostracon revealed via multispectral imaging. This
             ostracon, found at the desert fortress of Arad and dated to
             ca. 600 BCE (the eve of Judah's destruction by
             Nebuchadnezzar), has been on display for half a century. Its
             front side has been thoroughly studied, while its back side
             was considered blank. Our research revealed three lines of
             text on the supposedly blank side and four "new" lines on
             the front side. Our results demonstrate the need for
             multispectral image acquisition for both sides of all
             ancient ink ostraca. Moreover, in certain cases we recommend
             employing multispectral techniques for screening newly
             unearthed ceramic potsherds prior to disposal.},
   Doi = {10.1371/journal.pone.0178400},
   Key = {fds339338}
}

@article{fds339339,
   Author = {Anat Mendel-Geberovich, and Arie Shaus, and Shira
             Faigenbaum-Golovin, and Barak Sober, and Michael Cordonsky, and Eli Piasetzky, and Israel Finkelstein},
   Title = {A Brand New Old Inscription: Arad Ostracon 16 Rediscovered
             via Multispectral Imaging},
   Journal = {Bulletin of the American Schools of Oriental
             Research},
   Number = {378},
   Pages = {113-113},
   Year = {2017},
   url = {http://dx.doi.org/10.5615/bullamerschoorie.378.0113},
   Doi = {10.5615/bullamerschoorie.378.0113},
   Key = {fds339339}
}


%% Stern, Mark A.   
@article{fds339911,
   Author = {Lipnowski, M and Stern, M},
   Title = {Geometry of the Smallest 1-form Laplacian Eigenvalue on
             Hyperbolic Manifolds},
   Journal = {Geometrical and Functional Analysis Gafa},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1007/s00039-018-0471-x},
   Abstract = {© 2018, Springer Nature Switzerland AG. We relate small
             1-form Laplacian eigenvalues to relative cycle complexity on
             closed hyperbolic manifolds: small eigenvalues correspond to
             closed geodesics no multiple of which bounds a surface of
             small genus. We describe potential applications of this
             equivalence principle toward proving optimal torsion
             homology growth in families of hyperbolic 3-manifolds
             Benjamini–Schramm converging to H3.},
   Doi = {10.1007/s00039-018-0471-x},
   Key = {fds339911}
}

@article{fds330393,
   Title = {"Nonlinear Harmonic Forms and Indefinite Bochner Formulas "
             in Hodge Theory and L^2-Analysis},
   Volume = {39},
   Publisher = {Higher Education Press},
   Year = {2017},
   Key = {fds330393}
}


%% Tarokh, Vahid   
@article{fds339856,
   Author = {Ding, J and Tarokh, V and Yang, Y},
   Title = {Model Selection Techniques: An Overview},
   Journal = {Ieee Signal Processing Magazine},
   Volume = {35},
   Number = {6},
   Pages = {16-34},
   Year = {2018},
   Month = {November},
   url = {http://dx.doi.org/10.1109/MSP.2018.2867638},
   Abstract = {© 2018 IEEE. In the era of big data, analysts usually
             explore various statistical models or machine-learning
             methods for observed data to facilitate scientific
             discoveries or gain predictive power. Whatever data and
             fitting procedures are employed, a crucial step is to select
             the most appropriate model or method from a set of
             candidates. Model selection is a key ingredient in data
             analysis for reliable and reproducible statistical inference
             or prediction, and thus it is central to scientific studies
             in such fields as ecology, economics, engineering, finance,
             political science, biology, and epidemiology. There has been
             a long history of model selection techniques that arise from
             researches in statistics, information theory, and signal
             processing. A considerable number of methods has been
             proposed, following different philosophies and exhibiting
             varying performances. The purpose of this article is to
             provide a comprehensive overview of them, in terms of their
             motivation, large sample performance, and applicability. We
             provide integrated and practically relevant discussions on
             theoretical properties of state-of-the-art model selection
             approaches. We also share our thoughts on some controversial
             views on the practice of model selection.},
   Doi = {10.1109/MSP.2018.2867638},
   Key = {fds339856}
}

@article{fds338599,
   Author = {Ding, J and Diao, E and Zhou, J and Tarokh, V},
   Title = {A Penalized Method for the Predictive Limit of
             Learning},
   Journal = {2015 Ieee International Conference on Acoustics, Speech, and
             Signal Processing (Icassp)},
   Volume = {2018-April},
   Pages = {4414-4418},
   Year = {2018},
   Month = {September},
   ISBN = {9781538646588},
   url = {http://dx.doi.org/10.1109/ICASSP.2018.8461832},
   Abstract = {© 2018 IEEE. Machine learning systems learn from and make
             predictions by building models from observed data. Because
             large models tend to overfit while small models tend to
             underfit for a given fixed dataset, a critical challenge is
             to select an appropriate model (e.g. set of
             variables/features). Model selection aims to strike a
             balance between the goodness of fit and model complexity,
             and thus to gain reliable predictive power. In this paper,
             we study a penalized model selection technique that
             asymptotically achieves the optimal expected prediction loss
             (referred to as the limit of learning) offered by a set of
             candidate models. We prove that the proposed procedure is
             both statistically efficient in the sense that it
             asymptotically approaches the limit of learning, and
             computationally efficient in the sense that it can be much
             faster than cross validation methods. Our theory applies for
             a wide variety of model classes, loss functions, and high
             dimensions (in the sense that the models' complexity can
             grow with data size). We released a python package with our
             proposed method for general usage like logistic regression
             and neural networks.},
   Doi = {10.1109/ICASSP.2018.8461832},
   Key = {fds338599}
}

@article{fds339263,
   Author = {Banerjee, T and Choi, J and Pesaran, B and Ba, D and Tarokh,
             V},
   Title = {Wavelet Shrinkage and Thresholding Based Robust
             Classification for Brain-Computer Interface},
   Journal = {2015 Ieee International Conference on Acoustics, Speech, and
             Signal Processing (Icassp)},
   Volume = {2018-April},
   Pages = {836-840},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1109/ICASSP.2018.8462321},
   Abstract = {© 2018 IEEE. A macaque monkey is trained to perform two
             different kinds of tasks, memory aided and visually aided.
             In each task, the monkey saccades to eight possible target
             locations. A classifier is proposed for direction decoding
             and task decoding based on local field potentials (LFP)
             collected from the prefrontal cortex. The LFP time-series
             data is modeled in a nonparametric regression framework, as
             a function corrupted by Gaussian noise. It is shown that if
             the function belongs to Besov bodies, then the proposed
             wavelet shrinkage and thresholding based classifier is
             robust and consistent. The classifier is then applied to the
             LFP data to achieve high decoding performance. The proposed
             classifier is also quite general and can be applied for the
             classification of other types of time-series data as well,
             not necessarily brain data.},
   Doi = {10.1109/ICASSP.2018.8462321},
   Key = {fds339263}
}

@article{fds339264,
   Author = {Xiang, Y and Ding, J and Tarokh, V},
   Title = {Evolutionary Spectra Based on the Multitaper Method with
             Application to Stationarity Test},
   Journal = {2015 Ieee International Conference on Acoustics, Speech, and
             Signal Processing (Icassp)},
   Volume = {2018-April},
   Pages = {3994-3998},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1109/ICASSP.2018.8461443},
   Abstract = {© 2018 IEEE. In this work, we propose a new inference
             procedure for understanding non-stationary processes, under
             the framework of evolutionary spectra developed by
             Priestley. Among various frameworks of modeling
             non-stationary processes, the distinguishing feature of the
             evolutionary spectra is its focus on the physical meaning of
             frequency. The classical estimate of the evolutionary
             spectral density is based on a double-window technique
             consisting of a short-Fourier transform and a smoothing.
             However, smoothing is known to suffer from the so-called
             bias leakage problem. By incorporating Thomson's multitaper
             method that was originally designed for stationary
             processes, we propose an improved estimate of the
             evolutionary spectral density, and analyze its
             bias/variance/resolution tradeoff. As an application of the
             new estimate, we further propose a non-parametric rank-based
             stationarity test, and provide various experimental
             studies.},
   Doi = {10.1109/ICASSP.2018.8461443},
   Key = {fds339264}
}

@article{fds338434,
   Author = {Banerjee, T and Whipps, G and Gurram, P and Tarokh,
             V},
   Title = {Sequential Event Detection Using Multimodal Data in
             Nonstationary Environments},
   Journal = {2018 21st International Conference on Information Fusion,
             Fusion 2018},
   Pages = {1940-1947},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.23919/ICIF.2018.8455835},
   Abstract = {© 2018 ISIF The problem of sequential detection of
             anomalies in multimodal data is considered. The objective is
             to observe physical sensor data from CCTV cameras, and
             social media data from Twitter and Instagram to detect
             anomalous behaviors or events. Data from each modality is
             transformed to discrete time count data by using an
             artificial neural network to obtain counts of objects in
             CCTV images and by counting the number of tweets or
             Instagram posts in a geographical area. The anomaly
             detection problem is then formulated as a problem of
             quickest detection of changes in count statistics. The
             quickest detection problem is then solved using the
             framework of partially observable Markov decision processes
             (POMDP), and structural results on the optimal policy are
             obtained. The resulting optimal policy is then applied to
             real multimodal data collected from New York City around a
             5K race to detect the race. The count data both before and
             after the change is found to be nonstationary in nature. The
             proposed mathematical approach to this problem provides a
             framework for event detection in such nonstationary
             environments and across multiple data modalities.},
   Doi = {10.23919/ICIF.2018.8455835},
   Key = {fds338434}
}

@article{fds338435,
   Author = {Banerjee, T and Choi, J and Pesaran, B and Ba, D and Tarokh,
             V},
   Title = {Classification of Local Field Potentials using Gaussian
             Sequence Model},
   Journal = {2018 Ieee Statistical Signal Processing Workshop, Ssp
             2018},
   Pages = {218-222},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1109/SSP.2018.8450778},
   Abstract = {© 2018 IEEE. A problem of classification of local field
             potentials (LFPs), recorded from the prefrontal cortex of a
             macaque monkey, is considered. An adult macaque monkey is
             trained to perform a memory based saccade. The objective is
             to decode the eye movement goals from the LFP collected
             during a memory period. The LFP classification problem is
             modeled as that of classification of smooth functions
             embedded in Gaussian noise. It is then argued that using
             minimax function estimators as features would lead to
             consistent LFP classifiers. The theory of Gaussian sequence
             models allows us to represent minimax estimators as finite
             dimensional objects. The LFP classifier resulting from this
             mathematical endeavor is a spectrum based technique, where
             Fourier series coefficients of the LFP data, followed by
             appropriate shrinkage and thresholding, are used as features
             in a linear discriminant classifier. The classifier is then
             applied to the LFP data to achieve high decoding accuracy.
             The function classification approach taken in the paper also
             provides a systematic justification for using Fourier
             series, with shrinkage and thresholding, as features for the
             problem, as opposed to using the power spectrum. It also
             suggests that phase information is crucial to the decision
             making.},
   Doi = {10.1109/SSP.2018.8450778},
   Key = {fds338435}
}

@article{fds336637,
   Author = {Ding, J and Shahrampour, S and Heal, K and Tarokh,
             V},
   Title = {Analysis of Multistate Autoregressive Models},
   Journal = {Ieee Transactions on Signal Processing},
   Volume = {66},
   Number = {9},
   Pages = {2429-2440},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1109/TSP.2018.2811757},
   Doi = {10.1109/TSP.2018.2811757},
   Key = {fds336637}
}

@article{fds336660,
   Author = {Magnusson, S and Enyioha, C and Li, N and Fischione, C and Tarokh,
             V},
   Title = {Convergence of Limited Communication Gradient
             Methods},
   Journal = {Ieee Transactions on Automatic Control},
   Volume = {63},
   Number = {5},
   Pages = {1356-1371},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1109/TAC.2017.2743678},
   Doi = {10.1109/TAC.2017.2743678},
   Key = {fds336660}
}

@article{fds336638,
   Author = {Soloveychik, I and Xiang, Y and Tarokh, V},
   Title = {Pseudo-Wigner Matrices},
   Journal = {Ieee Transactions on Information Theory},
   Volume = {64},
   Number = {4},
   Pages = {3170-3178},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1109/TIT.2017.2777464},
   Doi = {10.1109/TIT.2017.2777464},
   Key = {fds336638}
}

@article{fds336639,
   Author = {Soloveychik, I and Xiang, Y and Tarokh, V},
   Title = {Symmetric Pseudo-Random Matrices},
   Journal = {Ieee Transactions on Information Theory},
   Volume = {64},
   Number = {4},
   Pages = {3179-3196},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1109/TIT.2018.2800004},
   Doi = {10.1109/TIT.2018.2800004},
   Key = {fds336639}
}

@article{fds336640,
   Author = {Ding, J and Zhou, J and Tarokh, V},
   Title = {Optimal prediction of data with unknown abrupt change
             points},
   Journal = {2017 Ieee Global Conference on Signal and Information
             Processing, Globalsip 2017 Proceedings},
   Volume = {2018-January},
   Pages = {928-932},
   Year = {2018},
   Month = {March},
   ISBN = {9781509059904},
   url = {http://dx.doi.org/10.1109/GlobalSIP.2017.8309096},
   Abstract = {© 2017 IEEE. We develop a novel methodology for predicting
             time series under unknown abrupt changes in data generating
             distributions. Based on Kolmogorov and Tikhomirov's e
             entropy, we propose a concept called e-predictability that
             quantifies the size of a model class and the maximal number
             of structural changes that allows the achievability of
             asymptotic optimal prediction. To predict under abrupt
             changes, our basic idea is to apply ϵ-net to discretize a
             nonparametric or parametric model class with an
             appropriately chosen e, and then apply a kinetic model
             averaging over the quantizers. Under reasonable assumptions,
             we prove that the average predictive performance is
             asymptotically as good as the oracle, i.e. when all the data
             generating distributions are known in advance. We show that
             the assumptions hold for a rather wide class of time
             variations. The results also address some puzzles related to
             the 'prediction-inference dilemma' in the context of change
             point analysis.},
   Doi = {10.1109/GlobalSIP.2017.8309096},
   Key = {fds336640}
}

