Mathematics Faculty: Publications since January 2016
List all publications in the database. :chronological alphabetical combined listing:
%% Abel, Michael
@article{fds317698,
Title = {HOMFLYPT 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: onecolumn partitions},
Year = {2016},
Month = {February},
url = {http://arxiv.org/abs/1510.05330},
Key = {fds311722}
}
%% Agarwal, Pankaj K.
@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 = {7.17.12},
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 smallsize subset H of vertices of G such
that by placing charging stations at vertices in H, every
shortest path in G becomes EVfeasible, 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
bicriteria approximation algorithm with running time
nearlinear 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 EVfeasible path between two
query vertices of G.},
Doi = {10.4230/LIPIcs.ISAAC.2016.7},
Key = {fds323822}
}
@article{fds323823,
Author = {Ying, R and Pan, J and Fox, K and Agarwal, PK},
Title = {A simple efficient approximation algorithm for dynamic time
warping},
Journal = {GIS: Proceedings of the ACM International Symposium on
Advances in Geographic Information Systems},
Year = {2016},
Month = {October},
ISBN = {9781450345897},
url = {http://dx.doi.org/10.1145/2996913.2996954},
Abstract = {© 2016 ACM.Dynamic time warping (DTW) is a widely used
curve similarity measure. We present a simple and efficient
(1 + ∈) approximation algorithm for DTW between a pair of
point sequences, say, P and Q, each of which is sampled from
a curve. We prove that the running time of the algorithm is
O( κ2/∈ n log σ) for a pair of κpacked 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 κpacked 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 realworld 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 510%. 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 812
times speedup using our algorithm as a subroutine in these
applications, without compromising much in
accuracy.},
Doi = {10.1145/2996913.2996954},
Key = {fds323823}
}
@article{fds323790,
Author = {Nath, A and Fox, K and Agarwal, PK and Munagala, K},
Title = {Massively parallel algorithms for computing TIN DEMs and
contour trees for large terrains},
Journal = {GIS: Proceedings of the ACM International Symposium on
Advances in Geographic Information Systems},
Year = {2016},
Month = {October},
ISBN = {9781450345897},
url = {http://dx.doi.org/10.1145/2996913.2996952},
Abstract = {© 2016 ACM.We propose parallel algorithms in the massively
parallel communication (MPC) model (e.g. MapReduce) for
processing large terrain elevation data (represented as a 3D
point cloud) that are too big to fit on one machine. In
particular, given a set S of 3D points that is distributed
across multiple machines, we present a simple randomized
algorithm to construct a TIN DEM of S by computing the
Delaunay triangulation of the xyprojections 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 HarPeled, S and Phillips, JM and Yi, K and Zhang, W},
Title = {NearestNeighbor Searching Under Uncertainty
II},
Journal = {ACM Transactions on Algorithms},
Volume = {13},
Number = {1},
Pages = {125},
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 = {Rangemax queries on uncertain data},
Journal = {Proceedings of the ACM SIGACTSIGMODSIGART Symposium on
Principles of Database Systems},
Volume = {26June01July2016},
Pages = {465476},
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 ℝd,
where each point pi ∈ P is associated with a real value vi
and a probability αi ∈ (0,1] of existence, i.e., each pi
exists with an independent probability αi. We present
algorithms for building an index on P so that for a
ddimensional query rectangle ρ, the expected maximum value
or the mostlikely maximum value in ρ can be computed
quickly. The specific contributions of our paper include the
following: (i) The first index of subquadratic size to
achieve a sublinear query time in any dimension d ≥ 1. It
also provides a tradeoff between query time and size of the
index. (ii) A conditional lower bound for the mostlikely
rangemax queries, based on the conjectured hardness of the
setintersection problem, which suggests that in the worst
case the product (query time)2 x (index size) is
Ω(n2/polylog(n)). (iii) A linearsize index for estimating
the expected rangemax value within approximation factor 1/2
in O(logcn) 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 topk values of the
rangemax.},
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
nearestneighbor searching data structures},
Journal = {Proceedings of the ACM SIGACTSIGMODSIGART Symposium on
Principles of Database Systems},
Volume = {26June01July2016},
Pages = {429440},
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 kdtrees, range trees, and BBDtrees 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 = {6.16.16},
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
doublestruck Rd, 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 nearlinear time for
point sequences drawn from κpacked or κbounded curves,
and subquadratic time for backbone sequences. Roughly
