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Mathematics Faculty: Publications since January 2016

List all publications in the database.    :chronological  alphabetical  combined listing:
%% Abel, Michael   
@article{fds317698,
   Title = {HOMFLY-PT homology for general link diagrams and braidlike
             isotopy},
   Year = {2016},
   Month = {June},
   url = {http://arxiv.org/abs/1607.00314},
   Key = {fds317698}
}

@article{fds311722,
   Author = {M. Abel and M. Hogancamp},
   Title = {Stable homology of torus links via categorified Young
             symmetrizers II: one-column partitions},
   Year = {2016},
   Month = {February},
   url = {http://arxiv.org/abs/1510.05330},
   Key = {fds311722}
}


%% Agarwal, Pankaj K.   
@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 = {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 = {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 = {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 R d for constant
             d, be two point sets with |R| + |B| = n, and let λ: R∪B
             → ℕ such that Σ r∈R λ(r) = Σ b∈B λ (b) be demand
             functions over R and B. Let d(·, ·) be a suitable distance
             function such as the L p distance. The transportation
             problem asks to find a map τ: R × B → ℕ such that Σ
             b∈B τ(r, b) = λ(r), Σ r∈R τ(r, b) = λ(b), and σ
             r∈Rb∈B τ(r, b)d(r, b) is minimized. We present three
             new results for the transportation problem when d(·, ·) is
             any L p metric: • For any constant ϵ > 0, an O(n 1+ϵ )
             expected time randomized algorithm that returns a
             transportation map with expected cost O(log 2 (1/ϵ)) times
             the optimal cost. • For any ϵ > 0, a (1 +
             ϵ)-approximation in O(n 3/2 ϵ -d polylog(U) polylog(n))
             time, where U = max p∈Rcup;B λ (p). •An exact strongly
             polynomial O(n 2 polylogn) 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{fds323822,
   Author = {Agarwal, PK and Pan, J and Victor, W},
   Title = {An efficient algorithm for placing electric vehicle charging
             stations},
   Journal = {LIPIcs},
   Volume = {64},
   Pages = {7.1-7.12},
   Year = {2016},
   Month = {December},
   ISBN = {9783959770262},
   url = {http://dx.doi.org/10.4230/LIPIcs.ISAAC.2016.7},
   Abstract = {© Pankaj K. Agarwal, Jiangwei Pan, and Will Victor.
             Motivated by the increasing popularity of electric vehicles
             (EV) and a lack of charging stations in the road network, we
             study the shortest path hitting set (SPHS) problem. Roughly
             speaking, given an input graph G, the goal is to compute a
             small-size subset H of vertices of G such that by placing
             charging stations at vertices in H, every shortest path in G
             becomes EV-feasible, i.e., an EV can travel between any two
             vertices of G through the shortest path with a full charge.
             In this paper, we propose a bi-criteria approximation
             algorithm with running time near-linear in the size of G
             that has a logarithmic approximation on |H| and may require
             the EV to slightly deviate from the shortest path. We also
             present a data structure for computing an EV-feasible path
             between two query vertices of G.},
   Doi = {10.4230/LIPIcs.ISAAC.2016.7},
   Key = {fds323822}
}

@article{fds323823,
   Author = {Ying, R and Pan, J and Fox, K and Agarwal, PK},
   Title = {A simple efficient approximation algorithm for dynamic time
             warping},
   Journal = {GIS: Proceedings of the ACM International Symposium on
             Advances in Geographic Information Systems},
   Year = {2016},
   Month = {October},
   ISBN = {9781450345897},
   url = {http://dx.doi.org/10.1145/2996913.2996954},
   Abstract = {© 2016 ACM. Dynamic time warping (DTW) is a widely used
             curve similarity measure. We present a simple and efficient
             (1 + ∈)- approximation algorithm for DTW between a pair of
             point sequences, say, P and Q, each of which is sampled from
             a curve. We prove that the running time of the algorithm is
             O( κ 2 /∈ n log σ) for a pair of κ-packed curves with a
             total of n points, assuming that the spreads of P and Q are
             bounded by σ. The spread of a point set is the ratio of the
             maximum to the minimum pairwise distance, and a curve is
             called κ-packed if the length of its intersection with any
             disk of radius r is at most κr. Although an algorithm with
             similar asymptotic time complexity was presented in [1], our
             algorithm is considerably simpler and more efficient in
             practice. We have implemented our algorithm. Our experiments
             on both synthetic and real-world data sets show that it is
             an order of magnitude faster than the standard exact DP
             algorithm on point sequences of length 5; 000 or more while
             keeping the approximation error within 5-10%. We demonstrate
             the eficacy of our algorithm by using it in two applications
             computing the k most similar trajectories to a query
             trajectory, and running the iterative closest point method
             for a pair of trajectories. We show that we can achieve 8-12
             times speedup using our algorithm as a subroutine in these
             applications, without compromising much in
             accuracy.},
   Doi = {10.1145/2996913.2996954},
   Key = {fds323823}
}

@article{fds323790,
   Author = {Nath, A and Fox, K and Agarwal, PK and Munagala, K},
   Title = {Massively parallel algorithms for computing TIN DEMs and
             contour trees for large terrains},
   Journal = {GIS: Proceedings of the ACM International Symposium on
             Advances in Geographic Information Systems},
   Year = {2016},
   Month = {October},
   ISBN = {9781450345897},
   url = {http://dx.doi.org/10.1145/2996913.2996952},
   Abstract = {© 2016 ACM. We propose parallel algorithms in the massively
             parallel communication (MPC) model (e.g. MapReduce) for
             processing large terrain elevation data (represented as a 3D
             point cloud) that are too big to fit on one machine. In
             particular, given a set S of 3D points that is distributed
             across multiple machines, we present a simple randomized
             algorithm to construct a TIN DEM of S by computing the
             Delaunay triangulation of the xy-projections of points in S,
             which is also stored across multiple machines. With high
             probability, the algorithm works in O(1) rounds and the
             total work performed is O(n log n). Next, we describe an
             efficient algorithm in the MPC model for computing the
             contour tree of the resulting DEM. Under some assumptions on
             the input, the algorithm works in O(1) rounds and the total
             work performed is O(n log n).},
   Doi = {10.1145/2996913.2996952},
   Key = {fds323790}
}

@article{fds318110,
   Author = {Agarwal, PK and Aronov, B and Har-Peled, S and Phillips, JM and Yi, K and Zhang, W},
   Title = {Nearest-Neighbor Searching Under Uncertainty
             II},
   Journal = {ACM Transactions on Algorithms},
   Volume = {13},
   Number = {1},
   Pages = {1-25},
   Year = {2016},
   Month = {October},
   url = {http://dx.doi.org/10.1145/2955098},
   Doi = {10.1145/2955098},
   Key = {fds318110}
}

@article{fds318111,
   Author = {Agarwal, PK and Kumar, N and Sintos, S and Suri, S},
   Title = {Range-max queries on uncertain data},
   Journal = {Proceedings of the ACM SIGACT-SIGMOD-SIGART Symposium on
             Principles of Database Systems},
   Volume = {26-June-01-July-2016},
   Pages = {465-476},
   Year = {2016},
   Month = {June},
   ISBN = {9781450341912},
   url = {http://dx.doi.org/10.1145/2902251.2902281},
   Abstract = {© 2016 ACM. Let P be a set of n uncertain points in ℝ d ,
             where each point p i ∈ P is associated with a real value v
             i and a probability α i ∈ (0,1] of existence, i.e., each
             p i exists with an independent probability α i . 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. The specific contributions of our paper include the
             following: (i) The first index of sub-quadratic size to
             achieve a sub-linear query time in any dimension d ≥ 1. It
             also provides a trade-off between query time and size of the
             index. (ii) A conditional lower bound for the most-likely
             range-max queries, based on the conjectured hardness of the
             set-intersection problem, which suggests that in the worst
             case the product (query time) 2 x (index size) is Ω(n 2
             /polylog (n) ). (iii) A linear-size index for estimating the
             expected range-max value within approximation factor 1/2 in
             O(log c n) time, for some constant c > 0; that is, if the
             expected maximum value is μ then the query procedure
             returns a value μ′ with μ/2 ≤ μ′ ≤ μ. (iv)
             Extensions of our algorithm to more general uncertainty
             models and for computing the top-k values of the
             range-max.},
   Doi = {10.1145/2902251.2902281},
   Key = {fds318111}
}

@article{fds318112,
   Author = {Agarwal, PK and Fox, K and Munagala, K and Nath, A},
   Title = {Parallel algorithms for constructing range and
             nearest-neighbor searching data structures},
   Journal = {Proceedings of the ACM SIGACT-SIGMOD-SIGART Symposium on
             Principles of Database Systems},
   Volume = {26-June-01-July-2016},
   Pages = {429-440},
   Year = {2016},
   Month = {June},
   ISBN = {9781450341912},
   url = {http://dx.doi.org/10.1145/2902251.2902303},
   Abstract = {© 2016 ACM. With the massive amounts of data available
             today, it is common to store and process data using multiple
             machines. Parallel programming platforms such as MapReduce
             and its variants are popular frameworks for handling such
             large data. We present the first provably efficient
             algorithms to compute, store, and query data structures for
             range queries and approximate nearest neighbor queries in a
             popular parallel computing abstraction that captures the
             salient features of MapReduce and other massively parallel
             communication (MPC) models. In particular, we describe
             algorithms for kd-trees, range trees, and BBD-trees that
             only require O(1) rounds of communication for both
             preprocessing and querying while staying competitive in
             terms of running time and workload to their classical
             counterparts. Our algorithms are randomized, but they can be
             made deterministic at some increase in their running time
             and workload while keeping the number of rounds of
             communication to be constant.},
   Doi = {10.1145/2902251.2902303},
   Key = {fds318112}
}

@article{fds318113,
   Author = {Agarwal, PK and Fox, K and Pan, J and Ying, R},
   Title = {Approximating dynamic time warping and edit distance for a
             pair of point sequences},
   Journal = {LIPIcs},
   Volume = {51},
   Pages = {6.1-6.16},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.4230/LIPIcs.SoCG.2016.6},
   Abstract = {© Pankaj K. Agarwal, Kyle Fox, Jiangwei Pan, and Rex Ying.
             We present the first subquadratic algorithms for computing
             similarity between a pair of point sequences in
             double-struck R d , for any fixed d > 1, using dynamic time
             warping (DTW) and edit distance, assuming that the point
             sequences are drawn from certain natural families of curves.
             In particular, our algorithms compute (1 +
             ε)-approximations of DTW and ED in near-linear time for
             point sequences drawn from κ-packed or κ-bounded curves,
             and subquadratic time for backbone sequences. Roughly
             speaking, a curve is κ-packed if the length of its
             intersection with any ball of radius r is at most κ · r,
             and it is κ-bounded if the sub-curve between two curve
             points does not go too far from the two points compared to
             the distance between the two points. In backbone sequences,
             consecutive points are spaced at approximately equal
             distances apart, and no two points lie very close together.
             Recent results suggest that a subquadratic algorithm for DTW
             or ED is unlikely for an arbitrary pair of point sequences
             even for d = 1. The commonly used dynamic programming
             algorithms for these distance measures reduce the problem to
             computing a minimum-weight path in a grid graph. Our
             algorithms work by constructing a small set of rectangular
             regions that cover the grid vertices. The weights of
             vertices inside each rectangle are roughly the same, and we
             develop efficient procedures to compute the approximate
             minimum-weight paths through these rectangles.},
   Doi = {10.4230/LIPIcs.SoCG.2016.6},
   Key = {fds318113}
}

@article{fds314402,
   Author = {Yu, A and Agarwal, PK and Yang, J},
   Title = {Top-$k$ Preferences in High Dimensions},
   Journal = {IEEE Transactions on Knowledge and Data Engineering},
   Volume = {28},
   Number = {2},
   Pages = {311-325},
   Year = {2016},
   Month = {February},
   ISSN = {1041-4347},
   url = {http://dx.doi.org/10.1109/TKDE.2015.2451630},
   Doi = {10.1109/TKDE.2015.2451630},
   Key = {fds314402}
}

@article{fds315094,
   Author = {Agarwal, PK and Fox, K and Salzman, O},
   Title = {An efficient algorithm for computing high-quality paths amid
             polygonal obstacles},
   Journal = {Proceedings of the Annual ACM-SIAM Symposium on Discrete
             Algorithms},
   Volume = {2},
   Pages = {1179-1192},
   Year = {2016},
   Month = {January},
   ISBN = {9781510819672},
   Abstract = {© Copyright (2016) by SIAM: Society for Industrial and
             Applied Mathematics. We study a path-planning problem amid a
             set 0 of obstacles in R2, in which we wish to compute a
             short path between two points while also maintaining a high
             clearance from 0; the clearance of a point is its distance
             from a nearest obstacle in 0. 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 0(n2/ϵ2 log n/ϵ) a path
             of total cost at most (1 + ϵ) times the cost of the optimal
             path.},
   Key = {fds315094}
}

@article{fds321561,
   Author = {Pan, J and Rao, V and Agarwal, PK and Gelfand, AE},
   Title = {Markov-modulated marked poisson processes for check-in
             data},
   Journal = {33rd International Conference on Machine Learning, ICML
             2016},
   Volume = {5},
   Pages = {3311-3320},
   Year = {2016},
   Month = {January},
   ISBN = {9781510829008},
   Abstract = {© 2016 by the author(s). We develop continuous-time
             probabilistic models to study trajectory data consisting of
             times and locations of user 'check-ins'. We model the data
             as realizations of a marked point process, with intensity
             and mark-distribution modulated by a latent Markov jump
             process (MJP). We also include user-heterogeneity in our
             model by assigning each user a vector of 'preferred
             locations'. Our model extends latent Dirichlet allocation by
             dropping the bag-of-words assumption and operating in
             continuous time. We show how an appropriate choice of priors
             allows efficient posterior inference. Our experiments
             demonstrate the usefulness of our approach by comparing with
             various baselines on a variety of tasks.copyright},
   Key = {fds321561}
}


%% Arlotto, Alessandro   
@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 and Algorithms},
   Volume = {52},
   Number = {1},
   Pages = {41-53},
   Publisher = {Wiley},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1002/rsa.20728},
   Abstract = {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 O(log
             n) of optimal. Our construction provides a direct and
             natural way for proving the O(log n)-optimality gap. An
             earlier proof of the same result made crucial use of a key
             inequality of Bruss and Delbaen (2001) and of
             de-Poissonization.},
   Doi = {10.1002/rsa.20728},
   Key = {fds330134}
}

@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{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},
   Year = {2018},
   url = {http://dx.doi.org/10.1007/s11009-016-9522-7},
   Doi = {10.1007/s11009-016-9522-7},
   Key = {fds330136}
}

@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}
}

@article{fds322098,
   Author = {Arlotto, A and Steele, JM},
   Title = {A central limit theorem for temporally nonhomogenous Markov
             chains with applications to dynamic programming},
   Journal = {Mathematics of Operations Research},
   Volume = {41},
   Number = {4},
   Pages = {1448-1468},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.1287/moor.2016.0784},
   Doi = {10.1287/moor.2016.0784},
   Key = {fds322098}
}

@article{fds322099,
   Author = {Arlotto, A and Mossel, E and Steele, JM},
   Title = {Quickest online selection of an increasing subsequence of
             specified size},
   Journal = {Random Structures and Algorithms},
   Volume = {49},
   Number = {2},
   Pages = {235-252},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.1002/rsa.20634},
   Doi = {10.1002/rsa.20634},
   Key = {fds322099}
}

@article{fds330138,
   Author = {Arlotto, A and Steele, JM},
   Title = {Beardwood–Halton–Hammersley theorem for stationary
             ergodic sequences: a counterexample},
   Journal = {The annals of applied probability : an official journal of
             the Institute of Mathematical Statistics},
   Volume = {26},
   Number = {4},
   Pages = {2141-2168},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.1214/15-AAP1142},
   Doi = {10.1214/15-AAP1142},
   Key = {fds330138}
}


%% Beale, J. Thomas   
@article{fds322466,
   Author = {Beale, JT and Ying, W and Wilson, JR},
   Title = {A Simple Method for Computing Singular or Nearly Singular
             Integrals on Closed Surfaces},
   Journal = {Communications in computational physics},
   Volume = {20},
   Number = {03},
   Pages = {733-753},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.4208/cicp.030815.240216a},
   Doi = {10.4208/cicp.030815.240216a},
   Key = {fds322466}
}


%% Bendich, Paul L   
@article{fds324396,
   Author = {Bendich, P and Chin, SP and Clark, J and Desena, J and Harer, J and Munch,
             E and Newman, A and Porter, D and Rouse, D and Strawn, N and Watkins,
             A},
   Title = {Topological and statistical behavior classifiers for
             tracking applications},
   Journal = {IEEE Transactions on Aerospace and Electronic
             Systems},
   Volume = {52},
   Number = {6},
   Pages = {2644-2661},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1109/TAES.2016.160405},
   Abstract = {© 1965-2011 IEEE.This paper introduces a method to
             integrate target behavior into the multiple hypothesis
             tracker (MHT) likelihood ratio. In particular, a periodic
             track appraisal based on behavior is introduced. The track
             appraisal uses elementary topological data analysis coupled
             with basic machine-learning techniques, and it adjusts the
             traditional kinematic data association likelihood (i.e.,
             track score) using an established formulation for
             feature-aided data association. The proposed method is
             tested and demonstrated on synthetic vehicular data
             representing an urban traffic scene generated by the
             Simulation of Urban Mobility package. The vehicles in the
             scene exhibit different driving behaviors. The proposed
             method distinguishes those behaviors and shows improved data
             association decisions relative to a conventional, kinematic
             MHT.},
   Doi = {10.1109/TAES.2016.160405},
   Key = {fds324396}
}

@article{fds321986,
   Author = {Bendich, P and Gasparovic, E and Harer, J and Tralie,
             C},
   Title = {Geometric models for musical audio data},
   Journal = {LIPIcs},
   Volume = {51},
   Pages = {65.1-65.5},
   Year = {2016},
   Month = {June},
   ISBN = {9783959770095},
   url = {http://dx.doi.org/10.4230/LIPIcs.SoCG.2016.65},
   Abstract = {© Paul Bendich, Ellen Gasparovic, John Harer, and
             Christopher Tralie. We study the geometry of sliding window
             embeddings of audio features that summarize perceptual
             information about audio, including its pitch and timbre.
             These embeddings can be viewed as point clouds in high
             dimensions, and we add structure to the point clouds using a
             cover tree with adaptive thresholds based on multi-scale
             local principal component analysis to automatically assign
             points to clusters. We connect neighboring clusters in a
             scaffolding graph, and we use knowledge of stratified space
             structure to refine our estimates of dimension in each
             cluster, demonstrating in our music applications that
             choruses and verses have higher dimensional structure, while
             transitions between them are lower dimensional. We showcase
             our technique with an interactive web-based application
             powered by Javascript and WebGL which plays music
             synchronized with a principal component analysis embedding
             of the point cloud down to 3D. We also render the clusters
             and the scaffolding on top of this projection to visualize
             the transitions between different sections of the
             music.},
   Doi = {10.4230/LIPIcs.SoCG.2016.65},
   Key = {fds321986}
}

@article{fds315426,
   Author = {Bendich, P and Marron, JS and Miller, E and Pieloch, A and Skwerer,
             S},
   Title = {Persistent homology analysis of brain artery
             trees},
   Journal = {Annals of Applied Statistics},
   Volume = {10},
   Number = {1},
   Pages = {19 pages},
   Year = {2016},
   Month = {January},
   ISSN = {1932-6157},
   url = {http://hdl.handle.net/10161/11157 Duke open
             access},
   Abstract = {New representations of tree-structured data objects, using
             ideas from topological data analysis, enable improved
             statistical analyses of a population of brain artery trees.
             A number of representations of each data tree arise from
             persistence diagrams that quantify branching and looping of
             vessels at multiple scales. Novel approaches to the
             statistical analysis, through various summaries of the
             persistence diagrams, lead to heightened correlations with
             covariates such as age and sex, relative to earlier analyses
             of this data set. The correlation with age continues to be
             significant even after controlling for correlations from
             earlier significant summaries},
   Doi = {10.1214/15-AOAS886},
   Key = {fds315426}
}

@article{fds311346,
   Author = {Paul Bendich and Ellen Gasparovic and John Harer and Christopher
             J. Tralie},
   Title = {Scaffoldings and Spines: Organizing High-Dimensional Data
             Using Cover Trees, Local Principal Component Analysis, and
             Persistent Homology},
   Year = {2016},
   url = {http://arxiv.org/abs/1602.06245},
   Key = {fds311346}
}


%% 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{fds300017,
   Author = {Bray, HL and Jauregui, JL and Mars, M},
   Title = {Time Flat Surfaces and the Monotonicity of the Spacetime
             Hawking Mass II},
   Journal = {Annales Henri Poincaré},
   Volume = {17},
   Number = {6},
   Pages = {1457-1475},
   Publisher = {Springer Basel},
   Year = {2016},
   Month = {June},
   ISSN = {1424-0637},
   url = {http://arxiv.org/abs/1402.3287},
   Abstract = {In this sequel paper we give a shorter, second proof of the
             monotonicity of the Hawking mass for time flat surfaces
             under spacelike uniformly area expanding flows in spacetimes
             that satisfy the dominant energy condition. We also include
             a third proof which builds on a known formula and describe a
             class of sufficient conditions of divergence type for the
             monotonicity of the Hawking mass. These flows of surfaces
             may have connections to the problem in general relativity of
             bounding the total mass of a spacetime from below by the
             quasi-local mass of spacelike 2-surfaces in the
             spacetime.},
   Doi = {10.1007/s00023-015-0420-2},
   Key = {fds300017}
}


%% Bryant, Robert   
@article{fds325462,
   Author = {Bryant, RL 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{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},
   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 = {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.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.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.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}
}

@article{fds326882,
   Author = {Reboredo, H and Renna, F and Calderbank, R and Rodrigues,
             MRD},
   Title = {Bounds on the Number of Measurements for Reliable
             Compressive Classification},
   Journal = {IEEE Transactions on Signal Processing},
   Volume = {64},
   Number = {22},
   Pages = {5778-5793},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.1109/TSP.2016.2599496},
   Doi = {10.1109/TSP.2016.2599496},
   Key = {fds326882}
}

@article{fds326883,
   Author = {Thompson, A and Robles, FE and Wilson, JW and Deb, S and Calderbank, R and Warren, WS},
   Title = {Dual-wavelength pump-probe microscopy analysis of melanin
             composition.},
   Journal = {Scientific Reports},
   Volume = {6},
   Pages = {36871},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.1038/srep36871},
   Abstract = {Pump-probe microscopy is an emerging technique that provides
             detailed chemical information of absorbers with
             sub-micrometer spatial resolution. Recent work has shown
             that the pump-probe signals from melanin in human skin
             cancers correlate well with clinical concern, but it has
             been difficult to infer the molecular origins of these
             differences. Here we develop a mathematical framework to
             describe the pump-probe dynamics of melanin in human
             pigmented tissue samples, which treats the ensemble of
             individual chromophores that make up melanin as Gaussian
             absorbers with bandwidth related via Frenkel excitons. Thus,
             observed signals result from an interplay between the
             spectral bandwidths of the individual underlying
             chromophores and spectral proximity of the pump and probe
             wavelengths. The model is tested using a dual-wavelength
             pump-probe approach and a novel signal processing method
             based on gnomonic projections. Results show signals can be
             described by a single linear transition path with different
             rates of progress for different individual pump-probe
             wavelength pairs. Moreover, the combined dual-wavelength
             data shows a nonlinear transition that supports our
             mathematical framework and the excitonic model to describe
             the optical properties of melanin. The novel gnomonic
             projection analysis can also be an attractive generic tool
             for analyzing mixing paths in biomolecular and analytical
             chemistry.},
   Doi = {10.1038/srep36871},
   Key = {fds326883}
}

@article{fds326750,
   Author = {Renna, F and Wang, L and Yuan, X and Yang, J and Reeves, G and Calderbank,
             R and Carin, L and Rodrigues, MRD},
   Title = {Classification and Reconstruction of High-Dimensional
             Signals From Low-Dimensional Features in the Presence of
             Side Information},
   Journal = {IEEE Transactions on Information Theory},
   Volume = {62},
   Number = {11},
   Pages = {6459-6492},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.1109/TIT.2016.2606646},
   Doi = {10.1109/TIT.2016.2606646},
   Key = {fds326750}
}

@article{fds326751,
   Author = {Kumar, S and Calderbank, R and Pfister, HD},
   Title = {Beyond double transitivity: Capacity-achieving cyclic codes
             on erasure channels},
   Journal = {2016 IEEE Information Theory Workshop, ITW
             2016},
   Pages = {241-245},
   Year = {2016},
   Month = {October},
   ISBN = {9781509010905},
   url = {http://dx.doi.org/10.1109/ITW.2016.7606832},
   Abstract = {© 2016 IEEE. Recently, sequences of error-correcting codes
             with doubly-transitive permutation groups were shown to
             achieve capacity on erasure channels under symbol-wise
             maximum a posteriori (MAP) decoding. From this, it follows
             that Reed-Muller and primitive narrow-sense BCH codes
             achieve capacity in the same setting. In this article, we
             extend this result to a large family of cyclic codes by
             considering codes whose permutation groups satisfy a
             condition weaker than double transitivity. The article
             combines two simple technical contributions. First, we show
             that the transition width of a monotone boolean function is
             O(1/log k), where k is the size of the smallest orbit
             induced by its symmetry group. The proof is based on
             Talagrand's lower bound on influences for monotone boolean
             functions. Second, we consider the extrinsic information
             transfer (EXIT) function of an Fq-linear cyclic code whose
             blocklength N divides q t -1 and is coprime with q-1. We
             show that this EXIT function is a monotone boolean function
             whose symmetry group contains no orbits of size smaller than
             the smallest prime divisor of t. Combining these, we show
             that sequences of cyclic codes, whose blocklengths satisfy
             the above conditions, achieve capacity on the q-ary erasure
             channel if all prime divisors of t tend to
             infinity.},
   Doi = {10.1109/ITW.2016.7606832},
   Key = {fds326751}
}

@article{fds326752,
   Author = {Mappouras, G and Vahid, A and Calderbank, R and Sorin,
             DJ},
   Title = {Methuselah flash: Rewriting codes for extra long storage
             lifetime},
   Journal = {Proceedings - 46th Annual IEEE/IFIP International Conference
             on Dependable Systems and Networks, DSN 2016},
   Pages = {180-191},
   Year = {2016},
   Month = {September},
   ISBN = {9781467388917},
   url = {http://dx.doi.org/10.1109/DSN.2016.25},
   Abstract = {© 2016 IEEE. Motivated by embedded systems and datacenters
             that require long-life components, we extend the lifetime of
             Flash memory using rewriting codes that allow for multiple
             writes to a page before it needs to be erased. Although
             researchers have previously explored rewriting codes for
             this purpose, we make two significant contributions beyond
             prior work. First, we remove the assumption of idealized -
             and unrealistically optimistic - Flash cells used in prior
             work on endurance codes. Unfortunately, current Flash
             technology has a non-ideal interface, due to its underlying
             physical design, and does not, for example, allow all
             seemingly possible increases in a cell's level. We show how
             to provide the ideal multi-level cell interface, by
             developing a virtual Flash cell, and we evaluate its impact
             on existing endurance codes. Our second contribution is our
             development of novel endurance codes, called Methuselah
             Flash Codes (MFC), that provide better cost/lifetime
             trade-offs than previously studied codes.},
   Doi = {10.1109/DSN.2016.25},
   Key = {fds326752}
}

@article{fds326884,
   Author = {Vahid, A and Calderbank, R},
   Title = {Two-User Erasure Interference Channels With Local Delayed
             CSIT},
   Journal = {IEEE Transactions on Information Theory},
   Volume = {62},
   Number = {9},
   Pages = {4910-4923},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.1109/TIT.2016.2594224},
   Doi = {10.1109/TIT.2016.2594224},
   Key = {fds326884}
}