@article{fds336641,
   Author = {DIng, J and Xiang, Y and Shen, L and Tarokh, V},
   Title = {Detecting structural changes in dependent
             data},
   Journal = {2017 Ieee Global Conference on Signal and Information
             Processing, Globalsip 2017 Proceedings},
   Volume = {2018-January},
   Pages = {750-754},
   Year = {2018},
   Month = {March},
   ISBN = {9781509059904},
   url = {http://dx.doi.org/10.1109/GlobalSIP.2017.8309060},
   Abstract = {© 2017 IEEE. In the era of big data, a frequently
             encountered task is to model and identify structural changes
             in the data generating process. It is quite challenging
             especially when data are dependent and massive, requiring
             computationally efficient analysis. To address the
             challenge, we model the data generating process as a
             segment-wise autoregression, and propose a multi-window
             method that is both effective and efficient for discovering
             the structural changes. The proposed approach was motivated
             by transforming a segment-wise autoregression into a
             multivariate time series that is asymptotically segment-wise
             independent and identically distributed. We then derive
             theoretical guarantees for (almost surely) selecting the
             true number of change points of segment-wise independent
             multivariate time series. In particular, we prove that a
             wide variety of penalized selection procedure produces a
             strongly consistent selection of the optimal number of
             change points, under mild assumptions. We demonstrate the
             theory and strength of the proposed algorithms by
             experiments on both synthetic and real-world
             data.},
   Doi = {10.1109/GlobalSIP.2017.8309060},
   Key = {fds336641}
}

@article{fds336642,
   Author = {Han, Q and Ding, J and Airoldi, E and Tarokh, V},
   Title = {Modeling nonlinearity in multi-dimensional dependent
             data},
   Journal = {2017 Ieee Global Conference on Signal and Information
             Processing, Globalsip 2017 Proceedings},
   Volume = {2018-January},
   Pages = {206-210},
   Year = {2018},
   Month = {March},
   ISBN = {9781509059904},
   url = {http://dx.doi.org/10.1109/GlobalSIP.2017.8308633},
   Abstract = {© 2017 IEEE. Given massive data that may be time dependent
             and multi-dimensional, how to efficiently explore the
             underlying functional relationships across different
             dimensions and time lags? In this work, we propose a
             methodology to sequentially and adaptively model nonlinear
             multivariate time series data. Data at each time step and
             dimension is modeled as a nonlinear function of past values
             corrupted by noise, and the underlying nonlinear function is
             assumed to be approximately expandable in a spline basis. We
             cast the modeling of data as finding a good fit
             representation in the linear span of multi-dimensional
             spline basis, and use a variant of h-penalty regularization
             in order to reduce the dimensionality of representation.
             Using adaptive filtering techniques, we design our online
             algorithm to automatically tune the underlying parameters
             based on the minimization of the regularized sequential
             prediction error. We demonstrate the generality and
             flexibility of the proposed approach on both synthetic and
             real-world datasets. Moreover, we analytically investigate
             the performance of our algorithm by obtaining bounds of the
             prediction errors.},
   Doi = {10.1109/GlobalSIP.2017.8308633},
   Key = {fds336642}
}

@article{fds336643,
   Author = {Soloveychik, I and Xiang, Y and Tarokh, V},
   Title = {Explicit symmetric pseudo-random matrices},
   Journal = {Ieee International Symposium on Information Theory
             Proceedings},
   Volume = {2018-January},
   Pages = {424-428},
   Year = {2018},
   Month = {January},
   ISBN = {9781509030972},
   url = {http://dx.doi.org/10.1109/ITW.2017.8277999},
   Abstract = {© 2017 IEEE. We consider the problem of generating
             symmetric pseudo-random sign (±1) matrices based on the
             similarity of their spectra to Wigner's semicircular law.
             Using binary m-sequences (Golomb sequences) of lengths n =
             2m- 1, we give a simple explicit construction of circulant n
             × n sign matrices and show that their spectra converge to
             the semicircular law when n grows. The Kolmogorov complexity
             of the proposed matrices equals to that of Golomb sequences
             and is at most 2log2(n) bits.},
   Doi = {10.1109/ITW.2017.8277999},
   Key = {fds336643}
}

@article{fds336644,
   Author = {Shahrampour, S and Tarokh, V},
   Title = {Nonlinear sequential accepts and rejects for identification
             of top arms in stochastic bandits},
   Journal = {55th Annual Allerton Conference on Communication, Control,
             and Computing, Allerton 2017},
   Volume = {2018-January},
   Pages = {228-235},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1109/ALLERTON.2017.8262742},
   Abstract = {© 2017 IEEE. We address the M-best-Arm identification
             problem in multi-Armed bandits. A player has a limited
             budget to explore K arms (M < K), and once pulled, each arm
             yields a reward drawn (independently) from a fixed, unknown
             distribution. The goal is to find the top M arms in the
             sense of expected reward. We develop an algorithm which
             proceeds in rounds to deactivate arms iteratively. At each
             round, the budget is divided by a nonlinear function of
             remaining arms, and the arms are pulled correspondingly.
             Based on a decision rule, the deactivated arm at each round
             may be accepted or rejected. The algorithm outputs the
             accepted arms that should ideally be the top M arms. We
             characterize the decay rate of the misidentification
             probability and establish that the nonlinear budget
             allocation proves to be useful for different problem
             environments (described by the number of competitive arms).
             We provide comprehensive numerical experiments showing that
             our algorithm outperforms the state-of-The-Art using
             suitable nonlinearity.},
   Doi = {10.1109/ALLERTON.2017.8262742},
   Key = {fds336644}
}

@article{fds336645,
   Author = {Soloveychik, I and Tarokh, V and Paulson, JA},
   Title = {On the spectral norms of pseudo-wigner and related
             matrices},
   Journal = {55th Annual Allerton Conference on Communication, Control,
             and Computing, Allerton 2017},
   Volume = {2018-January},
   Pages = {61-66},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1109/ALLERTON.2017.8262719},
   Abstract = {© 2017 IEEE. We investigate the spectral norms of symmetric
             N × N matrices from two pseudo-random ensembles. The first
             is the pseudo-Wigner ensemble introduced in 'Pseudo-Wigner
             Matrices' by Soloveychik, Xiang and Tarokh and the second is
             its sample covariance-Type analog defined in this work. Both
             ensembles are defined through the concept of r-independence
             by controlling the amount of randomness in the underlying
             matrices, and can be constructed from dual BCH codes. We
             show that when the measure of randomness r grows as Np,
             where p (0,1] and ϵ > 0, the norm of the matrices is almost
             surely within o(log1 + ϵN/Nmin[ρ, 2/3]) distance from 1.
             Numerical simulations verifying the obtained results are
             provided.},
   Doi = {10.1109/ALLERTON.2017.8262719},
   Key = {fds336645}
}

@article{fds336662,
   Author = {Enyioha, C and Magnusson, S and Heal, K and Li, N and Fischione, C and Tarokh, V},
   Title = {On Variability of Renewable Energy and Online Power
             Allocation},
   Journal = {Ieee Transactions on Power Systems},
   Volume = {33},
   Number = {1},
   Pages = {451-462},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1109/TPWRS.2017.2709544},
   Doi = {10.1109/TPWRS.2017.2709544},
   Key = {fds336662}
}

@article{fds339923,
   Author = {Ding, J and Zhou, J and Tarokh, V},
   Title = {Asymptotically Optimal Prediction for Time-Varying Data
             Generating Processes},
   Journal = {Ieee Transactions on Information Theory},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1109/TIT.2018.2882819},
   Abstract = {IEEE We develop a methodology (referred to as kinetic
             prediction) for predicting time series undergoing unknown
             changes in their data generating distributions. Based on
             Kolmogorov-Tikhomirov&#x2019;s &#x03B5;-entropy, we propose
             a concept called "-predictability that quantifies the size
             of a model class (which can be parametric or nonparametric)
             and the maximal number of abrupt structural changes that
             guarantee the achievability of asymptotically optimal
             prediction. Moreover, for parametric distribution families,
             we extend the aforementioned kinetic prediction with
             discretized function spaces to its counterpart with
             continuous function spaces, and propose a sequential Monte
             Carlo based implementation. We also extend our methodology
             for predicting smoothly varying data generating
             distributions. Under reasonable assumptions, we prove that
             the average predictive performance converges almost surely
             to the oracle bound, which corresponds to the case that the
             data generating distributions are known in advance. The
             results also shed some light on the so called
             &#x201C;prediction-inference dilemma&#x201D;. Various
             examples and numerical results are provided to demonstrate
             the wide applicability of our methodology.},
   Doi = {10.1109/TIT.2018.2882819},
   Key = {fds339923}
}

@article{fds336646,
   Author = {Magnusson, S and Enyioha, C and Li, N and Fichione, C and Tarokh,
             V},
   Title = {Communication Complexity of Dual Decomposition Methods for
             Distributed Resource Allocation Optimization},
   Journal = {Ieee Journal of Selected Topics in Signal
             Processing},
   Pages = {1-1},
   Year = {2018},
   url = {http://dx.doi.org/10.1109/JSTSP.2018.2848718},
   Doi = {10.1109/JSTSP.2018.2848718},
   Key = {fds336646}
}

@article{fds339985,
   Author = {Magnússon, S and Enyioha, C and Li, N and Fischione, C and Tarokh,
             V},
   Title = {Convergence of Limited Communication Gradient
             Methods.},
   Journal = {Ieee Trans. Automat. Contr.},
   Volume = {63},
   Pages = {1356-1371},
   Year = {2018},
   Key = {fds339985}
}

@article{fds339989,
   Author = {Banerjee, T and Whipps, GT and Gurram, P and Tarokh,
             V},
   Title = {Cyclostationary Statistical Models and Algorithms for
             Anomaly Detection Using Multi-Modal Data.},
   Journal = {Corr},
   Volume = {abs/1807.06945},
   Year = {2018},
   Key = {fds339989}
}

@article{fds339991,
   Author = {Banerjee, T and Choi, JS and Pesaran, B and Ba, D and Tarokh,
             V},
   Title = {Classification of Local Field Potentials using Gaussian
             Sequence Model.},
   Journal = {Ssp},
   Pages = {683-687},
   Publisher = {IEEE},
   Year = {2018},
   ISBN = {978-1-5386-1571-3},
   Key = {fds339991}
}

@article{fds339992,
   Author = {Banerjee, T and Whipps, GT and Gurram, P and Tarokh,
             V},
   Title = {Sequential Event Detection Using Multimodal Data in
             Nonstationary Environments.},
   Journal = {Fusion},
   Pages = {1940-1947},
   Publisher = {IEEE},
   Year = {2018},
   ISBN = {978-0-9964527-6-2},
   Key = {fds339992}
}

@article{fds339990,
   Author = {Magnússon, S and Enyioha, C and Li, N and Fischione, C and Tarokh,
             V},
   Title = {Communication Complexity of Dual Decomposition Methods for
             Distributed Resource Allocation Optimization.},
   Journal = {J. Sel. Topics Signal Processing},
   Volume = {12},
   Pages = {717-732},
   Year = {2018},
   Key = {fds339990}
}

@article{fds339986,
   Author = {Shahrampour, S and Beirami, A and Tarokh, V},
   Title = {On Data-Dependent Random Features for Improved
             Generalization in Supervised Learning.},
   Journal = {Aaai},
   Pages = {4026-4033},
   Publisher = {AAAI Press},
   Editor = {McIlraith, SA and Weinberger, KQ},
   Year = {2018},
   Key = {fds339986}
}

@article{fds339987,
   Author = {Soloveychik, I and Tarokh, V},
   Title = {Stationary Geometric Graphical Model Selection.},
   Journal = {Corr},
   Volume = {abs/1806.03571},
   Year = {2018},
   Key = {fds339987}
}

@article{fds339988,
   Author = {Ding, J and Tarokh, V and Yang, J-Y},
   Title = {Bridging AIC and BIC: A New Criterion for
             Autoregression.},
   Journal = {Ieee Trans. Information Theory},
   Volume = {64},
   Pages = {4024-4043},
   Year = {2018},
   Key = {fds339988}
}

@article{fds336647,
   Author = {Han, Q and Ding, J and Airoldi, EM and Tarokh, V},
   Title = {SLANTS: Sequential Adaptive Nonlinear Modeling of Time
             Series},
   Journal = {Ieee Transactions on Signal Processing},
   Volume = {65},
   Number = {19},
   Pages = {4994-5005},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1109/TSP.2017.2716898},
   Doi = {10.1109/TSP.2017.2716898},
   Key = {fds336647}
}

@article{fds339993,
   Author = {Boyer, R and Babadi, B and Kalouptsidis, N and Tarokh,
             V},
   Title = {Asymptotic Achievability of the Cramer-Rao Bound for Noisy
             Compressive Sampling (vol 57, pg 1233, 2009)},
   Journal = {Ieee Transactions on Signal Processing},
   Volume = {65},
   Number = {18},
   Pages = {4973-4974},
   Publisher = {IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS
             INC},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1109/TSP.2017.2723352},
   Doi = {10.1109/TSP.2017.2723352},
   Key = {fds339993}
}

@article{fds336648,
   Author = {Ding, J and Xiang, Y and Shen, L and Tarokh, V},
   Title = {Multiple Change Point Analysis: Fast Implementation and
             Strong Consistency},
   Journal = {Ieee Transactions on Signal Processing},
   Volume = {65},
   Number = {17},
   Pages = {4495-4510},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1109/TSP.2017.2711558},
   Doi = {10.1109/TSP.2017.2711558},
   Key = {fds336648}
}

@article{fds336649,
   Author = {Shahrampour, S and Noshad, M and Tarokh, V},
   Title = {On Sequential Elimination Algorithms for Best-Arm
             Identification in Multi-Armed Bandits},
   Journal = {Ieee Transactions on Signal Processing},
   Volume = {65},
   Number = {16},
   Pages = {4281-4292},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1109/TSP.2017.2706192},
   Doi = {10.1109/TSP.2017.2706192},
   Key = {fds336649}
}

@article{fds336650,
   Author = {Deng, Z and Ding, J and Heal, K and Tarokh, V},
   Title = {The number of independent sets in hexagonal
             graphs},
   Journal = {Ieee International Symposium on Information Theory
             Proceedings},
   Pages = {2910-2914},
   Year = {2017},
   Month = {August},
   ISBN = {9781509040964},
   url = {http://dx.doi.org/10.1109/ISIT.2017.8007062},
   Abstract = {© 2017 IEEE. We derive the tightest known bounds on η =
             2ν, where ν is the growth rate of the logarithm of the
             number of independent sets on a hexagonal lattice. To obtain
             these bounds, we generalize a method proposed by Calkin and
             Wilf. Their original strategy cannot immediately be used to
             derive bounds for η, due to the difference in symmetry
             between square and hexagonal lattices, so we propose a
             modified method and an algorithm to derive rigorous bounds
             on η. In particular, we prove that 1.546440708536001 ≤ η
             ≤ 1.5513, which improves upon the best known bounds of
             1.5463 ≤ η ≤ 1.5527 given by Nagy and Zeger. Our lower
             bound matches the numerical estimate of Baxter up to 9
             digits after the decimal point, and our upper bound can be
             further improved by following our method.},
   Doi = {10.1109/ISIT.2017.8007062},
   Key = {fds336650}
}