speaking, a curve is κpacked if the length of its
intersection with any ball of radius r is at most κ · r,
and it is κbounded if the subcurve 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 minimumweight 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
minimumweight 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 = {311325},
Year = {2016},
Month = {February},
ISSN = {10414347},
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 highquality paths amid
polygonal obstacles},
Journal = {Proceedings of the Annual ACMSIAM Symposium on Discrete
Algorithms},
Volume = {2},
Pages = {11791192},
Year = {2016},
Month = {January},
ISBN = {9781510819672},
Abstract = {© Copyright (2016) by SIAM: Society for Industrial and
Applied Mathematics.We study a pathplanning 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
polynomialtime 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 = {Markovmodulated marked poisson processes for checkin
data},
Journal = {33rd International Conference on Machine Learning, ICML
2016},
Volume = {5},
Pages = {33113320},
Year = {2016},
Month = {January},
ISBN = {9781510829008},
Abstract = {© 2016 by the author(s).We develop continuoustime
probabilistic models to study trajectory data consisting of
times and locations of user 'checkins'. We model the data
as realizations of a marked point process, with intensity
and markdistribution modulated by a latent Markov jump
process (MJP). We also include userheterogeneity in our
model by assigning each user a vector of 'preferred
locations'. Our model extends latent Dirichlet allocation by
dropping the bagofwords assumption and operating in
continuous time. We show how an appropriate choice of priors
allows efficient posterior inference. Our experiments
demonstrate the usefulness of our approach by comparing with
various baselines on a variety of tasks.copyright},
Key = {fds321561}
}
%% Arlotto, Alessandro
@article{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 = {14481468},
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 = {235252},
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 = {733753},
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{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 = {65.165.5},
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 multiscale
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 webbased application
powered by Javascript and WebGL which plays music
synchronized with a principal component analysis embedding
of the point cloud down to 3D. We also render the clusters
and the scaffolding on top of this projection to visualize
the transitions between different sections of the
music.},
Doi = {10.4230/LIPIcs.SoCG.2016.65},
Key = {fds321986}
}
@article{fds315426,
Author = {Bendich, P and Marron, JS and Miller, E and Pieloch, A and Skwerer,
S},
Title = {Persistent Homology Analysis of Brain Artery
Trees.},
Journal = {The annals of applied statistics},
Volume = {10},
Number = {1},
Pages = {198218},
Year = {2016},
Month = {January},
ISSN = {19326157},
url = {http://hdl.handle.net/10161/11157 Duke open
access},
Abstract = {New representations of treestructured 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 = {10.1214/15AOAS886},
Key = {fds315426}
}
@article{fds311346,
Author = {Paul Bendich and Ellen Gasparovic and John Harer and Christopher
J. Tralie},
Title = {Scaffoldings and Spines: Organizing HighDimensional 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 = {H1 solutions of a class of fourth order nonlinear equations
for image processing},
Journal = {Discrete And Continuous Dynamical Systems},
Volume = {10},
Number = {12},
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 = {14571475},
Publisher = {Springer Basel},
Year = {2016},
Month = {June},
ISSN = {14240637},
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
quasilocal mass of spacelike 2surfaces in the
spacetime.},
Doi = {10.1007/s0002301504202},
Key = {fds300017}
}
%% Daubechies, Ingrid
@article{fds318286,
Author = {Wu, HT 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 = {463472},
Year = {2016},
Month = {October},
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
computerbased 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 noncontact photoplethysmography
(PPG). As technologies move from contact to noncontact 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
noncontact sensors, on a beattobeat 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
beattobeat heart rate pattern (i.e., heart rate
variability).The adaptive harmonic model is applied to model
the contact or noncontact PPG signals, and a new
methodology, the Synchrosqueezing Transform (SST), is
applied to extract IHR. The body sway rhythm inherited in
the noncontact PPG signal is modeled and handled by the
notion of waveshape 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 noncontact 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.},
Key = {fds318286}
}
@article{fds323650,
Author = {Daubechies, I and Defrise, M and Mol, CD},
Title = {Sparsityenforcing regularisation and ISTA
revisited},
Journal = {Inverse Problems},