@article{fds326885,
   Author = {Nokleby, M and Beirami, A and Calderbank, R},
   Title = {Rate-distortion bounds on Bayes risk in supervised
             learning},
   Journal = {IEEE International Symposium on Information Theory -
             Proceedings},
   Volume = {2016-August},
   Pages = {2099-2103},
   Year = {2016},
   Month = {August},
   ISBN = {9781509018062},
   url = {http://dx.doi.org/10.1109/ISIT.2016.7541669},
   Abstract = {© 2016 IEEE. An information-theoretic framework is
             presented for estimating the number of labeled samples
             needed to train a classifier in a parametric Bayesian
             setting. Ideas from rate-distortion theory are used to
             derive bounds for the average L 1 or L ∞ distance between
             the learned classifier and the true maximum a posteriori
             classifier in terms of familiar information-theoretic
             quantities and the number of training samples available. The
             maximum a posteriori classifier is viewed as a random
             source, labeled training data are viewed as a finite-rate
             encoding of the source, and the L 1 or L ∞ Bayes risk is
             viewed as the average distortion. The result is a framework
             dual to the well-known probably approximately correct (PAC)
             framework. PAC bounds characterize worst-case learning
             performance of a family of classifiers whose complexity is
             captured by the Vapnik-Chervonenkis (VC) dimension. The
             rate-distortion framework, on the other hand, characterizes
             the average-case performance of a family of data
             distributions in terms of a quantity called the
             interpolation dimension, which represents the complexity of
             the family of data distributions. The resulting bounds do
             not suffer from the pessimism typical of the PAC framework,
             particularly when the training set is small.},
   Doi = {10.1109/ISIT.2016.7541669},
   Key = {fds326885}
}

@article{fds326886,
   Author = {Vahid, A and Calderbank, R},
   Title = {When does spatial correlation add value to delayed channel
             state information?},
   Journal = {IEEE International Symposium on Information Theory -
             Proceedings},
   Volume = {2016-August},
   Pages = {2624-2628},
   Year = {2016},
   Month = {August},
   ISBN = {9781509018062},
   url = {http://dx.doi.org/10.1109/ISIT.2016.7541774},
   Abstract = {© 2016 IEEE. Fast fading wireless networks with delayed
             knowledge of the channel state information have received
             significant attention in recent years. An exception is
             networks where channels are spatially correlated. This paper
             characterizes the capacity region of two-user erasure
             interference channels with delayed knowledge of the channel
             state information and spatially correlated channels. There
             are instances where spatial correlation eliminates any
             potential gain from delayed channel state information and
             instances where it enables the same performance that is
             possible with instantaneous knowledge of channel state. The
             key is an extremal entropy inequality for spatially
             correlated channels that separates the two types of
             instances. It is also shown that to achieve the capacity
             region, each transmitter only needs to rely on the delayed
             knowledge of the channels to which it is
             connected.},
   Doi = {10.1109/ISIT.2016.7541774},
   Key = {fds326886}
}

@article{fds326887,
   Author = {Sokolic, J and Renna, F and Calderbank, R and Rodrigues,
             MRD},
   Title = {Mismatch in the Classification of Linear Subspaces:
             Sufficient Conditions for Reliable Classification},
   Journal = {IEEE Transactions on Signal Processing},
   Volume = {64},
   Number = {12},
   Pages = {3035-3050},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1109/TSP.2016.2537272},
   Doi = {10.1109/TSP.2016.2537272},
   Key = {fds326887}
}

@article{fds326753,
   Author = {Wang, L and Renna, F and Yuan, X and Rodrigues, M and Calderbank, R and Carin, L},
   Title = {A general framework for reconstruction and classification
             from compressive measurements with side information},
   Journal = {IEEE International Conference on Acoustics Speech and Signal
             Processing},
   Volume = {2016-May},
   Pages = {4239-4243},
   Year = {2016},
   Month = {May},
   ISBN = {9781479999880},
   url = {http://dx.doi.org/10.1109/ICASSP.2016.7472476},
   Abstract = {© 2016 IEEE. We develop a general framework for compressive
             linear-projection measurements with side information. Side
             information is an additional signal correlated with the
             signal of interest. We investigate the impact of side
             information on classification and signal recovery from
             low-dimensional measurements. Motivated by real
             applications, two special cases of the general model are
             studied. In the first, a joint Gaussian mixture model is
             manifested on the signal and side information. The second
             example again employs a Gaussian mixture model for the
             signal, with side information drawn from a mixture in the
             exponential family. Theoretical results on recovery and
             classification accuracy are derived. The presence of side
             information is shown to yield improved performance, both
             theoretically and experimentally.},
   Doi = {10.1109/ICASSP.2016.7472476},
   Key = {fds326753}
}

@article{fds326888,
   Author = {Beirami, A and Calderbank, R and Christiansen, M and Duffy, K and Makhdoumi, A and Medard, M},
   Title = {A geometric perspective on guesswork},
   Journal = {2015 53rd Annual Allerton Conference on Communication,
             Control, and Computing, Allerton 2015},
   Pages = {941-948},
   Year = {2016},
   Month = {April},
   ISBN = {9781509018239},
   url = {http://dx.doi.org/10.1109/ALLERTON.2015.7447109},
   Abstract = {© 2015 IEEE. Guesswork is the position at which a random
             string drawn from a given probability distribution appears
             in the list of strings ordered from the most likely to the
             least likely. We define the tilt operation on probability
             distributions and show that it parametrizes an exponential
             family of distributions, which we refer to as the tilted
             family of the source. We prove that two sources result in
             the same guesswork, i.e., the same ordering from most likely
             to least likely on all strings, if and only if they belong
             to the same tilted family. We also prove that the strings
             whose guesswork is smaller than a given string are
             concentrated on the tilted family. Applying Laplace's
             method, we derive precise approximations on the distribution
             of guesswork on i.i.d. sources. The simulations show a good
             match between the approximations and the actual guesswork
             for i.i.d. sources.},
   Doi = {10.1109/ALLERTON.2015.7447109},
   Key = {fds326888}
}

@article{fds326889,
   Author = {Vahid, A and Shomorony, I and Calderbank, R},
   Title = {Informational bottlenecks in two-unicast wireless networks
             with delayed CSIT},
   Journal = {2015 53rd Annual Allerton Conference on Communication,
             Control, and Computing, Allerton 2015},
   Pages = {1256-1263},
   Year = {2016},
   Month = {April},
   ISBN = {9781509018239},
   url = {http://dx.doi.org/10.1109/ALLERTON.2015.7447152},
   Abstract = {© 2015 IEEE. We study the impact of delayed channel state
             information at the transmitters (CSIT) in two-unicast
             wireless networks with a layered topology and arbitrary
             connectivity. We introduce a technique to obtain outer
             bounds to the degrees-of-freedom (DoF) region through the
             new graph-theoretic notion of bottleneck nodes. Such nodes
             act as informational bottlenecks only under the assumption
             of delayed CSIT, and imply asymmetric DoF bounds of the form
             mD1 + D2 ≤ m. Combining this outer-bound technique with
             new achievability schemes, we characterize the sum DoF of a
             class of two-unicast wireless networks, which shows that,
             unlike in the case of instantaneous CSIT, the DoF of
             two-unicast networks with delayed CSIT can take an infinite
             set of values.},
   Doi = {10.1109/ALLERTON.2015.7447152},
   Key = {fds326889}
}

@article{fds326890,
   Author = {Huang, J and Qiu, Q and Calderbank, R},
   Title = {The Role of Principal Angles in Subspace
             Classification},
   Journal = {IEEE Transactions on Signal Processing},
   Volume = {64},
   Number = {8},
   Pages = {1933-1945},
   Year = {2016},
   Month = {April},
   url = {http://dx.doi.org/10.1109/TSP.2015.2500889},
   Doi = {10.1109/TSP.2015.2500889},
   Key = {fds326890}
}

@article{fds326754,
   Author = {Qiu, Q and Thompson, A and Calderbank, R and Sapiro,
             G},
   Title = {Data Representation Using the Weyl Transform},
   Journal = {IEEE Transactions on Signal Processing},
   Volume = {64},
   Number = {7},
   Pages = {1844-1853},
   Year = {2016},
   Month = {April},
   url = {http://dx.doi.org/10.1109/TSP.2015.2505661},
   Doi = {10.1109/TSP.2015.2505661},
   Key = {fds326754}
}

@article{fds326891,
   Author = {Goparaju, S and Rouayheb, SE and Calderbank, R},
   Title = {Can linear minimum storage regenerating codes be universally
             secure?},
   Journal = {Conference Record of the Asilomar Conference on Signals,
             Systems and Computers},
   Volume = {2016-February},
   Pages = {549-553},
   Year = {2016},
   Month = {February},
   ISBN = {9781467385763},
   url = {http://dx.doi.org/10.1109/ACSSC.2015.7421189},
   Abstract = {© 2015 IEEE. We study the problem of making a distributed
             storage system information-theoretically secure against a
             passive eavesdropper, and aim to characterize coding schemes
             that are universally secure for up to a given number of
             eavesdropped nodes. Specifically, we consider minimum
             storage regenerating (MSR) codes and ask the following
             question: For an MSR code where a failed node is repaired
             using all the remaining nodes, is it possible to
             simultaneously be optimally secure using a single linear
             coding scheme? We define a pareto-optimality associated with
             this simultaneity and show that there exists at least one
             linear coding scheme that is pareto-optimal.},
   Doi = {10.1109/ACSSC.2015.7421189},
   Key = {fds326891}
}

@article{fds326756,
   Author = {Carpenter, KLH and Sprechmann, P and Calderbank, R and Sapiro, G and Egger, HL},
   Title = {Quantifying Risk for Anxiety Disorders in Preschool
             Children: A Machine Learning Approach.},
   Journal = {PloS one},
   Volume = {11},
   Number = {11},
   Pages = {e0165524},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0165524},
   Abstract = {Early childhood anxiety disorders are common, impairing, and
             predictive of anxiety and mood disorders later in childhood.
             Epidemiological studies over the last decade find that the
             prevalence of impairing anxiety disorders in preschool
             children ranges from 0.3% to 6.5%. Yet, less than 15% of
             young children with an impairing anxiety disorder receive a
             mental health evaluation or treatment. One possible reason
             for the low rate of care for anxious preschoolers is the
             lack of affordable, timely, reliable and valid tools for
             identifying young children with clinically significant
             anxiety. Diagnostic interviews assessing psychopathology in
             young children require intensive training, take hours to
             administer and code, and are not available for use outside
             of research settings. The Preschool Age Psychiatric
             Assessment (PAPA) is a reliable and valid structured
             diagnostic parent-report interview for assessing
             psychopathology, including anxiety disorders, in 2 to 5 year
             old children. In this paper, we apply machine-learning tools
             to already collected PAPA data from two large community
             studies to identify sub-sets of PAPA items that could be
             developed into an efficient, reliable, and valid screening
             tool to assess a young child's risk for an anxiety disorder.
             Using machine learning, we were able to decrease by an order
             of magnitude the number of items needed to identify a child
             who is at risk for an anxiety disorder with an accuracy of
             over 96% for both generalized anxiety disorder (GAD) and
             separation anxiety disorder (SAD). Additionally, rather than
             considering GAD or SAD as discrete/binary entities, we
             present a continuous risk score representing the child's
             risk of meeting criteria for GAD or SAD. Identification of a
             short question-set that assesses risk for an anxiety
             disorder could be a first step toward development and
             validation of a relatively short screening tool feasible for
             use in pediatric clinics and daycare/preschool
             settings.},
   Doi = {10.1371/journal.pone.0165524},
   Key = {fds326756}
}

@article{fds326892,
   Author = {Thompson, A and Calderbank, R},
   Title = {Compressive imaging using fast transform
             coding},
   Journal = {Proceedings of SPIE - The International Society for Optical
             Engineering},
   Volume = {9992},
   Year = {2016},
   Month = {January},
   ISBN = {9781510603882},
   url = {http://dx.doi.org/10.1117/12.2239999},
   Abstract = {© 2016 SPIE. We propose deterministic sampling strategies
             for compressive imaging based on Delsarte-Goethals frames.
             We show that these sampling strategies result in multi-scale
             measurements which can be related to the 2D Haar wavelet
             transform. We demonstrate the effectiveness of our proposed
             strategies through numerical experiments.},
   Doi = {10.1117/12.2239999},
   Key = {fds326892}
}


%% 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 = {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 = {fds329931}
}

@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},
   Volume = {26},
   Number = {2},
   Pages = {751-764},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1109/TIP.2016.2623484},
   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},
   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}
}

@article{fds318286,
   Author = {Wu, H-T and Lewis, GF and Davila, MI and Daubechies, I and Porges,
             SW},
   Title = {Optimizing Estimates of Instantaneous Heart Rate from Pulse
             Wave Signals with the Synchrosqueezing Transform.},
   Journal = {Methods of information in medicine},
   Volume = {55},
   Number = {5},
   Pages = {463-472},
   Year = {2016},
   Month = {October},
   url = {http://dx.doi.org/10.3414/me16-01-0026},
   Abstract = {With recent advances in sensor and computer technologies,
             the ability to monitor peripheral pulse activity is no
             longer limited to the laboratory and clinic. Now inexpensive
             sensors, which interface with smartphones or other
             computer-based devices, are expanding into the consumer
             market. When appropriate algorithms are applied, these new
             technologies enable ambulatory monitoring of dynamic
             physiological responses outside the clinic in a variety of
             applications including monitoring fatigue, health, workload,
             fitness, and rehabilitation. Several of these applications
             rely upon measures derived from peripheral pulse waves
             measured via contact or non-contact photoplethysmography
             (PPG). As technologies move from contact to non-contact PPG,
             there are new challenges. The technology necessary to
             estimate average heart rate over a few seconds from a
             noncontact PPG is available. However, a technology to
             precisely measure instantaneous heat rate (IHR) from
             non-contact sensors, on a beat-to-beat basis, is more
             challenging.The objective of this paper is to develop an
             algorithm with the ability to accurately monitor IHR from
             peripheral pulse waves, which provides an opportunity to
             measure the neural regulation of the heart from the
             beat-to-beat heart rate pattern (i.e., heart rate
             variability).The adaptive harmonic model is applied to model
             the contact or non-contact PPG signals, and a new
             methodology, the Synchrosqueezing Transform (SST), is
             applied to extract IHR. The body sway rhythm inherited in
             the non-contact PPG signal is modeled and handled by the
             notion of wave-shape function.The SST optimizes the
             extraction of IHR from the PPG signals and the technique
             functions well even during periods of poor signal to noise.
             We contrast the contact and non-contact indices of PPG
             derived heart rate with a criterion electrocardiogram (ECG).
             ECG and PPG signals were monitored in 21 healthy subjects
             performing tasks with different physical demands. The root
             mean square error of IHR estimated by SST is significantly
             better than commonly applied methods such as autoregressive
             (AR) method. In the walking situation, while AR method
             fails, SST still provides a reasonably good result.The SST
             processed PPG data provided an accurate estimate of the ECG
             derived IHR and consistently performed better than commonly
             applied methods such as autoregressive method.},
   Doi = {10.3414/me16-01-0026},
   Key = {fds318286}
}

@article{fds323650,
   Author = {Daubechies, I and Defrise, M and Mol, CD},
   Title = {Sparsity-enforcing regularisation and ISTA
             revisited},
   Journal = {Inverse Problems},
   Volume = {32},
   Number = {10},
   Pages = {104001-104001},
   Year = {2016},
   Month = {October},
   url = {http://dx.doi.org/10.1088/0266-5611/32/10/104001},
   Doi = {10.1088/0266-5611/32/10/104001},
   Key = {fds323650}
}

@article{fds320873,
   Author = {O'Neal, WT and Wang, YG and Wu, H-T and Zhang, Z-M and Li, Y and Tereshchenko, LG and Estes, EH and Daubechies, I and Soliman,
             EZ},
   Title = {Electrocardiographic J Wave and Cardiovascular Outcomes in
             the General Population (from the Atherosclerosis Risk In
             Communities Study).},
   Journal = {The American Journal of Cardiology},
   Volume = {118},
   Number = {6},
   Pages = {811-815},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.1016/j.amjcard.2016.06.047},
   Abstract = {The association between the J wave, a key component of the
             early repolarization pattern, and adverse cardiovascular
             outcomes remains unclear. Inconsistencies have stemmed from
             the different methods used to measure the J wave. We
             examined the association between the J wave, detected by an
             automated method, and adverse cardiovascular outcomes in
             14,592 (mean age = 54 ± 5.8 years; 56% women; 26% black)
             participants from the Atherosclerosis Risk In Communities
             (ARIC) study. The J wave was detected at baseline (1987 to
             1989) and during follow-up study visits (1990 to 1992, 1993
             to 1995, and 1996 to 1998) using a fully automated method.
             Sudden cardiac death, coronary heart disease death, and
             cardiovascular mortality were ascertained from hospital
             discharge records, death certificates, and autopsy data
             through December 31, 2010. A total of 278 participants
             (1.9%) had evidence of a J wave. Over a median follow-up of
             22 years, 4,376 of the participants (30%) died. In a
             multivariable Cox regression analysis adjusted for
             demographics, cardiovascular risk factors, and potential
             confounders, the J wave was not associated with an increased
             risk of sudden cardiac death (hazard ratio [HR] 0.74, 95% CI
             0.36 to 1.50), coronary heart disease death (HR 0.72, 95% CI
             0.40 to 1.32), or cardiovascular mortality (HR 1.16, 95% CI
             0.87 to 1.56). An interaction was detected for
             cardiovascular mortality by gender with men (HR 1.54, 95% CI
             1.09 to 2.19) having a stronger association than women (HR
             0.74, 95% CI 0.43 to 1.25; P-interaction = 0.030). In
             conclusion, our findings suggest that the J wave is a benign
             entity that is not associated with an increased risk for
             sudden cardiac arrest in middle-aged adults in the United
             States.},
   Doi = {10.1016/j.amjcard.2016.06.047},
   Key = {fds320873}
}

@article{fds321988,
   Author = {Deligiannis, N and Mota, JFC and Cornelis, B and Rodrigues, MRD and Daubechies, I},
   Title = {X-ray image separation via coupled dictionary
             learning},
   Journal = {Proceedings / ICIP ... International Conference on Image
             Processing},
   Volume = {2016-August},
   Pages = {3533-3537},
   Year = {2016},
   Month = {August},
   ISBN = {9781467399616},
   url = {http://dx.doi.org/10.1109/ICIP.2016.7533017},
   Abstract = {© 2016 IEEE. In support of art investigation, we propose a
             new source separation method that unmixes a single X-ray
             scan acquired from double-sided paintings. Unlike prior
             source separation methods, which are based on statistical or
             structural incoherence of the sources, we use visual images
             taken from the front- and back-side of the panel to drive
             the separation process. The coupling of the two imaging
             modalities is achieved via a new multi-scale dictionary
             learning method. Experimental results demonstrate that our
             method succeeds in the discrimination of the sources, while
             state-of-the-art methods fail to do so.},
   Doi = {10.1109/ICIP.2016.7533017},
   Key = {fds321988}
}

@article{fds317216,
   Author = {Yin, R and Monson, E and Honig, E and Daubechies, I and Maggioni,
             M},
   Title = {Object recognition in art drawings: Transfer of a neural
             network},
   Journal = {IEEE International Conference on Acoustics Speech and Signal
             Processing},
   Volume = {2016-May},
   Pages = {2299-2303},
   Year = {2016},
   Month = {May},
   ISBN = {9781479999880},
   ISSN = {1520-6149},
   url = {http://dx.doi.org/10.1109/ICASSP.2016.7472087},
   Abstract = {© 2016 IEEE. We consider the problem of recognizing objects
             in collections of art works, in view of automatically
             labeling, searching and organizing databases of art works.
             To avoid manually labelling objects, we introduce a
             framework for transferring a convolutional neural network
             (CNN), trained on available large collections of labelled
             natural images, to the context of drawings. We retrain both
             the top and the bottom layer of the network, responsible for
             the high-level classiication output and the low-level
             features detection respectively, by transforming natural
             images into drawings. We apply this procedure to the
             drawings in the Jan Brueghel Wiki, and show the transferred
             CNN learns a discriminative metric on drawings and achieves
             good recognition accuracy. We also discuss why standard
             descriptor-based methods is problematic in the context of
             drawings.},
   Doi = {10.1109/ICASSP.2016.7472087},
   Key = {fds317216}
}

@article{fds315774,
   Author = {Daubechies, I and Wang, YG and Wu, H-T},
   Title = {ConceFT: concentration of frequency and time via a
             multitapered synchrosqueezed transform.},
   Journal = {Philosophical Transactions A},
   Volume = {374},
   Number = {2065},
   Pages = {20150193},
   Year = {2016},
   Month = {April},
   ISSN = {1364-503X},
   url = {http://dx.doi.org/10.1098/rsta.2015.0193},
   Abstract = {A new method is proposed to determine the time-frequency
             content of time-dependent signals consisting of multiple
             oscillatory components, with time-varying amplitudes and
             instantaneous frequencies. Numerical experiments as well as
             a theoretical analysis are presented to assess its
             effectiveness.},
   Doi = {10.1098/rsta.2015.0193},
   Key = {fds315774}
}

@article{fds315775,
   Author = {Huang, NE and Daubechies, I and Hou, TY},
   Title = {Adaptive data analysis: theory and applications.},
   Journal = {Philosophical Transactions A},
   Volume = {374},
   Number = {2065},
   Pages = {20150207},
   Year = {2016},
   Month = {April},
   ISSN = {1364-503X},
   url = {http://dx.doi.org/10.1098/rsta.2015.0207},
   Doi = {10.1098/rsta.2015.0207},
   Key = {fds315775}
}

@article{fds318287,
   Author = {Yin, R and Cornelis, B and Fodor, G and Ocon, N and Dunson, D and Daubechies, I},
   Title = {Removing Cradle Artifacts in X-Ray Images of
             Paintings},
   Journal = {SIAM Journal on Imaging Sciences},
   Volume = {9},
   Number = {3},
   Pages = {1247-1272},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1137/15M1053554},
   Doi = {10.1137/15M1053554},
   Key = {fds318287}
}


%% Dolbow, John E.   
@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}
}

@article{fds327049,
   Author = {Spencer, BW and Jiang, W and Dolbow, JE and Peco,
             C},
   Title = {Pellet cladding mechanical interaction modeling using the
             extended finite element method},
   Journal = {Top Fuel 2016: LWR Fuels with Enhanced Safety and
             Performance},
   Pages = {929-938},
   Year = {2016},
   Month = {January},
   ISBN = {9780894487309},
   Abstract = {Fracturing of ceramic light water reactor (LWR) fuel has
             multiple important effects on fuel performance. One
             particularly important concern is that cracks in the fuel
             cause elevated stresses in the cladding when pellet cladding
             mechanical interaction (PCMI) occurs. Modeling the effects
             of these cracks on the cladding stress is important for
             avoiding conditions when these elevated stresses could cause
             cladding failure. This can be readily done in fuel
             performance codes based on the finite element method by
             creating finite element meshes that incorporate discrete
             cracks defined a priori. The drawback of this approach,
             however, is that the crack geometry must be pre-determined
             rather than computed by the computational model. The
             extended finite element method (XFEM) is a powerful method
             to represent arbitrary propagating discrete cracks in finite
             element models. The use of XFEM has been previously
             demonstrated for modeling propagating discrete cracks in the
             BISON fuel performance code. This paper demonstrates an
             initial application of XFEM to model stress concentrations
             induced by fuel fractures at the fuel/cladding interface
             during PCMI. This is demonstrated on a study of a
             pre-defined stationary crack in a 2D cross-section model of
             a LWR fuel rod. The results from a model with a discrete
             crack defined with XFEM compare favorably with the results
             from a model with the same crack geometry defined in the
             finite element mesh. This study focuses on benchmarking the
             use of XFEM for PCMI modeling with a stationary crack, but
             this technique will be readily extended in the future to
             consider PCMI in conjunction with arbitrary, physics-driven
             crack propagation.},
   Key = {fds327049}
}


%% Dunson, David B.   
@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 et
             al.},
   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},
   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},
   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 : JMLR},
   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{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 = {July},
   url = {http://dx.doi.org/10.1080/01621459.2016.1208615},
   Doi = {10.1080/01621459.2016.1208615},
   Key = {fds326570}
}

@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},
   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{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 of London: Biological
             Sciences},
   Volume = {284},
   Number = {1855},
   Pages = {20170768-20170768},
   Year = {2017},
   Month = {May},
   url = {http://dx.doi.org/10.1098/rspb.2017.0768},
   Doi = {10.1098/rspb.2017.0768},
   Key = {fds329990}
}

@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{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 et
             al.},
   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 : a review journal of the Institute of
             Mathematical Statistics},
   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{fds325339,
   Author = {Johndrow, JE and Bhattacharya, A and Dunson, DB},
   Title = {Tensor decompositions and sparse log-linear
             models},
   Journal = {Annals of statistics},
   Volume = {45},
   Number = {1},
   Pages = {1-38},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1214/15-AOS1414},
   Doi = {10.1214/15-AOS1414},
   Key = {fds325339}
}

@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}
}

@article{fds329112,
   Author = {Bhattacharya, A and Dunson, DB and Pati, D and Pillai,
             NS},
   Title = {Sub-optimality of some continuous shrinkage
             priors},
   Journal = {Stochastic Processes and their Applications},
   Volume = {126},
   Number = {12},
   Pages = {3828-3842},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1016/j.spa.2016.08.007},
   Doi = {10.1016/j.spa.2016.08.007},
   Key = {fds329112}
}

@article{fds329113,
   Author = {Durante, D and Dunson, DB},
   Title = {Locally adaptive dynamic networks},
   Journal = {The annals of applied statistics},
   Volume = {10},
   Number = {4},
   Pages = {2203-2232},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1214/16-AOAS971},
   Doi = {10.1214/16-AOAS971},
   Key = {fds329113}
}

@article{fds327030,
   Author = {Datta, J and Dunson, DB},
   Title = {Bayesian inference on quasi-sparse count
             data},
   Journal = {Biometrika},
   Volume = {103},
   Number = {4},
   Pages = {971-983},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1093/biomet/asw053},
   Doi = {10.1093/biomet/asw053},
   Key = {fds327030}
}

@article{fds329114,
   Author = {Zhu, H and Strawn, N and Dunson, DB},
   Title = {Bayesian graphical models for multivariate functional
             data},
   Journal = {Journal of machine learning research : JMLR},
   Volume = {17},
   Pages = {1-27},
   Year = {2016},
   Month = {October},
   Abstract = {© 2016 Hongxiao Zhu, Nate Strawn, and David B. Dunson.
             Graphical models express conditional independence
             relationships among variables. Although methods for
             vector-valued data are well established, functional data
             graphical models remain underdeveloped. By functional data,
             we refer to data that are realizations of random functions
             varying over a continuum (e.g., images, signals). We
             introduce a notion of conditional independence between
             random functions, and construct a framework for Bayesian
             inference of undirected, decomposable graphs in the
             multivariate functional data context. This framework is
             based on extending Markov distributions and hyper Markov
             laws from random variables to random processes, providing a
             principled alternative to naive application of multivariate
             methods to discretized functional data. Markov properties
             facilitate the composition of likelihoods and priors
             according to the decomposition of a graph. Our focus is on
             Gaussian process graphical models using orthogonal basis
             expansions. We propose a hyper-inverse-Wishart-process prior
             for the covariance kernels of the infinite coeficient
             sequences of the basis expansion, and establish its
             existence and uniqueness. We also prove the strong hyper
             Markov property and the conjugacy of this prior under a
             finite rank condition of the prior kernel parameter.
             Stochastic search Markov chain Monte Carlo algorithms are
             developed for posterior inference, assessed through
             simulations, and applied to a study of brain activity and
             alcoholism.},
   Key = {fds329114}
}