@article{fds336651,
   Author = {Soloveychik, I and Xiang, Y and Tarokh, V},
   Title = {Pseudo-wigner matrices from dual BCH codes},
   Journal = {Ieee International Symposium on Information Theory
             Proceedings},
   Pages = {1381-1385},
   Year = {2017},
   Month = {August},
   ISBN = {9781509040964},
   url = {http://dx.doi.org/10.1109/ISIT.2017.8006755},
   Abstract = {© 2017 IEEE. We consider the problem of generating
             symmetric pseudo-random sign (±1) matrices based on the
             similarity of their spectra to Wigner's semicircular law. We
             introduce r-independent pseudo-Wigner ensembles and prove
             closeness of their spectra to the semicircular density in
             Kolmogorov distance. We give an explicit construction of a
             family of N × N pseudo-Wigner ensembles using dual BCH
             codes and show that the Kolmogorov complexity of the
             obtained matrices is of the order of log (N) bits for a
             fixed Kolmogorov distance precision. Finally, we provide
             numerical simulations verifying our theoretical
             results.},
   Doi = {10.1109/ISIT.2017.8006755},
   Key = {fds336651}
}

@article{fds336652,
   Author = {Jeong, S and Kang, J and Pahlavan, K and Tarokh, V},
   Title = {Fundamental Limits of TOA/DOA and Inertial Measurement
             Unit-Based Wireless Capsule Endoscopy Hybrid
             Localization},
   Journal = {International Journal of Wireless Information
             Networks},
   Volume = {24},
   Number = {2},
   Pages = {169-179},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1007/s10776-017-0342-7},
   Doi = {10.1007/s10776-017-0342-7},
   Key = {fds336652}
}

@article{fds339994,
   Author = {Farhadi, H and Xiang, Y and Jeong, S and Li, X and Guo, N and Sepulcre, J and Tarokh, V and Li, Q},
   Title = {Inferring the causality network of Abeta and Tau
             accumulation in the aging brain: a statistical inference
             approach},
   Journal = {Journal of Nuclear Medicine : Official Publication, Society
             of Nuclear Medicine},
   Volume = {58},
   Pages = {2 pages},
   Publisher = {SOC NUCLEAR MEDICINE INC},
   Year = {2017},
   Month = {May},
   Key = {fds339994}
}

@article{fds336653,
   Author = {Wei, L and Sarwate, AD and Corander, J and Hero, A and Tarokh,
             V},
   Title = {Analysis of a privacy-preserving PCA algorithm using random
             matrix theory},
   Journal = {2016 Ieee Global Conference on Signal and Information
             Processing, Globalsip 2016 Proceedings},
   Pages = {1335-1339},
   Year = {2017},
   Month = {April},
   ISBN = {9781509045457},
   url = {http://dx.doi.org/10.1109/GlobalSIP.2016.7906058},
   Abstract = {© 2016 IEEE. To generate useful summarization of data while
             maintaining privacy of sensitive information is a
             challenging task, especially in the big data era. The
             privacy-preserving principal component algorithm proposed in
             [1] is a promising approach when a low rank data
             summarization is desired. However, the analysis in [1] is
             limited to the case of a single principal component, which
             makes use of bounds on the vector-valued Bingham
             distribution in the unit sphere. By exploring the
             non-commutative structure of data matrices in the full
             Stiefel manifold, we extend the analysis to an arbitrary
             number of principal components. Our results are obtained by
             analyzing the asymptotic behavior of the matrix-variate
             Bingham distribution using tools from random matrix
             theory.},
   Doi = {10.1109/GlobalSIP.2016.7906058},
   Key = {fds336653}
}

@article{fds336654,
   Author = {Enyioha, C and Magnússon, S and Heal, K and Li, N and Fischione, C and Tarokh, V},
   Title = {Robustness analysis for an online decentralized descent
             power allocation algorithm},
   Journal = {2016 Information Theory and Applications Workshop, Ita
             2016},
   Year = {2017},
   Month = {March},
   ISBN = {9781509025299},
   url = {http://dx.doi.org/10.1109/ITA.2016.7888135},
   Abstract = {© 2016 IEEE. As independent service providers shift from
             conventional energy to renewable energy sources, the power
             distribution system will likely experience increasingly
             significant fluctuation in supply, given the uncertain and
             intermittent nature of renewable sources like wind and solar
             energy. These fluctuations in power generation, coupled with
             time-varying consumer demands of electricity and the massive
             scale of power distribution networks present the need to not
             only design real-time decentralized power allocation
             algorithms, but also characterize how effective they are
             given fast-changing consumer demands and power generation
             capacities. In this paper, we present an Online
             Decentralized Dual Descent (OD3) power allocation algorithm
             and determine (in the worst case) how much of observed
             social welfare and price volatility can be explained by
             fluctuations in generation capacity and consumer demand.
             Convergence properties and performance guarantees of the OD3
             algorithm are analyzed by characterizing the difference
             between the online decision and the optimal decision. The
             theoretical results in the paper are validated and
             illustrated by numerical experiments using real
             data.},
   Doi = {10.1109/ITA.2016.7888135},
   Key = {fds336654}
}

@article{fds336655,
   Author = {Kuiper, PK and Kolitz, SE and Tarokh, V},
   Title = {Base camp quality of life standardization and
             improvement},
   Journal = {Proceedings International Carnahan Conference on Security
             Technology},
   Year = {2017},
   Month = {January},
   ISBN = {9781509010707},
   url = {http://dx.doi.org/10.1109/CCST.2016.7815688},
   Abstract = {© 2016 IEEE. The United States (US) Army has over 66,000
             soldiers engaged in contingency operations across the world.
             Current budgetary constraints and an uncertain global
             security environment require these operations to be executed
             as efficiently as possible. Base camps are the secured areas
             where soldiers live when deployed to contingency operations.
             Base camps impose a significant financial and tactical
             burden during contingency operations and sub-optimal soldier
             quality of life decisions have significantly contributed to
             costs. Quality of life (QOL) refers to the non-security and
             non-mission related services that directly sustain the
             mission effectiveness of soldiers. Current US Army base camp
             tactics, techniques, and procedures (TTPs) do not
             sufficiently specify QOL services, and more detailed
             doctrine should be developed to support combat units
             executing contingency operations. In this investigation we
             employ quantitative methods to select decisions that improve
             QOL and inform doctrine. We leverage a QOL function and
             resource consumption data developed by US Army Natick
             Soldier Research, Development and Engineering Center's
             (Natick Labs) to build a model that improves QOL under the
             constraints of four fundamental resources: fuel, water,
             waste water, and solid waste. We employ a mixed integer
             linear program modeling approach and execute sensitivity
             analysis to evaluate the strength of our results. Our final
             model is formulated as a chance constraint optimization to
             address the uncertainty associated with resource
             availability in contingency operations. Our results provide
             QOL decisions that reduce resource consumption while
             maintaining an equivalent QOL level when compared to current
             TTPs. The model provides quantitative rigor, informing
             decision makers of specific base camp design principles for
             the development of doctrine.},
   Doi = {10.1109/CCST.2016.7815688},
   Key = {fds336655}
}

@article{fds336656,
   Author = {Kurien, BG and Ashcom, JB and Shah, VN and Rachlin, Y and Tarokh,
             V},
   Title = {Robust interferometric imaging via prior-less phase
             recovery: redundant spacing calibration with
             generalized-closure phases},
   Journal = {Monthly Notices of the Royal Astronomical
             Society},
   Volume = {464},
   Number = {2},
   Pages = {2356-2376},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1093/mnras/stw2323},
   Doi = {10.1093/mnras/stw2323},
   Key = {fds336656}
}

@article{fds336657,
   Author = {Jeong, S and Li, X and Yang, J and Li, Q and Tarokh,
             V},
   Title = {Dictionary learning and sparse coding-based denoising for
             high-resolution task functional connectivity MRI
             analysis},
   Journal = {Lecture Notes in Computer Science (Including Subseries
             Lecture Notes in Artificial Intelligence and Lecture Notes
             in Bioinformatics)},
   Volume = {10541 LNCS},
   Pages = {45-52},
   Year = {2017},
   Month = {January},
   ISBN = {9783319673882},
   url = {http://dx.doi.org/10.1007/978-3-319-67389-9_6},
   Abstract = {© 2017, Springer International Publishing AG. We propose a
             novel denoising framework for task functional Magnetic
             Resonance Imaging (tfMRI) data to delineate the
             high-resolution spatial pattern of the brain functional
             connectivity via dictionary learning and sparse coding
             (DLSC). In order to address the limitations of the
             unsupervised DLSC-based fMRI studies, we utilize the prior
             knowledge of task paradigm in the learning step to train a
             data-driven dictionary and to model the sparse
             representation. We apply the proposed DLSC-based method to
             Human Connectome Project (HCP) motor tfMRI dataset. Studies
             on the functional connectivity of cerebrocerebellar circuits
             in somatomotor networks show that the DLSC-based denoising
             framework can significantly improve the prominent
             connectivity patterns, in comparison to the temporal
             non-local means (tNLM)-based denoising method as well as the
             case without denoising, which is consistent and
             neuroscientifically meaningful within motor area. The
             promising results show that the proposed method can provide
             an important foundation for the high-resolution functional
             connectivity analysis, and provide a better approach for
             fMRI preprocessing.},
   Doi = {10.1007/978-3-319-67389-9_6},
   Key = {fds336657}
}

@article{fds336658,
   Author = {Beirami, A and Razaviyayn, M and Shahrampour, S and Tarokh,
             V},
   Title = {On optimal generalizability in parametric
             learning},
   Journal = {Advances in Neural Information Processing
             Systems},
   Volume = {2017-December},
   Pages = {3456-3466},
   Year = {2017},
   Month = {January},
   Abstract = {© 2017 Neural information processing systems foundation.
             All rights reserved. We consider the parametric learning
             problem, where the objective of the learner is determined by
             a parametric loss function. Employing empirical risk
             minimization with possibly regularization, the inferred
             parameter vector will be biased toward the training samples.
             Such bias is measured by the cross validation procedure in
             practice where the data set is partitioned into a training
             set used for training and a validation set, which is not
             used in training and is left to measure the outof-sample
             performance. A classical cross validation strategy is the
             leave-one-out cross validation (LOOCV) where one sample is
             left out for validation and training is done on the rest of
             the samples that are presented to the learner, and this
             process is repeated on all of the samples. LOOCV is rarely
             used in practice due to the high computational complexity.
             In this paper, we first develop a computationally efficient
             approximate LOOCV (ALOOCV) and provide theoretical
             guarantees for its performance. Then we use ALOOCV to
             provide an optimization algorithm for finding the
             regularizer in the empirical risk minimization framework. In
             our numerical experiments, we illustrate the accuracy and
             efficiency of ALOOCV as well as our proposed framework for
             the optimization of the regularizer.},
   Key = {fds336658}
}

@article{fds336659,
   Author = {Shahrampour, S and Noshad, M and Ding, J and Tarokh,
             V},
   Title = {Online Learning for Multimodal Data Fusion with Application
             to Object Recognition},
   Journal = {Ieee Transactions on Circuits and Systems Ii: Express
             Briefs},
   Volume = {65-II},
   Pages = {1-1},
   Year = {2017},
   url = {http://dx.doi.org/10.1109/TCSII.2017.2754141},
   Doi = {10.1109/TCSII.2017.2754141},
   Key = {fds336659}
}

@article{fds339996,
   Author = {Shahrampour, S and Beirami, A and Tarokh, V},
   Title = {On Data-Dependent Random Features for Improved
             Generalization in Supervised Learning.},
   Journal = {Corr},
   Volume = {abs/1712.07102},
   Year = {2017},
   Key = {fds339996}
}

@article{fds339995,
   Author = {Beirami, A and Razaviyayn, M and Shahrampour, S and Tarokh,
             V},
   Title = {On Optimal Generalizability in Parametric
             Learning.},
   Journal = {Nips},
   Pages = {3458-3468},
   Editor = {Guyon, I and Luxburg, UV and Bengio, S and Wallach, HM and Fergus, R and Vishwanathan, SVN and Garnett, R},
   Year = {2017},
   Key = {fds339995}
}

@article{fds339997,
   Author = {Soloveychik, I and Xiang, Y and Tarokh, V},
   Title = {Pseudo-Wigner Matrices from Dual BCH Codes.},
   Journal = {Corr},
   Volume = {abs/1701.05544},
   Year = {2017},
   Key = {fds339997}
}

@article{fds339998,
   Author = {Deng, Z and Ding, J and Heal, K and Tarokh, V},
   Title = {The number of independent sets in hexagonal
             graphs.},
   Journal = {Isit},
   Pages = {2910-2914},
   Publisher = {IEEE},
   Year = {2017},
   ISBN = {978-1-5090-4096-4},
   Key = {fds339998}
}

@article{fds339999,
   Author = {Jeong, S and Li, X and Yang, J and Li, Q and Tarokh,
             V},
   Title = {Dictionary Learning and Sparse Coding-Based Denoising for
             High-Resolution Task Functional Connectivity MRI
             Analysis.},
   Journal = {Mlmi@Miccai},
   Volume = {10541},
   Pages = {45-52},
   Publisher = {SPRINGER},
   Editor = {Wang, Q and Shi, Y and Suk, H-I and Suzuki, K},
   Year = {2017},
   ISBN = {978-3-319-67388-2},
   Key = {fds339999}
}

@article{fds340000,
   Author = {Boyer, R and Babadi, B and Kalouptsidis, N and Tarokh,
             V},
   Title = {Corrections to "Asymptotic Achievability of the Cramér-Rao
             Bound for Noisy Compressive Sampling".},
   Journal = {Ieee Trans. Signal Processing},
   Volume = {65},
   Pages = {4973-4974},
   Year = {2017},
   Key = {fds340000}
}

@article{fds340001,
   Author = {Shahrampour, S and Tarokh, V},
   Title = {Nonlinear Sequential Accepts and Rejects for Identification
             of Top Arms in Stochastic Bandits.},
   Journal = {Corr},
   Volume = {abs/1707.02649},
   Year = {2017},
   Key = {fds340001}
}


