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## Mathematics Faculty: Publications since January 2017

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article{fds328036,
Author = {Chen, Y and Sullivan, JC and Edwards, A and Layton,
AT},
Title = {Sex-specific computational models of the spontaneously
hypertensive rat kidneys: factors affecting nitric oxide
bioavailability.},
Journal = {American Journal of Physiology. Renal Physiology},
Volume = {313},
Number = {2},
Pages = {F174-F183},
Year = {2017},
Month = {August},
url = {http://dx.doi.org/10.1152/ajprenal.00482.2016},
Abstract = {The goals of this study were to 1) develop a computational
model of solute transport and oxygenation in the kidney of
the female spontaneously hypertensive rat (SHR), and 2)
apply that model to investigate sex differences in nitric
oxide (NO) levels in SHR and their effects on medullary
oxygenation and oxidative stress. To accomplish these goals,
we first measured NO synthase (NOS) 1 and NOS3 protein
expression levels in total renal microvessels of male and
female SHR. We found that the expression of both NOS1 and
NOS3 is higher in the renal vasculature of females compared
with males. To predict the implications of that finding on
medullary oxygenation and oxidative stress levels, we
developed a detailed computational model of the female SHR
kidney. The model was based on a published male kidney model
and represents solute transport and the biochemical
reactions among O2, NO, and superoxide ([Formula: see text])
in the renal medulla. Model simulations conducted using both
male and female SHR kidney models predicted significant
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
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
intake. A computational model that simulated UT-knockout
mouse models identified the individual contribution of each
UT in urine concentrating mechanism. Knocking out all UTs
also decreased the blood pressure and promoted the
maturation of the male reproductive system. Thus, functional
deficiency of all UTs caused a urea-selective
urine-concentrating defect with little physiological
abnormality in extrarenal organs.},
Doi = {10.1016/j.kint.2016.09.017},
Key = {fds323660}
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article{fds329286,
Author = {Randles, A and Frakes, DH and Leopold, JA},
Title = {Computational Fluid Dynamics and Additive Manufacturing to
Diagnose and Treat Cardiovascular Disease.},
Journal = {Trends in Biotechnology},
Volume = {35},
Number = {11},
Pages = {1049-1061},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1016/j.tibtech.2017.08.008},
Abstract = {Noninvasive engineering models are now being used for
diagnosing and planning the treatment of cardiovascular
disease. Techniques in computational modeling and additive
manufacturing have matured concurrently, and results from
simulations can inform and enable the design and
optimization of therapeutic devices and treatment
strategies. The emerging synergy between large-scale
simulations and 3D printing is having a two-fold benefit:
first, 3D printing can be used to validate the complex
simulations, and second, the flow models can be used to
improve treatment planning for cardiovascular disease. In
this review, we summarize and discuss recent methods and
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
atherogenic flow profiles (reversing unidirectional flow and
reversing multi-directional flow) on subcellular structures
relative to non-atherogenic flow (non-reversing flow).
Reversing flow lowers stresses and strains due to
viscoelastic effects, and multi-directional flow alters
stress on the ADJs perpendicular to the axial flow
direction. The simulations predict forces on integrins, ADJ
filaments and other substructures in the range that activate
mechanotransduction.},
Doi = {10.1098/rsif.2017.0185},
Key = {fds326715}
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article{fds338349,
Author = {Sober, B and Levin, D},
Title = {Computer aided restoration of handwritten character
strokes},
Journal = {Computer Aided Design},
Volume = {89},
Pages = {12-24},
Year = {2017},
Month = {August},
Key = {fds338349}
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article{fds328817,
Author = {Herry, CL and Frasch, M and Seely, AJ and Wu, H-T},
Title = {Heart beat classification from single-lead ECG using the
synchrosqueezing transform.},
Journal = {Physiological Measurement},
Volume = {38},
Number = {2},
Pages = {171-187},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1088/1361-6579/aa5070},
Abstract = {The processing of ECG signal provides a wealth of
information on cardiac function and overall cardiovascular
health. While multi-lead ECG recordings are often necessary
for a proper assessment of cardiac rhythms, they are not
always available or practical, for example in fetal ECG
applications. Moreover, a wide range of small non-obtrusive
single-lead ECG ambulatory monitoring devices are now
available, from which heart rate variability (HRV) and other
health-related metrics are derived. Proper beat detection
and classification of abnormal rhythms is important for
reliable HRV assessment and can be challenging in
single-lead ECG monitoring devices. In this manuscript, we
modelled the heart rate signal as an adaptive non-harmonic
model and used the newly developed synchrosqueezing
transform (SST) to characterize ECG patterns. We show how
the proposed model can be used to enhance heart beat
detection and classification between normal and abnormal
rhythms. In particular, using the Massachusetts Institute of
Technology-Beth Israel Hospital (MIT-BIH) arrhythmia
database and the Association for the Advancement of Medical
Instrumentation (AAMI) beat classes, we trained and
validated a support vector machine (SVM) classifier on a
portion of the annotated beat database using the SST-derived
instantaneous phase, the R-peak amplitudes and R-peak to
R-peak interval durations, based on a single ECG lead. We
obtained sentivities and positive predictive values
comparable to other published algorithms using multiple
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
Journal = {Complementary Therapies in Medicine},
Volume = {30},
Pages = {107-112},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1016/j.ctim.2016.12.005},
Abstract = {Our study aimed to correlate pulse wave parameters such as
augmentation index (AI) and heart rate variability with
traditional Chinese medicine (TCM) constitution for
evaluating health status.Out of 177 subjects, 69 healthy
subjects were enrolled in the present study, and others were
excluded because of cardiovascular, liver, kidney, or other
diseases. Each subject was invited to complete pulse wave
examination and the Constitution in Chinese Medicine
Questionnaire. Independent Student's t-tests, Mann-Whitney
tests, and binary logistic regression analysis were used to
analyse the correlation between pulse wave parameters and
TCM constitution.Qi-deficient individuals had higher AI
(p=0.006) and lower diastolic blood pressure (p=0.011);
yang-deficient individuals had lower dP/dt max (p=0.030),
systolic blood pressure (p=0.020), and pulse pressure
(p=0.048); and damp-heat individuals had higher
subendocardial viability index (SEVI) scores (p=0.011). We
then categorized the phlegm dampness and yang-deficiency
individuals into the cold group and those with damp-heat and
yin-deficiency into the heat group. A comparison of the two
constitution groups showed higher AI in the cold group
(p=0.026). Binary logistic regression analysis demonstrated
that only AI was a determinant, as evidenced by the finding
that an increase of one unit in AI corresponded to an
increase of 5% in the odds ratio for individuals to have a
cold constitution (p=0.026).Individuals with qi-deficient
and cold constitutions had higher AI and lower SEVI,
potentially reflecting an increase in arterial stiffness.
This study can provide a basis for further investigation of
the physiological indicators of TCM constitutions in modern
medicine.},
Doi = {10.1016/j.ctim.2016.12.005},
Key = {fds329944}
}