@article{fds329115,
   Author = {Sarkar, A and Dunson, DB},
   Title = {Bayesian Nonparametric Modeling of Higher Order Markov
             Chains},
   Journal = {Journal of the American Statistical Association},
   Volume = {111},
   Number = {516},
   Pages = {1791-1803},
   Year = {2016},
   Month = {October},
   url = {http://dx.doi.org/10.1080/01621459.2015.1115763},
   Doi = {10.1080/01621459.2015.1115763},
   Key = {fds329115}
}

@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},
   Pages = {1-15},
   Year = {2016},
   Month = {August},
   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{fds329116,
   Author = {Li, D and Heyer, L and Jennings, VH and Smith, CA and Dunson,
             DB},
   Title = {Personalised estimation of a woman's most fertile
             days.},
   Journal = {European Journal of Contraception and Reproductive Health
             Care},
   Volume = {21},
   Number = {4},
   Pages = {323-328},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.1080/13625187.2016.1196485},
   Abstract = {We propose a new, personalised approach of estimating a
             woman's most fertile days that only requires recording the
             first day of menses and can use a smartphone to convey this
             information to the user so that she can plan or prevent
             pregnancy.We performed a retrospective analysis of two
             cohort studies (a North Carolina-based study and the Early
             Pregnancy Study [EPS]) and a prospective multicentre trial
             (World Health Organization [WHO] study). The North Carolina
             study consisted of 68 sexually active women with either an
             intrauterine device or tubal ligation. The EPS comprised 221
             women who planned to become pregnant and had no known
             fertility problems. The WHO study consisted of 706 women
             from five geographically and culturally diverse settings.
             Bayesian statistical methods were used to design our
             proposed method, Dynamic Optimal Timing (DOT). Simulation
             studies were used to estimate the cumulative pregnancy
             risk.For the proposed method, simulation analyses indicated
             a 4.4% cumulative probability of pregnancy over 13 cycles
             with correct use. After a calibration window, this method
             flagged between 11 and 13 days when unprotected intercourse
             should be avoided per cycle. Eligible women should have
             cycle lengths between 20 and 40 days with a variability
             range less than or equal to 9 days.DOT can easily be
             implemented by computer or smartphone applications, allowing
             for women to make more informed decisions about their
             fertility. This approach is already incorporated into a
             patent-pending system and is available for free download on
             iPhones and Androids.},
   Doi = {10.1080/13625187.2016.1196485},
   Key = {fds329116}
}

@article{fds329993,
   Author = {Hultman, R and Mague, SD and Li, Q and Katz, BM and Michel, N and Lin, L and Wang, J and David, LK and Blount, C and Chandy, R and Carlson, D and Ulrich, K and Carin, L and Dunson, D and Kumar, S and Deisseroth, K and Moore, SD and Dzirasa, K},
   Title = {Dysregulation of Prefrontal Cortex-Mediated Slow-Evolving
             Limbic Dynamics Drives Stress-Induced Emotional
             Pathology.},
   Journal = {Neuron},
   Volume = {91},
   Number = {2},
   Pages = {439-452},
   Year = {2016},
   Month = {July},
   url = {http://dx.doi.org/10.1016/j.neuron.2016.05.038},
   Abstract = {Circuits distributed across cortico-limbic brain regions
             compose the networks that mediate emotional behavior. The
             prefrontal cortex (PFC) regulates ultraslow (<1 Hz)
             dynamics across these networks, and PFC dysfunction is
             implicated in stress-related illnesses including major
             depressive disorder (MDD). To uncover the mechanism whereby
             stress-induced changes in PFC circuitry alter emotional
             networks to yield pathology, we used a multi-disciplinary
             approach including in vivo recordings in mice and chronic
             social defeat stress. Our network model, inferred using
             machine learning, linked stress-induced behavioral pathology
             to the capacity of PFC to synchronize amygdala and VTA
             activity. Direct stimulation of PFC-amygdala circuitry with
             DREADDs normalized PFC-dependent limbic synchrony in
             stress-susceptible animals and restored normal behavior. In
             addition to providing insights into MDD mechanisms, our
             findings demonstrate an interdisciplinary approach that can
             be used to identify the large-scale network changes that
             underlie complex emotional pathologies and the specific
             network nodes that can be used to develop targeted
             interventions.},
   Doi = {10.1016/j.neuron.2016.05.038},
   Key = {fds329993}
}

@article{fds322536,
   Author = {Kunihama, T and Herring, AH and Halpern, CT and Dunson,
             DB},
   Title = {Nonparametric Bayes modeling with sample survey
             weights},
   Journal = {Statistics & Probability Letters},
   Volume = {113},
   Pages = {41-48},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.spl.2016.02.009},
   Doi = {10.1016/j.spl.2016.02.009},
   Key = {fds322536}
}

@article{fds322537,
   Author = {Rao, V and Lin, L and Dunson, DB},
   Title = {Data augmentation for models based on rejection
             sampling.},
   Journal = {Biometrika},
   Volume = {103},
   Number = {2},
   Pages = {319-335},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1093/biomet/asw005},
   Abstract = {We present a data augmentation scheme to perform Markov
             chain Monte Carlo inference for models where data generation
             involves a rejection sampling algorithm. Our idea is a
             simple scheme to instantiate the rejected proposals
             preceding each data point. The resulting joint probability
             over observed and rejected variables can be much simpler
             than the marginal distribution over the observed variables,
             which often involves intractable integrals. We consider
             three problems: modelling flow-cytometry measurements
             subject to truncation; the Bayesian analysis of the matrix
             Langevin distribution on the Stiefel manifold; and Bayesian
             inference for a nonparametric Gaussian process density
             model. The latter two are instances of doubly-intractable
             Markov chain Monte Carlo problems, where evaluating the
             likelihood is intractable. Our experiments demonstrate
             superior performance over state-of-the-art sampling
             algorithms for such problems.},
   Doi = {10.1093/biomet/asw005},
   Key = {fds322537}
}

@article{fds329994,
   Author = {Ovaskainen, O and Abrego, N and Halme, P and Dunson,
             D},
   Title = {Using latent variable models to identify large networks of
             species-to-species associations at different spatial
             scales},
   Journal = {Methods in Ecology and Evolution},
   Volume = {7},
   Number = {5},
   Pages = {549-555},
   Editor = {Warton, D},
   Year = {2016},
   Month = {May},
   url = {http://dx.doi.org/10.1111/2041-210X.12501},
   Doi = {10.1111/2041-210X.12501},
   Key = {fds329994}
}

@article{fds322538,
   Author = {Guhaniyogi, R and Dunson, DB},
   Title = {Compressed Gaussian process for manifold
             regression},
   Journal = {Journal of machine learning research : JMLR},
   Volume = {17},
   Year = {2016},
   Month = {May},
   Abstract = {©2016 Rajarshi Guhaniyogi and David B. Dunson.
             Nonparametric regression for large numbers of features (p)
             is an increasingly important problem. If the sample size n
             is massive, a common strategy is to partition the feature
             space, and then separately apply simple models to each
             partition set. This is not ideal when n is modest relative
             to p, and we propose an alternative approach relying on
             random compression of the feature vector combined with
             Gaussian process regression. The proposed approach is
             particularly motivated by the setting in which the response
             is conditionally independent of the features given the
             projection to a low dimensional manifold. Conditionally on
             the random compression matrix and a smoothness parameter,
             the posterior distribution for the regression surface and
             posterior predictive distributions are available
             analytically. Running the analysis in parallel for many
             random compression matrices and smoothness parameters, model
             averaging is used to combine the results. The algorithm can
             be implemented rapidly even in very large p and moderately
             large n nonparametric regression, has strong theoretical
             justification, and is found to yield state of the art
             predictive performance.},
   Key = {fds322538}
}

@article{fds329117,
   Author = {Yang, Y and Dunson, DB},
   Title = {Bayesian Conditional Tensor Factorizations for
             High-Dimensional Classification},
   Journal = {Journal of the American Statistical Association},
   Volume = {111},
   Number = {514},
   Pages = {656-669},
   Year = {2016},
   Month = {April},
   url = {http://dx.doi.org/10.1080/01621459.2015.1029129},
   Doi = {10.1080/01621459.2015.1029129},
   Key = {fds329117}
}

@article{fds322539,
   Author = {Kabisa, ST and Dunson, DB and Morris, JS},
   Title = {Online Variational Bayes Inference for High-Dimensional
             Correlated Data},
   Journal = {Journal of computational and graphical statistics : a joint
             publication of American Statistical Association, Institute
             of Mathematical Statistics, Interface Foundation of North
             America},
   Volume = {25},
   Number = {2},
   Pages = {426-444},
   Year = {2016},
   Month = {April},
   url = {http://dx.doi.org/10.1080/10618600.2014.998336},
   Doi = {10.1080/10618600.2014.998336},
   Key = {fds322539}
}

@article{fds322540,
   Author = {Yang, Y and Dunson, DB},
   Title = {Bayesian manifold regression},
   Journal = {Annals of statistics},
   Volume = {44},
   Number = {2},
   Pages = {876-905},
   Year = {2016},
   Month = {April},
   url = {http://dx.doi.org/10.1214/15-AOS1390},
   Doi = {10.1214/15-AOS1390},
   Key = {fds322540}
}

@article{fds322541,
   Author = {Zhou, J and Herring, AH and Bhattacharya, A and Olshan, AF and Dunson,
             DB and National Birth Defects Prevention Study},
   Title = {Nonparametric Bayes modeling for case control studies with
             many predictors.},
   Journal = {Biometrics},
   Volume = {72},
   Number = {1},
   Pages = {184-192},
   Year = {2016},
   Month = {March},
   url = {http://dx.doi.org/10.1111/biom.12411},
   Abstract = {It is common in biomedical research to run case-control
             studies involving high-dimensional predictors, with the main
             goal being detection of the sparse subset of predictors
             having a significant association with disease. Usual
             analyses rely on independent screening, considering each
             predictor one at a time, or in some cases on logistic
             regression assuming no interactions. We propose a
             fundamentally different approach based on a nonparametric
             Bayesian low rank tensor factorization model for the
             retrospective likelihood. Our model allows a very flexible
             structure in characterizing the distribution of multivariate
             variables as unknown and without any linear assumptions as
             in logistic regression. Predictors are excluded only if they
             have no impact on disease risk, either directly or through
             interactions with other predictors. Hence, we obtain an
             omnibus approach for screening for important predictors.
             Computation relies on an efficient Gibbs sampler. The
             methods are shown to have high power and low false discovery
             rates in simulation studies, and we consider an application
             to an epidemiology study of birth defects.},
   Doi = {10.1111/biom.12411},
   Key = {fds322541}
}

@article{fds322542,
   Author = {Tang, K and Dunson, DB and Su, Z and Liu, R and Zhang, J and Dong,
             J},
   Title = {Subspace segmentation by dense block and sparse
             representation.},
   Journal = {Neural Networks},
   Volume = {75},
   Pages = {66-76},
   Year = {2016},
   Month = {March},
   url = {http://dx.doi.org/10.1016/j.neunet.2015.11.011},
   Abstract = {Subspace segmentation is a fundamental topic in computer
             vision and machine learning. However, the success of many
             popular methods is about independent subspace segmentation
             instead of the more flexible and realistic disjoint subspace
             segmentation. Focusing on the disjoint subspaces, we provide
             theoretical and empirical evidence of inferior performance
             for popular algorithms such as LRR. To solve these problems,
             we propose a novel dense block and sparse representation
             (DBSR) for subspace segmentation and provide related
             theoretical results. DBSR minimizes a combination of the
             1,1-norm and maximum singular value of the representation
             matrix, leading to a combination of dense block and
             sparsity. We provide experimental results for synthetic and
             benchmark data showing that our method can outperform the
             state-of-the-art.},
   Doi = {10.1016/j.neunet.2015.11.011},
   Key = {fds322542}
}

@article{fds322543,
   Author = {Kunihama, T and Dunson, DB},
   Title = {Nonparametric Bayes inference on conditional
             independence},
   Journal = {Biometrika},
   Volume = {103},
   Number = {1},
   Pages = {35-47},
   Year = {2016},
   Month = {March},
   url = {http://dx.doi.org/10.1093/biomet/asv060},
   Doi = {10.1093/biomet/asv060},
   Key = {fds322543}
}

@article{fds322544,
   Author = {Van Den Boom and W and Dunson, D and Reeves, G},
   Title = {Quantifying uncertainty in variable selection with arbitrary
             matrices},
   Journal = {2015 IEEE 6th International Workshop on Computational
             Advances in Multi-Sensor Adaptive Processing, CAMSAP
             2015},
   Pages = {385-388},
   Year = {2016},
   Month = {January},
   ISBN = {9781479919635},
   url = {http://dx.doi.org/10.1109/CAMSAP.2015.7383817},
   Abstract = {© 2015 IEEE. Probabilistically quantifying uncertainty in
             parameters, predictions and decisions is a crucial component
             of broad scientific and engineering applications. This is
             however difficult if the number of parameters far exceeds
             the sample size. Although there are currently many methods
             which have guarantees for problems characterized by large
             random matrices, there is often a gap between theory and
             practice when it comes to measures of statistical
             significance for matrices encountered in real-world
             applications. This paper proposes a scalable framework that
             utilizes state-of-the-art methods to provide approximations
             to the marginal posterior distributions. This framework is
             used to approximate marginal posterior inclusion
             probabilities for Bayesian variable selection.},
   Doi = {10.1109/CAMSAP.2015.7383817},
   Key = {fds322544}
}

@article{fds328949,
   Author = {Chabout, J and Sarkar, A and Patel, SR and Radden, T and Dunson, DB and Fisher, SE and Jarvis, ED},
   Title = {A Foxp2 Mutation Implicated in Human Speech Deficits Alters
             Sequencing of Ultrasonic Vocalizations in Adult Male
             Mice.},
   Journal = {Frontiers in Behavioral Neuroscience},
   Volume = {10},
   Pages = {197},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.3389/fnbeh.2016.00197},
   Abstract = {Development of proficient spoken language skills is
             disrupted by mutations of the FOXP2 transcription factor. A
             heterozygous missense mutation in the KE family causes
             speech apraxia, involving difficulty producing words with
             complex learned sequences of syllables. Manipulations in
             songbirds have helped to elucidate the role of this gene in
             vocal learning, but findings in non-human mammals have been
             limited or inconclusive. Here, we performed a systematic
             study of ultrasonic vocalizations (USVs) of adult male mice
             carrying the KE family mutation. Using novel statistical
             tools, we found that Foxp2 heterozygous mice did not have
             detectable changes in USV syllable acoustic structure, but
             produced shorter sequences and did not shift to more complex
             syntax in social contexts where wildtype animals did.
             Heterozygous mice also displayed a shift in the position of
             their rudimentary laryngeal motor cortex (LMC) layer-5
             neurons. Our findings indicate that although mouse USVs are
             mostly innate, the underlying contributions of FoxP2 to
             sequencing of vocalizations are conserved with
             humans.},
   Doi = {10.3389/fnbeh.2016.00197},
   Key = {fds328949}
}

@article{fds321837,
   Author = {Yin, R and Cornelis, B and Fodor, G and Ocon, N and Dunson, D and Daubechies, I},
   Title = {Removing Cradle Artifacts in X-Ray Images of
             Paintings},
   Journal = {SIAM Journal on Imaging Sciences},
   Volume = {9},
   Number = {3},
   Pages = {1247-1272},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1137/15M1053554},
   Doi = {10.1137/15M1053554},
   Key = {fds321837}
}

@article{fds322545,
   Author = {Wang, X and Dunson, D and Leng, C},
   Title = {No penalty no tears: Least squares in high-dimensional
             linear models},
   Journal = {33rd International Conference on Machine Learning, ICML
             2016},
   Volume = {4},
   Pages = {2685-2706},
   Year = {2016},
   Month = {January},
   ISBN = {9781510829008},
   Abstract = {© 2016 by the author(s). Ordinary least squares (OI,S) is
             the default method for fitting linear models, but is not
             applicable for problems with dimensionality larger than the
             sample size. For these problems, we advocate the use of a
             generalized version of OLS motivated by ridge regression,
             and propose two novel three-step algorithms involving least
             squares fitting and hard thresholding. The algorithms are
             methodologically simple to understand intuitively,
             computationally easy to implement efficiently, and
             theoretically appealing for choosing models consistently.
             Numerical exercises comparing our methods with
             penalization-based approaches in simulations and data
             analyses illustrate the great potential of the proposed
             algorithms.},
   Key = {fds322545}
}

@article{fds327031,
   Author = {Wang, X and Dunson, D and Leng, C},
   Title = {DECOrrelated feature space partitioning for distributed
             sparse regression},
   Journal = {Advances in Neural Information Processing
             Systems},
   Pages = {802-810},
   Year = {2016},
   Month = {January},
   Abstract = {© 2016 NIPS Foundation - All Rights Reserved. Fitting
             statistical models is computationally challenging when the
             sample size or the dimension of the dataset is huge. An
             attractive approach for down-scaling the problem size is to
             first partition the dataset into subsets and then fit using
             distributed algorithms. The dataset can be partitioned
             either horizontally (in the sample space) or vertically (in
             the feature space). While the majority of the literature
             focuses on sample space partitioning, feature space
             partitioning is more effective when p > n. Existing methods
             for partitioning features, however, are either vulnerable to
             high correlations or inefficient in reducing the model
             dimension. In this paper, we solve these problems through a
             new embarrassingly parallel framework named DECO for
             distributed variable selection and parameter estimation. In
             DECO, variables are first partitioned and allocated to m
             distributed workers. The decorrelated subset data within
             each worker are then fitted via any algorithm designed for
             high-dimensional problems. We show that by incorporating the
             decorrelation step, DECO can achieve consistent variable
             selection and parameter estimation on each subset with
             (almost) no assumptions. In addition, the convergence rate
             is nearly minimax optimal for both sparse and weakly sparse
             models and does NOT depend on the partition number m.
             Extensive numerical experiments are provided to illustrate
             the performance of the new framework.},
   Key = {fds327031}
}

@article{fds329118,
   Author = {Canale, A and Dunson, DB},
   Title = {Multiscale Bernstein polynomials for densities},
   Journal = {Statistica Sinica},
   Year = {2016},
   url = {http://dx.doi.org/10.5705/ss.202015.0163},
   Doi = {10.5705/ss.202015.0163},
   Key = {fds329118}
}


%% Durrett, Richard T.   
@article{fds329932,
   Author = {Gleeson, JP and Durrett, R},
   Title = {Temporal profiles of avalanches on networks},
   Journal = {Nature Communications},
   Volume = {8},
   Number = {1},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1038/s41467-017-01212-0},
   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
             USA},
   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}
}

@article{fds323651,
   Author = {Durrett, R and Fan, W-TL},
   Title = {Genealogies in expanding populations},
   Journal = {The annals of applied probability : an official journal of
             the Institute of Mathematical Statistics},
   Volume = {26},
   Number = {6},
   Pages = {3456-3490},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1214/16-AAP1181},
   Doi = {10.1214/16-AAP1181},
   Key = {fds323651}
}

@article{fds323652,
   Author = {Cox, JT and Durrett, R},
   Title = {Evolutionary games on the torus with weak
             selection},
   Journal = {Stochastic Processes and their Applications},
   Volume = {126},
   Number = {8},
   Pages = {2388-2409},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.1016/j.spa.2016.02.004},
   Doi = {10.1016/j.spa.2016.02.004},
   Key = {fds323652}
}

@article{fds321819,
   Author = {Ryser, MD and Worni, M and Turner, EL and Marks, JR and Durrett, R and Hwang, ES},
   Title = {Outcomes of Active Surveillance for Ductal Carcinoma in
             Situ: A Computational Risk Analysis.},
   Journal = {Journal of the National Cancer Institute},
   Volume = {108},
   Number = {5},
   Year = {2016},
   Month = {May},
   url = {http://dx.doi.org/10.1093/jnci/djv372},
   Abstract = {Ductal carcinoma in situ (DCIS) is a noninvasive breast
             lesion with uncertain risk for invasive progression. Usual
             care (UC) for DCIS consists of treatment upon diagnosis,
             thus potentially overtreating patients with low propensity
             for progression. One strategy to reduce overtreatment is
             active surveillance (AS), whereby DCIS is treated only upon
             detection of invasive disease. Our goal was to perform a
             quantitative evaluation of outcomes following an AS strategy
             for DCIS.Age-stratified, 10-year disease-specific cumulative
             mortality (DSCM) for AS was calculated using a computational
             risk projection model based upon published estimates for
             natural history parameters, and Surveillance, Epidemiology,
             and End Results data for outcomes. AS projections were
             compared with the DSCM for patients who received UC. To
             quantify the propagation of parameter uncertainty, a 95%
             projection range (PR) was computed, and sensitivity analyses
             were performed.Under the assumption that AS cannot
             outperform UC, the projected median differences in 10-year
             DSCM between AS and UC when diagnosed at ages 40, 55, and 70
             years were 2.6% (PR = 1.4%-5.1%), 1.5% (PR = 0.5%-3.5%), and
             0.6% (PR = 0.0%-2.4), respectively. Corresponding median
             numbers of patients needed to treat to avert one breast
             cancer death were 38.3 (PR = 19.7-69.9), 67.3 (PR =
             28.7-211.4), and 157.2 (PR = 41.1-3872.8), respectively.
             Sensitivity analyses showed that the parameter with greatest
             impact on DSCM was the probability of understaging invasive
             cancer at diagnosis.AS could be a viable management strategy
             for carefully selected DCIS patients, particularly among
             older age groups and those with substantial competing
             mortality risks. The effectiveness of AS could be markedly
             improved by reducing the rate of understaging.},
   Doi = {10.1093/jnci/djv372},
   Key = {fds321819}
}

@article{fds243415,
   Author = {Durrett, R and Foo, J and Leder, K},
   Title = {Spatial Moran models, II: cancer initiation in spatially
             structured tissue.},
   Journal = {Journal of Mathematical Biology},
   Volume = {72},
   Number = {5},
   Pages = {1369-1400},
   Year = {2016},
   Month = {April},
   ISSN = {0303-6812},
   url = {http://dx.doi.org/10.1007/s00285-015-0912-1},
   Abstract = {We study the accumulation and spread of advantageous
             mutations in a spatial stochastic model of cancer initiation
             on a lattice. The parameters of this general model can be
             tuned to study a variety of cancer types and genetic
             progression pathways. This investigation contributes to an
             understanding of how the selective advantage of cancer cells
             together with the rates of mutations driving cancer, impact
             the process and timing of carcinogenesis. These results can
             be used to give insights into tumor heterogeneity and the
             "cancer field effect," the observation that a malignancy is
             often surrounded by cells that have undergone premalignant
             transformation.},
   Doi = {10.1007/s00285-015-0912-1},
   Key = {fds243415}
}


%% 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}
}

@article{fds321573,
   Author = {Oliveira, G},
   Title = {G 2-Monopoles with Singularities (Examples)},
   Journal = {Letters in Mathematical Physics},
   Volume = {106},
   Number = {11},
   Pages = {1479-1497},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.1007/s11005-016-0878-y},
   Doi = {10.1007/s11005-016-0878-y},
   Key = {fds321573}
}

@article{fds316671,
   Author = {Oliveira, G},
   Title = {Monopoles on AC 3-manifolds},
   Journal = {Journal of the London Mathematical Society},
   Volume = {93},
   Number = {3},
   Pages = {785-810},
   Year = {2016},
   Month = {June},
   ISSN = {0024-6107},
   url = {http://jlms.oxfordjournals.org/content/early/2016/05/06/jlms.jdw017.abstract},
   Doi = {10.1112/jlms/jdw017},
   Key = {fds316671}
}

@article{fds311851,
   Author = {Oliveira, G},
   Title = {Calabi–Yau Monopoles for the Stenzel Metric},
   Journal = {Communications in Mathematical Physics},
   Volume = {341},
   Number = {2},
   Pages = {699-728},
   Year = {2016},
   Month = {January},
   ISSN = {0010-3616},
   url = {http://hdl.handle.net/10161/11700 Duke open
             access},
   Doi = {10.1007/s00220-015-2534-2},
   Key = {fds311851}
}


%% Getz, Jayce R.   
@article{fds320411,
   Author = {Getz, JR},
   Title = {A four-variable automorphic kernel function},
   Journal = {Research in the Mathematical Sciences},
   Volume = {3},
   Number = {1},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1186/s40687-016-0069-6},
   Doi = {10.1186/s40687-016-0069-6},
   Key = {fds320411}
}


%% Hahn, Heekyoung   
@article{fds320417,
   Author = {Hahn, H},
   Title = {On Classical groups detected by the triple tensor product
             and the Littlewood–Richardson semigroup},
   Journal = {Research in Number Theory},
   Volume = {2},
   Number = {1},
   Pages = {1-12},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1007/s40993-016-0049-3},
   Doi = {10.1007/s40993-016-0049-3},
   Key = {fds320417}
}

@article{fds320109,
   Author = {Hahn, H},
   Title = {On tensor third $L$-functions of automorphic representations
             of $GL_n(\mathbb {A}_F)$},
   Journal = {Proceedings of the American Mathematical
             Society},
   Volume = {144},
   Number = {12},
   Pages = {5061-5069},
   Year = {2016},
   Month = {May},
   url = {http://dx.doi.org/10.1090/proc/13134},
   Doi = {10.1090/proc/13134},
   Key = {fds320109}
}

@article{fds305734,
   Author = {H. Hahn},
   Title = {On tensor thrid L-functions of automorphic representations
             of GL_n(A_F)},
   Journal = {Proc. Amer. Math. Soc.},
   Year = {2016},
   Key = {fds305734}
}

@article{fds227060,
   Author = {H. Hahn},
   Title = {On classical groups detected by the triple tensor product
             and the Littlewood-Richardson semigroup},
   Year = {2016},
   Key = {fds227060}
}


%% Hain, Richard   
@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}
}

@article{fds287213,
   Author = {Arapura, D and Dimca, A and Hain, R},
   Title = {On the fundamental groups of normal varieties},
   Journal = {Communications in Contemporary Mathematics},
   Volume = {18},
   Number = {04},
   Pages = {1550065-1550065},
   Year = {2016},
   Month = {August},
   ISSN = {0219-1997},
   url = {http://dx.doi.org/10.1142/S0219199715500650},
   Doi = {10.1142/S0219199715500650},
   Key = {fds287213}
}

@article{fds324840,
   Author = {Hain, R},
   Title = {Notes on the Universal Elliptic KZB Equation},
   Journal = {Pure and Applied Mathematics Quarterly},
   Volume = {12},
   Number = {2},
   Publisher = {International Press},
   Year = {2016},
   Month = {July},
   url = {http://arxiv.org/abs/1309.0580v3},
   Abstract = {The universal elliptic KZB equation is the integrable
             connection on the pro-vector bundle over M_{1,2} whose fiber
             over the point corresponding to the elliptic curve E and a
             non-zero point x of E is the unipotent completion of
             \pi_1(E-{0},x). This was written down independently by
             Calaque, Enriquez and Etingof (arXiv:math/0702670), and by
             Levin and Racinet (arXiv:math/0703237). It generalizes the
             KZ-equation in genus 0. These notes are in four parts. The
             first two parts provide a detailed exposition of this
             connection (following Levin-Racinet); the third is a
             leisurely exploration of the connection in which, for
             example, we compute the limit mixed Hodge structure on the
             unipotent fundamental group of the Tate curve minus its
             identity. In the fourth part we elaborate on ideas of Levin
             and Racinet and explicitly compute the connection over the
             moduli space of elliptic curves with a non-zero abelian
             differential, showing that it is defined over
             Q.},
   Key = {fds324840}
}