Volume = {32},
Number = {10},
Pages = {104001104001},
Year = {2016},
Month = {October},
url = {http://dx.doi.org/10.1088/02665611/32/10/104001},
Doi = {10.1088/02665611/32/10/104001},
Key = {fds323650}
}
@article{fds320873,
Author = {O'Neal, WT and Wang, YG and Wu, HT and Zhang, ZM 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 = {811815},
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 followup 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 followup 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; Pinteraction = 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 middleaged 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 = {Xray image separation via coupled dictionary
learning},
Journal = {Proceedings / ICIP ... International Conference on Image
Processing},
Volume = {2016August},
Pages = {35333537},
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 Xray
scan acquired from doublesided 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 backside of the panel to drive
the separation process. The coupling of the two imaging
modalities is achieved via a new multiscale dictionary
learning method. Experimental results demonstrate that our
method succeeds in the discrimination of the sources, while
stateoftheart 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 = {2016May},
Pages = {22992303},
Year = {2016},
Month = {May},
ISBN = {9781479999880},
ISSN = {15206149},
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 highlevel classiication output and the lowlevel
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
descriptorbased 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, HT},
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 = {1364503X},
url = {http://dx.doi.org/10.1098/rsta.2015.0193},
Abstract = {A new method is proposed to determine the timefrequency
content of timedependent signals consisting of multiple
oscillatory components, with timevarying 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 = {1364503X},
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 XRay Images of
Paintings},
Journal = {SIAM Journal on Imaging Sciences},
Volume = {9},
Number = {3},
Pages = {12471272},
Year = {2016},
Month = {January},
url = {http://dx.doi.org/10.1137/15M1053554},
Doi = {10.1137/15M1053554},
Key = {fds318287}
}
%% Dolbow, John E.
@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 = {12891314},
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 LevelSet model for dynamic fragmentation},
Journal = {Engineering Fracture Mechanics},
Volume = {172},
Pages = {3960},
Year = {2017},
Month = {March},
url = {http://dx.doi.org/10.1016/j.engfracmech.2016.12.012},
Doi = {10.1016/j.engfracmech.2016.12.012},
Key = {fds323719}
}
%% Dunson, David B.
@article{fds323700,
Author = {Lock, EF and Dunson, DB},
Title = {Bayesian genome and epigenomewide association studies with
gene level dependence.},
Journal = {Biometrics},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1111/biom.12649},
Abstract = {Highthroughput 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 genespecific
probabilities are modeled nonparametrically. This
hierarchical model allows for appropriate gene and
genomewide 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{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 = {4148},
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 = {319335},
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 flowcytometry 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 doublyintractable
Markov chain Monte Carlo problems, where evaluating the
likelihood is intractable. Our experiments demonstrate
superior performance over stateoftheart 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{fds322539,
Author = {Kabisa, ST and Dunson, DB and Morris, JS},
Title = {Online Variational Bayes Inference for HighDimensional
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 = {426444},
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 = {876905},
Year = {2016},
Month = {April},
url = {http://dx.doi.org/10.1214/15AOS1390},
Doi = {10.1214/15AOS1390},
Key = {fds322540}
}
@article{fds322541,
Author = {Zhou, J and Herring, AH and Bhattacharya, A and Olshan, AF and Dunson,
DB},
Title = {Nonparametric Bayes modeling for case control studies with
many predictors.},
Journal = {Biometrics},
Volume = {72},
Number = {1},
Pages = {184192},
Year = {2016},
Month = {March},
url = {http://dx.doi.org/10.1111/biom.12411},
Abstract = {It is common in biomedical research to run casecontrol
studies involving highdimensional 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 = {6676},
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
1,1norm 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
stateoftheart.},
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 = {3547},
Year = {2016},
Month = {March},
url = {http://dx.doi.org/10.1093/biomet/asv060},
Doi = {10.1093/biomet/asv060},
Key = {fds322543}
}
@article{fds322544,
Author = {Van Den Boom and W and Dunson, D and Reeves, G},
Title = {Quantifying uncertainty in variable selection with arbitrary
matrices},