%% Tralie, Christopher   
@article{fds330205,
   Author = {Tralie, CJ and Smith, A and Borggren, N and Hineman, J and Bendich, P and Zulch, P and Harer, J},
   Title = {Geometric Cross-Modal Comparison of Heterogeneous Sensor
             Data},
   Journal = {Proceedings of the 39th Ieee Aerospace Conference},
   Year = {2018},
   Month = {March},
   Abstract = {In this work, we address the problem of cross-modal
             comparison of aerial data streams. A variety of simulated
             automobile trajectories are sensed using two different
             modalities: full-motion video, and radio-frequency (RF)
             signals received by detectors at various locations. The
             information represented by the two modalities is compared
             using self-similarity matrices (SSMs) corresponding to
             time-ordered point clouds in feature spaces of each of these
             data sources; we note that these feature spaces can be of
             entirely different scale and dimensionality. Several metrics
             for comparing SSMs are explored, including a cutting-edge
             time-warping technique that can simultaneously handle local
             time warping and partial matches, while also controlling for
             the change in geometry between feature spaces of the two
             modalities. We note that this technique is quite general,
             and does not depend on the choice of modalities. In this
             particular setting, we demonstrate that the cross-modal
             distance between SSMs corresponding to the same trajectory
             type is smaller than the cross-modal distance between SSMs
             corresponding to distinct trajectory types, and we formalize
             this observation via precision-recall metrics in
             experiments. Finally, we comment on promising implications
             of these ideas for future integration into
             multiple-hypothesis tracking systems.},
   Key = {fds330205}
}

@article{fds330395,
   Author = {Tralie, CJ},
   Title = {Self-Similarity Based Time Warping},
   Year = {2017},
   Month = {November},
   Abstract = {In this work, we explore the problem of aligning two
             time-ordered point clouds which are spatially transformed
             and re-parameterized versions of each other. This has a
             diverse array of applications such as cross modal time
             series synchronization (e.g. MOCAP to video) and alignment
             of discretized curves in images. Most other works that
             address this problem attempt to jointly uncover a spatial
             alignment and correspondences between the two point clouds,
             or to derive local invariants to spatial transformations
             such as curvature before computing correspondences. By
             contrast, we sidestep spatial alignment completely by using
             self-similarity matrices (SSMs) as a proxy to the
             time-ordered point clouds, since self-similarity matrices
             are blind to isometries and respect global geometry. Our
             algorithm, dubbed "Isometry Blind Dynamic Time Warping"
             (IBDTW), is simple and general, and we show that its
             associated dissimilarity measure lower bounds the L1
             Gromov-Hausdorff distance between the two point sets when
             restricted to warping paths. We also present a local,
             partial alignment extension of IBDTW based on the Smith
             Waterman algorithm. This eliminates the need for tedious
             manual cropping of time series, which is ordinarily
             necessary for global alignment algorithms to function
             properly.},
   Key = {fds330395}
}

@article{fds330396,
   Author = {Tralie, C},
   Title = {Moebius Beats: The Twisted Spaces of Sliding Window Audio
             Novelty Functions with Rhythmic Subdivisions},
   Year = {2017},
   Month = {November},
   Abstract = {In this work, we show that the sliding window embeddings of
             certain audio novelty functions (ANFs) representing songs
             with rhythmic subdivisions concentrate on the boundary of
             non-orientable surfaces such as the Moebius strip. This
             insight provides a radically different topological approach
             to classifying types of rhythm hierarchies. In particular,
             we use tools from topological data analysis (TDA) to detect
             subdivisions, and we use thresholds derived from TDA to
             build graphs at different scales. The Laplacian eigenvectors
             of these graphs contain information which can be used to
             estimate tempos of the subdivisions. We show a proof of
             concept example on an audio snippet from the MIREX tempo
             training dataset, and we hope in future work to find a place
             for this in other MIR pipelines.},
   Key = {fds330396}
}

@article{fds330206,
   Author = {Tralie, CJ},
   Title = {Early MFCC And HPCP Fusion for Robust Cover Song
             Identification},
   Journal = {18th International Society for Music Information Retrieval
             (ISMIR)},
   Year = {2017},
   Month = {October},
   Abstract = {While most schemes for automatic cover song identification
             have focused on note-based features such as HPCP and chord
             profiles, a few recent papers surprisingly showed that local
             self-similarities of MFCC-based features also have
             classification power for this task. Since MFCC and HPCP
             capture complementary information, we design an unsupervised
             algorithm that combines normalized, beat-synchronous blocks
             of these features using cross-similarity fusion before
             attempting to locally align a pair of songs. As an added
             bonus, our scheme naturally incorporates structural
             information in each song to fill in alignment gaps where
             both feature sets fail. We show a striking jump in
             performance over MFCC and HPCP alone, achieving a state of
             the art mean reciprocal rank of 0.87 on the Covers80
             dataset. We also introduce a new medium-sized hand designed
             benchmark dataset called "Covers 1000," which consists of
             395 cliques of cover songs for a total of 1000 songs, and we
             show that our algorithm achieves an MRR of 0.9 on this
             dataset for the first correctly identified song in a clique.
             We provide the precomputed HPCP and MFCC features, as well
             as beat intervals, for all songs in the Covers 1000 dataset
             for use in further research.},
   Key = {fds330206}
}

@article{fds330397,
   Author = {Tralie, CJ and Perea, JA},
   Title = {(Quasi)Periodicity Quantification in Video Data, Using
             Topology},
   Volume = {11},
   Number = {2},
   Pages = {1049-1077},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1137/17M1150736},
   Abstract = {This work introduces a novel framework for quantifying the
             presence and strength of recurrent dynamics in video data.
             Specifically, we provide continuous measures of periodicity
             (perfect repetition) and quasiperiodicity (superposition of
             periodic modes with non-commensurate periods), in a way
             which does not require segmentation, training, object
             tracking or 1-dimensional surrogate signals. Our methodology
             operates directly on video data. The approach combines ideas
             from nonlinear time series analysis (delay embeddings) and
             computational topology (persistent homology), by translating
             the problem of finding recurrent dynamics in video data,
             into the problem of determining the circularity or
             toroidality of an associated geometric space. Through
             extensive testing, we show the robustness of our scores with
             respect to several noise models/levels; we show that our
             periodicity score is superior to other methods when compared
             to human-generated periodicity rankings; and furthermore, we
             show that our quasiperiodicity score clearly indicates the
             presence of biphonation in videos of vibrating vocal
             folds.},
   Doi = {10.1137/17M1150736},
   Key = {fds330397}
}


%% Turnage-Butterbaugh, Caroline   
@article{fds330816,
   Author = {Conrey, JB and Turnage-Butterbaugh, CL},
   Title = {On r-gaps between zeros of the Riemann zeta-function},
   Journal = {Bulletin of the London Mathematical Society},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1112/blms.12142},
   Abstract = {© 2018 London Mathematical Society. Under the Riemann
             Hypothesis, we prove for any natural number r there exist
             infinitely many natural numbers n such that
             (γn+r-γn)/(2πr/logγn) > 1+Θ/r and (γn+r-γn)/(2πr/logγn)
             < 1-θ/r for explicit absolute positive constants Θ and θ,
             where γ denotes an ordinate of a zero of the Riemann
             zeta-function on the critical line. Selberg published
             announcements of this result several times without
             proof.},
   Doi = {10.1112/blms.12142},
   Key = {fds330816}
}

@article{fds330817,
   Author = {Best, A and Dynes, P and Edelsbrunner, X and McDonald, B and Miller, SJ and Tor, K and Turnage-Butterbaugh, C and Weinstein,
             M},
   Title = {Benford Behavior of Generalized Zeckendorf
             Decompositions},
   Journal = {Springer Proceedings in Mathematics and Statistics},
   Volume = {220},
   Pages = {25-37},
   Publisher = {Springer},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1007/978-3-319-68032-3_3},
   Abstract = {© Springer International Publishing AG 2017. We prove
             connections between Zeckendorf decompositions and
             Benford’s law. Recall that if we define the Fibonacci
             numbers by F 1 = 1, F 2 = 2, and F n+1 = F n + F n−1 ,
             every positive integer can be written uniquely as a sum of
             nonadjacent elements of this sequence; this is called the
             Zeckendorf decomposition, and similar unique decompositions
             exist for sequences arising from recurrence relations of the
             form G n+1 = c 1 G n + … + c L G n+1−L with c i positive
             and some other restrictions. Additionally, a set S ⊂ ℤ
             is said to satisfy Benford’s law base 10 if the density of
             the elements in S with leading digit d is (Formula
             presented); in other words, smaller leading digits are more
             likely to occur. We prove that as n → ∞ for a randomly
             selected integer m in [0, G n+1 ) the distribution of the
             leading digits of the summands in its generalized Zeckendorf
             decomposition converges to Benford’s law almost surely.
             Our results hold more generally: One obtains similar
             theorems to those regarding the distribution of leading
             digits when considering how often values in sets with
             density are attained in the summands in the
             decompositions.},
   Doi = {10.1007/978-3-319-68032-3_3},
   Key = {fds330817}
}

@article{fds330335,
   Author = {Pierce, LB and Turnage-Butterbaugh, CL and Wood,
             MM},
   Title = {An effective Chebotarev density theorem for families of
             number fields, with an application to $\ell$-torsion in
             class groups},
   Journal = {(submitted)},
   Year = {2017},
   Abstract = {An effective Chebotarev density theorem for a fixed normal
             extension $L/\mathbb{Q}$ provides an asymptotic, with an
             explicit error term, for the number of primes of bounded
             size with a prescribed splitting type in $L$. In many
             applications one is most interested in the case where the
             primes are small (with respect to the absolute discriminant
             of $L$); this is well-known to be closely related to the
             Generalized Riemann Hypothesis for the Dedekind zeta
             function of $L$. In this work we prove a new effective
             Chebotarev density theorem, independent of GRH, that
             improves the previously known unconditional error term and
             allows primes to be taken quite small (certainly as small as
             an arbitrarily small power of the discriminant of $L$); this
             theorem holds for the Galois closures of "almost all" number
             fields that lie in an appropriate family of field
             extensions. Such a family has fixed degree, fixed Galois
             group of the Galois closure, and in certain cases a
             ramification restriction on all tamely ramified primes in
             each field; examples include totally ramified cyclic fields,
             degree $n$ $S_n$-fields with square-free discriminant, and
             degree $n$ $A_n$-fields. In all cases, our work is
             independent of GRH; in some cases we assume the strong Artin
             conjecture or hypotheses on counting number fields. The new
             effective Chebotarev theorem is expected to have many
             applications, of which we demonstrate two. First we prove
             (for all integers $\ell \geq 1$) nontrivial bounds for
             $\ell$-torsion in the class groups of "almost all" fields in
             the families of fields we consider. This provides the first
             nontrivial upper bounds for $\ell$-torsion, for all integers
             $\ell \geq 1$, applicable to infinite families of fields of
             arbitrarily large degree. Second, in answer to a question of
             Ruppert, we prove that within each family, "almost all"
             fields have a small generator.},
   Key = {fds330335}
}


%% Vafaee, Faramarz   
@article{fds337464,
   Author = {Greene, JE and Lewallen, S and Vafaee, F},
   Title = {(1, 1) L-space knots},
   Journal = {Compositio Mathematica},
   Volume = {154},
   Number = {5},
   Pages = {918-933},
   Publisher = {CAMBRIDGE UNIV PRESS},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1112/S0010437X17007989},
   Abstract = {© The Authors 2018. We characterize the knots in the
             3-sphere and lens spaces that admit non-trivial L-space
             surgeries. As a corollary, 1-bridge braids in these
             manifolds admit non-trivial L-space surgeries. We also
             recover a characterization of the Berge manifold among
             1-bridge braid exteriors.},
   Doi = {10.1112/S0010437X17007989},
   Key = {fds337464}
}


%% Venakides, Stephanos   
@article{fds335545,
   Author = {Aristotelous, AC and Crawford, JM and Edwards, GS and Kiehart, DP and Venakides, S},
   Title = {Mathematical models of dorsal closure.},
   Journal = {Progress in Biophysics and Molecular Biology},
   Volume = {137},
   Pages = {111-131},
   Year = {2018},
   Month = {September},
   url = {http://dx.doi.org/10.1016/j.pbiomolbio.2018.05.009},
   Abstract = {Dorsal closure is a model cell sheet movement that occurs
             midway through Drosophila embryogenesis. A dorsal hole,
             filled with amnioserosa, closes through the dorsalward
             elongation of lateral epidermal cell sheets. Closure
             requires contributions from 5 distinct tissues and well over
             140 genes (see Mortensen et al., 2018, reviewed in Kiehart
             et al., 2017 and Hayes and Solon, 2017). In spite of this
             biological complexity, the movements (kinematics) of closure
             are geometrically simple at tissue, and in certain cases, at
             cellular scales. This simplicity has made closure the target
             of a number of mathematical models that seek to explain and
             quantify the processes that underlie closure's kinematics.
             The first (purely kinematic) modeling approach recapitulated
             well the time-evolving geometry of closure even though the
             underlying physical principles were not known. Almost all
             subsequent models delve into the forces of closure (i.e. the
             dynamics of closure). Models assign elastic, contractile and
             viscous forces which impact tissue and/or cell mechanics.
             They write rate equations which relate the forces to one
             another and to other variables, including those which
             represent geometric, kinematic, and or signaling
             characteristics. The time evolution of the variables is
             obtained by computing the solution of the model's system of
             equations, with optimized model parameters. The basis of the
             equations range from the phenomenological to biophysical
             first principles. We review various models and present their
             contribution to our understanding of the molecular
             mechanisms and biophysics of closure. Models of closure will
             contribute to our understanding of similar movements that
             characterize vertebrate morphogenesis.},
   Doi = {10.1016/j.pbiomolbio.2018.05.009},
   Key = {fds335545}
}

@article{fds330525,
   Author = {Perez-Arancibia, C and Shipman, S and Turc, C and Venakides,
             S},
   Title = {DDM solutions of quasiperiodic transmission problems in
             layered media via robust boundary integral equations at all
             frequencies},
   Year = {2017},
   Month = {December},
   Key = {fds330525}
}