@article{fds320302,
   Author = {Hain, R},
   Title = {The Hodge-de Rham theory of modular groups},
   Volume = {427},
   Pages = {422-514},
   Booktitle = {Recent Advances in Hodge Theory Period Domains, Algebraic
             Cycles, and Arithmetic},
   Publisher = {Cambridge University Press},
   Editor = {Kerr, M and Pearlstein, G},
   Year = {2016},
   Month = {January},
   ISBN = {110754629X},
   Key = {fds320302}
}

@article{fds320426,
   Author = {Hain, R and Matsumoto, M},
   Title = {Universal Mixed Elliptic Motives},
   Journal = {Journal of the Institute of Mathematics of
             Jussieu},
   Year = {2016},
   url = {http://arxiv.org/abs/1512.03975},
   Abstract = {In this paper we construct a Q-linear tannakian category
             MEM_1 of universal mixed elliptic motives over the moduli
             space M_{1,1} of elliptic curves. It contains MTM, the
             category of mixed Tate motives unramified over the integers.
             Each object of MEM_1 is an object of MTM endowed with an
             action of SL_2(Z) that is compatible with its structure.
             Universal mixed elliptic motives can be thought of as
             motivic local systems over M_{1,1} whose fiber over the
             tangential base point d/dq at the cusp is a mixed Tate
             motive. The basic structure of the tannakian fundamental
             group of MEM is determined and the lowest order terms of all
             relations are found (using computations of Francis Brown),
             including the arithmetic relations, which describe the
             "infinitesimal Galois action". We use the presentation to
             give a new and more conceptual proof of the Ihara-Takao
             congruences.},
   Key = {fds320426}
}


%% Harer, John   
@article{fds324397,
   Author = {Bendich, P and Chin, SP and Clark, J and Desena, J and Harer, J and Munch,
             E and Newman, A and Porter, D and Rouse, D and Strawn, N and Watkins,
             A},
   Title = {Topological and statistical behavior classifiers for
             tracking applications},
   Journal = {IEEE Transactions on Aerospace and Electronic
             Systems},
   Volume = {52},
   Number = {6},
   Pages = {2644-2661},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1109/TAES.2016.160405},
   Abstract = {© 1965-2011 IEEE.This paper introduces a method to
             integrate target behavior into the multiple hypothesis
             tracker (MHT) likelihood ratio. In particular, a periodic
             track appraisal based on behavior is introduced. The track
             appraisal uses elementary topological data analysis coupled
             with basic machine-learning techniques, and it adjusts the
             traditional kinematic data association likelihood (i.e.,
             track score) using an established formulation for
             feature-aided data association. The proposed method is
             tested and demonstrated on synthetic vehicular data
             representing an urban traffic scene generated by the
             Simulation of Urban Mobility package. The vehicles in the
             scene exhibit different driving behaviors. The proposed
             method distinguishes those behaviors and shows improved data
             association decisions relative to a conventional, kinematic
             MHT.},
   Doi = {10.1109/TAES.2016.160405},
   Key = {fds324397}
}

@article{fds321989,
   Author = {McGoff, KA and Guo, X and Deckard, A and Kelliher, CM and Leman, AR and Francey, LJ and Hogenesch, JB and Haase, SB and Harer,
             JL},
   Title = {The Local Edge Machine: inference of dynamic models of gene
             regulation.},
   Journal = {Genome Biology: biology for the post-genomic
             era},
   Volume = {17},
   Number = {1},
   Pages = {214},
   Year = {2016},
   Month = {October},
   Abstract = {We present a novel approach, the Local Edge Machine, for the
             inference of regulatory interactions directly from
             time-series gene expression data. We demonstrate its
             performance, robustness, and scalability on in silico
             datasets with varying behaviors, sizes, and degrees of
             complexity. Moreover, we demonstrate its ability to
             incorporate biological prior information and make
             informative predictions on a well-characterized in vivo
             system using data from budding yeast that have been
             synchronized in the cell cycle. Finally, we use an atlas of
             transcription data in a mammalian circadian system to
             illustrate how the method can be used for discovery in the
             context of large complex networks.},
   Key = {fds321989}
}

@article{fds321990,
   Author = {Bendich, P and Gasparovic, E and Harer, J and Tralie,
             C},
   Title = {Geometric models for musical audio data},
   Journal = {LIPIcs},
   Volume = {51},
   Pages = {65.1-65.5},
   Year = {2016},
   Month = {June},
   ISBN = {9783959770095},
   url = {http://dx.doi.org/10.4230/LIPIcs.SoCG.2016.65},
   Abstract = {© Paul Bendich, Ellen Gasparovic, John Harer, and
             Christopher Tralie. We study the geometry of sliding window
             embeddings of audio features that summarize perceptual
             information about audio, including its pitch and timbre.
             These embeddings can be viewed as point clouds in high
             dimensions, and we add structure to the point clouds using a
             cover tree with adaptive thresholds based on multi-scale
             local principal component analysis to automatically assign
             points to clusters. We connect neighboring clusters in a
             scaffolding graph, and we use knowledge of stratified space
             structure to refine our estimates of dimension in each
             cluster, demonstrating in our music applications that
             choruses and verses have higher dimensional structure, while
             transitions between them are lower dimensional. We showcase
             our technique with an interactive web-based application
             powered by Javascript and WebGL which plays music
             synchronized with a principal component analysis embedding
             of the point cloud down to 3D. We also render the clusters
             and the scaffolding on top of this projection to visualize
             the transitions between different sections of the
             music.},
   Doi = {10.4230/LIPIcs.SoCG.2016.65},
   Key = {fds321990}
}


%% 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}
}


%% Hodel, Richard E.   
@book{fds302140,
   Author = {R.E. Hodel and Donald W. Loveland and Richard E. Hodel and S.G.
             Sterrett},
   Title = {Three Views of Logic: Mathematics, Philosophy, Computer
             Science},
   Year = {2016},
   Key = {fds302140}
}


%% Junge, Matthew S   
@article{fds329100,
   Author = {Hoffman, C and Johnson, T and Junge, M},
   Title = {Recurrence and transience for the frog model on
             trees},
   Journal = {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}
}

@article{fds325463,
   Author = {Hoffman, C and Johnson, T and Junge, M},
   Title = {From transience to recurrence with Poisson tree
             frogs},
   Journal = {The annals of applied probability : an official journal of
             the Institute of Mathematical Statistics},
   Volume = {26},
   Number = {3},
   Pages = {1620-1635},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1214/15-AAP1127},
   Doi = {10.1214/15-AAP1127},
   Key = {fds325463}
}

@article{fds325464,
   Author = {Benjamini, I and Foxall, E and Gurel-Gurevich, O and Junge, M and Kesten, H},
   Title = {Site recurrence for coalescing random walk},
   Journal = {Electronic Communications in Probability},
   Volume = {21},
   Year = {2016},
   url = {http://dx.doi.org/10.1214/16-ECP5},
   Doi = {10.1214/16-ECP5},
   Key = {fds325464}
}

@article{fds325465,
   Author = {Johnson, T and Junge, M},
   Title = {The critical density for the frog model is the degree of the
             tree},
   Journal = {Electronic Communications in Probability},
   Volume = {21},
   Year = {2016},
   url = {http://dx.doi.org/10.1214/16-ECP29},
   Doi = {10.1214/16-ECP29},
   Key = {fds325465}
}


%% Kiselev, Alexander A.   
@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 & 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 & 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}
}

@article{fds330281,
   Author = {Kiselev, A and Ryzhik, L and Yao, Y and Zlatoš, A},
   Title = {Finite time singularity for the modified SQG patch
             equation},
   Journal = {Annals of Mathematics},
   Volume = {184},
   Number = {3},
   Pages = {909-948},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.4007/annals.2016.184.3.7},
   Doi = {10.4007/annals.2016.184.3.7},
   Key = {fds330281}
}

@article{fds330282,
   Author = {Kiselev, A and Xu, X},
   Title = {Suppression of Chemotactic Explosion by Mixing},
   Journal = {Archive for Rational Mechanics and Analysis},
   Volume = {222},
   Number = {2},
   Pages = {1077-1112},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.1007/s00205-016-1017-8},
   Doi = {10.1007/s00205-016-1017-8},
   Key = {fds330282}
}

@article{fds330283,
   Author = {Popov, IY and Kurasov, PA and Naboko, SN and Kiselev, AA and Ryzhkov,
             AE and Yafyasov, AM and Miroshnichenko, GP and Karpeshina, YE and Kruglov, VI and Pankratova, TF and Popov, AI},
   Title = {A distinguished mathematical physicist Boris S.
             Pavlov},
   Pages = {782-788},
   Year = {2016},
   Month = {October},
   url = {http://dx.doi.org/10.17586/2220-8054-2016-7-5-782-788},
   Doi = {10.17586/2220-8054-2016-7-5-782-788},
   Key = {fds330283}
}


%% 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{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}
}

@article{fds320875,
   Author = {Layton, AT and Laghmani, K and Vallon, V and Edwards,
             A},
   Title = {Solute transport and oxygen consumption along the nephrons:
             effects of Na+ transport inhibitors.},
   Journal = {American Journal of Physiology: Renal Physiology},
   Volume = {311},
   Number = {6},
   Pages = {F1217-F1229},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1152/ajprenal.00294.2016},
   Abstract = {Sodium and its associated anions are the major determinant
             of extracellular fluid volume, and the reabsorption of Na+
             by the kidney plays a crucial role in long-term blood
             pressure control. The goal of this study was to investigate
             the extent to which inhibitors of transepithelial Na+
             transport (TNa) along the nephron alter urinary solute
             excretion and TNa efficiency and how those effects may vary
             along different nephron segments. To accomplish that goal,
             we used the multinephron model developed in the companion
             study (28). That model represents detailed transcellular and
             paracellular transport processes along the nephrons of a rat
             kidney. We simulated the inhibition of the Na+/H+ exchanger
             (NHE3), the bumetanide-sensitive Na+-K+-2Cl- transporter
             (NKCC2), the Na+-Cl- cotransporter (NCC), and the
             amiloride-sensitive Na+ channel (ENaC). Under baseline
             conditions, NHE3, NKCC2, NCC, and ENaC reabsorb 36, 22, 4,
             and 7%, respectively, of filtered Na+ The model predicted
             that inhibition of NHE3 substantially reduced proximal
             tubule TNa and oxygen consumption (QO2 ). Whole-kidney TNa
             efficiency, as reflected by the number of moles of Na+
             reabsorbed per moles of O2 consumed (denoted by the ratio
             TNa/QO2 ), decreased by ∼20% with 80% inhibition of NHE3.
             NKCC2 inhibition simulations predicted a substantial
             reduction in thick ascending limb TNa and QO2 ; however, the
             effect on whole-kidney TNa/QO2 was minor. Tubular K+
             transport was also substantially impaired, resulting in
             elevated urinary K+ excretion. The most notable effect of
             NCC inhibition was to increase the excretion of Na+, K+, and
             Cl-; its impact on whole-kidney TNa and its efficiency was
             minor. Inhibition of ENaC was predicted to have opposite
             effects on the excretion of Na+ (increased) and K+
             (decreased) and to have only a minor impact on whole-kidney
             TNa and TNa/QO2 Overall, model predictions agree well with
             measured changes in Na+ and K+ excretion in response to
             diuretics and Na+ transporter mutations.},
   Doi = {10.1152/ajprenal.00294.2016},
   Key = {fds320875}
}

@article{fds320876,
   Author = {Layton, AT and Vallon, V and Edwards, A},
   Title = {A computational model for simulating solute transport and
             oxygen consumption along the nephrons.},
   Journal = {American Journal of Physiology: Renal Physiology},
   Volume = {311},
   Number = {6},
   Pages = {F1378-F1390},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1152/ajprenal.00293.2016},
   Abstract = {The goal of this study was to investigate water and solute
             transport, with a focus on sodium transport (TNa) and
             metabolism along individual nephron segments under differing
             physiological and pathophysiological conditions. To
             accomplish this goal, we developed a computational model of
             solute transport and oxygen consumption (QO2 ) along
             different nephron populations of a rat kidney. The model
             represents detailed epithelial and paracellular transport
             processes along both the superficial and juxtamedullary
             nephrons, with the loop of Henle of each model nephron
             extending to differing depths of the inner medulla. We used
             the model to assess how changes in TNa may alter QO2 in
             different nephron segments and how shifting the TNa sites
             alters overall kidney QO2 Under baseline conditions, the
             model predicted a whole kidney TNa/QO2 , which denotes the
             number of moles of Na+ reabsorbed per moles of O2 consumed,
             of ∼15, with TNa efficiency predicted to be significantly
             greater in cortical nephron segments than in medullary
             segments. The TNa/QO2 ratio was generally similar among the
             superficial and juxtamedullary nephron segments, except for
             the proximal tubule, where TNa/QO2 was ∼20% higher in
             superficial nephrons, due to the larger luminal flow along
             the juxtamedullary proximal tubules and the resulting
             higher, flow-induced transcellular transport. Moreover, the
             model predicted that an increase in single-nephron
             glomerular filtration rate does not significantly affect
             TNa/QO2 in the proximal tubules but generally increases
             TNa/QO2 along downstream segments. The latter result can be
             attributed to the generally higher luminal [Na+], which
             raises paracellular TNa Consequently, vulnerable medullary
             segments, such as the S3 segment and medullary thick
             ascending limb, may be relatively protected from
             flow-induced increases in QO2 under pathophysiological
             conditions.},
   Doi = {10.1152/ajprenal.00293.2016},
   Key = {fds320876}
}

@article{fds320877,
   Author = {Sgouralis, I and Kett, MM and Ow, CPC and Abdelkader, A and Layton, AT and Gardiner, BS and Smith, DW and Lankadeva, YR and Evans,
             RG},
   Title = {Bladder urine oxygen tension for assessing renal medullary
             oxygenation in rabbits: experimental and modeling
             studies.},
   Journal = {American journal of physiology. Regulatory, integrative and
             comparative physiology},
   Volume = {311},
   Number = {3},
   Pages = {R532-R544},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.1152/ajpregu.00195.2016},
   Abstract = {Oxygen tension (Po2) of urine in the bladder could be used
             to monitor risk of acute kidney injury if it varies with
             medullary Po2 Therefore, we examined this relationship and
             characterized oxygen diffusion across walls of the ureter
             and bladder in anesthetized rabbits. A computational model
             was then developed to predict medullary Po2 from bladder
             urine Po2 Both intravenous infusion of [Phe(2),Ile(3),Orn(8)]-vasopressin
             and infusion of N(G)-nitro-l-arginine reduced urinary Po2
             and medullary Po2 (8-17%), yet had opposite effects on renal
             blood flow and urine flow. Changes in bladder urine Po2
             during these stimuli correlated strongly with changes in
             medullary Po2 (within-rabbit r(2) = 0.87-0.90). Differences
             in the Po2 of saline infused into the ureter close to the
             kidney could be detected in the bladder, although this was
             diminished at lesser ureteric flow. Diffusion of oxygen
             across the wall of the bladder was very slow, so it was not
             considered in the computational model. The model predicts
             Po2 in the pelvic ureter (presumed to reflect medullary Po2)
             from known values of bladder urine Po2, urine flow, and
             arterial Po2 Simulations suggest that, across a
             physiological range of urine flow in anesthetized rabbits
             (0.1-0.5 ml/min for a single kidney), a change in bladder
             urine Po2 explains 10-50% of the change in pelvic
             urine/medullary Po2 Thus, it is possible to infer changes in
             medullary Po2 from changes in urinary Po2, so urinary Po2
             may have utility as a real-time biomarker of risk of acute
             kidney injury.},
   Doi = {10.1152/ajpregu.00195.2016},
   Key = {fds320877}
}

@article{fds320878,
   Author = {Layton, AT},
   Title = {Recent advances in renal hypoxia: insights from bench
             experiments and computer simulations.},
   Journal = {American Journal of Physiology: Renal Physiology},
   Volume = {311},
   Number = {1},
   Pages = {F162-F165},
   Year = {2016},
   Month = {July},
   url = {http://dx.doi.org/10.1152/ajprenal.00228.2016},
   Abstract = {The availability of oxygen in renal tissue is determined by
             the complex interactions among a host of processes,
             including renal blood flow, glomerular filtration,
             arterial-to-venous oxygen shunting, medullary architecture,
             Na(+) transport, and oxygen consumption. When this delicate
             balance is disrupted, the kidney may become susceptible to
             hypoxic injury. Indeed, renal hypoxia has been implicated as
             one of the major causes of acute kidney injury and chronic
             kidney diseases. This review highlights recent advances in
             our understanding of renal hypoxia; some of these studies
             were published in response to a recent Call for Papers of
             this journal: Renal Hypoxia.},
   Doi = {10.1152/ajprenal.00228.2016},
   Key = {fds320878}
}

@article{fds320880,
   Author = {Layton, AT and Vallon, V and Edwards, A},
   Title = {Predicted consequences of diabetes and SGLT inhibition on
             transport and oxygen consumption along a rat
             nephron.},
   Journal = {American Journal of Physiology: Renal Physiology},
   Volume = {310},
   Number = {11},
   Pages = {F1269-F1283},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1152/ajprenal.00543.2015},
   Abstract = {Diabetes increases the reabsorption of Na(+) (TNa) and
             glucose via the sodium-glucose cotransporter SGLT2 in the
             early proximal tubule (S1-S2 segments) of the renal cortex.
             SGLT2 inhibitors enhance glucose excretion and lower
             hyperglycemia in diabetes. We aimed to investigate how
             diabetes and SGLT2 inhibition affect TNa and sodium
             transport-dependent oxygen consumption [Formula: see text]
             along the whole nephron. To do so, we developed a
             mathematical model of water and solute transport from the
             Bowman space to the papillary tip of a superficial nephron
             of the rat kidney. Model simulations indicate that, in the
             nondiabetic kidney, acute and chronic SGLT2 inhibition
             enhances active TNa in all nephron segments, thereby raising
             [Formula: see text] by 5-12% in the cortex and medulla.
             Diabetes increases overall TNa and [Formula: see text] by
             ∼50 and 100%, mainly because it enhances glomerular
             filtration rate (GFR) and transport load. In diabetes, acute
             and chronic SGLT2 inhibition lowers [Formula: see text] in
             the cortex by ∼30%, due to GFR reduction that lowers
             proximal tubule active TNa, but raises [Formula: see text]
             in the medulla by ∼7%. In the medulla specifically,
             chronic SGLT2 inhibition is predicted to increase [Formula:
             see text] by 26% in late proximal tubules (S3 segments), by
             2% in medullary thick ascending limbs (mTAL), and by 9 and
             21% in outer and inner medullary collecting ducts (OMCD and
             IMCD), respectively. Additional blockade of SGLT1 in S3
             segments enhances glucose excretion, reduces [Formula: see
             text] by 33% in S3 segments, and raises [Formula: see text]
             by <1% in mTAL, OMCD, and IMCD. In summary, the model
             predicts that SGLT2 blockade in diabetes lowers cortical
             [Formula: see text] and raises medullary [Formula: see
             text], particularly in S3 segments.},
   Doi = {10.1152/ajprenal.00543.2015},
   Key = {fds320880}
}

@article{fds320881,
   Author = {Liu, R and Layton, AT},
   Title = {Modeling the effects of positive and negative feedback in
             kidney blood flow control.},
   Journal = {Mathematical Biosciences},
   Volume = {276},
   Pages = {8-18},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.mbs.2016.02.007},
   Abstract = {Blood flow in the mammalian kidney is tightly autoregulated.
             One of the important autoregulation mechanisms is the
             myogenic response, which is activated by perturbations in
             blood pressure along the afferent arteriole. Another is the
             tubuloglomerular feedback, which is a negative feedback that
             responds to variations in tubular fluid [Cl(-)] at the
             macula densa.(1) When initiated, both the myogenic response
             and the tubuloglomerular feedback adjust the afferent
             arteriole muscle tone. A third mechanism is the connecting
             tubule glomerular feedback, which is a positive feedback
             mechanism located at the connecting tubule, downstream of
             the macula densa. The connecting tubule glomerular feedback
             is much less well studied. The goal of this study is to
             investigate the interactions among these feedback mechanisms
             and to better understand the effects of their interactions.
             To that end, we have developed a mathematical model of
             solute transport and blood flow control in the rat kidney.
             The model represents the myogenic response, tubuloglomerular
             feedback, and connecting tubule glomerular feedback. By
             conducting a bifurcation analysis, we studied the stability
             of the system under a range of physiologically-relevant
             parameters. The bifurcation results were confirmed by means
             of a comparison with numerical simulations. Additionally, we
             conducted numerical simulations to test the hypothesis that
             the interactions between the tubuloglomerular feedback and
             the connecting tubule glomerular feedback may give rise to a
             yet-to-be-explained low-frequency oscillation that has been
             observed in experimental records.},
   Doi = {10.1016/j.mbs.2016.02.007},
   Key = {fds320881}
}

@article{fds320882,
   Author = {Chen, Y and Fry, BC and Layton, AT},
   Title = {Modeling Glucose Metabolism in the Kidney.},
   Journal = {Bulletin of Mathematical Biology},
   Volume = {78},
   Number = {6},
   Pages = {1318-1336},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1007/s11538-016-0188-7},
   Abstract = {The mammalian kidney consumes a large amount of energy to
             support the reabsorptive work it needs to excrete metabolic
             wastes and to maintain homeostasis. Part of that energy is
             supplied via the metabolism of glucose. To gain insights
             into the transport and metabolic processes in the kidney, we
             have developed a detailed model of the renal medulla of the
             rat kidney. The model represents water and solute flows,
             transmural fluxes, and biochemical reactions in the luminal
             fluid of the nephrons and vessels. In particular, the model
             simulates the metabolism of oxygen and glucose. Using that
             model, we have identified parameters concerning glucose
             transport and basal metabolism that yield predicted blood
             glucose concentrations that are consistent with experimental
             measurements. The model predicts substantial axial gradients
             in blood glucose levels along various medullary structures.
             Furthermore, the model predicts that in the inner medulla,
             owing to the relatively limited blood flow and low tissue
             oxygen tension, anaerobic metabolism of glucose
             dominates.},
   Doi = {10.1007/s11538-016-0188-7},
   Key = {fds320882}
}

@article{fds320883,
   Author = {Nganguia, H and Young, Y-N and Layton, AT and Lai, M-C and Hu,
             W-F},
   Title = {Electrohydrodynamics of a viscous drop with
             inertia.},
   Journal = {Physical review. E},
   Volume = {93},
   Number = {5},
   Pages = {053114},
   Year = {2016},
   Month = {May},
   url = {http://dx.doi.org/10.1103/physreve.93.053114},
   Abstract = {Most of the existing numerical and theoretical
             investigations on the electrohydrodynamics of a viscous drop
             have focused on the creeping Stokes flow regime, where
             nonlinear inertia effects are neglected. In this work we
             study the inertia effects on the electrodeformation of a
             viscous drop under a DC electric field using a novel
             second-order immersed interface method. The inertia effects
             are quantified by the Ohnesorge number Oh, and the electric
             field is characterized by an electric capillary number
             Ca_{E}. Below the critical Ca_{E}, small to moderate
             electric field strength gives rise to steady equilibrium
             drop shapes. We found that, at a fixed Ca_{E}, inertia
             effects induce larger deformation for an oblate drop than a
             prolate drop, consistent with previous results in the
             literature. Moreover, our simulations results indicate that
             inertia effects on the equilibrium drop deformation are
             dictated by the direction of normal electric stress on the
             drop interface: Larger drop deformation is found when the
             normal electric stress points outward, and smaller drop
             deformation is found otherwise. To our knowledge, such
             inertia effects on the equilibrium drop deformation has not
             been reported in the literature. Above the critical Ca_{E},
             no steady equilibrium drop deformation can be found, and
             often the drop breaks up into a number of daughter droplets.
             In particular, our Navier-Stokes simulations show that, for
             the parameters we use, (1) daughter droplets are larger in
             the presence of inertia, (2) the drop deformation evolves
             more rapidly compared to creeping flow, and (3) complex
             distribution of electric stresses for drops with inertia
             effects. Our results suggest that normal electric pressure
             may be a useful tool in predicting drop pinch-off in oblate
             deformations.},
   Doi = {10.1103/physreve.93.053114},
   Key = {fds320883}
}

@article{fds320884,
   Author = {Sgouralis, I and Maroulas, V and Layton, AT},
   Title = {Transfer Function Analysis of Dynamic Blood Flow Control in
             the Rat Kidney.},
   Journal = {Bulletin of Mathematical Biology},
   Volume = {78},
   Number = {5},
   Pages = {923-960},
   Year = {2016},
   Month = {May},
   url = {http://dx.doi.org/10.1007/s11538-016-0168-y},
   Abstract = {Renal blood flow is regulated by the myogenic response (MR)
             and tubuloglomerular feedback (TGF). Both mechanisms
             function to buffer not only steady pressure perturbations
             but also transient ones. In this study, we develop two
             models of renal autoregulation-a comprehensive model and a
             simplified model-and use them to analyze the individual
             contributions of MR and TGF in buffering transient pressure
             perturbations. Both models represent a single nephron of a
             rat kidney together with the associated vasculature. The
             comprehensive model includes detailed representation of the
             vascular properties and cellular processes. In contrast, the
             simplified model represents a minimal set of key processes.
             To assess the degree to which fluctuations in renal
             perfusion pressure at different frequencies are attenuated,
             we derive a transfer function for each model. The transfer
             functions of both models predict resonance at 45 and
             180 mHz, which are associated with TGF and MR,
             respectively, effective autoregulation below [Formula: see
             text]100 mHz, and amplification of pressure perturbations
             above [Formula: see text]200 mHz. The predictions are in
             good agreement with experimental findings.},
   Doi = {10.1007/s11538-016-0168-y},
   Key = {fds320884}
}

@article{fds320180,
   Author = {Herschlag, G and Liu, J-G and Layton, AT},
   Title = {Fluid extraction across pumping and permeable walls in the
             viscous limit},
   Journal = {Physics of Fluids},
   Volume = {28},
   Number = {4},
   Pages = {041902-041902},
   Year = {2016},
   Month = {April},
   url = {http://dx.doi.org/10.1063/1.4946005},
   Doi = {10.1063/1.4946005},
   Key = {fds320180}
}

@article{fds320885,
   Author = {Sgouralis, I and Layton, AT},
   Title = {Conduction of feedback-mediated signal in a computational
             model of coupled nephrons.},
   Journal = {Mathematical Medicine and Biology: A Journal of the
             IMA},
   Volume = {33},
   Number = {1},
   Pages = {87-106},
   Year = {2016},
   Month = {March},
   url = {http://dx.doi.org/10.1093/imammb/dqv005},
   Abstract = {The nephron in the kidney regulates its fluid flow by
             several autoregulatory mechanisms. Two primary mechanisms
             are the myogenic response and the tubuloglomerular feedback
             (TGF). The myogenic response is a property of the
             pre-glomerular vasculature in which a rise in intravascular
             pressure elicits vasoconstriction that generates a
             compensatory increase in vascular resistance. TGF is a
             negative feedback response that balances glomerular
             filtration with tubular reabsorptive capacity. While each
             nephron has its own autoregulatory response, the responses
             of the kidney's many nephrons do not act autonomously but
             are instead coupled through the pre-glomerular vasculature.
             To better understand the conduction of these signals along
             the pre-glomerular arterioles and the impacts of
             internephron coupling on nephron flow dynamics, we developed
             a mathematical model of renal haemodynamics of two
             neighbouring nephrons that are coupled in that their
             afferent arterioles arise from a common cortical radial
             artery. Simulations were conducted to estimate internephron
             coupling strength, determine its dependence on vascular
             properties and to investigate the effect of coupling on
             TGF-mediated flow oscillations. Simulation results suggest
             that reduced gap-junctional conductances may yield stronger
             internephron TGF coupling and highly irregular TGF-mediated
             oscillations in nephron dynamics, both of which
             experimentally have been associated with hypertensive
             rats.},
   Doi = {10.1093/imammb/dqv005},
   Key = {fds320885}
}