Journal = {2015 IEEE 6th International Workshop on Computational
Advances in MultiSensor Adaptive Processing, CAMSAP
2015},
Pages = {385388},
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 realworld
applications. This paper proposes a scalable framework that
utilizes stateoftheart 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{fds321837,
Author = {Yin, R and Cornelis, B and Fodor, G and Ocon, N and Dunson, D and Daubechies, I},
Title = {Removing Cradle Artifacts in XRay Images of
Paintings},
Journal = {SIAM Journal on Imaging Sciences},
Volume = {9},
Number = {3},
Pages = {12471272},
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 highdimensional
linear models},
Journal = {33rd International Conference on Machine Learning, ICML
2016},
Volume = {4},
Pages = {26852706},
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 threestep 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
penalizationbased approaches in simulations and data
analyses illustrate the great potential of the proposed
algorithms.},
Key = {fds322545}
}
%% Durrett, Richard T.
@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 = {82107},
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, WTL},
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 = {34563490},
Year = {2016},
Month = {December},
url = {http://dx.doi.org/10.1214/16AAP1181},
Doi = {10.1214/16AAP1181},
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 = {23882409},
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.Agestratified, 10year diseasespecific 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 10year
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 = 19.769.9), 67.3 (PR =
28.7211.4), and 157.2 (PR = 41.13872.8), 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 = {13691400},
Year = {2016},
Month = {April},
ISSN = {03036812},
url = {http://dx.doi.org/10.1007/s0028501509121},
Doi = {10.1007/s0028501509121},
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 = {570580},
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 2Monopoles with Singularities (Examples)},
Journal = {Letters in Mathematical Physics},
Volume = {106},
Number = {11},
Pages = {14791497},
Year = {2016},
Month = {November},
url = {http://dx.doi.org/10.1007/s110050160878y},
Doi = {10.1007/s110050160878y},
Key = {fds321573}
}
@article{fds316671,
Author = {Oliveira, G},
Title = {Monopoles on AC 3manifolds},
Journal = {Journal of the London Mathematical Society},
Volume = {93},
Number = {3},
Pages = {785810},
Year = {2016},
Month = {June},
ISSN = {00246107},
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 = {699728},
Year = {2016},
Month = {January},
ISSN = {00103616},
url = {http://hdl.handle.net/10161/11700 Duke open
access},
Doi = {10.1007/s0022001525342},
Key = {fds311851}
}
%% Getz, Jayce R.
@article{fds320411,
Author = {Getz, JR},
Title = {A fourvariable automorphic kernel function},
Journal = {Research in the Mathematical Sciences},
Volume = {3},
Number = {1},
Year = {2016},
Month = {December},
url = {http://dx.doi.org/10.1186/s4068701600696},
Doi = {10.1186/s4068701600696},
Key = {fds320411}
}
%% Hahn, Heekyoung
@article{fds320417,
Author = {Hahn, H},
Title = {On classical groups detected by the triple tensor products
and the LittlewoodRichardson semigroup},
Journal = {Reserch in Number Theory},
Volume = {2},
Number = {1},
Pages = {112},
Year = {2016},
Month = {June},
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 = {50615069},
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 Lfunctions 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 LittlewoodRichardson 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 = {15500651550065},
Year = {2016},
Month = {August},
ISSN = {02191997},
url = {http://dx.doi.org/10.1142/S0219199715500650},
Doi = {10.1142/S0219199715500650},
Key = {fds287213}
}
@article{fds320302,
Author = {Hain, R},
Title = {The Hodgede Rham theory of modular groups},
Volume = {427},
Pages = {422514},
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 Qlinear 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 IharaTakao
congruences.},
Key = {fds320426}
}
@article{fds320425,
Author = {Hain, R},
Title = {DeligneBeilinson 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
DeligneBeilinson 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{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 postgenomic
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
timeseries 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 wellcharacterized 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 = {65.165.5},
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 multiscale
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 webbased application
powered by Javascript and WebGL which plays music
synchronized with a principal component analysis embedding
of the point cloud down to 3D. We also render the clusters
and the scaffolding on top of this projection to visualize
the transitions between different sections of the
music.},
Doi = {10.4230/LIPIcs.SoCG.2016.65},
Key = {fds321990}
}
%% 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}
}
%% Layton, Anita T.
