## Mathematics Faculty: Publications since January 2016

%% Abel, Michael
@article{fds317698,
Title = {HOMFLY-PT homology for general link diagrams and braidlike
isotopy},
Year = {2016},
Month = {June},
url = {http://arxiv.org/abs/1607.00314},
Key = {fds317698}
}

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

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

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

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

@article{fds329182,
Author = {Agarwal, PK and Fox, K and Panigrahi, D and Varadarajan, KR and Xiao,
A},
Title = {Faster algorithms for the geometric transportation
problem},
Journal = {LIPIcs},
Volume = {77},
Pages = {71-716},
Year = {2017},
Month = {June},
ISBN = {9783959770385},
url = {http://dx.doi.org/10.4230/LIPIcs.SoCG.2017.7},
Abstract = {© Pankaj K. Agarwal, Kyle Fox, Debmalya Panigrahi, Kasturi
R. Varadarajan, and Allen Xiao. Let R, B C R d for constant
d, be two point sets with |R| + |B| = n, and let λ: R∪B
→ ℕ such that Σ r∈R λ(r) = Σ b∈B λ (b) be demand
functions over R and B. Let d(·, ·) be a suitable distance
function such as the L p distance. The transportation
problem asks to find a map τ: R × B → ℕ such that Σ
b∈B τ(r, b) = λ(r), Σ r∈R τ(r, b) = λ(b), and σ
r∈Rb∈B τ(r, b)d(r, b) is minimized. We present three
new results for the transportation problem when d(·, ·) is
any L p metric: • For any constant ϵ > 0, an O(n 1+ϵ )
expected time randomized algorithm that returns a
transportation map with expected cost O(log 2 (1/ϵ)) times
the optimal cost. • For any ϵ > 0, a (1 +
ϵ)-approximation in O(n 3/2 ϵ -d polylog(U) polylog(n))
time, where U = max p∈Rcup;B λ (p). •An exact strongly
polynomial O(n 2 polylogn) time algorithm, for d =
2.},
Doi = {10.4230/LIPIcs.SoCG.2017.7},
Key = {fds329182}
}

@article{fds323822,
Author = {Agarwal, PK and Pan, J and Victor, W},
Title = {An efficient algorithm for placing electric vehicle charging
stations},
Journal = {LIPIcs},
Volume = {64},
Pages = {7.1-7.12},
Year = {2016},
Month = {December},
ISBN = {9783959770262},
url = {http://dx.doi.org/10.4230/LIPIcs.ISAAC.2016.7},
Abstract = {© Pankaj K. Agarwal, Jiangwei Pan, and Will Victor.
Motivated by the increasing popularity of electric vehicles
(EV) and a lack of charging stations in the road network, we
study the shortest path hitting set (SPHS) problem. Roughly
speaking, given an input graph G, the goal is to compute a
small-size subset H of vertices of G such that by placing
charging stations at vertices in H, every shortest path in G
becomes EV-feasible, i.e., an EV can travel between any two
vertices of G through the shortest path with a full charge.
In this paper, we propose a bi-criteria approximation
algorithm with running time near-linear in the size of G
that has a logarithmic approximation on |H| and may require
the EV to slightly deviate from the shortest path. We also
present a data structure for computing an EV-feasible path
between two query vertices of G.},
Doi = {10.4230/LIPIcs.ISAAC.2016.7},
Key = {fds323822}
}

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

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

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

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

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

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

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

@article{fds315094,
Author = {Agarwal, PK and Fox, K and Salzman, O},
Title = {An efficient algorithm for computing high-quality paths amid
polygonal obstacles},
Journal = {Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms},
Volume = {2},
Pages = {1179-1192},
Year = {2016},
Month = {January},
ISBN = {9781510819672},
Applied Mathematics. We study a path-planning problem amid a
set 0 of obstacles in R2, in which we wish to compute a
short path between two points while also maintaining a high
clearance from 0; the clearance of a point is its distance
from a nearest obstacle in 0. Specifically, the problem asks
for a path minimizing the reciprocal of the clearance
integrated over the length of the path. We present the first
polynomial-time approximation scheme for this problem. Let n
be the total number of obstacle vertices and let ϵ ∈ (0,
1]. Our algorithm computes in time 0(n2/ϵ2 log n/ϵ) a path
of total cost at most (1 + ϵ) times the cost of the optimal
path.},
Key = {fds315094}
}