@article{fds320886,
   Author = {Fry, BC and Edwards, A and Layton, AT},
   Title = {Impact of nitric-oxide-mediated vasodilation and oxidative
             stress on renal medullary oxygenation: a modeling
             study.},
   Journal = {American Journal of Physiology: Renal Physiology},
   Volume = {310},
   Number = {3},
   Pages = {F237-F247},
   Year = {2016},
   Month = {February},
   url = {http://dx.doi.org/10.1152/ajprenal.00334.2015},
   Abstract = {The goal of this study was to investigate the effects of
             nitric oxide (NO)-mediated vasodilation in preventing
             medullary hypoxia, as well as the likely pathways by which
             superoxide (O2(-)) conversely enhances medullary hypoxia. To
             do so, we expanded a previously developed mathematical model
             of solute transport in the renal medulla that accounts for
             the reciprocal interactions among oxygen (O2), NO, and O2(-)
             to include the vasoactive effects of NO on medullary
             descending vasa recta. The model represents the radial
             organization of the vessels and tubules, centered around
             vascular bundles in the outer medulla and collecting ducts
             in the inner medulla. Model simulations suggest that NO
             helps to prevent medullary hypoxia both by inducing
             vasodilation of the descending vasa recta (thus increasing
             O2 supply) and by reducing the active sodium transport rate
             (thus reducing O2 consumption). That is, the vasodilative
             properties of NO significantly contribute to maintaining
             sufficient medullary oxygenation. The model further predicts
             that a reduction in tubular transport efficiency (i.e., the
             ratio of active sodium transport per O2 consumption) is the
             main factor by which increased O2(-) levels lead to hypoxia,
             whereas hyperfiltration is not a likely pathway to medullary
             hypoxia due to oxidative stress. Finally, our results
             suggest that further increasing the radial separation
             between vessels and tubules would reduce the diffusion of NO
             towards descending vasa recta in the inner medulla, thereby
             diminishing its vasoactive effects therein and reducing O2
             delivery to the papillary tip.},
   Doi = {10.1152/ajprenal.00334.2015},
   Key = {fds320886}
}

@article{fds320181,
   Author = {Xie, L and Layton, AT and Wang, N and Larson, PEZ and Zhang, JL and Lee,
             VS and Liu, C and Johnson, GA},
   Title = {Dynamic contrast-enhanced quantitative susceptibility
             mapping with ultrashort echo time MRI for evaluating renal
             function.},
   Journal = {American Journal of Physiology: Renal Physiology},
   Volume = {310},
   Number = {2},
   Pages = {F174-F182},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1152/ajprenal.00351.2015},
   Abstract = {Dynamic contrast-enhanced (DCE) MRI can provide key insight
             into renal function. DCE MRI is typically achieved through
             an injection of a gadolinium (Gd)-based contrast agent,
             which has desirable T1 quenching and tracer kinetics.
             However, significant T2* blooming effects and signal voids
             can arise when Gd becomes very concentrated, especially in
             the renal medulla and pelvis. One MRI sequence designed to
             alleviate T2* effects is the ultrashort echo time (UTE)
             sequence. In the present study, we observed T2* blooming in
             the inner medulla of the mouse kidney, despite using UTE at
             an echo time of 20 microseconds and a low dose of 0.03
             mmol/kg Gd. We applied quantitative susceptibility mapping
             (QSM) and resolved the signal void into a positive
             susceptibility signal. The susceptibility values [in parts
             per million (ppm)] were converted into molar concentrations
             of Gd using a calibration curve. We determined the
             concentrating mechanism (referred to as the concentrating
             index) as a ratio of maximum Gd concentration in the inner
             medulla to the renal artery. The concentrating index was
             assessed longitudinally over a 17-wk course (3, 5, 7, 9, 13,
             17 wk of age). We conclude that the UTE-based DCE method is
             limited in resolving extreme T2* content caused by the
             kidney's strong concentrating mechanism. QSM was able to
             resolve and confirm the source of the blooming effect to be
             the large positive susceptibility of concentrated Gd. UTE
             with QSM can complement traditional magnitude UTE and offer
             a powerful tool to study renal pathophysiology.},
   Doi = {10.1152/ajprenal.00351.2015},
   Key = {fds320181}
}


%% 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 & 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}
}

@article{fds328058,
   Author = {Greene, J and Levine, A},
   Title = {Strong Heegaard diagrams and strong L–spaces},
   Journal = {Algebraic and Geometric Topology},
   Volume = {16},
   Number = {6},
   Pages = {3167-3208},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.2140/agt.2016.16.3167},
   Doi = {10.2140/agt.2016.16.3167},
   Key = {fds328058}
}

@article{fds328059,
   Author = {Hedden, M and Levine, AS},
   Title = {Splicing knot complements and bordered Floer
             homology},
   Journal = {Journal für die Reine und Angewandte Mathematik (Crelle's
             Journal)},
   Volume = {2016},
   Number = {720},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1515/crelle-2014-0064},
   Doi = {10.1515/crelle-2014-0064},
   Key = {fds328059}
}

@article{fds328060,
   Author = {LEVINE, ADAMSIMON},
   Title = {NONSURJECTIVE SATELLITE OPERATORS AND PIECEWISE-LINEAR
             CONCORDANCE},
   Journal = {Forum of Mathematics, Sigma},
   Volume = {4},
   Year = {2016},
   url = {http://dx.doi.org/10.1017/fms.2016.31},
   Doi = {10.1017/fms.2016.31},
   Key = {fds328060}
}


%% 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}
}


%% 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},
   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{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{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{fds329523,
   Author = {Huang, H and Liu, JG},
   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},
   Month = {January},
   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{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{fds320659,
   Author = {J.-G. Liu and J. Wang},
   Title = {A generalized Sz. Nagy inequality in higher dimensions and
             the critical thin film equation},
   Journal = {Nonlinearity},
   Volume = {30},
   Pages = {35-60},
   Year = {2017},
   Key = {fds320659}
}

@article{fds329169,
   Author = {Liu, J-G and Cong, W},
   Title = {Uniform $L^{\infty}$ boundedness for a degenerate
             parabolic-parabolic Keller-Segel model},
   Journal = {Discrete and Continuous Dynamical Systems - Series
             B},
   Volume = {22},
   Number = {2},
   Pages = {307-338},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.3934/dcdsb.2017015},
   Doi = {10.3934/dcdsb.2017015},
   Key = {fds329169}
}

@article{fds318453,
   Author = {Huang, H and Liu, J-G},
   Title = {A note on Monge–Ampère Keller–Segel
             equation},
   Journal = {Applied Mathematics Letters},
   Volume = {61},
   Pages = {26-34},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.1016/j.aml.2016.05.003},
   Doi = {10.1016/j.aml.2016.05.003},
   Key = {fds318453}
}

@article{fds323245,
   Author = {Huang, H and Liu, J-G},
   Title = {Error estimates of the aggregation-diffusion splitting
             algorithms for the Keller-Segel equations},
   Journal = {Discrete and Continuous Dynamical Systems - Series
             B},
   Volume = {21},
   Number = {10},
   Pages = {3463-3478},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.3934/dcdsb.2016107},
   Doi = {10.3934/dcdsb.2016107},
   Key = {fds323245}
}

@article{fds318454,
   Author = {Liu, J-G and Huang, H},
   Title = {Well-posedness for the Keller-Segel equation with fractional
             Laplacian and the theory of propagation of
             chaos},
   Journal = {Kinetic and Related Models},
   Volume = {9},
   Number = {4},
   Pages = {715-748},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.3934/krm.2016013},
   Doi = {10.3934/krm.2016013},
   Key = {fds318454}
}

@article{fds318455,
   Author = {Liu, J-G and Cong, W},
   Title = {A degenerate $p$-Laplacian Keller-Segel model},
   Journal = {Kinetic and Related Models},
   Volume = {9},
   Number = {4},
   Pages = {687-714},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.3934/krm.2016012},
   Doi = {10.3934/krm.2016012},
   Key = {fds318455}
}

@article{fds320551,
   Author = {Liu, J-G and Wang, J},
   Title = {A Note on L ∞ $L^{\infty}$ -Bound and Uniqueness to a
             Degenerate Keller-Segel Model},
   Journal = {Acta Applicandae Mathematicae},
   Volume = {142},
   Number = {1},
   Pages = {173-188},
   Year = {2016},
   Month = {April},
   ISSN = {0167-8019},
   url = {http://dx.doi.org/10.1007/s10440-015-0022-5},
   Doi = {10.1007/s10440-015-0022-5},
   Key = {fds320551}
}

@article{fds315797,
   Author = {Herschlag, G and Liu, J-G and Layton, AT},
   Title = {Fluid extraction across pumping and permeable walls in the
             viscous limit},
   Journal = {Physics of Fluids},
   Volume = {28},
   Number = {4},
   Pages = {041902-041902},
   Year = {2016},
   Month = {April},
   ISSN = {1070-6631},
   url = {http://dx.doi.org/10.1063/1.4946005},
   Doi = {10.1063/1.4946005},
   Key = {fds315797}
}

@article{fds320552,
   Author = {Liu, J-G and Pego, RL},
   Title = {On generating functions of Hausdorff moment
             sequences},
   Journal = {Transactions of the American Mathematical
             Society},
   Volume = {368},
   Number = {12},
   Pages = {8499-8518},
   Year = {2016},
   Month = {February},
   url = {http://dx.doi.org/10.1090/tran/6618},
   Doi = {10.1090/tran/6618},
   Key = {fds320552}
}

@article{fds329526,
   Author = {Chen, J and Liu, J-G and Zhou, Z},
   Title = {On a Schrödinger--Landau--Lifshitz System: Variational
             Structure and Numerical Methods},
   Journal = {Multiscale Modeling & Simulation},
   Volume = {14},
   Number = {4},
   Pages = {1463-1487},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M106947X},
   Doi = {10.1137/16M106947X},
   Key = {fds329526}
}

@article{fds323246,
   Author = {Liu, J-G and Xu, X},
   Title = {Existence Theorems for a Multidimensional Crystal Surface
             Model},
   Journal = {SIAM Journal on Mathematical Analysis},
   Volume = {48},
   Number = {6},
   Pages = {3667-3687},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M1059400},
   Doi = {10.1137/16M1059400},
   Key = {fds323246}
}

@article{fds320553,
   Author = {Liu, JG and Zhang, Y},
   Title = {Convergence of diffusion-drift many particle systems in
             probability under a sobolev norm},
   Journal = {Springer Proceedings in Mathematics and Statistics},
   Volume = {162},
   Series = {Proceedings of Particle Systems and Partial Differential
             Equations - III},
   Pages = {195-223},
   Publisher = {Springer},
   Year = {2016},
   Month = {January},
   ISBN = {9783319321424},
   url = {http://dx.doi.org/10.1007/978-3-319-32144-8_10},
   Abstract = {© Springer International Publishing Switzerland 2016. In
             this paperwedevelop a newmartingale method to showthe
             convergence of the regularized empirical measure of many
             particle systems in probability under a Sobolev norm to the
             corresponding mean field PDE. Our method works well for the
             simple case of Fokker Planck equation and we can estimate a
             lower bound of the rate of convergence. This method can be
             generalized to more complicated systems with
             interactions.},
   Doi = {10.1007/978-3-319-32144-8_10},
   Key = {fds320553}
}

@article{fds320649,
   Author = {J.-G. Liu and R. Yang},
   Title = {Propagation of chaos for large Brownian particle system with
             Coulomb interaction},
   Journal = {Research in the Mathematical Sciences},
   Volume = {3},
   Number = {40},
   Year = {2016},
   Key = {fds320649}
}

@article{fds320549,
   Author = {Y. Duan and J.-G. Liu},
   Title = {Error estimate of the particle method for the
             b-equation},
   Journal = {Methods and Applications of Analysis},
   Volume = {23},
   Pages = {119-154},
   Year = {2016},
   Key = {fds320549}
}

@article{fds320556,
   Author = {J.-G. Liu and Y. Zhang},
   Title = {Convergence of stochastic interacting particle systems in
             probability under a Sobolev norm},
   Journal = {Annals of Mathematical Sciences and Applications},
   Volume = {1},
   Pages = {251-299},
   Year = {2016},
   Key = {fds320556}
}

@article{fds320739,
   Author = {P. Degond and J.-G. Liu and S. Merino-Aceituno and T.
             Tardiveau},
   Title = {Continuum dynamics of the intention field under weakly
             cohesive social interactions},
   Journal = {Math. Models Methods Appl. Sci.},
   Year = {2016},
   Key = {fds320739}
}

@article{fds320743,
   Author = {Y. Gao and J.-G. Liu and J. Lu},
   Title = {Continuum limit of a mesoscopic model of step motion on
             vicinal surfaces},
   Journal = {J. Nonlinear Science},
   Year = {2016},
   Key = {fds320743}
}

@article{fds300225,
   Author = {J.-G. Liu and J. Wang},
   Title = {Refined hyper-contractivity and uniqueness for the
             Keller-Segel equations},
   Journal = {Applied Math Letter},
   Volume = {52},
   Pages = {212-219},
   Year = {2016},
   Key = {fds300225}
}


%% Lu, Jianfeng   
@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{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},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1016/j.cpc.2017.09.007},
   Doi = {10.1016/j.cpc.2017.09.007},
   Key = {fds329344}
}

@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},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1016/j.jcp.2017.09.012},
   Doi = {10.1016/j.jcp.2017.09.012},
   Key = {fds329343}
}

@article{fds328895,
   Author = {Lu, J and Steinerberger, S},
   Title = {A variation on the Donsker-Varadhan inequality for the
             principal eigenvalue.},
   Journal = {Proceedings of the Royal Society of London: 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 = {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{fds326081,
   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 = {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{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{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{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},
   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}
}

@article{fds321515,
   Author = {Mendl, CB and Lu, J and Lukkarinen, J},
   Title = {Thermalization of oscillator chains with onsite
             anharmonicity and comparison with kinetic
             theory.},
   Journal = {Physical review. E},
   Volume = {94},
   Number = {6-1},
   Pages = {062104},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1103/physreve.94.062104},
   Abstract = {We perform microscopic molecular dynamics simulations of
             particle chains with an onsite anharmonicity to study
             relaxation of spatially homogeneous states to equilibrium,
             and directly compare the simulations with the corresponding
             Boltzmann-Peierls kinetic theory. The Wigner function serves
             as a common interface between the microscopic and kinetic
             level. We demonstrate quantitative agreement after an
             initial transient time interval. In particular, besides
             energy conservation, we observe the additional
             quasiconservation of the phonon density, defined via an
             ensemble average of the related microscopic field variables
             and exactly conserved by the kinetic equations. On
             superkinetic time scales, density quasiconservation is lost
             while energy remains conserved, and we find evidence for
             eventual relaxation of the density to its canonical ensemble
             value. However, the precise mechanism remains unknown and is
             not captured by the Boltzmann-Peierls equations.},
   Doi = {10.1103/physreve.94.062104},
   Key = {fds321515}
}

@article{fds325891,
   Author = {Li, Q and Lu, J and Sun, W},
   Title = {Half-space kinetic equations with general boundary
             conditions},
   Journal = {Mathematics of Computation},
   Volume = {86},
   Number = {305},
   Pages = {1269-1301},
   Year = {2016},
   Month = {October},
   url = {http://dx.doi.org/10.1090/mcom/3155},
   Doi = {10.1090/mcom/3155},
   Key = {fds325891}
}

@article{fds320186,
   Author = {Yu, T-Q and Lu, J and Abrams, CF and Vanden-Eijnden,
             E},
   Title = {Multiscale implementation of infinite-swap replica exchange
             molecular dynamics.},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {113},
   Number = {42},
   Pages = {11744-11749},
   Year = {2016},
   Month = {October},
   url = {http://dx.doi.org/10.1073/pnas.1605089113},
   Abstract = {Replica exchange molecular dynamics (REMD) is a popular
             method to accelerate conformational sampling of complex
             molecular systems. The idea is to run several replicas of
             the system in parallel at different temperatures that are
             swapped periodically. These swaps are typically attempted
             every few MD steps and accepted or rejected according to a
             Metropolis-Hastings criterion. This guarantees that the
             joint distribution of the composite system of replicas is
             the normalized sum of the symmetrized product of the
             canonical distributions of these replicas at the different
             temperatures. Here we propose a different implementation of
             REMD in which (i) the swaps obey a continuous-time Markov
             jump process implemented via Gillespie's stochastic
             simulation algorithm (SSA), which also samples exactly the
             aforementioned joint distribution and has the advantage of
             being rejection free, and (ii) this REMD-SSA is combined
             with the heterogeneous multiscale method to accelerate the
             rate of the swaps and reach the so-called infinite-swap
             limit that is known to optimize sampling efficiency. The
             method is easy to implement and can be trivially
             parallelized. Here we illustrate its accuracy and efficiency
             on the examples of alanine dipeptide in vacuum and
             C-terminal β-hairpin of protein G in explicit solvent. In
             this latter example, our results indicate that the landscape
             of the protein is a triple funnel with two folded structures
             and one misfolded structure that are stabilized by
             H-bonds.},
   Doi = {10.1073/pnas.1605089113},
   Key = {fds320186}
}

@article{fds320187,
   Author = {Lu, J and Zhou, Z},
   Title = {Improved sampling and validation of frozen Gaussian
             approximation with surface hopping algorithm for
             nonadiabatic dynamics.},
   Journal = {Journal of Chemical Physics},
   Volume = {145},
   Number = {12},
   Pages = {124109},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.1063/1.4963107},
   Abstract = {In the spirit of the fewest switches surface hopping, the
             frozen Gaussian approximation with surface hopping (FGA-SH)
             method samples a path integral representation of the
             non-adiabatic dynamics in the semiclassical regime. An
             improved sampling scheme is developed in this work for
             FGA-SH based on birth and death branching processes. The
             algorithm is validated for the standard test examples of
             non-adiabatic dynamics.},
   Doi = {10.1063/1.4963107},
   Key = {fds320187}
}

@article{fds318293,
   Author = {Li, X and Lu, J},
   Title = {Traction boundary conditions for molecular static
             simulations},
   Journal = {Computer Methods in Applied Mechanics and
             Engineering},
   Volume = {308},
   Pages = {310-329},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.1016/j.cma.2016.05.002},
   Doi = {10.1016/j.cma.2016.05.002},
   Key = {fds318293}
}

@article{fds318294,
   Author = {Lin, L and Lu, J},
   Title = {Decay estimates of discretized Green’s functions for
             Schrödinger type operators},
   Journal = {Science China Mathematics},
   Volume = {59},
   Number = {8},
   Pages = {1561-1578},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.1007/s11425-016-0311-4},
   Doi = {10.1007/s11425-016-0311-4},
   Key = {fds318294}
}

@article{fds318295,
   Author = {Lai, R and Lu, J},
   Title = {Localized density matrix minimization and linear-scaling
             algorithms},
   Journal = {Journal of Computational Physics},
   Volume = {315},
   Pages = {194-210},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.jcp.2016.02.076},
   Doi = {10.1016/j.jcp.2016.02.076},
   Key = {fds318295}
}

@article{fds318296,
   Author = {Lu, J and Ying, L},
   Title = {Sparsifying preconditioner for soliton calculations},
   Journal = {Journal of Computational Physics},
   Volume = {315},
   Pages = {458-466},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.jcp.2016.03.061},
   Doi = {10.1016/j.jcp.2016.03.061},
   Key = {fds318296}
}

@article{fds316401,
   Author = {Lu, J and Wirth, B and Yang, H},
   Title = {Combining 2D synchrosqueezed wave packet transform with
             optimization for crystal image analysis},
   Journal = {Journal of the Mechanics and Physics of Solids},
   Volume = {89},
   Pages = {194-210},
   Year = {2016},
   Month = {April},
   ISSN = {0022-5096},
   url = {http://hdl.handle.net/10161/11296 Duke open
             access},
   Abstract = {© 2016 Elsevier Ltd. All rights reserved. We develop a
             variational optimization method for crystal analysis in
             atomic resolution images, which uses information from a 2D
             synchrosqueezed transform (SST) as input. The
             synchrosqueezed transform is applied to extract initial
             information from atomic crystal images: crystal defects,
             rotations and the gradient of elastic deformation. The
             deformation gradient estimate is then improved outside the
             identified defect region via a variational approach, to
             obtain more robust results agreeing better with the physical
             constraints. The variational model is optimized by a
             nonlinear projected conjugate gradient method. Both examples
             of images from computer simulations and imaging experiments
             are analyzed, with results demonstrating the effectiveness
             of the proposed method.},
   Doi = {10.1016/j.jmps.2016.01.002},
   Key = {fds316401}
}

@article{fds318297,
   Author = {Chen, J and Lu, J},
   Title = {Analysis of the divide-and-conquer method for electronic
             structure calculations},
   Journal = {Mathematics of Computation},
   Volume = {85},
   Number = {302},
   Pages = {2919-2938},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1090/mcom/3066},
   Doi = {10.1090/mcom/3066},
   Key = {fds318297}
}

@article{fds320188,
   Author = {Delgadillo, R and Lu, J and Yang, X},
   Title = {Gauge-Invariant Frozen Gaussian Approximation Method for the
             Schrödinger Equation with Periodic Potentials},
   Journal = {SIAM Journal on Scientific Computing},
   Volume = {38},
   Number = {4},
   Pages = {A2440-A2463},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1137/15M1040384},
   Doi = {10.1137/15M1040384},
   Key = {fds320188}
}


%% 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}
}

@article{fds328559,
   Author = {Iglesias, M and Lu, Y and Stuart, A},
   Title = {A Bayesian level set method for geometric inverse
             problems},
   Journal = {Interfaces and Free Boundaries},
   Volume = {18},
   Number = {2},
   Pages = {181-217},
   Year = {2016},
   url = {http://dx.doi.org/10.4171/IFB/362},
   Doi = {10.4171/IFB/362},
   Key = {fds328559}
}


%% Ma, Ding   
@article{fds318299,
   Author = {Ma, D},
   Title = {Inverse of some matrix related to double zeta values of odd
             weight},
   Journal = {Journal of Number Theory},
   Volume = {166},
   Pages = {166-180},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.1016/j.jnt.2016.02.007},
   Doi = {10.1016/j.jnt.2016.02.007},
   Key = {fds318299}
}

@article{fds318300,
   Author = {Ma, D},
   Title = {Period polynomial relations between formal double zeta
             values of odd weight},
   Journal = {Mathematische Annalen},
   Volume = {365},
   Number = {1-2},
   Pages = {345-362},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1007/s00208-015-1308-7},
   Doi = {10.1007/s00208-015-1308-7},
   Key = {fds318300}
}


%% Maggioni, Mauro   
@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{fds329467,
   Author = {Gerber, S and Maggioni, M},
   Title = {Multiscale strategies for computing optimal
             transport},
   Journal = {Journal of machine learning research : JMLR},
   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}
}

@article{fds320927,
   Author = {Liao, W and Maggioni, M and Vigogna, S},
   Title = {Learning adaptive multiscale approximations to data and
             functions near low-dimensional sets},
   Journal = {2016 IEEE Information Theory Workshop, ITW
             2016},
   Pages = {226-230},
   Year = {2016},
   Month = {October},
   ISBN = {9781509010905},
   url = {http://dx.doi.org/10.1109/ITW.2016.7606829},
   Abstract = {© 2016 IEEE. In the setting where a data set in D consists
             of samples from a probability measure ρ concentrated on or
             near an unknown d-dimensional set M, with D large but d ≪
             D, we consider two sets of problems: geometric approximation
             of M and regression of a function on M. In the first case we
             construct multiscale low-dimensional empirical
             approximations ofM, which are adaptive whenMhas geometric
             regularity that may vary at different locations and scales,
             and give performance guarantees. In the second case we
             exploit these empirical geometric approximations to
             construct multiscale approximations to on M, which adapt to
             the unknown regularity of even when this varies at different
             scales and locations. We prove guarantees showing that we
             attain the same learning rates as if was defined on a
             Euclidean domain of dimension d, instead of an unknown
             manifold M. All algorithms have complexity O(n log n), with
             constants scaling linearly in D and exponentially in
             d.},
   Doi = {10.1109/ITW.2016.7606829},
   Key = {fds320927}
}

@article{fds318319,
   Author = {Goetzmann, WN and Jones, PW and Maggioni, M and Walden,
             J},
   Title = {Beauty is in the bid of the beholder: An empirical basis for
             style},
   Journal = {Research in Economics},
   Volume = {70},
   Number = {3},
   Pages = {388-402},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.1016/j.rie.2016.05.004},
   Doi = {10.1016/j.rie.2016.05.004},
   Key = {fds318319}
}

@article{fds316563,
   Author = {Wang, Y and Chen, G and Maggioni, M},
   Title = {High-Dimensional Data Modeling Techniques for Detection of
             Chemical Plumes and Anomalies in Hyperspectral Images and
             Movies},
   Journal = {IEEE Journal of Selected Topics in Applied Earth
             Observations and Remote Sensing},
   Volume = {9},
   Number = {9},
   Pages = {4316-4324},
   Year = {2016},
   Month = {September},
   ISSN = {1939-1404},
   url = {http://dx.doi.org/10.1109/JSTARS.2016.2539968},
   Abstract = {We briefly review recent progress in techniques for modeling
             and analyzing hyperspectral images and movies, in particular
             for detecting plumes of both known and unknown chemicals.
             For detecting chemicals of known spectrum, we extend the
             technique of using a single subspace for modeling the
             background to a “mixture of subspaces” model to tackle
             more complicated background. Furthermore, we use partial
             least squares regression on a resampled training set to
             boost performance. For the detection of unknown chemicals,
             we view the problem as an anomaly detection problem and use
             novel estimators with low-sampled complexity for
             intrinsically low-dimensional data in high dimensions that
             enable us to model the “normal” spectra and detect
             anomalies. We apply these algorithms to benchmark datasets
             made available by the Automated Target Detection program
             cofunded by NSF, DTRA, and NGA, and compare, when
             applicable, to current state-of-the-art algorithms, with
             favorable results.},
   Doi = {10.1109/JSTARS.2016.2539968},
   Key = {fds316563}
}

@article{fds317218,
   Author = {Yin, R and Monson, E and Honig, E and Daubechies, I and Maggioni,
             M},
   Title = {Object recognition in art drawings: Transfer of a neural
             network},
   Journal = {IEEE International Conference on Acoustics Speech and Signal
             Processing},
   Volume = {2016-May},
   Pages = {2299-2303},
   Year = {2016},
   Month = {May},
   ISBN = {9781479999880},
   ISSN = {1520-6149},
   url = {http://dx.doi.org/10.1109/ICASSP.2016.7472087},
   Abstract = {© 2016 IEEE. We consider the problem of recognizing objects
             in collections of art works, in view of automatically
             labeling, searching and organizing databases of art works.
             To avoid manually labelling objects, we introduce a
             framework for transferring a convolutional neural network
             (CNN), trained on available large collections of labelled
             natural images, to the context of drawings. We retrain both
             the top and the bottom layer of the network, responsible for
             the high-level classiication output and the low-level
             features detection respectively, by transforming natural
             images into drawings. We apply this procedure to the
             drawings in the Jan Brueghel Wiki, and show the transferred
             CNN learns a discriminative metric on drawings and achieves
             good recognition accuracy. We also discuss why standard
             descriptor-based methods is problematic in the context of
             drawings.},
   Doi = {10.1109/ICASSP.2016.7472087},
   Key = {fds317218}
}