@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 = {338351},
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
ureaselective 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 allUTknockout
mice. Daily urine output was nearly 3.5fold higher, with
significantly lower urine osmolality in allUTknockout mice
than that in wildtype mice. AllUTknockout mice were not
able to increase urinary urea concentration and osmolality
after water deprivation, acute urea loading, or high protein
intake. A computational model that simulated UTknockout
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 ureaselective
urineconcentrating 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 = {F1217F1229},
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 longterm 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 bumetanidesensitive Na+K+2Cl transporter
(NKCC2), the Na+Cl cotransporter (NCC), and the
amiloridesensitive 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 ). Wholekidney 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 wholekidney 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 wholekidney 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 wholekidney
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 = {F1378F1390},
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, flowinduced transcellular transport. Moreover, the
model predicted that an increase in singlenephron
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
flowinduced increases in QO2 under pathophysiological
conditions.},
Doi = {10.1152/ajprenal.00293.2016},
Key = {fds320876}
}
@article{fds320877,
Author = {Sgouralis, I and Kett, MM and Ow, CP 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 = {R532R544},
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)nitrolarginine reduced urinary Po2
and medullary Po2 (817%), 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 (withinrabbit r(2) = 0.870.90). 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
(0.10.5 ml/min for a single kidney), a change in bladder
urine Po2 explains 1050% 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 realtime 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 = {F162F165},
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,
arterialtovenous 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{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},
Year = {2016},
Month = {June},
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[Formula:
see text], which is an indicator of renal hypoxia, is
predicted near the thick ascending limbs. Interstitial
tissue P[Formula: see text] exhibits a general decrease
along the inner medullary axis, but urine P[Formula: see
text] increases significantly along the ureter. Thus,
bladder urinary P[Formula: see text] is predicted to be
substantially higher than medullary P[Formula: see text] 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.},
Key = {fds320879}
}
@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 = {F1269F1283},
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 sodiumglucose cotransporter SGLT2 in the
early proximal tubule (S1S2 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
transportdependent 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 512% in the cortex and medulla.
Diabetes increases overall TNa and [Formula: see text] by
∼50 and 100%, mainly because it enhances glomerular
filtration rate (GFR) and transport load. In diabetes, acute
and chronic SGLT2 inhibition lowers [Formula: see text] in
the cortex by ∼30%, due to GFR reduction that lowers
proximal tubule active TNa, but raises [Formula: see text]
in the medulla by ∼7%. In the medulla specifically,
chronic SGLT2 inhibition is predicted to increase [Formula:
see text] by 26% in late proximal tubules (S3 segments), by
2% in medullary thick ascending limbs (mTAL), and by 9 and
21% in outer and inner medullary collecting ducts (OMCD and
IMCD), respectively. Additional blockade of SGLT1 in S3
segments enhances glucose excretion, reduces [Formula: see
text] by 33% in S3 segments, and raises [Formula: see text]
by <1% in mTAL, OMCD, and IMCD. In summary, the model
predicts that SGLT2 blockade in diabetes lowers cortical