@article{fds330399,
   Author = {Bruno, OP and Shipman, SP and Turc, C and Venakides,
             S},
   Title = {Three-dimensional quasi-periodic shifted Green function
             throughout the spectrum, including Wood anomalies},
   Journal = {Proceedings. Mathematical, Physical, and Engineering
             Sciences},
   Volume = {473},
   Number = {2207},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1098/rspa.2017.0242},
   Abstract = {© 2017 The Author(s) Published by the Royal Society. All
             rights reserved. This work, part II in a series, presents an
             efficient method for evaluation of wave scattering by doubly
             periodic diffraction gratings at or near what are commonly
             called ‘Wood anomaly frequencies’. At these frequencies,
             there is a grazing Rayleigh wave, and the quasi-periodic
             Green function ceases to exist. We present a modification of
             the Green function by adding two types of terms to its
             lattice sum. The first type are transversely shifted Green
             functions with coefficients that annihilate the growth in
             the original lattice sum and yield algebraic convergence.
             The second type are quasi-periodic plane wave solutions of
             the Helmholtz equation which reinstate certain necessary
             grazing modes without leading to blowup at Wood anomalies.
             Using the new quasi-periodic Green function, we establish,
             for the first time, that the Dirichlet problem of scattering
             by a smooth doubly periodic scattering surface at a Wood
             frequency is uniquely solvable. We also present an efficient
             high-order numerical method based on this new Green function
             for scattering by doubly periodic surfaces at and around
             Wood frequencies. We believe this is the first solver able
             to handle Wood frequencies for doubly periodic scattering
             problems in three dimensions.We demonstrate the method by
             applying it to acoustic scattering.},
   Doi = {10.1098/rspa.2017.0242},
   Key = {fds330399}
}

@article{fds329310,
   Author = {Kiehart, DP and Crawford, JM and Aristotelous, A and Venakides, S and Edwards, GS},
   Title = {Cell Sheet Morphogenesis: Dorsal Closure in Drosophila
             melanogaster as a Model System.},
   Journal = {Annual Review of Cell and Developmental Biology},
   Volume = {33},
   Pages = {169-202},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1146/annurev-cellbio-111315-125357},
   Abstract = {Dorsal closure is a key process during Drosophila
             morphogenesis that models cell sheet movements in chordates,
             including neural tube closure, palate formation, and wound
             healing. Closure occurs midway through embryogenesis and
             entails circumferential elongation of lateral epidermal cell
             sheets that close a dorsal hole filled with amnioserosa
             cells. Signaling pathways regulate the function of cellular
             structures and processes, including Actomyosin and
             microtubule cytoskeletons, cell-cell/cell-matrix adhesion
             complexes, and endocytosis/vesicle trafficking. These
             orchestrate complex shape changes and movements that entail
             interactions between five distinct cell types. Genetic and
             laser perturbation studies establish that closure is robust,
             resilient, and the consequence of redundancy that
             contributes to four distinct biophysical processes:
             contraction of the amnioserosa, contraction of supracellular
             Actomyosin cables, elongation (stretching?) of the lateral
             epidermis, and zipping together of two converging cell
             sheets. What triggers closure and what the emergent
             properties are that give rise to its extraordinary
             resilience and fidelity remain key, extant
             questions.},
   Doi = {10.1146/annurev-cellbio-111315-125357},
   Key = {fds329310}
}


%% Viel, Shira   
@article{fds337147,
   Author = {Barnard, E and Meehan, E and Reading, N and Viel,
             S},
   Title = {Universal Geometric Coefficients for the Four-Punctured
             Sphere},
   Journal = {Annals of Combinatorics},
   Volume = {22},
   Number = {1},
   Pages = {1-44},
   Year = {2018},
   Month = {March},
   url = {http://dx.doi.org/10.1007/s00026-018-0378-0},
   Doi = {10.1007/s00026-018-0378-0},
   Key = {fds337147}
}


%% Wang, Jiuya   
@article{fds338600,
   Author = {Boston, N and Wang, J},
   Title = {The 2-class tower of ℚ(√-5460)},
   Volume = {251},
   Pages = {71-80},
   Booktitle = {Springer Proceedings in Mathematics and Statistics},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1007/978-3-319-97379-1_5},
   Abstract = {© Springer Nature Switzerland AG 2018. The seminal papers
             in the field of root-discriminant bounds are those of
             Odlyzko and Martinet. Both papers include the question of
             whether the field ℚ(√-5460) has finite or infinite
             2-class tower. This is a critical case that will either
             substantially lower the best known upper bound for lim inf
             of root discriminants (if infinite) or else give a
             counter-example to what is often termed Martinet’s
             conjecture or question (if finite). Using extensive
             computation and introducing some new techniques, we give
             strong evidence that the tower is in fact finite,
             establishing other properties of its Galois group en
             route.},
   Doi = {10.1007/978-3-319-97379-1_5},
   Key = {fds338600}
}


%% Watson, Alexander   
@article{fds338113,
   Author = {Watson, A and Weinstein, MI},
   Title = {Wavepackets in Inhomogeneous Periodic Media: Propagation
             Through a One-Dimensional Band Crossing},
   Journal = {Communications in Mathematical Physics},
   Volume = {363},
   Number = {2},
   Pages = {655-698},
   Year = {2018},
   Month = {October},
   url = {http://dx.doi.org/10.1007/s00220-018-3213-x},
   Abstract = {© 2018, Springer-Verlag GmbH Germany, part of Springer
             Nature. We consider a model of an electron in a crystal
             moving under the influence of an external electric
             field:Schrödinger’s equation in one spatial dimension
             with a potential which is the sum of a periodic function V
             and a smooth function W. We assume that the period of V is
             much shorter than the scale of variation of W and denote the
             ratio of these scales by ϵ. We consider the dynamics of
             semiclassical wavepacket asymptotic (in the limit ϵ↓ 0)
             solutions which are spectrally localized near to a crossing
             of two Bloch band dispersion functions of the periodic
             operator -12∂z2+V(z). We show that the dynamics is
             qualitatively different from the case where bands are
             well-separated: at the time the wavepacket is incident on
             the band crossing, a second wavepacket is ‘excited’
             which has opposite group velocity to the incident
             wavepacket. We then show that our result is consistent with
             the solution of a ‘Landau–Zener’-type
             model.},
   Doi = {10.1007/s00220-018-3213-x},
   Key = {fds338113}
}

@article{fds328439,
   Author = {Watson, AB and Lu, J and Weinstein, MI},
   Title = {Wavepackets in inhomogeneous periodic media: Effective
             particle-field dynamics and Berry curvature},
   Journal = {Journal of Mathematical Physics},
   Volume = {58},
   Number = {2},
   Pages = {021503-021503},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1063/1.4976200},
   Doi = {10.1063/1.4976200},
   Key = {fds328439}
}


%% Witelski, Thomas P.   
@article{fds336414,
   Author = {Chiou, J-G and Ramirez, SA and Elston, TC and Witelski, TP and Schaeffer, DG and Lew, DJ},
   Title = {Principles that govern competition or co-existence in
             Rho-GTPase driven polarization.},
   Journal = {Plos Computational Biology},
   Volume = {14},
   Number = {4},
   Pages = {e1006095},
   Year = {2018},
   Month = {April},
   url = {http://dx.doi.org/10.1371/journal.pcbi.1006095},
   Abstract = {Rho-GTPases are master regulators of polarity establishment
             and cell morphology. Positive feedback enables concentration
             of Rho-GTPases into clusters at the cell cortex, from where
             they regulate the cytoskeleton. Different cell types
             reproducibly generate either one (e.g. the front of a
             migrating cell) or several clusters (e.g. the multiple
             dendrites of a neuron), but the mechanistic basis for
             unipolar or multipolar outcomes is unclear. The design
             principles of Rho-GTPase circuits are captured by
             two-component reaction-diffusion models based on conserved
             aspects of Rho-GTPase biochemistry. Some such models display
             rapid winner-takes-all competition between clusters,
             yielding a unipolar outcome. Other models allow prolonged
             co-existence of clusters. We investigate the behavior of a
             simple class of models and show that while the timescale of
             competition varies enormously depending on model parameters,
             a single factor explains a large majority of this variation.
             The dominant factor concerns the degree to which the maximal
             active GTPase concentration in a cluster approaches a
             "saturation point" determined by model parameters. We
             suggest that both saturation and the effect of saturation on
             competition reflect fundamental properties of the Rho-GTPase
             polarity machinery, regardless of the specific feedback
             mechanism, which predict whether the system will generate
             unipolar or multipolar outcomes.},
   Doi = {10.1371/journal.pcbi.1006095},
   Key = {fds336414}
}

@article{fds332862,
   Author = {Ji, H and Witelski, TP},
   Title = {Instability and dynamics of volatile thin
             films},
   Journal = {Physical Review Fluids},
   Volume = {3},
   Number = {2},
   Year = {2018},
   Month = {February},
   url = {http://dx.doi.org/10.1103/PhysRevFluids.3.024001},
   Abstract = {© 2018 American Physical Society. Volatile viscous fluids
             on partially wetting solid substrates can exhibit
             interesting interfacial instabilities and pattern formation.
             We study the dynamics of vapor condensation and fluid
             evaporation governed by a one-sided model in a
             low-Reynolds-number lubrication approximation incorporating
             surface tension, intermolecular effects, and evaporative
             fluxes. Parameter ranges for evaporation-dominated and
             condensation-dominated regimes and a critical case are
             identified. Interfacial instabilities driven by the
             competition between the disjoining pressure and evaporative
             effects are studied via linear stability analysis. Transient
             pattern formation in nearly flat evolving films in the
             critical case is investigated. In the weak evaporation limit
             unstable modes of finite-amplitude nonuniform steady states
             lead to rich droplet dynamics, including flattening,
             symmetry breaking, and droplet merging. Numerical
             simulations show that long-time behaviors leading to
             evaporation or condensation are sensitive to transitions
             between filmwise and dropwise dynamics.},
   Doi = {10.1103/PhysRevFluids.3.024001},
   Key = {fds332862}
}

@article{fds325294,
   Author = {Gao, Y and Ji, H and Liu, J-G and Witelski, TP},
   Title = {Global existence of solutions to a tear film model with
             locally elevated evaporation rates},
   Journal = {Physica D: Nonlinear Phenomena},
   Volume = {350},
   Pages = {13-25},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1016/j.physd.2017.03.005},
   Doi = {10.1016/j.physd.2017.03.005},
   Key = {fds325294}
}

@article{fds320453,
   Author = {Ji, H and Witelski, TP},
   Title = {Finite-time thin film rupture driven by modified evaporative
             loss},
   Journal = {Physica D: Nonlinear Phenomena},
   Volume = {342},
   Pages = {1-15},
   Year = {2017},
   Month = {March},
   url = {http://dx.doi.org/10.1016/j.physd.2016.10.002},
   Doi = {10.1016/j.physd.2016.10.002},
   Key = {fds320453}
}

@article{fds338527,
   Author = {Gao, Y and Ji, H and Liu, J-G and P. Witelski and T},
   Title = {A vicinal surface model for epitaxial growth with
             logarithmic free energy},
   Journal = {Discrete & Continuous Dynamical Systems B},
   Volume = {22},
   Number = {11},
   Pages = {1-21},
   Year = {2017},
   url = {http://dx.doi.org/10.3934/dcdsb.2018170},
   Doi = {10.3934/dcdsb.2018170},
   Key = {fds338527}
}


%% Wong, Jeffrey T   
@article{fds335546,
   Author = {Mavromoustaki, A and Wang, L and Wong, J and Bertozzi,
             AL},
   Title = {Surface tension effects for particle settling and
             resuspension in viscous thin films},
   Journal = {Nonlinearity},
   Volume = {31},
   Number = {7},
   Pages = {3151-3173},
   Year = {2018},
   Month = {July},
   url = {http://dx.doi.org/10.1088/1361-6544/aab91d},
   Abstract = {© 2018 IOP Publishing Ltd & London Mathematical Society. We
             consider flow of a thin film on an incline with negatively
             buoyant particles. We derive a one-dimensional lubrication
             model, including the effect of surface tension, which is a
             nontrivial extension of a previous model (Murisic et al 2013
             J. Fluid Mech. 717 203-31). We show that the surface
             tension, in the form of high order derivatives, not only
             regularizes the previous model as a high order diffusion,
             but also modifies the fluxes. As a result, it leads to a
             different stratification in the particle concentration along
             the direction perpendicular to the motion of the fluid
             mixture. The resulting equations are of mixed
             hyperbolic-parabolic type and different from the well-known
             lubrication theory for a clear fluid or fluid with
             surfactant. To study the system numerically, we formulate a
             semi-implicit scheme that is able to preserve the particle
             maximum packing fraction. We show extensive numerical
             results for this model including a qualitative comparison
             with two-dimensional laboratory experiments.},
   Doi = {10.1088/1361-6544/aab91d},
   Key = {fds335546}
}


%% Wu, Hau-Tieng   
@article{fds335552,
   Author = {Katz, O and Talmon, R and Lo, Y-L and Wu, H-T},
   Title = {Alternating diffusion maps for multimodal data
             fusion},
   Journal = {Information Fusion},
   Volume = {45},
   Pages = {346-360},
   Year = {2019},
   Month = {January},
   url = {http://dx.doi.org/10.1016/j.inffus.2018.01.007},
   Doi = {10.1016/j.inffus.2018.01.007},
   Key = {fds335552}
}

@article{fds337335,
   Author = {Lin, CY and Wu, HT},
   Title = {Embeddings of Riemannian manifolds with finite eigenvector
             fields of connection Laplacian},
   Journal = {Calculus of Variations and Partial Differential
             Equations},
   Volume = {57},
   Number = {5},
   Year = {2018},
   Month = {October},
   url = {http://dx.doi.org/10.1007/s00526-018-1401-3},
   Abstract = {© 2018, Springer-Verlag GmbH Germany, part of Springer
             Nature. We study the problem asking if one can embed
             manifolds into finite dimensional Euclidean spaces by taking
             finite number of eigenvector fields of the connection
             Laplacian. This problem is essential for the dimension
             reduction problem in manifold learning. In this paper, we
             provide a positive answer to the problem. Specifically, we
             use eigenvector fields to construct local coordinate charts
             with low distortion, and show that the distortion constants
             depend only on geometric properties of manifolds with
             metrics in the little Hölder space c2,α. Next, we use the
             coordinate charts to embed the entire manifold into a finite
             dimensional Euclidean space. The proof of the results relies
             on solving the elliptic system and providing estimates for
             eigenvector fields and the heat kernel and their gradients.
             We also provide approximation results for eigenvector field
             under the c2,αperturbation.},
   Doi = {10.1007/s00526-018-1401-3},
   Key = {fds337335}
}