@article{fds314792,
   Author = {Maggioni, M and Minsker, S and Strawn, N},
   Title = {Multiscale dictionary learning: Non-asymptotic bounds and
             robustness},
   Journal = {Journal of machine learning research : JMLR},
   Volume = {17},
   Year = {2016},
   Month = {January},
   ISSN = {1532-4435},
   url = {http://arxiv.org/abs/1401.5833},
   Abstract = {© 2016 Mauro Maggioni, Stanislav Minsker, and Nate Strawn.
             High-dimensional datasets are well-approximated by
             low-dimensional structures. Over the past decade, this
             empirical observation motivated the investigation of
             detection, measurement, and modeling techniques to exploit
             these low-dimensional intrinsic structures, yielding
             numerous implications for high-dimensional statistics,
             machine learning, and signal processing. Manifold learning
             (where the low-dimensional structure is a manifold) and
             dictionary learning (where the low-dimensional structure is
             the set of sparse linear combinations of vectors from a
             finite dictionary) are two prominent theoretical and
             computational frameworks in this area. Despite their
             ostensible distinction, the recently-introduced Geometric
             Multi-Resolution Analysis (GMRA) provides a robust,
             computationally eficient, multiscale procedure for
             simultaneously learning manifolds and dictionaries. In this
             work, we prove non-asymptotic probabilistic bounds on the
             approximation error of GMRA for a rich class of
             data-generating statistical models that includes "noisy"
             manifolds, thereby establishing the theoretical robustness
             of the procedure and confirming empirical observations. In
             particular, if a dataset aggregates near a low-dimensional
             manifold, our results show that the approximation error of
             the GMRA is completely independent of the ambient dimension.
             Our work therefore establishes GMRA as a provably fast
             algorithm for dictionary learning with approximation and
             sparsity guarantees. We include several numerical
             experiments confirming these theoretical results, and our
             theoretical framework provides new tools for assessing the
             behavior of manifold learning and dictionary learning
             procedures on a large class of interesting
             models.},
   Key = {fds314792}
}

@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}
}


%% 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},
   Year = {2017},
   Month = {August},
   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.},
   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},
   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}
}

@article{fds318321,
   Author = {Hairer, M and Mattingly, J},
   Title = {The strong Feller property for singular stochastic
             PDEs},
   Year = {2016},
   Abstract = {We show that the Markov semigroups generated by a large
             class of singular stochastic PDEs satisfy the strong Feller
             property. These include for example the KPZ equation and the
             dynamical $\Phi^4_3$ model. As a corollary, we prove that
             the Brownian bridge measure is the unique invariant measure
             for the KPZ equation with periodic boundary
             conditions.},
   Key = {fds318321}
}

@article{fds318322,
   Author = {Tempkin, JOB and Koten, BV and Mattingly, JC and Dinner, AR and Weare,
             J},
   Title = {Trajectory stratification of stochastic dynamics},
   Year = {2016},
   Abstract = {We present a general mathematical framework for trajectory
             stratification for simulating rare events. Trajectory
             stratification involves decomposing trajectories of the
             underlying process into fragments limited to restricted
             regions of state space (strata), computing averages over the
             distributions of the trajectory fragments within the strata
             with minimal communication between them, and combining those
             averages with appropriate weights to yield averages with
             respect to the original underlying process. Our framework
             reveals the full generality and flexibility of trajectory
             stratification, and it illuminates a common mathematical
             structure shared by existing algorithms for sampling rare
             events. We demonstrate the power of the framework by
             defining strata in terms of both points in time and
             path-dependent variables for efficiently estimating averages
             that were not previously tractable.},
   Key = {fds318322}
}


%% Miller, Ezra   
@article{fds320533,
   Author = {Berenstein, A and Braverman, M and Miller, E and Retakh, V and Weitsman,
             J},
   Title = {Andrei Zelevinsky, 1953–2013},
   Journal = {Advances in Mathematics},
   Volume = {300},
   Pages = {1-4},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.1016/j.aim.2016.06.006},
   Doi = {10.1016/j.aim.2016.06.006},
   Key = {fds320533}
}

@article{fds320534,
   Author = {Berenstein, A and Braverman, M and Miller, E and Retakh, V and Weitsman,
             J},
   Title = {Andrei Zelevinsky, 1953-2013},
   Journal = {Advances in Mathematics},
   Volume = {299},
   Pages = {601-604},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.1016/j.aim.2016.05.020},
   Doi = {10.1016/j.aim.2016.05.020},
   Key = {fds320534}
}

@article{fds303557,
   Author = {Kahle, T and Miller, E and O’Neill, C},
   Title = {Irreducible decomposition of binomial ideals},
   Journal = {Compositio Mathematica},
   Volume = {152},
   Number = {06},
   Pages = {1319-1332},
   Year = {2016},
   Month = {June},
   url = {http://arxiv.org/abs/1503.02607},
   Abstract = {Building on coprincipal mesoprimary decomposition [Kahle and
             Miller, 2014], we combinatorially construct an irreducible
             decomposition of any given binomial ideal. In a parallel
             manner, for congruences in commutative monoids we construct
             decompositions that are direct combinatorial analogues of
             binomial irreducible decompositions, and for binomial ideals
             we construct decompositions into ideals that are as
             irreducible as possible while remaining binomial. We provide
             an example of a binomial ideal that is not an intersection
             of irreducible binomial ideals, thus answering a question of
             Eisenbud and Sturmfels [1996].},
   Doi = {10.1112/S0010437X16007272},
   Key = {fds303557}
}

@article{fds303556,
   Author = {Bendich, P and Marron, JS and Miller, E and Pieloch, A and Skwerer,
             S},
   Title = {Persistent homology analysis of brain artery
             trees},
   Journal = {Annals of Applied Statistics},
   Volume = {10},
   Number = {1},
   Pages = {19 pages},
   Year = {2016},
   Month = {January},
   url = {http://arxiv.org/abs/1411.6652v1},
   Abstract = {New representations of tree-structured data objects, using
             ideas from topological data analysis, enable improved
             statistical analyses of a population of brain artery trees.
             A number of representations of each data tree arise from
             persistence diagrams that quantify branching and looping of
             vessels at multiple scales. Novel approaches to the
             statistical analysis, through various summaries of the
             persistence diagrams, lead to heightened correlations with
             covariates such as age and sex, relative to earlier analyses
             of this data set. The correlation with age continues to be
             significant even after controlling for correlations from
             earlier significant summaries},
   Key = {fds303556}
}


%% 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}
}

@article{fds318324,
   Author = {F.C. Motta and Francis C. Motta, and Patrick D. Shipman, and Bethany D.
             Springer},
   Title = {Optimally Topologically Transitive Orbits in Discrete
             Dynamical Systems},
   Journal = {American Mathematical Monthly},
   Volume = {123},
   Number = {2},
   Pages = {115-115},
   Year = {2016},
   url = {http://dx.doi.org/10.4169/amer.math.monthly.123.2.115},
   Doi = {10.4169/amer.math.monthly.123.2.115},
   Key = {fds318324}
}


%% Mukherjee, Sayan   
@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{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{fds322049,
   Author = {Snyder-Mackler, N and Majoros, WH and Yuan, ML and Shaver, AO and Gordon, JB and Kopp, GH and Schlebusch, SA and Wall, JD and Alberts, SC and Mukherjee, S and Zhou, X and Tung, J},
   Title = {Efficient Genome-Wide Sequencing and Low-Coverage Pedigree
             Analysis from Noninvasively Collected Samples.},
   Journal = {Genetics},
   Volume = {203},
   Number = {2},
   Pages = {699-714},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1534/genetics.116.187492},
   Abstract = {Research on the genetics of natural populations was
             revolutionized in the 1990s by methods for genotyping
             noninvasively collected samples. However, these methods have
             remained largely unchanged for the past 20 years and lag far
             behind the genomics era. To close this gap, here we report
             an optimized laboratory protocol for genome-wide capture of
             endogenous DNA from noninvasively collected samples, coupled
             with a novel computational approach to reconstruct pedigree
             links from the resulting low-coverage data. We validated
             both methods using fecal samples from 62 wild baboons,
             including 48 from an independently constructed extended
             pedigree. We enriched fecal-derived DNA samples up to
             40-fold for endogenous baboon DNA and reconstructed
             near-perfect pedigree relationships even with extremely
             low-coverage sequencing. We anticipate that these methods
             will be broadly applicable to the many research systems for
             which only noninvasive samples are available. The lab
             protocol and software ("WHODAD") are freely available at
             www.tung-lab.org/protocols-and-software.html and
             www.xzlab.org/software.html, respectively.},
   Doi = {10.1534/genetics.116.187492},
   Key = {fds322049}
}

@article{fds323271,
   Author = {Zhao, S and Gao, C and Mukherjee, S and Engelhardt,
             BE},
   Title = {Bayesian group factor analysis with structured
             sparsity},
   Journal = {Journal of machine learning research : JMLR},
   Volume = {17},
   Pages = {1-47},
   Year = {2016},
   Month = {April},
   Abstract = {© 2016 Shiwen Zhao, Chuan Gao, Sayan Mukherjee, and Barbara
             E. Engelhardt.Latent factor models are the canonical
             statistical tool for exploratory analyses of lowdimensional
             linear structure for a matrix of p features across n
             samples. We develop a structured Bayesian group factor
             analysis model that extends the factor model to multiple
             coupled observation matrices; in the case of two
             observations, this reduces to a Bayesian model of canonical
             correlation analysis. Here, we carefully de-ne a structured
             Bayesian prior that encourages both element-wise and
             column-wise shrinkage and leads to desirable behavior on
             high-dimensional data. In particular, our model puts a
             structured prior on the joint factor loading matrix,
             regularizing at three levels, which enables element-wise
             sparsity and unsupervised recovery of latent factors
             corresponding to structured variance across arbitrary
             subsets of the observations. In addition, our structured
             prior allows for both dense and sparse latent factors so
             that covariation among either all features or only a subset
             of features can be recovered. We use fast parameter-expanded
             expectation-maximization for parameter estimation in this
             model. We validate our method on simulated data with
             substantial structure. We show results of our method applied
             to three high-dimensional data sets, comparing results
             against a number of state-of-The-Art approaches. These
             results illustrate useful properties of our model, including
             i) recovering sparse signal in the presence of dense
             effects; ii) the ability to scale naturally to large numbers
             of observations; iii) exible observation-and factor-specific
             regularization to recover factors with a wide variety of
             sparsity levels and percentage of variance explained; and
             iv) tractable inference that scales to modern genomic and
             text data sizes.},
   Key = {fds323271}
}

@article{fds323272,
   Author = {Galinsky, KJ and Bhatia, G and Loh, P-R and Georgiev, S and Mukherjee,
             S and Patterson, NJ and Price, AL},
   Title = {Fast Principal-Component Analysis Reveals Convergent
             Evolution of ADH1B in Europe and East Asia.},
   Journal = {The American Journal of Human Genetics},
   Volume = {98},
   Number = {3},
   Pages = {456-472},
   Year = {2016},
   Month = {March},
   url = {http://dx.doi.org/10.1016/j.ajhg.2015.12.022},
   Abstract = {Searching for genetic variants with unusual differentiation
             between subpopulations is an established approach for
             identifying signals of natural selection. However, existing
             methods generally require discrete subpopulations. We
             introduce a method that infers selection using principal
             components (PCs) by identifying variants whose
             differentiation along top PCs is significantly greater than
             the null distribution of genetic drift. To enable the
             application of this method to large datasets, we developed
             the FastPCA software, which employs recent advances in
             random matrix theory to accurately approximate top PCs while
             reducing time and memory cost from quadratic to linear in
             the number of individuals, a computational improvement of
             many orders of magnitude. We apply FastPCA to a cohort of
             54,734 European Americans, identifying 5 distinct
             subpopulations spanning the top 4 PCs. Using the PC-based
             test for natural selection, we replicate previously known
             selected loci and identify three new genome-wide significant
             signals of selection, including selection in Europeans at
             ADH1B. The coding variant rs1229984(∗)T has previously
             been associated to a decreased risk of alcoholism and shown
             to be under selection in East Asians; we show that it is a
             rare example of independent evolution on two continents. We
             also detect selection signals at IGFBP3 and IGH, which have
             also previously been associated to human
             disease.},
   Doi = {10.1016/j.ajhg.2015.12.022},
   Key = {fds323272}
}

@misc{fds323273,
   Author = {Huang, B and Jarrett, NWD and Babu, S and Mukherjee, S and Yang,
             J},
   Title = {Cümülön: MatrixBased data analytics in the cloud with
             spot instances},
   Volume = {9},
   Pages = {156-167},
   Booktitle = {Proceedings of the VLDB Endowment},
   Year = {2016},
   Month = {January},
   Abstract = {We describe Cümülön, a system aimed at helping users
             develop and deploy matrix-based data analysis programs in a
             public cloud. A key feature of Cümülön is its end-to-end
             support for the so-called spot instances-machines whose
             market price fluctuates over time but is usually much lower
             than the regular fixed price. A user sets a bid price when
             acquiring spot instances, and loses them as soon as the
             market price exceeds the bid price. While spot instances can
             potentially save cost, they are difficult to use
             effectively, and run the risk of not finishing work while
             costing more. Cümülön provides a highly elastic
             computation and storage engine on top of spot instances, and
             offers automatic cost-based optimization of execution,
             deployment, and bidding strategies. Cümülön further
             quantifies how the uncertainty in the market price
             translates into the cost uncertainty of its recommendations,
             and allows users to specify their risk tolerance as an
             optimization constraint.},
   Key = {fds323273}
}


%% Ng, Lenhard L.   
@article{fds320427,
   Author = {Cornwell, C and Ng, L and Sivek, S},
   Title = {Obstructions to Lagrangian concordance},
   Journal = {Algebraic and Geometric Topology},
   Volume = {16},
   Number = {2},
   Pages = {797-824},
   Year = {2016},
   Month = {April},
   url = {http://dx.doi.org/10.2140/agt.2016.16.797},
   Doi = {10.2140/agt.2016.16.797},
   Key = {fds320427}
}


%% Nolen, James H.   
@article{fds316609,
   Author = {Mourrat, J-C and Nolen, J},
   Title = {Scaling limit of the corrector in stochastic
             homogenization},
   Journal = {The annals of applied probability : an official journal of
             the Institute of Mathematical Statistics},
   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}
}

@article{fds316608,
   Author = {Gloria, A and Nolen, J},
   Title = {A Quantitative Central Limit Theorem for the Effective
             Conductance on the Discrete Torus},
   Journal = {Communications on Pure & Applied Mathematics},
   Volume = {69},
   Number = {12},
   Pages = {2304-2348},
   Year = {2016},
   Month = {December},
   ISSN = {0010-3640},
   url = {http://dx.doi.org/10.1002/cpa.21614},
   Doi = {10.1002/cpa.21614},
   Key = {fds316608}
}

@article{fds316661,
   Author = {Nolen, J},
   Title = {Normal approximation for the net flux through a random
             conductor},
   Journal = {Stochastic Partial Differential Equations: Analysis and
             Computations},
   Volume = {4},
   Number = {3},
   Pages = {439-476},
   Year = {2016},
   Month = {September},
   ISSN = {2194-0401},
   url = {http://arxiv.org/abs/1406.2186},
   Doi = {10.1007/s40072-015-0068-4},
   Key = {fds316661}
}

@article{fds318326,
   Author = {Nolen, JH and Roquejoffre, J-M and Ryzhik, L},
   Title = {Refined long time asymptotics for Fisher-KPP
             fronts},
   Year = {2016},
   Key = {fds318326}
}

@article{fds320462,
   Author = {Hamel, F and Nolen, J and Roquejoffre, J-M and Ryzhik,
             L},
   Title = {The logarithmic delay of KPP fronts in a periodic
             medium},
   Journal = {Journal of the European Mathematical Society},
   Volume = {18},
   Number = {3},
   Pages = {465-505},
   Year = {2016},
   url = {http://arxiv.org/abs/1211.6173},
   Doi = {10.4171/JEMS/595},
   Key = {fds320462}
}


%% Orizaga, Saulo   
@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}
}

@article{fds329008,
   Author = {Glasner, K and Orizaga, S},
   Title = {Improving the accuracy of convexity splitting methods for
             gradient flow equations},
   Journal = {Journal of Computational Physics},
   Volume = {315},
   Pages = {52-64},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.jcp.2016.03.042},
   Doi = {10.1016/j.jcp.2016.03.042},
   Key = {fds329008}
}

@article{fds329009,
   Author = {Orizaga, S and Glasner, K},
   Title = {Instability and reorientation of block copolymer
             microstructure by imposed electric fields.},
   Journal = {Physical review. E},
   Volume = {93},
   Number = {5},
   Pages = {052504},
   Year = {2016},
   Month = {May},
   url = {http://dx.doi.org/10.1103/physreve.93.052504},
   Abstract = {The influence of electric fields on lamellar block copolymer
             microstructure is studied in the context of a density
             functional model and its sharp interface limit. A free
             boundary problem for domain interfaces of strongly
             segregated polymers is derived, which includes coupling of
             interface and electric field orientation. The linearized
             dynamics of lamellar configurations is computed in this
             context, leading to quantitative criteria for instability as
             a function of pattern wavelength, field magnitude, and
             orientation. Numerical simulations of the full model in two
             and three dimensions are used to study the nonlinear
             development of instabilities. In three dimensions,
             sufficiently large electric field magnitude always leads to
             instability. In two dimensions, the field has either
             stabilizing or destabilizing effects depending on the
             misorientation of the field and pattern. Even when linear
             instabilities are present, the dynamics can lead to stable
             corrugated domain interfaces which do not align with the
             electric field. Sufficiently high field strengths, on the
             other hand, produce topological rearrangement which may lead
             to alignment.},
   Doi = {10.1103/physreve.93.052504},
   Key = {fds329009}
}


%% 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}
}

@book{fds51036,
   Author = {A. O. Petters and X. Dong},
   Title = {An Introduction to Mathematical Finance: Understanding and
             Building Financial Intuition},
   Series = {SUMAT},
   Publisher = {Springer, in preparation},
   Year = {2016},
   Month = {Winter},
   Key = {fds51036}
}


%% Pfister, Henry   
@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},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1103/PhysRevE.96.032129},
   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}
}

@article{fds322709,
   Author = {Kumar, S and Calderbank, R and Pfister, HD},
   Title = {Beyond double transitivity: Capacity-achieving cyclic codes
             on erasure channels},
   Journal = {2016 IEEE Information Theory Workshop, ITW
             2016},
   Pages = {241-245},
   Year = {2016},
   Month = {October},
   ISBN = {9781509010905},
   url = {http://dx.doi.org/10.1109/ITW.2016.7606832},
   Abstract = {© 2016 IEEE. Recently, sequences of error-correcting codes
             with doubly-transitive permutation groups were shown to
             achieve capacity on erasure channels under symbol-wise
             maximum a posteriori (MAP) decoding. From this, it follows
             that Reed-Muller and primitive narrow-sense BCH codes
             achieve capacity in the same setting. In this article, we
             extend this result to a large family of cyclic codes by
             considering codes whose permutation groups satisfy a
             condition weaker than double transitivity. The article
             combines two simple technical contributions. First, we show
             that the transition width of a monotone boolean function is
             O(1/log k), where k is the size of the smallest orbit
             induced by its symmetry group. The proof is based on
             Talagrand's lower bound on influences for monotone boolean
             functions. Second, we consider the extrinsic information
             transfer (EXIT) function of an Fq-linear cyclic code whose
             blocklength N divides q t -1 and is coprime with q-1. We
             show that this EXIT function is a monotone boolean function
             whose symmetry group contains no orbits of size smaller than
             the smallest prime divisor of t. Combining these, we show
             that sequences of cyclic codes, whose blocklengths satisfy
             the above conditions, achieve capacity on the q-ary erasure
             channel if all prime divisors of t tend to
             infinity.},
   Doi = {10.1109/ITW.2016.7606832},
   Key = {fds322709}
}

@article{fds322710,
   Author = {Hager, C and Amat, AGI and Pfister, HD and Brannstrom,
             F},
   Title = {Density evolution for deterministic generalized product
             codes with higher-order modulation},
   Journal = {International Symposium on Turbo Codes and Iterative
             Information Processing, ISTC},
   Volume = {2016-October},
   Pages = {236-240},
   Year = {2016},
   Month = {October},
   ISBN = {9781509034017},
   url = {http://dx.doi.org/10.1109/ISTC.2016.7593112},
   Abstract = {© 2016 IEEE. Generalized product codes (GPCs) are
             extensions of product codes (PCs) where coded bits are
             protected by two component codes but not necessarily
             arranged in a rectangular array. It has recently been shown
             that there exists a large class of deterministic GPCs
             (including, e.g., irregular PCs, half-product codes,
             staircase codes, and certain braided codes) for which the
             asymptotic performance under iterative bounded-distance
             decoding over the binary erasure channel (BEC) can be
             rigorously characterized in terms of a density evolution
             analysis. In this paper, the analysis is extended to the
             case where transmission takes place over parallel BECs with
             different erasure probabilities. We use this model to
             predict the code performance in a coded modulation setup
             with higher-order signal constellations. We also discuss the
             design of the bit mapper that determines the allocation of
             the coded bits to the modulation bits of the signal
             constellation.},
   Doi = {10.1109/ISTC.2016.7593112},
   Key = {fds322710}
}

@article{fds322711,
   Author = {Sanatkar, MR and Pfister, HD},
   Title = {Increasing the rate of spatially-coupled codes via optimized
             irregular termination},
   Journal = {International Symposium on Turbo Codes and Iterative
             Information Processing, ISTC},
   Volume = {2016-October},
   Pages = {31-35},
   Year = {2016},
   Month = {October},
   ISBN = {9781509034017},
   url = {http://dx.doi.org/10.1109/ISTC.2016.7593071},
   Abstract = {© 2016 IEEE. In this paper, we consider the rate-loss
             problem for spatially-coupled LDPC (SC-LDPC) codes on the
             binary erasure channel. Although SC-LDPC codes have good
             noise thresholds under belief-propagation (BP) decoding,
             they also suffer a rate-loss due to termination that is
             significant at moderate blocklengths. Our idea is to attach
             additional variable nodes at the boundary using an irregular
             degree distribution. Then, this degree distribution is
             optimized to improve the code rate without reducing the BP
             threshold. The optimization is formulated as an linear
             program and solved numerically. Our results show that the
             code rate can be increased by a reasonable amount without
             decreasing the BP threshold.},
   Doi = {10.1109/ISTC.2016.7593071},
   Key = {fds322711}
}

@article{fds322712,
   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 International Symposium on Information Theory -
             Proceedings},
   Volume = {2016-August},
   Pages = {310-314},
   Year = {2016},
   Month = {August},
   ISBN = {9781509018062},
   url = {http://dx.doi.org/10.1109/ISIT.2016.7541311},
   Abstract = {© 2016 IEEE. A single-letter upper bound on the feedback
             capacity of a unifilar finite-state channel is derived. The
             upper bound is tight for all cases where the feedback
             capacity is known. Its efficiency is also demonstrated by
             direct application of the bound on the dicode erasure
             channel, which results in a new capacity result. The bound
             is based on a new technique, called the Q-contexts mapping,
             where the channel outputs are recursively quantized to a
             finite set, called the contexts set.},
   Doi = {10.1109/ISIT.2016.7541311},
   Key = {fds322712}
}

@article{fds322713,
   Author = {Pfister, HD and Urbanke, R},
   Title = {Near-optimal finite-length scaling for polar codes over
             large alphabets},
   Journal = {IEEE International Symposium on Information Theory -
             Proceedings},
   Volume = {2016-August},
   Pages = {215-219},
   Year = {2016},
   Month = {August},
   ISBN = {9781509018062},
   url = {http://dx.doi.org/10.1109/ISIT.2016.7541292},
   Abstract = {© 2016 IEEE. For any prime power q, Mori and Tanaka
             introduced a family of q-ary polar codes based on q by q
             Reed-Solomon polarization kernels. For transmission over a
             q-ary erasure channel, they also derived a closed-form
             recursion for the erasure probability of each effective
             channel. In this paper, we use that expression to analyze
             the finite-length scaling of these codes on q-ary erasure
             channel with erasure probability ϵ ⋯ (0, 1). Our primary
             result is that, for any γ > 0 and δ > 0, there is a q 0
             such that, for all q ≥ q 0 , the fraction of effective
             channels with erasure rate at most N -γ is at least 1 - ϵ
             - O(N -1/2+δ ), where N = q n is the blocklength. Since the
             gap to the channel capacity 1 - ϵ cannot vanish faster than
             O(N-1/2), this establishes near-optimal finite-length
             scaling for this family of codes. Our approach can be seen
             as an extension of a similar analysis for binary polar codes
             by Mondelli, Hassani, and Urbanke.},
   Doi = {10.1109/ISIT.2016.7541292},
   Key = {fds322713}
}

@article{fds322714,
   Author = {Reeves, G and Pfister, HD},
   Title = {The replica-symmetric prediction for compressed sensing with
             Gaussian matrices is exact},
   Journal = {IEEE International Symposium on Information Theory -
             Proceedings},
   Volume = {2016-August},
   Pages = {665-669},
   Year = {2016},
   Month = {August},
   ISBN = {9781509018062},
   url = {http://dx.doi.org/10.1109/ISIT.2016.7541382},
   Abstract = {© 2016 IEEE. This paper considers the fundamental limit of
             compressed sensing for i.i.d. signal distributions and
             i.i.d. Gaussian measurement matrices. Its main contribution
             is a rigorous characterization of the asymptotic mutual
             information (MI) and minimum mean-square error (MMSE) in
             this setting. Under mild technical conditions, our results
             show that the limiting MI and MMSE are equal to the values
             predicted by the replica method from statistical physics.
             This resolves a well-known problem that has remained open
             for over a decade.},
   Doi = {10.1109/ISIT.2016.7541382},
   Key = {fds322714}
}

@article{fds319310,
   Author = {Hager, C and Pfister, HD and Graell I Amat and A and Brannstrom,
             F},
   Title = {Deterministic and ensemble-based spatially-coupled product
             codes},
   Journal = {IEEE International Symposium on Information Theory -
             Proceedings},
   Volume = {2016-August},
   Pages = {2114-2118},
   Year = {2016},
   Month = {August},
   ISBN = {9781509018062},
   url = {http://dx.doi.org/10.1109/ISIT.2016.7541672},
   Abstract = {© 2016 IEEE. Several authors have proposed
             spatially-coupled (or convolutional-like) variants of
             product codes (PCs). In this paper, we focus on a
             parametrized family of generalized PCs that recovers some of
             these codes (e.g., staircase and block-wise braided codes)
             as special cases and study the iterative decoding
             performance over the binary erasure channel. Even though our
             code construction is deterministic (and not based on a
             randomized ensemble), we show that it is still possible to
             rigorously derive the density evolution (DE) equations that
             govern the asymptotic performance. The obtained DE equations
             are then compared to those for a related spatially-coupled
             PC ensemble. In particular, we show that there exists a
             family of (deterministic) braided codes that follows the
             same DE equation as the ensemble, for any spatial length and
             coupling width.},
   Doi = {10.1109/ISIT.2016.7541672},
   Key = {fds319310}
}

@article{fds319311,
   Author = {Kumar, S and Calderbank, R and Pfister, HD},
   Title = {Reed-muller codes achieve capacity on the quantum erasure
             channel},
   Journal = {IEEE International Symposium on Information Theory -
             Proceedings},
   Volume = {2016-August},
   Pages = {1750-1754},
   Year = {2016},
   Month = {August},
   ISBN = {9781509018062},
   url = {http://dx.doi.org/10.1109/ISIT.2016.7541599},
   Abstract = {© 2016 IEEE. The quantum erasure channel is the simplest
             example of a quantum communication channel and its
             information capacity is known precisely. The subclass of
             quantum error-correcting codes called stabilizer codes is
             known to contain capacity-achieving sequences for the
             quantum erasure channel, but no efficient method is known to
             construct these sequences. In this article, we explicitly
             describe a capacity-achieving code sequence for the quantum
             erasure channel. In particular, we show that
             Calderbank-Shor-Steane (CSS) stabilizer codes constructed
             from self-orthogonal binary linear codes are
             capacity-achieving on the quantum erasure channel if the
             binary linear codes are capacity-achieving on the binary
             erasure channel. Recently, Reed-Muller codes were shown to
             achieve capacity on classical erasure channels. Using this,
             we show that CSS codes constructed from binary Reed-Muller
             codes achieve the capacity of the quantum erasure channel.
             The capacity-achieving nature of these CSS codes is also
             explained from a GF(4) perspective.},
   Doi = {10.1109/ISIT.2016.7541599},
   Key = {fds319311}
}