[Formula: see text] and raises medullary [Formula: see
text], particularly in S3 segments.},
Doi = {10.1152/ajprenal.00543.2015},
Key = {fds320880}
}
@article{fds320881,
Author = {Liu, R and Layton, AT},
Title = {Modeling the effects of positive and negative feedback in
kidney blood flow control.},
Journal = {Mathematical Biosciences},
Volume = {276},
Pages = {818},
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 physiologicallyrelevant
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
yettobeexplained lowfrequency 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 = {13181336},
Year = {2016},
Month = {June},
url = {http://dx.doi.org/10.1007/s1153801601887},
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/s1153801601887},
Key = {fds320882}
}
@article{fds320883,
Author = {Nganguia, H and Young, YN and Layton, AT and Lai, MC and Hu,
WF},
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
secondorder 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 NavierStokes 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 pinchoff 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 = {923960},
Year = {2016},
Month = {May},
url = {http://dx.doi.org/10.1007/s115380160168y},
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 autoregulationa comprehensive model and a
simplified modeland 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/s115380160168y},
Key = {fds320884}
}
@article{fds320180,
Author = {Herschlag, G and Liu, JG and Layton, AT},
Title = {Fluid extraction across pumping and permeable walls in the
viscous limit},
Journal = {Physics of Fluids},
Volume = {28},
Number = {4},
Pages = {041902041902},
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 feedbackmediated signal in a computational
model of coupled nephrons.},
Journal = {Mathematical Medicine and Biology: A Journal of the
IMA},
Volume = {33},
Number = {1},
Pages = {87106},
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
preglomerular 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 preglomerular vasculature.
To better understand the conduction of these signals along
the preglomerular 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
TGFmediated flow oscillations. Simulation results suggest
that reduced gapjunctional conductances may yield stronger
internephron TGF coupling and highly irregular TGFmediated
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 nitricoxidemediated vasodilation and oxidative
stress on renal medullary oxygenation: a modeling
study.},
Journal = {American Journal of Physiology: Renal Physiology},
Volume = {310},
Number = {3},
Pages = {F237F247},
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 contrastenhanced quantitative susceptibility
mapping with ultrashort echo time MRI for evaluating renal
function.},
Journal = {American Journal of Physiology: Renal Physiology},
Volume = {310},
Number = {2},
Pages = {F174F182},
Year = {2016},
Month = {January},
url = {http://dx.doi.org/10.1152/ajprenal.00351.2015},
Abstract = {Dynamic contrastenhanced (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 17wk course (3, 5, 7, 9, 13,
17 wk of age). We conclude that the UTEbased 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}
}
%% Liu, JianGuo
@article{fds323838,
Author = {Degond, P and Liu, JG and MerinoAceituno, 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 = {159182},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1142/S021820251740005X},
Doi = {10.1142/S021820251740005X},
Key = {fds323838}
}
@article{fds320670,
Author = {W. Cong and J.G. Liu},
Title = {Uniform $L^\infty$ boundedness for a degenerate
parabolicparabolic KellerSegel model},
Journal = {Discrete and Continuous Dynamical Systems  Series
B},
Volume = {22},
Pages = {307338},
Year = {2017},
Key = {fds320670}
}
@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 = {3560},
Year = {2017},
Key = {fds320659}
}
@article{fds318453,
Author = {Huang, H and Liu, JG},
Title = {A note on Monge–Ampère Keller–Segel
equation},
Journal = {Applied Mathematics Letters},
Volume = {61},
Pages = {2634},
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, JG},
Title = {Error estimates of the aggregationdiffusion splitting
algorithms for the KellerSegel equations},
Journal = {Discrete and Continuous Dynamical Systems  Series