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

%% Arlotto, Alessandro
@article{fds322098,
Author = {Arlotto, A and Steele, JM},
Title = {A Central Limit Theorem for Temporally Nonhomogenous Markov
Chains with Applications to Dynamic Programming},
Journal = {Mathematics of Operations Research},
Volume = {41},
Number = {4},
Pages = {1448-1468},
Year = {2016},
Month = {November},
url = {http://dx.doi.org/10.1287/moor.2016.0784},
Doi = {10.1287/moor.2016.0784},
Key = {fds322098}
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

%% Daubechies, Ingrid
@article{fds325388,
Author = {Deligiannis, N and Mota, JFC and Cornelis, B and Rodrigues, MRD and Daubechies, I},
Title = {Multi-Modal Dictionary Learning for Image Separation With
Application in Art Investigation},
Journal = {IEEE Transactions on Image Processing},
Volume = {26},
Number = {2},
Pages = {751-764},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1109/TIP.2016.2623484},
Doi = {10.1109/TIP.2016.2623484},
Key = {fds325388}
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article{fds329109,
Author = {Li, C and Srivastava, S and Dunson, DB},
Title = {Simple, scalable and accurate posterior interval
estimation},
Journal = {Biometrika},
Volume = {104},
Number = {3},
Pages = {665-680},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1093/biomet/asx033},
Doi = {10.1093/biomet/asx033},
Key = {fds329109}
}

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

@article{fds329110,
Author = {Srivastava, S and Engelhardt, BE and Dunson, DB},
Title = {Expandable factor analysis},
Journal = {Biometrika},
Volume = {104},
Number = {3},
Pages = {649-663},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1093/biomet/asx030},
Doi = {10.1093/biomet/asx030},
Key = {fds329110}
}

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

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

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

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

@article{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 et
al.},
Title = {The Genetic Basis of Hepatosplenic T-cell
Lymphoma.},
Journal = {Cancer Discovery},
Volume = {7},
Number = {4},
Pages = {369-379},
Year = {2017},
Month = {April},
url = {http://dx.doi.org/10.1158/2159-8290.cd-16-0330},
Abstract = {Hepatosplenic T-cell lymphoma (HSTL) is a rare and lethal
lymphoma; the genetic drivers of this disease are unknown.
Through whole-exome sequencing of 68 HSTLs, we define
recurrently mutated driver genes and copy-number alterations
in the disease. Chromatin-modifying genes, including SETD2,
INO80, and ARID1B, were commonly mutated in HSTL, affecting
62% of cases. HSTLs manifest frequent mutations in STAT5B
(31%), STAT3 (9%), and PIK3CD (9%), for which there
currently exist potential targeted therapies. In addition,
we noted less frequent events in EZH2, KRAS, and TP53SETD2
was the most frequently silenced gene in HSTL. We
experimentally demonstrated that SETD2 acts as a tumor
suppressor gene. In addition, we found that mutations in
STAT5B and PIK3CD activate critical signaling pathways
important to cell survival in HSTL. Our work thus defines
the genetic landscape of HSTL and implicates gene mutations
linked to HSTL pathogenesis and potential treatment
targets.Significance: We report the first systematic
application of whole-exome sequencing to define the genetic
basis of HSTL, a rare but lethal disease. Our work defines
SETD2 as a tumor suppressor gene in HSTL and implicates
genes including INO80 and PIK3CD in the disease. Cancer
Discov; 7(4); 369-79. ©2017 AACR.See related commentary by
the In This Issue feature, p. 339.},
Doi = {10.1158/2159-8290.cd-16-0330},
Key = {fds326037}
}