@article{fds338042,
   Author = {Malik, J and Lo, YL and Wu, HT},
   Title = {Sleep-wake classification via quantifying heart rate
             variability by convolutional neural network},
   Journal = {Physiological Measurement},
   Volume = {39},
   Number = {8},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1088/1361-6579/aad5a9},
   Abstract = {© 2018 Institute of Physics and Engineering in Medicine.
             Objective: Fluctuations in heart rate are intimately related
             to changes in the physiological state of the organism. We
             exploit this relationship by classifying a human
             participant's wake/sleep status using his instantaneous
             heart rate (IHR) series. Approach: We use a convolutional
             neural network (CNN) to build features from the IHR series
             extracted from a whole-night electrocardiogram (ECG) and
             predict every 30 s whether the participant is awake or
             asleep. Our training database consists of 56 normal
             participants, and we consider three different databases for
             validation; one is private, and two are public with
             different races and apnea severities. Main results: On our
             private database of 27 participants, our accuracy,
             sensitivity, specificity, and values for predicting the wake
             stage are , 52.4%, 89.4%, and 0.83, respectively. Validation
             performance is similar on our two public databases. When we
             use the photoplethysmography instead of the ECG to obtain
             the IHR series, the performance is also comparable. A
             robustness check is carried out to confirm the obtained
             performance statistics. Significance: This result advocates
             for an effective and scalable method for recognizing changes
             in physiological state using non-invasive heart rate
             monitoring. The CNN model adaptively quantifies IHR
             fluctuation as well as its location in time and is suitable
             for differentiating between the wake and sleep
             stages.},
   Doi = {10.1088/1361-6579/aad5a9},
   Key = {fds338042}
}

@article{fds335547,
   Author = {Wu, H-T and Wu, J-C and Huang, P-C and Lin, T-Y and Wang, T-Y and Huang,
             Y-H and Lo, Y-L},
   Title = {Phenotype-Based and Self-Learning Inter-Individual Sleep
             Apnea Screening With a Level IV-Like Monitoring
             System},
   Journal = {Frontiers in Physiology},
   Volume = {9},
   Year = {2018},
   Month = {July},
   url = {http://dx.doi.org/10.3389/fphys.2018.00723},
   Doi = {10.3389/fphys.2018.00723},
   Key = {fds335547}
}

@article{fds337015,
   Author = {Wu, HT and Liu, YW},
   Title = {Analyzing transient-evoked otoacoustic emissions by
             concentration of frequency and time},
   Journal = {The Journal of the Acoustical Society of
             America},
   Volume = {144},
   Number = {1},
   Pages = {448-466},
   Year = {2018},
   Month = {July},
   url = {http://dx.doi.org/10.1121/1.5047749},
   Abstract = {© 2018 Acoustical Society of America. The linear part of
             transient evoked otoacoustic emission (TEOAE) is thought to
             be generated via coherent reflection near the characteristic
             place of constituent wave components. Because of the
             tonotopic organization of the cochlea, high frequency
             emissions return earlier than low frequencies; however, due
             to the random nature of coherent reflection, the
             instantaneous frequency (IF) and amplitude envelope of
             TEOAEs both fluctuate. Multiple reflection components and
             synchronized spontaneous emissions can further make it
             difficult to extract the IF by linear transforms. This paper
             proposes to model TEOAEs as a sum of intrinsic mode-type
             functions and analyze it by a nonlinear-type time-frequency
             (T-F) analysis technique called concentration of frequency
             and time (ConceFT). When tested with synthetic otoacoustic
             emission signals with possibly multiple oscillatory
             components, the present method is able to produce clearly
             visualized traces of individual components on the T-F plane.
             Further, when the signal is noisy, the proposed method is
             compared with existing linear and bilinear methods in its
             accuracy for estimating the fluctuating IF. Results suggest
             that ConceFT outperforms the best of these methods in terms
             of optimal transport distance, reducing the error by 10% to
             21% when the signal to noise ratio is 10 dB or
             below.},
   Doi = {10.1121/1.5047749},
   Key = {fds337015}
}

@article{fds335548,
   Author = {Liu, TC and Wu, HT and Chen, YH and Fang, TY and Wang, PC and Liu,
             YW},
   Title = {Analysis of click-evoked otoacoustic emissions by
             concentration of frequency and time: Preliminary results
             from normal hearing and Ménière's disease
             ears},
   Journal = {Aip Conference Proceedings},
   Volume = {1965},
   Year = {2018},
   Month = {May},
   ISBN = {9780735416703},
   url = {http://dx.doi.org/10.1063/1.5038538},
   Abstract = {© 2018 Author(s). The presence of click-evoked (CE)
             otoacoustic emissions (OAEs) has been clinically accepted as
             an indicator of normal cochlear processing of sounds. For
             treatment and diagnostic purposes, however, clinicians do
             not typically pay attention to the detailed spectrum and
             waveform of CEOAEs. A possible reason is due to the lack of
             noise-robust signal processing tools to estimate
             physiologically meaningful time-frequency properties of
             CEOAEs, such as the latency of spectral components. In this
             on-going study, we applied a modern tool called
             concentration of frequency and time (ConceFT, [1]) to
             analyze CEOAE waveforms. Randomly combined orthogonal
             functions are used as windowing functions for time-frequency
             analysis. The resulting spectrograms are subject to
             nonlinear time-frequency reassignment so as to enhance the
             concentration of time-varying sinusoidal components. The
             results after reassignment could be further averaged across
             the random choice of windows. CEOAE waveforms are acquired
             by a linear averaging paradigm, and longitudinal data are
             currently being collected from patients with Ménière's
             disease (MD) and a control group of normal hearing subjects.
             When CEOAE is present, the ConceFT plots show traces of
             decreasing but fluctuating instantaneous frequency against
             time. For comparison purposes, same processing methods are
             also applied to analyze CEOAE data from cochlear mechanics
             simulation.},
   Doi = {10.1063/1.5038538},
   Key = {fds335548}
}

@article{fds335549,
   Author = {Wu, H-T and Soliman, EZ},
   Title = {A new approach for analysis of heart rate variability and QT
             variability in long-term ECG recording.},
   Journal = {Biomedical Engineering Online},
   Volume = {17},
   Number = {1},
   Pages = {54},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1186/s12938-018-0490-8},
   Abstract = {With the emergence of long-term electrocardiogram (ECG)
             recordings that extend several days beyond the typical
             24-48 h, the development of new tools to measure heart rate
             variability (HRV) and QT variability is needed to utilize
             the full potential of such extra-long-term ECG recordings.In
             this report, we propose a new nonlinear time-frequency
             analysis approach, the concentration of frequency and time
             (ConceFT), to study the HRV QT variability from
             extra-long-term ECG recordings. This approach is a
             generalization of Short Time Fourier Transform and
             Continuous Wavelet Transform approaches.As proof of concept,
             we used 14-day ECG recordings to show that the ConceFT
             provides a sharpened and stabilized spectrogram by taking
             the phase information of the time series and the multitaper
             technique into account.The ConceFT has the potential to
             provide a sharpened and stabilized spectrogram for the heart
             rate variability and QT variability in 14-day ECG
             recordings.},
   Doi = {10.1186/s12938-018-0490-8},
   Key = {fds335549}
}

@article{fds337127,
   Author = {Frasch, MG and Lobmaier, SM and Stampalija, T and Desplats, P and Pallarés, ME and Pastor, V and Brocco, MA and Wu, H-T and Schulkin, J and Herry, CL and Seely, AJE and Metz, GAS and Louzoun, Y and Antonelli,
             MC},
   Title = {Non-invasive biomarkers of fetal brain development
             reflecting prenatal stress: An integrative multi-scale
             multi-species perspective on data collection and
             analysis},
   Journal = {Neuroscience and Biobehavioral Reviews},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1016/j.neubiorev.2018.05.026},
   Doi = {10.1016/j.neubiorev.2018.05.026},
   Key = {fds337127}
}

@article{fds335550,
   Author = {Zhang, J-T and Cheng, M-Y and Wu, H-T and Zhou, B},
   Title = {A new test for functional one-way ANOVA with applications to
             ischemic heart screening},
   Journal = {Computational Statistics & Data Analysis},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1016/j.csda.2018.05.004},
   Doi = {10.1016/j.csda.2018.05.004},
   Key = {fds335550}
}

@article{fds339912,
   Author = {Wu, JC and Wang, CW and Huang, YH and Wu, HT and Huang, PC and Lo,
             YL},
   Title = {A Portable Monitoring System with Automatic Event Detection
             for Sleep Apnea Level-IV Evaluation},
   Journal = {Proceedings Ieee International Symposium on Circuits and
             Systems},
   Volume = {2018-May},
   Year = {2018},
   Month = {April},
   ISBN = {9781538648810},
   url = {http://dx.doi.org/10.1109/ISCAS.2018.8351221},
   Abstract = {© 2018 IEEE. To meet the demands on a comfortable
             screening, or even diagnostic, equipment without interfering
             with the sleep, this study develops a level IV portable
             system, equipped with two tri-axial accelerometers (TAA)
             measuring the thoracic and abdominal respiratory efforts,
             and one oximeter measuring the oxygen saturation (SpO2), to
             identify obstructive sleep apnea (OSA), central sleep apnea
             (CSA), and hypopnea (HYP) events. The prototype integrates
             all the hardware and software for physiological information
             extraction. In addition, an automatic event detection
             algorithm is proposed to reduce the labor-intensive work on
             scoring the events. Based on 63 subjects, with 80% data for
             training and 20% for validation, the classification accuracy
             of the apnea hypopnea-index (AHI) is 84.13%. The results
             indicate that the proposed algorithm has great potential to
             classify the severity of patients in clinical examinations
             for both the screening and the homecare purposes.},
   Doi = {10.1109/ISCAS.2018.8351221},
   Key = {fds339912}
}

@article{fds332750,
   Author = {Shen, C and Frasch, MG and Wu, HT and Herry, CL and Cao, M and Desrochers,
             A and Fecteau, G and Burns, P},
   Title = {Non-invasive acquisition of fetal ECG from the maternal
             xyphoid process: a feasibility study in pregnant sheep and a
             call for open data sets.},
   Journal = {Physiological Measurement},
   Volume = {39},
   Number = {3},
   Pages = {035005},
   Year = {2018},
   Month = {March},
   url = {http://dx.doi.org/10.1088/1361-6579/aaaaa4},
   Abstract = {The utility of fetal heart rate (FHR) monitoring can only be
             achieved with an acquisition sampling rate that preserves
             the underlying physiological information on the millisecond
             time scale (1000 Hz rather than 4 Hz). For such acquisition,
             fetal ECG (fECG) is required, rather than the ultrasound to
             derive FHR. We tested one recently developed algorithm,
             SAVER, and two widely applied algorithms to extract fECG
             from a single-channel maternal ECG signal recorded over the
             xyphoid process rather than the routine abdominal signal.At
             126dG, ECG was attached to near-term ewe and fetal
             shoulders, manubrium and xyphoid processes
             (n  =  12). fECG served as the ground-truth to which
             the fetal ECG signal extracted from the simultaneously-acquired
             maternal ECG was compared. All fetuses were in good health
             during surgery (pH 7.29  ±  0.03, pO2
             33.2  ±  8.4, pCO2 56.0  ±  7.8, O2Sat
             78.3  ±  7.6, lactate 2.8  ±  0.6,
             BE  -0.3  ±  2.4).In all animals, single lead
             fECG extraction algorithm could not extract fECG from the
             maternal ECG signal over the xyphoid process with the F1
             less than 50%.The applied fECG extraction algorithms might
             be unsuitable for the maternal ECG signal over the xyphoid
             process, or the latter does not contain strong enough fECG
             signal, although the lead is near the mother's abdomen.
             Fetal sheep model is widely used to mimic various fetal
             conditions, yet ECG recordings in a public data set form are
             not available to test the predictive ability of fECG and
             FHR. We are making this data set openly available to other
             researchers to foster non-invasive fECG acquisition in this
             animal model.},
   Doi = {10.1088/1361-6579/aaaaa4},
   Key = {fds332750}
}

@article{fds338084,
   Author = {Wu, HT and Wu, N},
   Title = {Think globally, fit locally under the manifold setup:
             Asymptotic analysis of locally linear embedding},
   Journal = {The Annals of Statistics},
   Volume = {46},
   Number = {6B},
   Pages = {3805-3837},
   Publisher = {INST MATHEMATICAL STATISTICS},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1214/17-AOS1676},
   Abstract = {© Institute of Mathematical Statistics, 2018. Since its
             introduction in 2000, Locally Linear Embedding (LLE) has
             been widely applied in data science. We provide an
             asymptotical analysis of LLE under the manifold setup. We
             show that for a general manifold, asymptotically we may not
             obtain the Laplace–Beltrami operator, and the result may
             depend on nonuniform sampling unless a correct
             regularization is chosen. We also derive the corresponding
             kernel function, which indicates that LLE is not a Markov
             process. A comparison with other commonly applied nonlinear
             algorithms, particularly a diffusion map, is provided and
             its relationship with locally linear regression is also
             discussed.},
   Doi = {10.1214/17-AOS1676},
   Key = {fds338084}
}

@article{fds333710,
   Author = {Talmon, R and Wu, H-T},
   Title = {Latent common manifold learning with alternating diffusion:
             Analysis and applications},
   Journal = {Applied and Computational Harmonic Analysis},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1016/j.acha.2017.12.006},
   Doi = {10.1016/j.acha.2017.12.006},
   Key = {fds333710}
}

@article{fds328822,
   Author = {Kowalski, M and Meynard, A and Wu, H-T},
   Title = {Convex Optimization approach to signals with fast varying
             instantaneous frequency},
   Journal = {Applied and Computational Harmonic Analysis},
   Volume = {44},
   Number = {1},
   Pages = {89-122},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1016/j.acha.2016.03.008},
   Doi = {10.1016/j.acha.2016.03.008},
   Key = {fds328822}
}

@article{fds335551,
   Author = {Tan, C and Zhang, L and Wu, H-T},
   Title = {A Novel Blaschke Unwinding Adaptive Fourier Decomposition
             based Signal Compression Algorithm with Application on ECG
             Signals},
   Journal = {Ieee Journal of Biomedical and Health Informatics},
   Pages = {1-1},
   Year = {2018},
   url = {http://dx.doi.org/10.1109/JBHI.2018.2817192},
   Abstract = {IEEE This paper presents a novel signal compression
             algorithm based on the Blaschke unwinding adaptive Fourier
             decomposition (AFD). The Blaschke unwinding AFD is a newly
             developed signal decomposition theory. It utilizes the
             Nevanlinna factorization and the maximal selection principle
             in each decomposition step, and achieves a faster
             convergence rate with higher fidelity. The proposed
             compression algorithm is applied to the electrocardiogram
             signal. To assess the performance of the proposed
             compression algorithm, in addition to the generic assessment
             criteria, we consider the less discussed criteria related to
             the clinical needs - for the heart rate variability analysis
             purpose, how accurate the R peak information is preserved is
             evaluated. The experiments are conducted on the MIT-BIH
             arrhythmia benchmark database. The results show that the
             proposed algorithm performs better than other
             state-of-theart approaches. Meanwhile, it also well
             preserves the R peak information.},
   Doi = {10.1109/JBHI.2018.2817192},
   Key = {fds335551}
}