B},
Volume = {21},
Number = {10},
Pages = {34633478},
Year = {2016},
Month = {November},
url = {http://dx.doi.org/10.3934/dcdsb.2016107},
Doi = {10.3934/dcdsb.2016107},
Key = {fds323245}
}
@article{fds318454,
Author = {Liu, JG and Huang, H},
Title = {Wellposedness for the KellerSegel equation with fractional
Laplacian and the theory of propagation of
chaos},
Journal = {Kinetic and Related Models},
Volume = {9},
Number = {4},
Pages = {715748},
Year = {2016},
Month = {September},
url = {http://dx.doi.org/10.3934/krm.2016013},
Doi = {10.3934/krm.2016013},
Key = {fds318454}
}
@article{fds318455,
Author = {Liu, JG and Cong, W},
Title = {A degenerate $p$Laplacian KellerSegel model},
Journal = {Kinetic and Related Models},
Volume = {9},
Number = {4},
Pages = {687714},
Year = {2016},
Month = {September},
url = {http://dx.doi.org/10.3934/krm.2016012},
Doi = {10.3934/krm.2016012},
Key = {fds318455}
}
@article{fds320551,
Author = {Liu, JG and Wang, J},
Title = {A Note on L ∞ $L^{\infty}$ Bound and Uniqueness to a
Degenerate KellerSegel Model},
Journal = {Acta Applicandae Mathematicae},
Volume = {142},
Number = {1},
Pages = {173188},
Year = {2016},
Month = {April},
ISSN = {01678019},
url = {http://dx.doi.org/10.1007/s1044001500225},
Doi = {10.1007/s1044001500225},
Key = {fds320551}
}
@article{fds315797,
Author = {Herschlag, G and Liu, JG and Layton, AT},
Title = {Fluid extraction across pumping and permeable walls in the
viscous limit},
Journal = {Physics of Fluids},
Volume = {28},
Number = {4},
Pages = {041902041902},
Year = {2016},
Month = {April},
ISSN = {10706631},
url = {http://dx.doi.org/10.1063/1.4946005},
Doi = {10.1063/1.4946005},
Key = {fds315797}
}
@article{fds320552,
Author = {Liu, JG and Pego, RL},
Title = {On generating functions of Hausdorff moment
sequences},
Journal = {Transactions of the American Mathematical
Society},
Volume = {368},
Number = {12},
Pages = {84998518},
Year = {2016},
Month = {February},
url = {http://dx.doi.org/10.1090/tran/6618},
Doi = {10.1090/tran/6618},
Key = {fds320552}
}
@article{fds323246,
Author = {Liu, JG and Xu, X},
Title = {Existence Theorems for a Multidimensional Crystal Surface
Model},
Journal = {SIAM Journal on Mathematical Analysis},
Volume = {48},
Number = {6},
Pages = {36673687},
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 diffusiondrift many particle systems in
probability under a sobolev norm},
Volume = {162},
Series = {Proceedings of Particle Systems and Partial Differential
Equations  III},
Pages = {195223},
Publisher = {Springer},
Year = {2016},
Month = {January},
ISBN = {9783319321424},
url = {http://dx.doi.org/10.1007/9783319321448_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 = {10.1007/9783319321448_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{fds320652,
Author = {J. Chen and J.G. Liu and Z. Zhou},
Title = {On a SchrodingerLandauLifshitz system: Variational struc
ture and numerical methods},
Journal = {Multiscale Modeling and Simulation},
Volume = {14},
Pages = {14631487},
Year = {2016},
Key = {fds320652}
}
@article{fds320549,
Author = {Y. Duan and J.G. Liu},
Title = {Error estimate of the particle method for the
bequation},
Journal = {Methods and Applications of Analysis},
Volume = {23},
Pages = {119154},
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 = {251299},
Year = {2016},
Key = {fds320556}
}
@article{fds320739,
Author = {P. Degond and J.G. Liu and S. MerinoAceituno 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{fds320717,
Author = {P. Degond and J.G. Liu and R.L. Pego},
Title = {Coagulationfragmentation model for animal groupsize
statistics},
Journal = {J. Nonlinear Science},
Year = {2016},
Key = {fds320717}
}
@article{fds320738,
Author = {H. Huang and J.G. Liu},
Title = {Error estimate of a random particle blob method for the
KellerSegel equation},
Journal = {Math. Comp.},
Year = {2016},
Key = {fds320738}
}
@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{fds320744,
Author = {J.G. Liu and J. Wang},
Title = {Global existence for a thin film equation with subcritical
mass},
Journal = {Discrete and Continuous Dynamical Systems  Series
B},
Year = {2016},
Key = {fds320744}
}
@article{fds300225,
Author = {J.G. Liu and J. Wang},