@article{fds319312,
   Author = {Kudekar, S and Kumar, S and Mondelli, M and Pfister, HD and Urbankez,
             R},
   Title = {Comparing the bit-MAP and block-MAP decoding thresholds of
             reed-muller codes on BMS channels},
   Journal = {IEEE International Symposium on Information Theory -
             Proceedings},
   Volume = {2016-August},
   Pages = {1755-1759},
   Year = {2016},
   Month = {August},
   ISBN = {9781509018062},
   url = {http://dx.doi.org/10.1109/ISIT.2016.7541600},
   Abstract = {© 2016 IEEE. The question whether RM codes are
             capacity-achieving is a long-standing open problem in coding
             theory that was recently answered in the affirmative for
             transmission over erasure channels [1], [2] . Remarkably,
             the proof does not rely on specific properties of RM codes,
             apart from their symmetry. Indeed, the main technical result
             consists in showing that any sequence of linear codes, with
             doubly-transitive permutation groups, achieves capacity on
             the memoryless erasure channel under bit-MAP decoding. Thus,
             a natural question is what happens under block-MAP decoding.
             In [1], [2] , by exploiting further symmetries of the code,
             the bit-MAP threshold was shown to be sharp enough so that
             the block erasure probability also converges to 0. However,
             this technique relies heavily on the fact that the
             transmission is over an erasure channel. We present an
             alternative approach to strengthen results regarding the
             bit-MAP threshold to block-MAP thresholds. This approach is
             based on a careful analysis of the weight distribution of RM
             codes. In particular, the flavor of the main result is the
             following: assume that the bit-MAP error probability decays
             as N -δ , for some δ > 0. Then, the block-MAP error
             probability also converges to 0. This technique applies to
             transmission over any binary memoryless symmetric channel.
             Thus, it can be thought of as a first step in extending the
             proof that RM codes are capacity-achieving to the general
             case.},
   Doi = {10.1109/ISIT.2016.7541600},
   Key = {fds319312}
}

@article{fds322715,
   Author = {Hager, C and Pfister, HD and Amat, AG and Brannstrom,
             F},
   Title = {Density evolution and error floor analysis for staircase and
             braided codes},
   Journal = {2016 Optical Fiber Communications Conference and Exhibition,
             OFC 2016},
   Year = {2016},
   Month = {August},
   ISBN = {9781943580071},
   Abstract = {© 2016 OSA. We analyze deterministically constructed (i.e.,
             non-ensemble-based) codes in the waterfall and error floor
             region. The analysis directly applies to several FEC classes
             proposed for high-speed OTNs such as staircase and braided
             codes.},
   Key = {fds322715}
}

@article{fds319313,
   Author = {Kudekar, S and Pfister, HD and Kumar, S and Şaşoǧlu, E and Mondelli,
             M and Urbanke, R},
   Title = {Reed-Muller codes achieve capacity on erasure
             channels},
   Journal = {Proceedings of the Annual ACM Symposium on Theory of
             Computing},
   Volume = {19-21-June-2016},
   Pages = {658-669},
   Year = {2016},
   Month = {June},
   ISBN = {9781450341325},
   url = {http://dx.doi.org/10.1145/2897518.2897584},
   Abstract = {© 2016 ACM. We introduce a new approach to proving that a
             sequence of deterministic linear codes achieves capacity on
             an erasure channel under maximum a posteriori decoding.
             Rather than relying on the precise structure of the codes,
             our method exploits code symmetry. In particular, the
             technique applies to any sequence of linear codes where the
             block lengths are strictly increasing, the code rates
             converge, and the permutation group of each code is doubly
             transitive. In a nutshell, we show that symmetry alone
             implies near-optimal performance. An important consequence
             of this result is that a sequence of Reed-Muller codes with
             increasing block length and converging rate achieves
             capacity. This possibility has been suggested previously in
             the literature, but it has only been proven for cases where
             the limiting code rate is 0 or 1. Moreover, these results
             extend naturally to affine-invariant codes and, thus, to all
             extended primitive narrow-sense BCH codes. This is used to
             resolve, in the affirmative, the existence question for
             capacity-achieving sequences of binary cyclic codes. The
             primary tools used in the proofs are the sharp threshold
             property for symmetric monotone boolean functions and the
             area theorem for extrinsic information transfer (EXIT)
             functions.},
   Doi = {10.1145/2897518.2897584},
   Key = {fds319313}
}

@article{fds322716,
   Author = {Kumar, S and Vem, A and Narayanan, K and Pfister,
             HD},
   Title = {Spatially-coupled codes for write-once memories},
   Journal = {2015 53rd Annual Allerton Conference on Communication,
             Control, and Computing, Allerton 2015},
   Pages = {125-131},
   Year = {2016},
   Month = {April},
   ISBN = {9781509018239},
   url = {http://dx.doi.org/10.1109/ALLERTON.2015.7446994},
   Abstract = {© 2015 IEEE. The focus of this article is on low-complexity
             capacity-achieving coding schemes for write-once memory
             (WOM) systems. The construction is based on
             spatially-coupled compound LDGM/LDPC codes. Both noiseless
             systems and systems with read errors are considered.
             Compound LDGM/LDPC codes are known to achieve capacity under
             MAP decoding for the closely related Gelfand-Pinsker problem
             and their coset decomposition provides an elegant way to
             encode the messages while simultaneously providing error
             protection. The application of compound codes to the WOM
             system is new. The main result is that spatial coupling
             enables these codes to achieve the capacity region of the
             2-write WOM system with low-complexity message-passing
             encoding and decoding algorithms.},
   Doi = {10.1109/ALLERTON.2015.7446994},
   Key = {fds322716}
}

@article{fds322717,
   Author = {Lian, M and Pfister, HD},
   Title = {Belief-propagation reconstruction for compressed sensing:
             Quantization vs. Gaussian approximation},
   Journal = {2015 53rd Annual Allerton Conference on Communication,
             Control, and Computing, Allerton 2015},
   Pages = {1106-1113},
   Year = {2016},
   Month = {April},
   ISBN = {9781509018239},
   url = {http://dx.doi.org/10.1109/ALLERTON.2015.7447132},
   Abstract = {© 2015 IEEE. This work considers the compressed sensing
             (CS) of i.i.d. signals with sparse measurement matrices and
             belief-propagation (BP) reconstruction. In general, BP
             reconstruction for CS requires the passing of messages that
             are distributions over the real numbers. To implement this
             in practice, one typically uses either quantized
             distributions or a Gaussian approximation. In this work, we
             use density evolution to compare the reconstruction
             performance of these two methods. Since the reconstruction
             performance depends on the signal realization, this analysis
             makes use of a novel change of variables to analyze the
             performance for a typical signal. Simulation results are
             provided to support the results.},
   Doi = {10.1109/ALLERTON.2015.7447132},
   Key = {fds322717}
}

@article{fds323532,
   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 = {STOC},
   Pages = {658-669},
   Publisher = {ACM},
   Editor = {Wichs, D and Mansour, Y},
   Year = {2016},
   ISBN = {978-1-4503-4132-5},
   url = {http://dx.doi.org/10.1145/2897518.2897584},
   Doi = {10.1145/2897518.2897584},
   Key = {fds323532}
}


%% Pierce, Lillian B.   
@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{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},
   Year = {2017},
   Month = {September},
   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{fds330204,
   Author = {Pierce, LB},
   Title = {The Vinogradov Mean Value Theorem [after Wooley, and
             Bourgain, Demeter and Guth]},
   Journal = {Asterisque},
   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 für die Reine und Angewandte Mathematik (Crelle's
             Journal)},
   Volume = {2017},
   Number = {727},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1515/crelle-2014-0112},
   Doi = {10.1515/crelle-2014-0112},
   Key = {fds320389}
}

@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 and 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}
}

@article{fds320387,
   Author = {Pierce, LB},
   Title = {Burgess bounds for multi-dimensional short mixed character
             sums},
   Journal = {Journal of Number Theory},
   Volume = {163},
   Pages = {172-210},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.jnt.2015.08.022},
   Doi = {10.1016/j.jnt.2015.08.022},
   Key = {fds320387}
}

@article{fds320386,
   Author = {Pierce, LB and Schindler, D and Wood, MM},
   Title = {Representations of integers by systems of three quadratic
             forms},
   Journal = {Proceedings of the London Mathematical Society},
   Volume = {3},
   Number = {113},
   Pages = {289-344},
   Publisher = {London Mathematical Society},
   Year = {2016},
   url = {http://dx.doi.org/10.1112/plms/pdw027},
   Abstract = {It is classically known that the circle method produces an
             asymptotic for the number of representations of a tuple of
             integers $(n_1,\ldots,n_R)$ by a system of quadratic forms
             $Q_1,\ldots, Q_R$ in $k$ variables, as long as $k$ is
             sufficiently large; reducing the required number of
             variables remains a significant open problem. In this work,
             we consider the case of 3 forms and improve on the classical
             result by reducing the number of required variables to $k
             \geq 10$ for "almost all" tuples, under appropriate
             nonsingularity assumptions on the forms $Q_1,Q_2,Q_3$. To
             accomplish this, we develop a three-dimensional analogue of
             Kloosterman's circle method, in particular capitalizing on
             geometric properties of appropriate systems of three
             quadratic forms.},
   Doi = {10.1112/plms/pdw027},
   Key = {fds320386}
}


%% Plesser, Ronen   
@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}
}


%% Randles, Amanda   
@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 = {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}
}

@article{fds323711,
   Author = {Gounley, J and Chaudhury, R and Vardhan, M and Driscoll, M and Pathangey, G and Winarta, K and Ryan, J and Frakes, D and Randles,
             A},
   Title = {Does the degree of coarctation of the aorta influence wall
             shear stress focal heterogeneity?},
   Journal = {Annual International Conference of the IEEE Engineering in
             Medicine and Biology - Proceedings},
   Volume = {2016},
   Pages = {3429-3432},
   Year = {2016},
   Month = {August},
   ISBN = {9781457702204},
   url = {http://dx.doi.org/10.1109/embc.2016.7591465},
   Abstract = {The development of atherosclerosis in the aorta is
             associated with low and oscillatory wall shear stress for
             normal patients. Moreover, localized differences in wall
             shear stress heterogeneity have been correlated with the
             presence of complex plaques in the descending aorta. While
             it is known that coarctation of the aorta can influence
             indices of wall shear stress, it is unclear how the degree
             of narrowing influences resulting patterns. We hypothesized
             that the degree of coarctation would have a strong influence
             on focal heterogeneity of wall shear stress. To test this
             hypothesis, we modeled the fluid dynamics in a
             patient-specific aorta with varied degrees of coarctation.
             We first validated a massively parallel computational model
             against experimental results for the patient geometry and
             then evaluated local shear stress patterns for a range of
             degrees of coarctation. Wall shear stress patterns at two
             cross sectional slices prone to develop atherosclerotic
             plaques were evaluated. Levels at different focal regions
             were compared to the conventional measure of average
             circumferential shear stress to enable localized
             quantification of coarctation-induced shear stress
             alteration. We find that the coarctation degree causes
             highly heterogeneous changes in wall shear
             stress.},
   Doi = {10.1109/embc.2016.7591465},
   Key = {fds323711}
}


%% Reed, Michael C.   
@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{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{fds320464,
   Author = {Samaranayake, S and Abdalla, A and Robke, R and Nijhout, HF and Reed,
             MC and Best, J and Hashemi, P},
   Title = {A voltammetric and mathematical analysis of histaminergic
             modulation of serotonin in the mouse hypothalamus.},
   Journal = {Journal of Neurochemistry},
   Volume = {138},
   Number = {3},
   Pages = {374-383},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.1111/jnc.13659},
   Abstract = {Histamine and serotonin are neuromodulators which facilitate
             numerous, diverse neurological functions. Being co-localized
             in many brain regions, these two neurotransmitters are
             thought to modulate one another's chemistry and are often
             implicated in the etiology of disease. Thus, it is desirable
             to interpret the in vivo chemistry underlying
             neurotransmission of these two molecules to better define
             their roles in health and disease. In this work, we describe
             a voltammetric approach to monitoring serotonin and
             histamine simultaneously in real time. Via electrical
             stimulation of the axonal bundles in the medial forebrain
             bundle, histamine release was evoked in the mouse
             premammillary nucleus. We found that histamine release was
             accompanied by a rapid, potent inhibition of serotonin in a
             concentration-dependent manner. We developed mathematical
             models to capture the experimental time courses of histamine
             and serotonin, which necessitated incorporation of an
             inhibitory receptor on serotonin neurons. We employed
             pharmacological experiments to verify that this serotonin
             inhibition was mediated by H3 receptors. Our novel approach
             provides fundamental mechanistic insights that can be used
             to examine the full extent of interconnectivity between
             histamine and serotonin in the brain. Histamine and
             serotonin are co-implicated in many of the brain's
             functions. In this paper, we develop a novel voltammetric
             method for simultaneous real-time monitoring of histamine
             and serotonin in the mouse premammillary nucleus. Electrical
             stimulation of the medial forebrain bundle evokes histamine
             and inhibits serotonin release. We show voltammetrically,
             mathematically, and pharmacologically that this serotonin
             inhibition is H3 receptor mediated.},
   Doi = {10.1111/jnc.13659},
   Key = {fds320464}
}

@article{fds320465,
   Author = {Lawley, SD and Best, JA and Reed, MC},
   Title = {Neurotransmitter concentrations in the presence of neural
             switching in one dimension},
   Journal = {Discrete and Continuous Dynamical Systems - Series
             B},
   Volume = {21},
   Number = {7},
   Pages = {2255-2273},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.3934/dcdsb.2016046},
   Doi = {10.3934/dcdsb.2016046},
   Key = {fds320465}
}

@article{fds320466,
   Author = {Temamogullari, NE and Nijhout, HF and C Reed and M},
   Title = {Mathematical modeling of perifusion cell culture experiments
             on GnRH signaling.},
   Journal = {Mathematical Biosciences},
   Volume = {276},
   Pages = {121-132},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.mbs.2016.03.016},
   Abstract = {The effects of pulsatile GnRH stimulation on anterior
             pituitary cells are studied using perifusion cell cultures,
             where constantly moving culture medium over the immobilized
             cells allows intermittent GnRH delivery. The LH content of
             the outgoing medium serves as a readout of the GnRH
             signaling pathway activation in the cells. The challenge
             lies in relating the LH content of the medium leaving the
             chamber to the cellular processes producing LH secretion. To
             investigate this relation we developed and analyzed a
             mathematical model consisting of coupled partial
             differential equations describing LH secretion in a
             perifusion cell culture. We match the mathematical model to
             three different data sets and give cellular mechanisms that
             explain the data. Our model illustrates the importance of
             the negative feedback in the signaling pathway and receptor
             desensitization. We demonstrate that different LH outcomes
             in oxytocin and GnRH stimulations might originate from
             different receptor dynamics and concentration. We analyze
             the model to understand the influence of parameters, like
             the velocity of the medium flow or the fraction collection
             time, on the LH outcomes. We show that slow velocities lead
             to high LH outcomes. Also, we show that fraction collection
             times, which do not divide the GnRH pulse period evenly,
             lead to irregularities in the data. We examine the influence
             of the rate of binding and dissociation of GnRH on the GnRH
             movement down the chamber. Our model serves as an important
             tool that can help in the design of perifusion experiments
             and the interpretation of results.},
   Doi = {10.1016/j.mbs.2016.03.016},
   Key = {fds320466}
}

@article{fds320467,
   Author = {Thanacoody, HKR and Nijhout, FH and Reed, MC and Thomas,
             SHL},
   Title = {Mathematical modelling of the effect of a high dose
             acetylcysteine regimen based on the SNAP trial on hepatic
             glutathione regeneration and hepatocyte death},
   Journal = {Clinical Toxicology},
   Volume = {54},
   Number = {4},
   Pages = {494-494},
   Year = {2016},
   Key = {fds320467}
}

@article{fds321771,
   Author = {Reed, MC and Nijhout, HF and Kurtz, T},
   Title = {Mathematical modeling of cell metabolism},
   Booktitle = {Encyclopedia of Applied and Computational
             Mathematics},
   Publisher = {Springer},
   Editor = {Engquist, B},
   Year = {2016},
   Key = {fds321771}
}


%% 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}
}

@article{fds320189,
   Author = {Robles, C},
   Title = {Classification of horizontal s},
   Journal = {Compositio Mathematica},
   Volume = {152},
   Number = {05},
   Pages = {918-954},
   Year = {2016},
   Month = {May},
   url = {http://dx.doi.org/10.1112/S0010437X15007691},
   Doi = {10.1112/S0010437X15007691},
   Key = {fds320189}
}

@article{fds320190,
   Author = {Robles, C},
   Title = {Characteristic cohomology of the infinitesimal period
             relation},
   Journal = {Asian Journal of Mathematics},
   Volume = {20},
   Number = {4},
   Pages = {725-758},
   Year = {2016},
   url = {http://dx.doi.org/10.4310/AJM.2016.v20.n4.a7},
   Doi = {10.4310/AJM.2016.v20.n4.a7},
   Key = {fds320190}
}


%% Saper, Leslie   
@article{fds320662,
   Author = {Saper, L},
   Title = {Perverse sheaves and the reductive Borel-Serre
             compactification},
   Booktitle = {Hodge Theory and L² Analysis},
   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}
}

@article{fds320773,
   Author = {Saper, L},
   Title = {ℒ-modules and micro-support},
   Journal = {to appear in Annals of Mathematics},
   Year = {2017},
   Key = {fds320773}
}


%% Sapiro, Guillermo   
@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{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},
   Year = {2017},
   Month = {June},
   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{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 = {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.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.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.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}
}

@article{fds322212,
   Author = {Lezama, J and Mukherjee, D and McNabb, RP and Sapiro, G and Kuo, AN and Farsiu, S},
   Title = {Segmentation guided registration of wide field-of-view
             retinal optical coherence tomography volumes.},
   Journal = {Biomedical Optics Express},
   Volume = {7},
   Number = {12},
   Pages = {4827-4846},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1364/boe.7.004827},
   Abstract = {Patient motion artifacts are often visible in densely
             sampled or large wide field-of-view (FOV) retinal optical
             coherence tomography (OCT) volumes. A popular strategy for
             reducing motion artifacts is to capture two orthogonally
             oriented volumetric scans. However, due to larger volume
             sizes, longer acquisition times, and corresponding larger
             motion artifacts, the registration of wide FOV scans remains
             a challenging problem. In particular, gaps in data
             acquisition due to eye motion, such as saccades, can be
             significant and their modeling becomes critical for
             successful registration. In this article, we develop a
             complete computational pipeline for the automatic motion
             correction and accurate registration of wide FOV
             orthogonally scanned OCT images of the human retina. The
             proposed framework utilizes the retinal boundary
             segmentation as a guide for registration and requires only a
             minimal transformation of the acquired data to produce a
             successful registration. It includes saccade detection and
             correction, a custom version of the optical flow algorithm
             for dense lateral registration and a linear optimization
             approach for axial registration. Utilizing a wide FOV swept
             source OCT system, we acquired retinal volumes of 12
             subjects and we provide qualitative and quantitative
             experimental results to validate the state-of-the-art
             effectiveness of the proposed technique. The source code
             corresponding to the proposed algorithm is available
             online.},
   Doi = {10.1364/boe.7.004827},
   Key = {fds322212}
}

@article{fds322672,
   Author = {Aguerrebere, C and Delbracio, M and Bartesaghi, A and Sapiro,
             G},
   Title = {Fundamental Limits in Multi-Image Alignment},
   Journal = {IEEE Transactions on Signal Processing},
   Volume = {64},
   Number = {21},
   Pages = {5707-5722},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.1109/TSP.2016.2600517},
   Doi = {10.1109/TSP.2016.2600517},
   Key = {fds322672}
}

@article{fds322673,
   Author = {Elhamifar, E and Sapiro, G and Sastry, SS},
   Title = {Dissimilarity-Based Sparse Subset Selection.},
   Journal = {IEEE Transactions on Pattern Analysis and Machine
             Intelligence},
   Volume = {38},
   Number = {11},
   Pages = {2182-2197},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.1109/tpami.2015.2511748},
   Abstract = {Finding an informative subset of a large collection of data
             points or models is at the center of many problems in
             computer vision, recommender systems, bio/health informatics
             as well as image and natural language processing. Given
             pairwise dissimilarities between the elements of a 'source
             set' and a 'target set,' we consider the problem of finding
             a subset of the source set, called representatives or
             exemplars, that can efficiently describe the target set. We
             formulate the problem as a row-sparsity regularized trace
             minimization problem. Since the proposed formulation is, in
             general, NP-hard, we consider a convex relaxation. The
             solution of our optimization finds representatives and the
             assignment of each element of the target set to each
             representative, hence, obtaining a clustering. We analyze
             the solution of our proposed optimization as a function of
             the regularization parameter. We show that when the two sets
             jointly partition into multiple groups, our algorithm finds
             representatives from all groups and reveals clustering of
             the sets. In addition, we show that the proposed framework
             can effectively deal with outliers. Our algorithm works with
             arbitrary dissimilarities, which can be asymmetric or
             violate the triangle inequality. To efficiently implement
             our algorithm, we consider an Alternating Direction Method
             of Multipliers (ADMM) framework, which results in quadratic
             complexity in the problem size. We show that the ADMM
             implementation allows to parallelize the algorithm, hence
             further reducing the computational time. Finally, by
             experiments on real-world datasets, we show that our
             proposed algorithm improves the state of the art on the two
             problems of scene categorization using representative images
             and time-series modeling and segmentation using
             representative models.},
   Doi = {10.1109/tpami.2015.2511748},
   Key = {fds322673}
}

@article{fds322674,
   Author = {Fiori, M and Muse, P and Tepper, M and Sapiro, G},
   Title = {Tell me where you are and i tell you where you are going:
             Estimation of dynamic mobility graphs},
   Journal = {Proceedings of the IEEE Sensor Array and Multichannel Signal
             Processing Workshop},
   Volume = {2016-September},
   Year = {2016},
   Month = {September},
   ISBN = {9781509021031},
   url = {http://dx.doi.org/10.1109/SAM.2016.7569685},
   Abstract = {© 2016 IEEE. The interest in problems related to graph
             inference has been increasing significantly during the last
             decade. However, the vast majority of the problems addressed
             are either static, or systems where changes in one node are
             immediately reflected in other nodes. In this paper we
             address the problem of mobility graph estimation, when the
             available dataset has an asynchronous and time-variant
             nature. We present a formulation for this problem consisting
             on an optimization of a cost function having a fitting term
             to explain the observations with the dynamics of the system,
             and a sparsity promoting penalty term, in order to select
             the paths actually used. The formulation is tested on two
             publicly available real datasets on US aviation and NY taxi
             traffic, showing the importance of the problem and the
             applicability of the proposed framework.},
   Doi = {10.1109/SAM.2016.7569685},
   Key = {fds322674}
}

@article{fds322675,
   Author = {Giryes, R and Sapiro, G and Bronstein, AM},
   Title = {Deep Neural Networks with Random Gaussian Weights: A
             Universal Classification Strategy?},
   Journal = {IEEE Transactions on Signal Processing},
   Volume = {64},
   Number = {13},
   Pages = {3444-3457},
   Year = {2016},
   Month = {July},
   url = {http://dx.doi.org/10.1109/TSP.2016.2546221},
   Doi = {10.1109/TSP.2016.2546221},
   Key = {fds322675}
}

@article{fds322676,
   Author = {Tepper, M and Sapiro, G},
   Title = {A short-graph fourier transform via personalized pagerank
             vectors},
   Journal = {IEEE International Conference on Acoustics Speech and Signal
             Processing},
   Volume = {2016-May},
   Pages = {4806-4810},
   Year = {2016},
   Month = {May},
   ISBN = {9781479999880},
   url = {http://dx.doi.org/10.1109/ICASSP.2016.7472590},
   Abstract = {© 2016 IEEE. The short-time Fourier transform (STFT) is
             widely used to analyze the spectra of temporal signals that
             vary through time. Signals defined over graphs, due to their
             intrinsic complexity, exhibit large variations in their
             patterns. In this work we propose a new formulation for an
             STFT for signals defined over graphs. This formulation draws
             on recent ideas from spectral graph theory, using
             personalized PageRank vectors as its fundamental building
             block. Furthermore, this work establishes and explores the
             connection between local spectral graph theory and localized
             spectral analysis of graph signals. We accompany the
             presentation with synthetic and real-world examples, showing
             the suitability of the proposed approach.},
   Doi = {10.1109/ICASSP.2016.7472590},
   Key = {fds322676}
}

@article{fds322677,
   Author = {Tepper, M and Sapiro, G},
   Title = {Compressed Nonnegative Matrix Factorization Is Fast and
             Accurate},
   Journal = {IEEE Transactions on Signal Processing},
   Volume = {64},
   Number = {9},
   Pages = {2269-2283},
   Year = {2016},
   Month = {May},
   url = {http://dx.doi.org/10.1109/TSP.2016.2516971},
   Doi = {10.1109/TSP.2016.2516971},
   Key = {fds322677}
}

@article{fds322678,
   Author = {Qiu, Q and Thompson, A and Calderbank, R and Sapiro,
             G},
   Title = {Data Representation Using the Weyl Transform},
   Journal = {IEEE Transactions on Signal Processing},
   Volume = {64},
   Number = {7},
   Pages = {1844-1853},
   Year = {2016},
   Month = {April},
   url = {http://dx.doi.org/10.1109/TSP.2015.2505661},
   Doi = {10.1109/TSP.2015.2505661},
   Key = {fds322678}
}

@article{fds322213,
   Author = {Carpenter, KLH and Sprechmann, P and Calderbank, R and Sapiro, G and Egger, HL},
   Title = {Quantifying Risk for Anxiety Disorders in Preschool
             Children: A Machine Learning Approach.},
   Journal = {PloS one},
   Volume = {11},
   Number = {11},
   Pages = {e0165524},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0165524},
   Abstract = {Early childhood anxiety disorders are common, impairing, and
             predictive of anxiety and mood disorders later in childhood.
             Epidemiological studies over the last decade find that the
             prevalence of impairing anxiety disorders in preschool
             children ranges from 0.3% to 6.5%. Yet, less than 15% of
             young children with an impairing anxiety disorder receive a
             mental health evaluation or treatment. One possible reason
             for the low rate of care for anxious preschoolers is the
             lack of affordable, timely, reliable and valid tools for
             identifying young children with clinically significant
             anxiety. Diagnostic interviews assessing psychopathology in
             young children require intensive training, take hours to
             administer and code, and are not available for use outside
             of research settings. The Preschool Age Psychiatric
             Assessment (PAPA) is a reliable and valid structured
             diagnostic parent-report interview for assessing
             psychopathology, including anxiety disorders, in 2 to 5 year
             old children. In this paper, we apply machine-learning tools
             to already collected PAPA data from two large community
             studies to identify sub-sets of PAPA items that could be
             developed into an efficient, reliable, and valid screening
             tool to assess a young child's risk for an anxiety disorder.
             Using machine learning, we were able to decrease by an order
             of magnitude the number of items needed to identify a child
             who is at risk for an anxiety disorder with an accuracy of
             over 96% for both generalized anxiety disorder (GAD) and
             separation anxiety disorder (SAD). Additionally, rather than
             considering GAD or SAD as discrete/binary entities, we
             present a continuous risk score representing the child's
             risk of meeting criteria for GAD or SAD. Identification of a
             short question-set that assesses risk for an anxiety
             disorder could be a first step toward development and
             validation of a relatively short screening tool feasible for
             use in pediatric clinics and daycare/preschool
             settings.},
   Doi = {10.1371/journal.pone.0165524},
   Key = {fds322213}
}