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

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

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

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

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

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

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

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

@article{fds327388,
Author = {Durante, D and Dunson, DB and Vogelstein, JT},
Title = {Nonparametric Bayes Modeling of Populations of
Networks},
Journal = {Journal of the American Statistical Association},
Pages = {1-15},
Year = {2016},
Month = {August},
url = {http://dx.doi.org/10.1080/01621459.2016.1219260},
Abstract = {© 2017 American Statistical Association Replicated network
data are increasingly available in many research fields. For
example, in connectomic applications, interconnections among
brain regions are collected for each patient under study,
motivating statistical models which can flexibly
characterize the probabilistic generative mechanism
underlying these network-valued data. Available models for a
single network are not designed specifically for inference
on the entire probability mass function of a network-valued
random variable and therefore lack flexibility in
characterizing the distribution of relevant topological
structures. We propose a flexible Bayesian nonparametric
approach for modeling the population distribution of
network-valued data. The joint distribution of the edges is
defined via a mixture model that reduces dimensionality and
efficiently incorporates network information within each
mixture component by leveraging latent space
representations. The formulation leads to an efficient Gibbs
sampler and provides simple and coherent strategies for
inference and goodness-of-fit assessments. We provide
theoretical results on the flexibility of our model and
illustrate improved performance—compared to
state-of-the-art models—in simulations and application to
human brain networks. Supplementary materials for this
article are available online.},
Doi = {10.1080/01621459.2016.1219260},
Key = {fds327388}
}

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

@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},
Pages = {1-13},
Year = {2016},
Month = {July},
url = {http://dx.doi.org/10.1080/01621459.2016.1208615},
Doi = {10.1080/01621459.2016.1208615},
Key = {fds326570}
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article{fds320425,
Author = {Hain, R},
Title = {Deligne-Beilinson Cohomology of Affine Groups},
Year = {2016},
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{fds324397,
Author = {Bendich, P and Chin, SP and Clark, J and Desena, J and Harer, J and Munch,
E and Newman, A and Porter, D and Rouse, D and Strawn, N and Watkins,
A},
Title = {Topological and statistical behavior classifiers for
tracking applications},
Journal = {IEEE Transactions on Aerospace and Electronic
Systems},
Volume = {52},
Number = {6},
Pages = {2644-2661},
Year = {2016},
Month = {December},
url = {http://dx.doi.org/10.1109/TAES.2016.160405},
Abstract = {© 1965-2011 IEEE.This paper introduces a method to
integrate target behavior into the multiple hypothesis
tracker (MHT) likelihood ratio. In particular, a periodic
track appraisal based on behavior is introduced. The track
appraisal uses elementary topological data analysis coupled
with basic machine-learning techniques, and it adjusts the
traditional kinematic data association likelihood (i.e.,
track score) using an established formulation for
feature-aided data association. The proposed method is
tested and demonstrated on synthetic vehicular data
representing an urban traffic scene generated by the
Simulation of Urban Mobility package. The vehicles in the
scene exhibit different driving behaviors. The proposed
method distinguishes those behaviors and shows improved data
association decisions relative to a conventional, kinematic
MHT.},
Doi = {10.1109/TAES.2016.160405},
Key = {fds324397}
}

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

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

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

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

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

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

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

%% Layton, Anita T.
@article{fds329189,
Author = {Edwards, A and Layton, AT},
Title = {Cell Volume Regulation in the Proximal Tubule of Rat Kidney
: Proximal Tubule Cell Volume Regulation.},
Journal = {Bulletin of Mathematical Biology},
Year = {2017},
Month = {September},
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}
}

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

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

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

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

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

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

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

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

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

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

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

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

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

@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 & Its Ramifications},
Volume = {26},
Number = {02},
Pages = {1740004-1740004},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1142/S0218216517400041},
Doi = {10.1142/S0218216517400041},
Key = {fds328057}
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article{fds329344,
Author = {Yu, VW-Z and Corsetti, F and García, A and Huhn, WP and Jacquelin, M and Jia, W and Lange, B and Lin, L and Lu, J and Mi, W and Seifitokaldani, A and Vázquez-Mayagoitia, Á and Yang, C and Yang, H and Blum,
V},
Title = {ELSI: A unified software interface for Kohn–Sham
electronic structure solvers},
Journal = {Computer Physics Communications},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1016/j.cpc.2017.09.007},
Doi = {10.1016/j.cpc.2017.09.007},
Key = {fds329344}
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

%% Pfister, Henry
@article{fds328986,
Author = {Charbonneau, P and Li, YC and Pfister, HD and Yaida,
S},
Title = {Cycle-expansion method for the Lyapunov exponent,
susceptibility, and higher moments},
Journal = {Physical review. E},
Volume = {96},
Number = {3},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1103/PhysRevE.96.032129},
Doi = {10.1103/PhysRevE.96.032129},
Key = {fds328986}
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article{fds323532,
Author = {Kudekar, S and Kumar, S and Mondelli, M and Pfister, HD and Sasoglu, E and Urbanke, RL},
Title = {Reed-Muller codes achieve capacity on erasure
channels.},
Journal = {STOC},
Pages = {658-669},
Publisher = {ACM},
Editor = {Wichs, D and Mansour, Y},
Year = {2016},
ISBN = {978-1-4503-4132-5},
url = {http://dx.doi.org/10.1145/2897518.2897584},
Doi = {10.1145/2897518.2897584},
Key = {fds323532}
}