@article{fds329941,
   Author = {Wu, H-K and Ko, Y-S and Lin, Y-S and Wu, H-T and Tsai, T-H and Chang,
             H-H},
   Title = {Corrigendum to "The correlation between pulse diagnosis and
             constitution identification in traditional Chinese medicine"
             [Complementary Ther. Med. 30 (2017) 107-112].},
   Journal = {Complementary Therapies in Medicine},
   Volume = {35},
   Pages = {145},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1016/j.ctim.2017.09.004},
   Doi = {10.1016/j.ctim.2017.09.004},
   Key = {fds329941}
}

@article{fds329940,
   Author = {Chao, Y-S and Wu, H-T and Scutari, M and Chen, T-S and Wu, C-J and Durand,
             M and Boivin, A},
   Title = {A network perspective on patient experiences and health
             status: the Medical Expenditure Panel Survey 2004 to
             2011.},
   Journal = {Bmc Health Services Research},
   Volume = {17},
   Number = {1},
   Pages = {579},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1186/s12913-017-2496-5},
   Abstract = {There is a growing emphasis on the need to engage patients
             in order to improve the quality of health care and improve
             health outcomes. However, we are still lacking a
             comprehensive understanding on how different measures of
             patient experiences interact with one another or relate to
             health status. This study takes a network perspective to 1)
             study the associations between patient characteristics and
             patient experience in health care and 2) identify factors
             that could be prioritized to improve health status.This
             study uses data from the two-year panels from the Medical
             Expenditure Panel Survey (MEPS) initiated between 2004 and
             2011 in the United States. The 88 variables regarding
             patient health and experience with health care were
             identified through the MEPS documentation. Sex, age,
             race/ethnicity, and years of education were also included
             for analysis. The bnlearn package within R (v3.20) was used
             to 1) identify the structure of the network of variables, 2)
             assess the model fit of candidate algorithms, 3)
             cross-validate the network, and 4) fit conditional
             probabilities with the given structure.There were 51,023
             MEPS interviewees aged 18 to 85 years (mean = 44, 95%
             CI = 43.9 to 44.2), with years of education ranging from 1
             to 19 (mean = 7.4, 95% CI = 7.40 to 7.46). Among all,
             55% and 74% were female and white, respectively. There were
             nine networks identified and 17 variables not linked to
             others, including death in the second years, sex, entry
             years to the MEPS, and relations of proxies. The health
             status in the second years was directly linked to that in
             the first years. The health care ratings were associated
             with how often professionals listened to them and whether
             professionals' explanation was understandable.It is
             feasible to construct Bayesian networks with information on
             patient characteristics and experiences in health care.
             Network models help to identify significant predictors of
             health care quality ratings. With temporal relationships
             established, the structure of the variables can be
             meaningful for health policy researchers, who search for one
             or a few key priorities to initiate interventions or health
             care quality improvement programs.},
   Doi = {10.1186/s12913-017-2496-5},
   Key = {fds329940}
}

@article{fds328812,
   Author = {Lin, T-Y and Fang, Y-F and Huang, S-H and Wang, T-Y and Kuo, C-H and Wu,
             H-T and Kuo, H-P and Lo, Y-L},
   Title = {Capnography monitoring the hypoventilation during the
             induction of bronchoscopic sedation: A randomized controlled
             trial.},
   Journal = {Scientific Reports},
   Volume = {7},
   Number = {1},
   Pages = {8685},
   Year = {2017},
   Month = {August},
   url = {http://dx.doi.org/10.1038/s41598-017-09082-8},
   Abstract = {We hypothesize that capnography could detect hypoventilation
             during induction of bronchoscopic sedation and starting
             bronchoscopy following hypoventilation, may decrease
             hypoxemia. Patients were randomized to: starting
             bronchoscopy when hypoventilation (hypopnea, two successive
             breaths of at least 50% reduction of the peak wave compared
             to baseline or apnea, no wave for 10 seconds) (Study
             group, n = 55), or when the Observer Assessment of
             Alertness and Sedation scale (OAAS) was less than 4 (Control
             group, n = 59). Propofol infusion was titrated to
             maintain stable vital signs and sedative levels. The
             hypoventilation during induction in the control group and
             the sedative outcome were recorded. The patient
             characteristics and procedures performed were similar.
             Hypoventilation was observed in 74.6% of the patients before
             achieving OAAS < 4 in the control group. Apnea occurred
             more than hypopnea (p < 0.0001). Hypoventilation
             preceded OAAS < 4 by 96.5 ± 88.1 seconds. In the
             study group, the induction time was shorter (p = 0.03)
             and subjects with any two events of hypoxemia during
             sedation, maintenance or recovery were less than the control
             group (1.8 vs. 18.6%, p < 0.01). Patient tolerance,
             wakefulness during sedation, and cooperation were similar in
             both groups. Significant hypoventilation occurred during the
             induction and start bronchoscopy following hypoventilation
             may decrease hypoxemia without compromising patient
             tolerance.},
   Doi = {10.1038/s41598-017-09082-8},
   Key = {fds328812}
}

@article{fds328814,
   Author = {Georgiou, A and Bello-Rivas, J and Gear, C and Wu, H-T and Chiavazzo, E and Kevrekidis, I},
   Title = {An Exploration Algorithm for Stochastic Simulators Driven by
             Energy Gradients},
   Journal = {Entropy},
   Volume = {19},
   Number = {7},
   Pages = {294-294},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.3390/e19070294},
   Doi = {10.3390/e19070294},
   Key = {fds328814}
}

@article{fds328813,
   Author = {Malik, J and Reed, N and Wang, C-L and Wu, H-T},
   Title = {Single-lead f-wave extraction using diffusion
             geometry.},
   Journal = {Physiological Measurement},
   Volume = {38},
   Number = {7},
   Pages = {1310-1334},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1088/1361-6579/aa707c},
   Abstract = {A novel single-lead f-wave extraction algorithm based on the
             modern diffusion geometry data analysis framework is
             proposed.The algorithm is essentially an averaged beat
             subtraction algorithm, where the ventricular activity
             template is estimated by combining a newly designed metric,
             the 'diffusion distance', and the non-local Euclidean median
             based on the non-linear manifold setup. We coined the
             algorithm [Formula: see text].Two simulation schemes are
             considered, and the new algorithm [Formula: see text]
             outperforms traditional algorithms, including the average
             beat subtraction, principal component analysis, and adaptive
             singular value cancellation, in different evaluation metrics
             with statistical significance.The clinical potential is
             shown in the real Holter signal, and we introduce a new
             score to evaluate the performance of the
             algorithm.},
   Doi = {10.1088/1361-6579/aa707c},
   Key = {fds328813}
}

@article{fds328815,
   Author = {Sheu, Y-L and Hsu, L-Y and Chou, P-T and Wu, H-T},
   Title = {Entropy-based time-varying window width selection for
             nonlinear-type time–frequency analysis},
   Journal = {International Journal of Data Science and
             Analytics},
   Volume = {3},
   Number = {4},
   Pages = {231-245},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1007/s41060-017-0053-2},
   Doi = {10.1007/s41060-017-0053-2},
   Key = {fds328815}
}

@article{fds328817,
   Author = {Herry, CL and Frasch, M and Seely, AJ and Wu, H-T},
   Title = {Heart beat classification from single-lead ECG using the
             synchrosqueezing transform.},
   Journal = {Physiological Measurement},
   Volume = {38},
   Number = {2},
   Pages = {171-187},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1088/1361-6579/aa5070},
   Abstract = {The processing of ECG signal provides a wealth of
             information on cardiac function and overall cardiovascular
             health. While multi-lead ECG recordings are often necessary
             for a proper assessment of cardiac rhythms, they are not
             always available or practical, for example in fetal ECG
             applications. Moreover, a wide range of small non-obtrusive
             single-lead ECG ambulatory monitoring devices are now
             available, from which heart rate variability (HRV) and other
             health-related metrics are derived. Proper beat detection
             and classification of abnormal rhythms is important for
             reliable HRV assessment and can be challenging in
             single-lead ECG monitoring devices. In this manuscript, we
             modelled the heart rate signal as an adaptive non-harmonic
             model and used the newly developed synchrosqueezing
             transform (SST) to characterize ECG patterns. We show how
             the proposed model can be used to enhance heart beat
             detection and classification between normal and abnormal
             rhythms. In particular, using the Massachusetts Institute of
             Technology-Beth Israel Hospital (MIT-BIH) arrhythmia
             database and the Association for the Advancement of Medical
             Instrumentation (AAMI) beat classes, we trained and
             validated a support vector machine (SVM) classifier on a
             portion of the annotated beat database using the SST-derived
             instantaneous phase, the R-peak amplitudes and R-peak to
             R-peak interval durations, based on a single ECG lead. We
             obtained sentivities and positive predictive values
             comparable to other published algorithms using multiple
             leads and many more features.},
   Doi = {10.1088/1361-6579/aa5070},
   Key = {fds328817}
}

@article{fds329944,
   Author = {Wu, H-K and Ko, Y-S and Lin, Y-S and Wu, H-T and Tsai, T-H and Chang,
             H-H},
   Title = {The correlation between pulse diagnosis and constitution
             identification in traditional Chinese medicine.},
   Journal = {Complementary Therapies in Medicine},
   Volume = {30},
   Pages = {107-112},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1016/j.ctim.2016.12.005},
   Abstract = {Our study aimed to correlate pulse wave parameters such as
             augmentation index (AI) and heart rate variability with
             traditional Chinese medicine (TCM) constitution for
             evaluating health status.Out of 177 subjects, 69 healthy
             subjects were enrolled in the present study, and others were
             excluded because of cardiovascular, liver, kidney, or other
             diseases. Each subject was invited to complete pulse wave
             examination and the Constitution in Chinese Medicine
             Questionnaire. Independent Student's t-tests, Mann-Whitney
             tests, and binary logistic regression analysis were used to
             analyse the correlation between pulse wave parameters and
             TCM constitution.Qi-deficient individuals had higher AI
             (p=0.006) and lower diastolic blood pressure (p=0.011);
             yang-deficient individuals had lower dP/dt max (p=0.030),
             systolic blood pressure (p=0.020), and pulse pressure
             (p=0.048); and damp-heat individuals had higher
             subendocardial viability index (SEVI) scores (p=0.011). We
             then categorized the phlegm dampness and yang-deficiency
             individuals into the cold group and those with damp-heat and
             yin-deficiency into the heat group. A comparison of the two
             constitution groups showed higher AI in the cold group
             (p=0.026). Binary logistic regression analysis demonstrated
             that only AI was a determinant, as evidenced by the finding
             that an increase of one unit in AI corresponded to an
             increase of 5% in the odds ratio for individuals to have a
             cold constitution (p=0.026).Individuals with qi-deficient
             and cold constitutions had higher AI and lower SEVI,
             potentially reflecting an increase in arterial stiffness.
             This study can provide a basis for further investigation of
             the physiological indicators of TCM constitutions in modern
             medicine.},
   Doi = {10.1016/j.ctim.2016.12.005},
   Key = {fds329944}
}

@article{fds331926,
   Author = {Coifman, RR and Steinerberger, S and Wu, HT},
   Title = {Carrier frequencies, holomorphy. And unwinding},
   Journal = {Siam Journal on Mathematical Analysis},
   Volume = {49},
   Number = {6},
   Pages = {4838-4864},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1081087},
   Abstract = {© 2017 Society for Industrial and Applied Mathematics. We
             prove that functions of intrinsic-mode type (a classical
             models for signals) behave essentially like holomorphic
             functions: Adding a pure carrier frequency eint ensures that
             the anti- holomorphic part is much smaller than the
             holomorphic part lP-(f)||L 2 ≪||-P+(f)||L 2 . This enables
             us to use techniques from complex analysis, in particular
             the unwinding series. We study its stability and convergence
             properties and show that the unwinding scries can provide a
             high-resolution, noise- robust time-frequency
             representation.},
   Doi = {10.1137/16M1081087},
   Key = {fds331926}
}

@article{fds328816,
   Author = {Li, R and Frasch, MG and Wu, H-T},
   Title = {Efficient Fetal-Maternal ECG Signal Separation from Two
             Channel Maternal Abdominal ECG via Diffusion-Based Channel
             Selection.},
   Journal = {Frontiers in Physiology},
   Volume = {8},
   Pages = {277},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.3389/fphys.2017.00277},
   Abstract = {There is a need for affordable, widely deployable
             maternal-fetal ECG monitors to improve maternal and fetal
             health during pregnancy and delivery. Based on the
             diffusion-based channel selection, here we present the
             mathematical formalism and clinical validation of an
             algorithm capable of accurate separation of maternal and
             fetal ECG from a two channel signal acquired over maternal
             abdomen. The proposed algorithm is the first algorithm, to
             the best of the authors' knowledge, focusing on the fetal
             ECG analysis based on two channel maternal abdominal ECG
             signal, and we apply it to two publicly available databases,
             the PhysioNet non-invasive fECG database (adfecgdb) and the
             2013 PhysioNet/Computing in Cardiology Challenge (CinC2013),
             to validate the algorithm. The state-of-the-art results are
             achieved when compared with other available algorithms.
             Particularly, the F1 score for the R peak detection achieves
             99.3% for the adfecgdb and 87.93% for the CinC2013, and the
             mean absolute error for the estimated R peak locations is
             4.53 ms for the adfecgdb and 6.21 ms for the CinC2013. The
             method has the potential to be applied to other fetal
             cardiogenic signals, including cardiac doppler
             signals.},
   Doi = {10.3389/fphys.2017.00277},
   Key = {fds328816}
}

@article{fds329942,
   Author = {Frasch, MG and Boylan, GB and Wu, H-T and Devane,
             D},
   Title = {Commentary: Computerised interpretation of fetal heart rate
             during labour (INFANT): a randomised controlled
             trial.},
   Journal = {Frontiers in Physiology},
   Volume = {8},
   Pages = {721},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.3389/fphys.2017.00721},
   Doi = {10.3389/fphys.2017.00721},
   Key = {fds329942}
}