@article{fds322680,
   Author = {Chang, Z and Qiu, Q and Sapiro, G},
   Title = {Synthesis-based low-cost gaze analysis},
   Journal = {Communications in Computer and Information
             Science},
   Volume = {618},
   Pages = {95-100},
   Year = {2016},
   Month = {January},
   ISBN = {9783319405414},
   url = {http://dx.doi.org/10.1007/978-3-319-40542-1_15},
   Abstract = {© Springer International Publishing Switzerland 2016. Gaze
             analysis has gained much popularity over the years due to
             its relevance in a wide array of applications, including
             humancomputer interaction, fatigue detection, and clinical
             mental health diagnosis. However, accurate gaze estimation
             from low resolution images outside of the lab (in the wild)
             still proves to be a challenging task. The new Intel
             low-cost RealSense 3D camera, capable of acquiring
             submillimeter resolution depth information, is currently
             available in laptops, and such technology is expected to
             become ubiquitous in other portable devices. In this paper,
             we focus on low-cost, scalable and real time analysis of
             human gaze using this RealSense camera. We exploit the
             direct measurement of eye surface geometry captured by the
             RGB-D camera, and perform gaze estimation through novel
             synthesis-based training and testing. Furthermore, we
             synthesize different eye movement appearances using a linear
             approach. From each 3D eye training sample captured by the
             RealSense camera, we synthesize multiple novel 2D views by
             varying the view angle to simulate head motions expected at
             testing. We then learn from the synthesized 2D eye images a
             gaze regression model using regression forests. At testing,
             for each captured RGB-D eye image, we first repeat the same
             synthesis process. For each synthesized image, we estimate
             the gaze from our gaze regression model, and factor-out the
             associated camera/head motion. In this way, we obtain
             multiple gaze estimations for each RGB-D eye image, and the
             consensus is adopted. We show that this synthesis-based
             training and testing significantly improves the precision in
             gaze estimation, opening the door to true low-cost
             solutions.},
   Doi = {10.1007/978-3-319-40542-1_15},
   Key = {fds322680}
}

@article{fds322681,
   Author = {Lyzinski, V and Fishkind, DE and Fiori, M and Vogelstein, JT and Priebe,
             CE and Sapiro, G},
   Title = {Graph Matching: Relax at Your Own Risk.},
   Journal = {IEEE Transactions on Pattern Analysis and Machine
             Intelligence},
   Volume = {38},
   Number = {1},
   Pages = {60-73},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1109/tpami.2015.2424894},
   Abstract = {Graph matching-aligning a pair of graphs to minimize their
             edge disagreements-has received wide-spread attention from
             both theoretical and applied communities over the past
             several decades, including combinatorics, computer vision,
             and connectomics. Its attention can be partially attributed
             to its computational difficulty. Although many heuristics
             have previously been proposed in the literature to
             approximately solve graph matching, very few have any
             theoretical support for their performance. A common
             technique is to relax the discrete problem to a continuous
             problem, therefore enabling practitioners to bring
             gradient-descent-type algorithms to bear. We prove that an
             indefinite relaxation (when solved exactly) almost always
             discovers the optimal permutation, while a common convex
             relaxation almost always fails to discover the optimal
             permutation. These theoretical results suggest that
             initializing the indefinite algorithm with the convex
             optimum might yield improved practical performance. Indeed,
             experimental results illuminate and corroborate these
             theoretical findings, demonstrating that excellent results
             are achieved in both benchmark and real data problems by
             amalgamating the two approaches.},
   Doi = {10.1109/tpami.2015.2424894},
   Key = {fds322681}
}


%% Smith, David A.   
@article{fds323466,
   Author = {Smith, DA and Fey, JT},
   Title = {Algebra as Part of an Integrated High School
             Curriculum},
   Pages = {119-129},
   Booktitle = {And the Rest is Just Algebra},
   Publisher = {Springer},
   Editor = {Stewart, S},
   Year = {2016},
   Month = {October},
   ISBN = {3319450530},
   Keywords = {integrated curriculum school algebra functions problem based
             learning mathematical modeling applications},
   Abstract = {Chapter 7 Algebra as Part of an Integrated High School
             Curriculum James T. Fey and David A. Smith Abstract
             Traditional high school mathematics curricula in the United
             States devote 2 years almost exclusively to development of
             student&nbsp;...},
   Key = {fds323466}
}


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

@article{fds317670,
   Author = {Sergey A. Cherkis and Andres Larrain-Hubach and Mark
             Stern},
   Title = {Instantons on multi-Taub-NUT Spaces I: Asymptotic Form and
             Index Theorem},
   Journal = {arXiv:1608.00018},
   Year = {2016},
   Month = {August},
   Abstract = {We study finite action anti-self-dual Yang-Mills connections
             on the multi-Taub-NUT space. We establish the curvature and
             the harmonic spinors decay rates and compute the index of
             the associated Dirac operator. This is the first in a series
             of papers proving the completeness of the bow construction
             of instantons on multi-Taub-NUT spaces and exploring it in
             detail.},
   Key = {fds317670}
}


%% 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},
   Year = {2017},
   Month = {April},
   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.},
   Key = {fds330397}
}

@article{fds330207,
   Author = {Tralie, C},
   Title = {High Dimensional Geometry of Sliding Window Embeddings of
             Periodic Videos},
   Journal = {Proceedings of the 32st International Symposium on
             Computational Geometry (SOCG)},
   Year = {2016},
   Month = {June},
   Abstract = {We explore the high dimensional geometry of sliding windows
             of periodic videos. Under a reas- onable model for periodic
             videos, we show that the sliding window is necessary to
             disambiguate all states within a period, and we show that a
             video embedding with a sliding window of an appropriate
             dimension lies on a topological loop along a hypertorus.
             This hypertorus has an in- dependent ellipse for each
             harmonic of the motion. Natural motions with sharp
             transitions from foreground to background have many
             harmonics and are hence in higher dimensions, so linear
             subspace projections such as PCA do not accurately summarize
             the geometry of these videos. Noting this, we invoke tools
             from topological data analysis and cohomology to
             parameterize mo- tions in high dimensions with circular
             coordinates after the embeddings. We show applications to
             videos in which there is obvious periodic motion and to
             videos in which the motion is hidden.},
   Key = {fds330207}
}

@article{fds330208,
   Author = {Bendich, P and Gasparovic, E and Harer, J and Tralie,
             C},
   Title = {Geometric Models for Musical Audio Data},
   Journal = {Proceedings of the 32st International Symposium on
             Computational Geometry (SOCG)},
   Year = {2016},
   Month = {June},
   Key = {fds330208}
}


%% Turnage-Butterbaugh, Caroline   
@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},
   Year = {2017},
   Month = {September},
   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}
}

@book{fds320234,
   Author = {Mackall, B and Miller, SJ and Rapti, C and Turnage-Butterbaugh, C and Winsor, K},
   Title = {Some Results in the Theory of Low-lying Zeros},
   Booktitle = {Families of Automorphic Forms and the Trace
             Formula},
   Publisher = {Springer},
   Year = {2016},
   Month = {September},
   ISBN = {3319414240},
   Abstract = {Featuring the work of twenty-three internationally-recognized
             experts, this volume explores the trace formula, spectra of
             locally symmetric spaces, p-adic families, and other recent
             techniques from harmonic analysis and representation
             ...},
   Key = {fds320234}
}

@article{fds318339,
   Author = {Bui, HM and Heap, WP and Turnage-Butterbaugh, CL},
   Title = {GAPS BETWEEN ZEROS OF DEDEKIND ZETA-FUNCTIONS OF QUADRATIC
             NUMBER FIELDS. II},
   Journal = {Quarterly Journal of Mathematics},
   Volume = {67},
   Number = {3},
   Pages = {467-482},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.1093/qmath/haw021},
   Doi = {10.1093/qmath/haw021},
   Key = {fds318339}
}

@book{fds318340,
   Author = {Barrett, O and Firk, F and Miller, SJ and Turnage-Butterbaugh,
             C},
   Title = {From Quantum Systems to L-Functions: Pair Correlation
             Statistics and Beyond},
   Pages = {123-171},
   Booktitle = {Open Problems in Mathematics},
   Publisher = {Springer},
   Editor = {John Nash Jr. and Michael Th. Rassias},
   Year = {2016},
   Month = {August},
   ISBN = {3319321625},
   url = {http://arxiv.org/abs/1505.07481},
   Key = {fds318340}
}

@article{fds318341,
   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 = {Gaussian distribution of the number of summands in
             generalized Zeckendorf decomposition in small
             intervals},
   Journal = {Integers},
   Volume = {16},
   Pages = {13 pages},
   Year = {2016},
   Key = {fds318341}
}


%% Venakides, Stephanos   
@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 = {Proc. R. Soc. A 2017 473 20170242},
   Year = {2017},
   Month = {November},
   url = {http://dx.doi.org/10.1098/rspa.2017.0242},
   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}
}

@article{fds320428,
   Author = {Komineas, S and Shipman, SP and Venakides, S},
   Title = {Lossless polariton solitons},
   Journal = {Physica D: Nonlinear Phenomena},
   Volume = {316},
   Pages = {43-56},
   Year = {2016},
   Month = {February},
   url = {http://dx.doi.org/10.1016/j.physd.2015.10.018},
   Abstract = {© 2015 Elsevier B.V. All rights reserved. Photons and
             excitons in a semiconductor microcavity interact to form
             exciton-polariton condensates. These are governed by a
             nonlinear quantum-mechanical system involving exciton and
             photon wavefunctions. We calculate all non-traveling
             harmonic soliton solutions for the one-dimensional lossless
             system. There are two frequency bands of bright solitons
             when the inter-exciton interactions produce an attractive
             nonlinearity and two frequency bands of dark solitons when
             the nonlinearity is repulsive. In addition, there are two
             frequency bands for which the exciton wavefunction is
             discontinuous at its symmetry point, where it undergoes a
             phase jump of π. A band of continuous dark solitons merges
             with a band of discontinuous dark solitons, forming a larger
             band over which the soliton far-field amplitude varies from
             0 to ∞ ; the discontinuity is initiated when the operating
             frequency exceeds the free exciton frequency. The far fields
             of the solitons in the lowest and highest frequency bands
             (one discontinuous and one continuous dark) are linearly
             unstable, whereas the other four bands have linearly stable
             far fields, including the merged band of dark
             solitons.},
   Doi = {10.1016/j.physd.2015.10.018},
   Key = {fds320428}
}


%% Watson, Alexander   
@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{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{fds320454,
   Author = {George, C and Virgin, LN and Witelski, T},
   Title = {Experimental study of regular and chaotic transients in a
             non-smooth system},
   Journal = {International Journal of Non-Linear Mechanics},
   Volume = {81},
   Pages = {55-64},
   Year = {2016},
   Month = {May},
   url = {http://dx.doi.org/10.1016/j.ijnonlinmec.2015.12.006},
   Doi = {10.1016/j.ijnonlinmec.2015.12.006},
   Key = {fds320454}
}

@article{fds320455,
   Author = {Sanaei, P and Richardson, GW and Witelski, T and Cummings,
             LJ},
   Title = {Flow and fouling in a pleated membrane filter},
   Journal = {Journal of Fluid Mechanics},
   Volume = {795},
   Pages = {36-59},
   Year = {2016},
   Month = {May},
   url = {http://dx.doi.org/10.1017/jfm.2016.194},
   Doi = {10.1017/jfm.2016.194},
   Key = {fds320455}
}

@article{fds317250,
   Author = {Smolka, LB and McLaughlin, CK and Witelski, TP},
   Title = {Oil capture from a water surface by a falling
             sphere},
   Journal = {Colloids and Surfaces A: Physicochemical and Engineering
             Aspects},
   Volume = {497},
   Pages = {126-132},
   Year = {2016},
   Month = {May},
   ISSN = {0927-7757},
   url = {http://dx.doi.org/10.1016/j.colsurfa.2016.02.026},
   Doi = {10.1016/j.colsurfa.2016.02.026},
   Key = {fds317250}
}


%% Wong, Jeffrey T   
@article{fds329103,
   Author = {Wong, JT and Bertozzi, AL},
   Title = {A conservation law model for bidensity suspensions on an
             incline},
   Journal = {Physica D: Nonlinear Phenomena},
   Volume = {330},
   Pages = {47-57},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.1016/j.physd.2016.05.002},
   Doi = {10.1016/j.physd.2016.05.002},
   Key = {fds329103}
}


%% Wu, Hau-Tieng   
@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{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},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1186/s12913-017-2496-5},
   Doi = {10.1186/s12913-017-2496-5},
   Key = {fds329940}
}

@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},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1016/j.ctim.2017.09.004},
   Doi = {10.1016/j.ctim.2017.09.004},
   Key = {fds329941}
}

@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},
   Year = {2017},
   Month = {September},
   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},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.3389/fphys.2017.00701},
   Doi = {10.3389/fphys.2017.00701},
   Key = {fds329943}
}

@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{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 = {July},
   url = {http://dx.doi.org/10.1088/1361-6579/aa707c},
   Doi = {10.1088/1361-6579/aa707c},
   Key = {fds328813}
}

@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 (Basel, Switzerland)},
   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{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{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},
   Year = {2017},
   Month = {May},
   url = {http://dx.doi.org/10.3389/fphys.2017.00277},
   Doi = {10.3389/fphys.2017.00277},
   Key = {fds328816}
}

@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{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 Biomedical 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}
}

@article{fds329072,
   Author = {Wu, C-H and Wang, T-D and Hsieh, C-H and Huang, S-H and Lin, J-W and Hsu,
             S-C and Wu, H-T and Wu, Y-M and Liu, T-M},
   Title = {Imaging Cytometry of Human Leukocytes with Third Harmonic
             Generation Microscopy},
   Journal = {Scientific Reports},
   Volume = {6},
   Number = {1},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1038/srep37210},
   Doi = {10.1038/srep37210},
   Key = {fds329072}
}

@article{fds328820,
   Author = {Marchesini, S and Tu, Y-C and Wu, H-T},
   Title = {Alternating projection, ptychographic imaging and phase
             synchronization},
   Journal = {Applied and Computational Harmonic Analysis},
   Volume = {41},
   Number = {3},
   Pages = {815-851},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.1016/j.acha.2015.06.005},
   Doi = {10.1016/j.acha.2015.06.005},
   Key = {fds328820}
}

@article{fds328301,
   Author = {Wu, H-T and Lewis, GF and Davila, MI and Daubechies, I and Porges,
             SW},
   Title = {Optimizing Estimates of Instantaneous Heart Rate from Pulse
             Wave Signals with the Synchrosqueezing Transform.},
   Journal = {Methods of information in medicine},
   Volume = {55},
   Number = {5},
   Pages = {463-472},
   Year = {2016},
   Month = {October},
   url = {http://dx.doi.org/10.3414/me16-01-0026},
   Abstract = {With recent advances in sensor and computer technologies,
             the ability to monitor peripheral pulse activity is no
             longer limited to the laboratory and clinic. Now inexpensive
             sensors, which interface with smartphones or other
             computer-based devices, are expanding into the consumer
             market. When appropriate algorithms are applied, these new
             technologies enable ambulatory monitoring of dynamic
             physiological responses outside the clinic in a variety of
             applications including monitoring fatigue, health, workload,
             fitness, and rehabilitation. Several of these applications
             rely upon measures derived from peripheral pulse waves
             measured via contact or non-contact photoplethysmography
             (PPG). As technologies move from contact to non-contact PPG,
             there are new challenges. The technology necessary to
             estimate average heart rate over a few seconds from a
             noncontact PPG is available. However, a technology to
             precisely measure instantaneous heat rate (IHR) from
             non-contact sensors, on a beat-to-beat basis, is more
             challenging.The objective of this paper is to develop an
             algorithm with the ability to accurately monitor IHR from
             peripheral pulse waves, which provides an opportunity to
             measure the neural regulation of the heart from the
             beat-to-beat heart rate pattern (i.e., heart rate
             variability).The adaptive harmonic model is applied to model
             the contact or non-contact PPG signals, and a new
             methodology, the Synchrosqueezing Transform (SST), is
             applied to extract IHR. The body sway rhythm inherited in
             the non-contact PPG signal is modeled and handled by the
             notion of wave-shape function.The SST optimizes the
             extraction of IHR from the PPG signals and the technique
             functions well even during periods of poor signal to noise.
             We contrast the contact and non-contact indices of PPG
             derived heart rate with a criterion electrocardiogram (ECG).
             ECG and PPG signals were monitored in 21 healthy subjects
             performing tasks with different physical demands. The root
             mean square error of IHR estimated by SST is significantly
             better than commonly applied methods such as autoregressive
             (AR) method. In the walking situation, while AR method
             fails, SST still provides a reasonably good result.The SST
             processed PPG data provided an accurate estimate of the ECG
             derived IHR and consistently performed better than commonly
             applied methods such as autoregressive method.},
   Doi = {10.3414/me16-01-0026},
   Key = {fds328301}
}

@article{fds328821,
   Author = {Lin, Y-T and Flandrin, P and Wu, H-T},
   Title = {When Interpolation-Induced Reflection Artifact Meets
             Time-Frequency Analysis.},
   Journal = {IEEE Transactions on Biomedical Engineering},
   Volume = {63},
   Number = {10},
   Pages = {2133-2141},
   Year = {2016},
   Month = {October},
   url = {http://dx.doi.org/10.1109/tbme.2015.2510580},
   Abstract = {While extracting the temporal dynamical features based on
             the time-frequency analyses, like the reassignment and
             synchrosqueezing transform, attracts more and more interest
             in biomedical data analysis, we should be careful about
             artifacts generated by interpolation schemes, in particular
             when the sampling rate is not significantly higher than the
             frequency of the oscillatory component we are interested
             in.We formulate the problem called the reflection effect and
             provide a theoretical justification of the statement. We
             also show examples in the anesthetic depth analysis with
             clear but undesirable artifacts.The artifact associated with
             the reflection effect exists not only theoretically but
             practically as well. Its influence is pronounced when we
             apply the time-frequency analyses to extract the
             time-varying dynamics hidden inside the signal.We have to
             carefully deal with the artifact associated with the
             reflection effect by choosing a proper interpolation
             scheme.},
   Doi = {10.1109/tbme.2015.2510580},
   Key = {fds328821}
}

@article{fds328302,
   Author = {O'Neal, WT and Wang, YG and Wu, H-T and Zhang, Z-M and Li, Y and Tereshchenko, LG and Estes, EH and Daubechies, I and Soliman,
             EZ},
   Title = {Electrocardiographic J Wave and Cardiovascular Outcomes in
             the General Population (from the Atherosclerosis Risk In
             Communities Study).},
   Journal = {The American Journal of Cardiology},
   Volume = {118},
   Number = {6},
   Pages = {811-815},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.1016/j.amjcard.2016.06.047},
   Abstract = {The association between the J wave, a key component of the
             early repolarization pattern, and adverse cardiovascular
             outcomes remains unclear. Inconsistencies have stemmed from
             the different methods used to measure the J wave. We
             examined the association between the J wave, detected by an
             automated method, and adverse cardiovascular outcomes in
             14,592 (mean age = 54 ± 5.8 years; 56% women; 26% black)
             participants from the Atherosclerosis Risk In Communities
             (ARIC) study. The J wave was detected at baseline (1987 to
             1989) and during follow-up study visits (1990 to 1992, 1993
             to 1995, and 1996 to 1998) using a fully automated method.
             Sudden cardiac death, coronary heart disease death, and
             cardiovascular mortality were ascertained from hospital
             discharge records, death certificates, and autopsy data
             through December 31, 2010. A total of 278 participants
             (1.9%) had evidence of a J wave. Over a median follow-up of
             22 years, 4,376 of the participants (30%) died. In a
             multivariable Cox regression analysis adjusted for
             demographics, cardiovascular risk factors, and potential
             confounders, the J wave was not associated with an increased
             risk of sudden cardiac death (hazard ratio [HR] 0.74, 95% CI
             0.36 to 1.50), coronary heart disease death (HR 0.72, 95% CI
             0.40 to 1.32), or cardiovascular mortality (HR 1.16, 95% CI
             0.87 to 1.56). An interaction was detected for
             cardiovascular mortality by gender with men (HR 1.54, 95% CI
             1.09 to 2.19) having a stronger association than women (HR
             0.74, 95% CI 0.43 to 1.25; P-interaction = 0.030). In
             conclusion, our findings suggest that the J wave is a benign
             entity that is not associated with an increased risk for
             sudden cardiac arrest in middle-aged adults in the United
             States.},
   Doi = {10.1016/j.amjcard.2016.06.047},
   Key = {fds328302}
}

@article{fds329946,
   Author = {Chui, CK and Lin, Y-T and Wu, H-T},
   Title = {Real-time dynamics acquisition from irregular samples —
             With application to anesthesia evaluation},
   Journal = {Analysis & Applications},
   Volume = {14},
   Number = {04},
   Pages = {537-590},
   Year = {2016},
   Month = {July},
   url = {http://dx.doi.org/10.1142/S0219530515500165},
   Doi = {10.1142/S0219530515500165},
   Key = {fds329946}
}

@article{fds328303,
   Author = {Daubechies, I and Wang, YG and Wu, H-T},
   Title = {ConceFT: concentration of frequency and time via a
             multitapered synchrosqueezed transform.},
   Journal = {Philosophical Transactions A},
   Volume = {374},
   Number = {2065},
   Pages = {20150193},
   Year = {2016},
   Month = {April},
   url = {http://dx.doi.org/10.1098/rsta.2015.0193},
   Abstract = {A new method is proposed to determine the time-frequency
             content of time-dependent signals consisting of multiple
             oscillatory components, with time-varying amplitudes and
             instantaneous frequencies. Numerical experiments as well as
             a theoretical analysis are presented to assess its
             effectiveness.},
   Doi = {10.1098/rsta.2015.0193},
   Key = {fds328303}
}

@article{fds328823,
   Author = {El Karoui and N and Wu, H-T},
   Title = {Graph connection Laplacian methods can be made robust to
             noise},
   Journal = {Annals of statistics},
   Volume = {44},
   Number = {1},
   Pages = {346-372},
   Year = {2016},
   Month = {February},
   url = {http://dx.doi.org/10.1214/14-AOS1275},
   Doi = {10.1214/14-AOS1275},
   Key = {fds328823}
}

@article{fds329947,
   Author = {Herry, CL and Cortes, M and Wu, H-T and Durosier, LD and Cao, M and Burns,
             P and Desrochers, A and Fecteau, G and Seely, AJE and Frasch,
             MG},
   Title = {Temporal Patterns in Sheep Fetal Heart Rate Variability
             Correlate to Systemic Cytokine Inflammatory Response: A
             Methodological Exploration of Monitoring Potential Using
             Complex Signals Bioinformatics.},
   Journal = {PloS one},
   Volume = {11},
   Number = {4},
   Pages = {e0153515},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0153515},
   Abstract = {Fetal inflammation is associated with increased risk for
             postnatal organ injuries. No means of early detection exist.
             We hypothesized that systemic fetal inflammation leads to
             distinct alterations of fetal heart rate variability (fHRV).
             We tested this hypothesis deploying a novel series of
             approaches from complex signals bioinformatics. In
             chronically instrumented near-term fetal sheep, we induced
             an inflammatory response with lipopolysaccharide (LPS)
             injected intravenously (n = 10) observing it over 54 hours;
             seven additional fetuses served as controls. Fifty-one fHRV
             measures were determined continuously every 5 minutes using
             Continuous Individualized Multi-organ Variability Analysis
             (CIMVA). CIMVA creates an fHRV measures matrix across five
             signal-analytical domains, thus describing complementary
             properties of fHRV. We implemented, validated and tested
             methodology to obtain a subset of CIMVA fHRV measures that
             matched best the temporal profile of the inflammatory
             cytokine IL-6. In the LPS group, IL-6 peaked at 3 hours. For
             the LPS, but not control group, a sharp increase in
             standardized difference in variability with respect to
             baseline levels was observed between 3 h and 6 h abating to
             baseline levels, thus tracking closely the IL-6 inflammatory
             profile. We derived fHRV inflammatory index (FII) consisting
             of 15 fHRV measures reflecting the fetal inflammatory
             response with prediction accuracy of 90%. Hierarchical
             clustering validated the selection of 14 out of 15 fHRV
             measures comprising FII. We developed methodology to
             identify a distinctive subset of fHRV measures that tracks
             inflammation over time. The broader potential of this
             bioinformatics approach is discussed to detect physiological
             responses encoded in HRV measures.},
   Doi = {10.1371/journal.pone.0153515},
   Key = {fds329947}
}

@article{fds328824,
   Author = {Wu, H-T and Wu, H-K and Wang, C-L and Yang, Y-L and Wu, W-H and Tsai, T-H and Chang, H-H},
   Title = {Modeling the Pulse Signal by Wave-Shape Function and
             Analyzing by Synchrosqueezing Transform.},
   Journal = {PloS one},
   Volume = {11},
   Number = {6},
   Pages = {e0157135},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0157135},
   Abstract = {We apply the recently developed adaptive non-harmonic model
             based on the wave-shape function, as well as the
             time-frequency analysis tool called synchrosqueezing
             transform (SST) to model and analyze oscillatory
             physiological signals. To demonstrate how the model and
             algorithm work, we apply them to study the pulse wave
             signal. By extracting features called the spectral pulse
             signature, and based on functional regression, we
             characterize the hemodynamics from the radial pulse wave
             signals recorded by the sphygmomanometer. Analysis results
             suggest the potential of the proposed signal processing
             approach to extract health-related hemodynamics
             features.},
   Doi = {10.1371/journal.pone.0157135},
   Key = {fds328824}
}


%% 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}
}

@article{fds303562,
   Author = {Lu, J and Wirth, B and Yang, H},
   Title = {Combining 2D synchrosqueezed wave packet transform with
             optimization for crystal image analysis},
   Journal = {Journal of the Mechanics and Physics of Solids},
   Volume = {89},
   Pages = {194-210},
   Publisher = {Elsevier},
   Editor = {Bhattacharya, K},
   Year = {2016},
   Month = {April},
   ISSN = {0022-5096},
   url = {http://hdl.handle.net/10161/11296 Duke open
             access},
   Abstract = {© 2016 Elsevier Ltd. All rights reserved. We develop a
             variational optimization method for crystal analysis in
             atomic resolution images, which uses information from a 2D
             synchrosqueezed transform (SST) as input. The
             synchrosqueezed transform is applied to extract initial
             information from atomic crystal images: crystal defects,
             rotations and the gradient of elastic deformation. The
             deformation gradient estimate is then improved outside the
             identified defect region via a variational approach, to
             obtain more robust results agreeing better with the physical
             constraints. The variational model is optimized by a
             nonlinear projected conjugate gradient method. Both examples
             of images from computer simulations and imaging experiments
             are analyzed, with results demonstrating the effectiveness
             of the proposed method.},
   Doi = {10.1016/j.jmps.2016.01.002},
   Key = {fds303562}
}


%% 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}
}

@article{fds323592,
   Author = {Jin, S and Sparber, C and Zhou, Z},
   Title = {On the classical limit of a time-dependent self-consistent
             field system: Analysis and computation},
   Journal = {Kinetic and Related Models},
   Volume = {10},
   Number = {1},
   Pages = {263-298},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.3934/krm.2017011},
   Doi = {10.3934/krm.2017011},
   Key = {fds323592}
}

@article{fds322468,
   Author = {Chen, J and Liu, J-G and Zhou, Z},
   Title = {On a Schrödinger--Landau--Lifshitz System: Variational
             Structure and Numerical Methods},
   Journal = {Multiscale Modeling & Simulation},
   Volume = {14},
   Number = {4},
   Pages = {1463-1487},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1137/16M106947X},
   Doi = {10.1137/16M106947X},
   Key = {fds322468}
}

 

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

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