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

@article{fds328811,
Author = {Heath-Brown, DR and Pierce, LB},
Title = {Averages and moments associated to class numbers of
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{fds320389,
Author = {Heath-Brown, DR and Pierce, LB},
Title = {Simultaneous integer values of pairs of quadratic
forms},
Journal = {Journal für die Reine und Angewandte Mathematik (Crelle's
Journal)},
Volume = {2017},
Number = {727},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1515/crelle-2014-0112},
Doi = {10.1515/crelle-2014-0112},
Key = {fds320389}
}

@article{fds320660,
Author = {Ellenberg, J and Pierce, LB and Wood, MM},
Title = {On $\ell$-torsion in class groups of number
fields},
Journal = {arXiv:1606.06103 [math]},
Year = {2016},
Month = {June},
Abstract = {For each integer $\ell \geq 1$, we prove an unconditional
upper bound on the size of the $\ell$-torsion subgroup of
the class group, which holds for all but a zero-density set
of field extensions of $\mathbb{Q}$ of degree $d$, for any
fixed $d \in \{2,3,4,5\}$ (with the additional restriction
in the case $d=4$ that the field be non-$D_4$). For
sufficiently large $\ell$ (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.},
Key = {fds320660}
}

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

@article{fds320661,
Author = {Guo, S and Pierce, LB and Roos, J and Yung, P},
Title = {Polynomial Carleson operators along monomial curves in the
plane},
Journal = {arXiv:1605.05812 [math]},
Year = {2016},
Month = {May},
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}
}

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

%% Randles, Amanda
@article{fds329286,
Author = {Randles, A and Frakes, DH and Leopold, JA},
Title = {Computational Fluid Dynamics and Additive Manufacturing to
Diagnose and Treat Cardiovascular Disease.},
Journal = {Trends in Biotechnology},
Year = {2017},
Month = {September},
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 = {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}
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article{fds327666,
Author = {Pisharady, PK and Sotiropoulos, SN and Duarte-Carvajalino, JM and Sapiro, G and Lenglet, C},
Title = {Estimation of white matter fiber parameters from compressed
multiresolution diffusion MRI using sparse Bayesian
learning.},
Journal = {NeuroImage},
Year = {2017},
Month = {June},
url = {http://dx.doi.org/10.1016/j.neuroimage.2017.06.052},
Abstract = {We present a sparse Bayesian unmixing algorithm BusineX:
Bayesian Unmixing for Sparse Inference-based Estimation of
Fiber Crossings (X), for estimation of white matter fiber
parameters from compressed (under-sampled) diffusion MRI
(dMRI) data. BusineX combines compressive sensing with
linear unmixing and introduces sparsity to the previously
proposed multiresolution data fusion algorithm RubiX,
resulting in a method for improved reconstruction,
especially from data with lower number of diffusion
gradients. We formulate the estimation of fiber parameters
as a sparse signal recovery problem and propose a linear
unmixing framework with sparse Bayesian learning for the
recovery of sparse signals, the fiber orientations and
volume fractions. The data is modeled using a parametric
spherical deconvolution approach and represented using a
dictionary created with the exponential decay components
along different possible diffusion directions. Volume
fractions of fibers along these directions define the
dictionary weights. The proposed sparse inference, which is
based on the dictionary representation, considers the
sparsity of fiber populations and exploits the spatial
redundancy in data representation, thereby facilitating
inference from under-sampled q-space. The algorithm improves
parameter estimation from dMRI through data-dependent local
learning of hyperparameters, at each voxel and for each
possible fiber orientation, that moderate the strength of
priors governing the parameter variances. Experimental
results on synthetic and in-vivo data show improved accuracy
with a lower uncertainty in fiber parameter estimates.
BusineX resolves a higher number of second and third fiber
crossings. For under-sampled data, the algorithm is also
shown to produce more reliable estimates.},
Doi = {10.1016/j.neuroimage.2017.06.052},
Key = {fds327666}
}