@article{fds329943,
   Author = {Cicone, A and Wu, H-T},
   Title = {How Nonlinear-Type Time-Frequency Analysis Can Help in
             Sensing Instantaneous Heart Rate and Instantaneous
             Respiratory Rate from Photoplethysmography in a Reliable
             Way.},
   Journal = {Frontiers in Physiology},
   Volume = {8},
   Pages = {701},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.3389/fphys.2017.00701},
   Abstract = {Despite the population of the noninvasive, economic,
             comfortable, and easy-to-install photoplethysmography (PPG),
             it is still lacking a mathematically rigorous and stable
             algorithm which is able to simultaneously extract from a
             single-channel PPG signal the instantaneous heart rate (IHR)
             and the instantaneous respiratory rate (IRR). In this paper,
             a novel algorithm called deppG is provided to tackle this
             challenge. deppG is composed of two theoretically solid
             nonlinear-type time-frequency analyses techniques, the
             de-shape short time Fourier transform and the
             synchrosqueezing transform, which allows us to extract the
             instantaneous physiological information from the PPG signal
             in a reliable way. To test its performance, in addition to
             validating the algorithm by a simulated signal and
             discussing the meaning of "instantaneous," the algorithm is
             applied to two publicly available batch databases, the
             Capnobase and the ICASSP 2015 signal processing cup. The
             former contains PPG signals relative to spontaneous or
             controlled breathing in static patients, and the latter is
             made up of PPG signals collected from subjects doing intense
             physical activities. The accuracies of the estimated IHR and
             IRR are compared with the ones obtained by other methods,
             and represent the state-of-the-art in this field of
             research. The results suggest the potential of deppG to
             extract instantaneous physiological information from a
             signal acquired from widely available wearable devices, even
             when a subject carries out intense physical
             activities.},
   Doi = {10.3389/fphys.2017.00701},
   Key = {fds329943}
}

@article{fds329945,
   Author = {Liu, W-T and Wu, H-T and Juang, J-N and Wisniewski, A and Lee, H-C and Wu,
             D and Lo, Y-L},
   Title = {Prediction of the severity of obstructive sleep apnea by
             anthropometric features via support vector
             machine.},
   Journal = {Plos One},
   Volume = {12},
   Number = {5},
   Pages = {e0176991},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0176991},
   Abstract = {To develop an applicable prediction for obstructive sleep
             apnea (OSA) is still a challenge in clinical practice. We
             apply a modern machine learning method, the support vector
             machine to establish a predicting model for the severity of
             OSA. The support vector machine was applied to build up a
             prediction model based on three anthropometric features
             (neck circumference, waist circumference, and body mass
             index) and age on the first database. The established model
             was then valided independently on the second database. The
             anthropometric features and age were combined to generate
             powerful predictors for OSA. Following the common practice,
             we predict if a subject has the apnea-hypopnea index greater
             then 15 or not as well as 30 or not. Dividing by genders and
             age, for the AHI threhosld 15 (respectively 30), the cross
             validation and testing accuracy for the prediction were
             85.3% and 76.7% (respectively 83.7% and 75.5%) in young
             female, while the negative likelihood ratio for the AHI
             threhosld 15 (respectively 30) for the cross validation and
             testing were 0.2 and 0.32 (respectively 0.06 and 0.1) in
             young female. The more accurate results with lower negative
             likelihood ratio in the younger patients, especially the
             female subgroup, reflect the potential of the proposed model
             for the screening purpose and the importance of approaching
             by different genders and the effects of aging.},
   Doi = {10.1371/journal.pone.0176991},
   Key = {fds329945}
}

@article{fds328818,
   Author = {Lin, Y-T and Wu, H-T},
   Title = {ConceFT for Time-Varying Heart Rate Variability Analysis as
             a Measure of Noxious Stimulation During General
             Anesthesia.},
   Journal = {Ieee Transactions on Bio Medical Engineering},
   Volume = {64},
   Number = {1},
   Pages = {145-154},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1109/tbme.2016.2549048},
   Abstract = {Heart rate variability (HRV) offers a noninvasive way to
             peek into the physiological status of the human body. When
             this physiological status is dynamic, traditional HRV
             indices calculated from power spectrum do not resolve the
             dynamic situation due to the issue of nonstationarity.
             Clinical anesthesia is a typically dynamic situation that
             calls for time-varying HRV analysis. Concentration of
             frequency and time (ConceFT) is a nonlinear time-frequency
             (TF) analysis generalizing the multitaper technique and the
             synchrosqueezing transform. The result is a sharp TF
             representation capturing the dynamics inside HRV. Companion
             indices of the commonly applied HRV indices, including
             time-varying low-frequency power (tvLF), time-varying
             high-frequency power, and time-varying low-high ratio, are
             considered as measures of noxious stimulation.To evaluate
             the feasibility of the proposed indices, we apply these
             indices to study two different types of noxious stimulation,
             the endotracheal intubation and surgical skin incision,
             under general anesthesia. The performance was compared with
             traditional HRV indices, the heart rate reading, and indices
             from electroencephalography.The results indicate that the
             tvLF index performs best and outperforms not only the
             traditional HRV index, but also the commonly used heart rate
             reading.With the help of ConceFT, the proposed HRV indices
             are potential to provide a better quantification of the
             dynamic change of the autonomic nerve system.Our proposed
             scheme of time-varying HRV analysis could contribute to the
             clinical assessment of analgesia under general
             anesthesia.},
   Doi = {10.1109/tbme.2016.2549048},
   Key = {fds328818}
}

@article{fds328819,
   Author = {Wu, H-T},
   Title = {Embedding Riemannian manifolds by the heat kernel of the
             connection Laplacian},
   Journal = {Advances in Mathematics},
   Volume = {304},
   Pages = {1055-1079},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1016/j.aim.2016.05.023},
   Doi = {10.1016/j.aim.2016.05.023},
   Key = {fds328819}
}


%% Wu, Nan   
@article{fds339455,
   Author = {Wu, HT and Wu, N},
   Title = {Think globally, fit locally under the manifold setup:
             Asymptotic analysis of locally linear embedding},
   Journal = {The Annals of Statistics},
   Volume = {46},
   Number = {6B},
   Pages = {3805-3837},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1214/17-AOS1676},
   Abstract = {© Institute of Mathematical Statistics, 2018. Since its
             introduction in 2000, Locally Linear Embedding (LLE) has
             been widely applied in data science. We provide an
             asymptotical analysis of LLE under the manifold setup. We
             show that for a general manifold, asymptotically we may not
             obtain the Laplace–Beltrami operator, and the result may
             depend on nonuniform sampling unless a correct
             regularization is chosen. We also derive the corresponding
             kernel function, which indicates that LLE is not a Markov
             process. A comparison with other commonly applied nonlinear
             algorithms, particularly a diffusion map, is provided and
             its relationship with locally linear regression is also
             discussed.},
   Doi = {10.1214/17-AOS1676},
   Key = {fds339455}
}


%% Yang, Haizhao   
@article{fds325968,
   Author = {Lu, J and Yang, H},
   Title = {A cubic scaling algorithm for excited states calculations in
             particle–particle random phase approximation},
   Journal = {Journal of Computational Physics},
   Volume = {340},
   Pages = {297-308},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1016/j.jcp.2017.03.055},
   Doi = {10.1016/j.jcp.2017.03.055},
   Key = {fds325968}
}

@article{fds311605,
   Author = {Li, Y and Yang, H and Ying, L},
   Title = {Multidimensional butterfly factorization},
   Journal = {Applied and Computational Harmonic Analysis},
   Publisher = {Elsevier},
   Year = {2017},
   Month = {April},
   ISSN = {1096-603X},
   url = {http://hdl.handle.net/10161/11651 Duke open
             access},
   Doi = {10.1016/j.acha.2017.04.002},
   Key = {fds311605}
}

@article{fds311606,
   Author = {Cornelis, B and Yang, H and Goodfriend, A and Ocon, N and Lu, J and Daubechies, I},
   Title = {Removal of Canvas Patterns in Digital Acquisitions of
             Paintings.},
   Journal = {IEEE Transactions on Image Processing},
   Volume = {26},
   Number = {1},
   Pages = {160-171},
   Publisher = {Institute of Electrical and Electronics Engineers
             (IEEE)},
   Year = {2017},
   Month = {January},
   ISSN = {1941-0042},
   url = {http://hdl.handle.net/10161/11650 Duke open
             access},
   Abstract = {We address the removal of canvas artifacts from
             high-resolution digital photographs and X-ray images of
             paintings on canvas. Both imaging modalities are common
             investigative tools in art history and art conservation.
             Canvas artifacts manifest themselves very differently
             according to the acquisition modality; they can hamper the
             visual reading of the painting by art experts, for instance,
             in preparing a restoration campaign. Computer-aided canvas
             removal is desirable for restorers when the painting on
             canvas they are preparing to restore has acquired over the
             years a much more salient texture. We propose a new
             algorithm that combines a cartoon-texture decomposition
             method with adaptive multiscale thresholding in the
             frequency domain to isolate and suppress the canvas
             components. To illustrate the strength of the proposed
             method, we provide various examples, for acquisitions in
             both imaging modalities, for paintings with different types
             of canvas and from different periods. The proposed algorithm
             outperforms previous methods proposed for visual photographs
             such as morphological component analysis and Wiener
             filtering and it also works for the digital removal of
             canvas artifacts in X-ray images.},
   Doi = {10.1109/tip.2016.2621413},
   Key = {fds311606}
}

@article{fds312767,
   Author = {Lu, J and Yang, H},
   Title = {Preconditioning Orbital Minimization Method for Planewave
             Discretization},
   Journal = {Multiscale Modeling & Simulation},
   Volume = {15},
   Number = {1},
   Pages = {254-273},
   Year = {2017},
   Month = {January},
   url = {http://hdl.handle.net/10161/11833 Duke open
             access},
   Abstract = {We present an efficient preconditioner for the orbital
             minimization method when the Hamiltonian is discretized
             using planewaves (i.e., pseudospectral method). This novel
             preconditioner is based on an approximate Fermi operator
             projection by pole expansion, combined with the sparsifying
             preconditioner to efficiently evaluate the pole expansion
             for a wide range of Hamiltonian operators. Numerical results
             validate the performance of the new preconditioner for the
             orbital minimization method, in particular, the iteration
             number is reduced to $O(1)$ and often only a few iterations
             are enough for convergence.},
   Doi = {10.1137/16M1068670},
   Key = {fds312767}
}

@article{fds315394,
   Author = {Li, Y and Yang, H},
   Title = {Interpolative Butterfly Factorization},
   Journal = {SIAM Journal on Scientific Computing},
   Volume = {39},
   Number = {2},
   Pages = {A503-A531},
   Year = {2017},
   Month = {January},
   url = {http://arxiv.org/abs/1605.03616},
   Doi = {10.1137/16M1074941},
   Key = {fds315394}
}

@article{fds311604,
   Author = {Yang, H},
   Title = {Statistical analysis of synchrosqueezed transforms},
   Journal = {Applied and Computational Harmonic Analysis},
   Publisher = {Elsevier},
   Year = {2017},
   Month = {January},
   ISSN = {1096-603X},
   url = {http://hdl.handle.net/10161/11652 Duke open
             access},
   Doi = {10.1016/j.acha.2017.01.001},
   Key = {fds311604}
}


%% Zhou, Zhennan   
@article{fds323230,
   Author = {Liu, J-G and Ma, Z and Zhou, Z},
   Title = {Explicit and Implicit TVD Schemes for Conservation Laws with
             Caputo Derivatives},
   Journal = {Journal of Scientific Computing},
   Volume = {72},
   Number = {1},
   Pages = {291-313},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1007/s10915-017-0356-4},
   Abstract = {© 2017 Springer Science+Business Media New YorkIn this
             paper, we investigate numerical approximations of the scalar
             conservation law with the Caputo derivative, which
             introduces the memory effect. We construct the first order
             and the second order explicit upwind schemes for such
             equations, which are shown to be conditionally (Formula
             presented.) contracting and TVD. However, the Caputo
             derivative leads to the modified CFL-type stability
             condition, (Formula presented.), where (Formula presented.)
             is the fractional exponent in the derivative. When (Formula
             presented.) is small, such strong constraint makes the
             numerical implementation extremely impractical. We have then
             proposed the implicit upwind scheme to overcome this issue,
             which is proved to be unconditionally (Formula presented.)
             contracting and TVD. Various numerical tests are presented
             to validate the properties of the methods and provide more
             numerical evidence in interpreting the memory effect in
             conservation laws.},
   Doi = {10.1007/s10915-017-0356-4},
   Key = {fds323230}
}

@article{fds326270,
   Author = {Lu, J and Zhou, Z},
   Title = {Path integral molecular dynamics with surface hopping for
             thermal equilibrium sampling of nonadiabatic
             systems.},
   Journal = {Journal of Chemical Physics},
   Volume = {146},
   Number = {15},
   Pages = {154110},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1063/1.4981021},
   Abstract = {In this work, a novel ring polymer representation for a
             multi-level quantum system is proposed for thermal average
             calculations. The proposed representation keeps the
             discreteness of the electronic states: besides position and
             momentum, each bead in the ring polymer is also
             characterized by a surface index indicating the electronic
             energy surface. A path integral molecular dynamics with
             surface hopping (PIMD-SH) dynamics is also developed to
             sample the equilibrium distribution of the ring polymer
             configurational space. The PIMD-SH sampling method is
             validated theoretically and by numerical
             examples.},
   Doi = {10.1063/1.4981021},
   Key = {fds326270}
}

@article{fds318345,
   Author = {Ma, Z and Zhang, Y and Zhou, Z},
   Title = {An improved semi-Lagrangian time splitting spectral method
             for the semi-classical Schrödinger equation with vector
             potentials using NUFFT},
   Journal = {Applied Numerical Mathematics},
   Volume = {111},
   Pages = {144-159},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1016/j.apnum.2016.08.015},
   Doi = {10.1016/j.apnum.2016.08.015},
   Key = {fds318345}
}


%% Zhu, Wei   
@article{fds333669,
   Author = {Zhu, W and Qiu, Q and Huang, J and Calderbank, AR and Sapiro, G and Daubechies, I},
   Title = {LDMNet: Low Dimensional Manifold Regularized Neural
             Networks.},
   Journal = {CoRR},
   Volume = {abs/1711.06246},
   Year = {2017},
   Key = {fds333669}
}

 

dept@math.duke.edu
ph: 919.660.2800
fax: 919.660.2821

Mathematics Department
Duke University, Box 90320
Durham, NC 27708-0320