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

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

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

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

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

@article{fds328818,
Author = {Lin, Y-T and Wu, H-T},
Title = {ConceFT for Time-Varying Heart Rate Variability Analysis as
a Measure of Noxious Stimulation During General
Anesthesia.},
Journal = {Ieee Transactions on Bio Medical Engineering},
Volume = {64},
Number = {1},
Pages = {145-154},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1109/tbme.2016.2549048},
Abstract = {Heart rate variability (HRV) offers a noninvasive way to
peek into the physiological status of the human body. When
this physiological status is dynamic, traditional HRV
indices calculated from power spectrum do not resolve the
dynamic situation due to the issue of nonstationarity.
Clinical anesthesia is a typically dynamic situation that
calls for time-varying HRV analysis. Concentration of
frequency and time (ConceFT) is a nonlinear time-frequency
(TF) analysis generalizing the multitaper technique and the
synchrosqueezing transform. The result is a sharp TF
representation capturing the dynamics inside HRV. Companion
indices of the commonly applied HRV indices, including
time-varying low-frequency power (tvLF), time-varying
high-frequency power, and time-varying low-high ratio, are
considered as measures of noxious stimulation.To evaluate
the feasibility of the proposed indices, we apply these
indices to study two different types of noxious stimulation,
the endotracheal intubation and surgical skin incision,
under general anesthesia. The performance was compared with
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},
Volume = {304},
Pages = {1055-1079},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1016/j.aim.2016.05.023},
Doi = {10.1016/j.aim.2016.05.023},
Key = {fds328819}
}

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

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

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

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

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

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

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

%% Zhou, Zhennan
@article{fds323230,
Author = {Liu, J-G and Ma, Z and Zhou, Z},
Title = {Explicit and Implicit TVD Schemes for Conservation Laws with
Caputo Derivatives},
Journal = {Journal of Scientific Computing},
Volume = {72},
Number = {1},
Pages = {291-313},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1007/s10915-017-0356-4},
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
systems.},
Journal = {Journal of Chemical Physics},
Volume = {146},
Number = {15},
Pages = {154110},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1063/1.4981021},
Abstract = {In this work, a novel ring polymer representation for a
multi-level quantum system is proposed for thermal average
calculations. The proposed representation keeps the
discreteness of the electronic states: besides position and
momentum, each bead in the ring polymer is also
characterized by a surface index indicating the electronic
energy surface. A path integral molecular dynamics with
surface hopping (PIMD-SH) dynamics is also developed to
sample the equilibrium distribution of the ring polymer
configurational space. The PIMD-SH sampling method is
validated theoretically and by numerical
examples.},
Doi = {10.1063/1.4981021},
Key = {fds326270}
}

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

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



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

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