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

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

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

@article{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 = {Lecture notes in computer science},
Volume = {10433 LNCS},
Pages = {602-610},
Year = {2017},
Month = {January},
ISBN = {9783319661810},
url = {http://dx.doi.org/10.1007/978-3-319-66182-7_69},
Abstract = {© 2017, Springer International Publishing AG. 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{fds326840,
Author = {Gunalan, K and Chaturvedi, A and Howell, B and Duchin, Y and Lempka, SF and Patriat, R and Sapiro, G and Harel, N and McIntyre,
CC},
Title = {Creating and parameterizing patient-specific deep brain
stimulation pathway-activation models using the hyperdirect
pathway as an example.},
Journal = {PloS one},
Volume = {12},
Number = {4},
Pages = {e0176132},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1371/journal.pone.0176132},
Abstract = {Deep brain stimulation (DBS) is an established clinical
therapy and computational models have played an important
role in advancing the technology. Patient-specific DBS
models are now common tools in both academic and industrial
research, as well as clinical software systems. However, the
exact methodology for creating patient-specific DBS models
can vary substantially and important technical details are
often missing from published reports.Provide a detailed
description of the assembly workflow and parameterization of
a patient-specific DBS pathway-activation model (PAM) and
predict the response of the hyperdirect pathway to clinical
stimulation.Integration of multiple software tools (e.g.
COMSOL, MATLAB, FSL, NEURON, Python) enables the creation
and visualization of a DBS PAM. An example DBS PAM was
developed using 7T magnetic resonance imaging data from a
single unilaterally implanted patient with Parkinson's
disease (PD). This detailed description implements our best
computational practices and most elaborate parameterization
steps, as defined from over a decade of technical
evolution.Pathway recruitment curves and strength-duration
relationships highlight the non-linear response of axons to
changes in the DBS parameter settings.Parameterization of
patient-specific DBS models can be highly detailed and
constrained, thereby providing confidence in the simulation
predictions, but at the expense of time demanding technical
implementation steps. DBS PAMs represent new tools for
investigating possible correlations between brain pathway
activation patterns and clinical symptom
modulation.},
Doi = {10.1371/journal.pone.0176132},
Key = {fds326840}
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article{fds318341,
Author = {Best, A and Dynes, P and Edelsbrunner, X and McDonald, B and Miller, SJ and Tor, K and Turnage-Butterbaugh, C and Weinstein,
M},
Title = {Gaussian distribution of the number of summands in
generalized Zeckendorf decomposition in small
intervals},
Journal = {Integers},
Volume = {16},
Pages = {13 pages},
Year = {2016},
Key = {fds318341}
}

%% Venakides, Stephanos
@article{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}
}

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

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

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

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

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

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

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

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

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

@article{fds328813,
Author = {Malik, J and Reed, N and Wang, C-L and Wu, H-T},
Title = {Single-lead f-wave extraction using diffusion
geometry},
Journal = {Physiological Measurement},
Volume = {38},
Number = {7},
Pages = {1310-1334},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1088/1361-6579/aa707c},
Doi = {10.1088/1361-6579/aa707c},
Key = {fds328813}
}

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

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

@article{fds328816,
Author = {Li, R and Frasch, MG and Wu, H-T},
Title = {Efficient Fetal-Maternal ECG Signal Separation from Two
Channel Maternal Abdominal ECG via Diffusion-Based Channel
Selection},
Journal = {Frontiers in Physiology},
Volume = {8},
Year = {2017},
Month = {May},
url = {http://dx.doi.org/10.3389/fphys.2017.00277},
Doi = {10.3389/fphys.2017.00277},
Key = {fds328816}
}

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

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

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

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

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

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

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

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

@article{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},
Year = {2016},
Month = {April},
url = {http://dx.doi.org/10.1016/j.acha.2016.03.008},
Doi = {10.1016/j.acha.2016.03.008},
Key = {fds328822}
}

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

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

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

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

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

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

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

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

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

%% Zhou, Zhennan
@article{fds323230,
Author = {Liu, J-G and Ma, Z and Zhou, Z},
Title = {Explicit and Implicit TVD Schemes for Conservation Laws with
Caputo Derivatives},
Journal = {Journal of Scientific Computing},
Volume = {72},
Number = {1},
Pages = {291-313},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1007/s10915-017-0356-4},
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}
}

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

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