Title = {Refined hypercontractivity and uniqueness for the
KellerSegel equations},
Journal = {Applied Math Letter},
Volume = {52},
Pages = {212219},
Year = {2016},
Key = {fds300225}
}
%% Lu, Jianfeng
@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 = {242258},
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{fds323661,
Author = {Li, Q and Lu, J and Sun, W},
Title = {Validity and Regularization of Classical HalfSpace
Equations},
Journal = {Journal of Statistical Physics},
Volume = {166},
Number = {2},
Pages = {398433},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1007/s1095501616884},
Doi = {10.1007/s1095501616884},
Key = {fds323661}
}
@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},
Year = {2016},
Month = {December},
url = {http://dx.doi.org/10.1103/PhysRevE.94.062104},
Doi = {10.1103/PhysRevE.94.062104},
Key = {fds321515}
}
@article{fds320186,
Author = {Yu, TQ and Lu, J and Abrams, CF and VandenEijnden,
E},
Title = {Multiscale implementation of infiniteswap replica exchange
molecular dynamics.},
Journal = {Proceedings of the National Academy of Sciences of
USA},
Volume = {113},
Number = {42},
Pages = {1174411749},
Year = {2016},
Month = {October},
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
MetropolisHastings 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 continuoustime 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 REMDSSA is combined
with the heterogeneous multiscale method to accelerate the
rate of the swaps and reach the socalled infiniteswap
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
Cterminal βhairpin 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
Hbonds.},
Key = {fds320186}
}
@article{fds320187,
Author = {Lu, J and Zhou, Z},
Title = {Improved sampling and validation of frozen Gaussian
approximation with surface hopping algorithm for
nonadiabatic dynamics.},
Journal = {Journal of Chemical Physics},
Volume = {145},
Number = {12},
Pages = {124109},
Year = {2016},
Month = {September},
url = {http://dx.doi.org/10.1063/1.4963107},
Abstract = {In the spirit of the fewest switches surface hopping, the
frozen Gaussian approximation with surface hopping (FGASH)
method samples a path integral representation of the
nonadiabatic dynamics in the semiclassical regime. An
improved sampling scheme is developed in this work for
FGASH based on birth and death branching processes. The
algorithm is validated for the standard test examples of
nonadiabatic dynamics.},
Doi = {10.1063/1.4963107},
Key = {fds320187}
}
@article{fds318293,
Author = {Li, X and Lu, J},
Title = {Traction boundary conditions for molecular static
simulations},
Journal = {Computer Methods in Applied Mechanics and
Engineering},
Volume = {308},
Pages = {310329},
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 = {15611578},
Year = {2016},
Month = {August},
url = {http://dx.doi.org/10.1007/s1142501603114},
Doi = {10.1007/s1142501603114},
Key = {fds318294}
}
@article{fds318295,
Author = {Lai, R and Lu, J},
Title = {Localized density matrix minimization and linearscaling
algorithms},
Journal = {Journal of Computational Physics},
Volume = {315},
Pages = {194210},
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 = {458466},
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 = {194210},
Year = {2016},
Month = {April},
ISSN = {00225096},
url = {http://hdl.handle.net/10161/11296 Duke open
access},
Abstract = {© 2016 Elsevier Ltd. All rights reserved.We develop a
variational optimization method for crystal analysis in
atomic resolution images, which uses information from a 2D
synchrosqueezed transform (SST) as input. The
synchrosqueezed transform is applied to extract initial
information from atomic crystal images: crystal defects,
rotations and the gradient of elastic deformation. The
deformation gradient estimate is then improved outside the
identified defect region via a variational approach, to
obtain more robust results agreeing better with the physical
constraints. The variational model is optimized by a
nonlinear projected conjugate gradient method. Both examples
of images from computer simulations and imaging experiments
are analyzed, with results demonstrating the effectiveness
of the proposed method.},
Doi = {10.1016/j.jmps.2016.01.002},
Key = {fds316401}
}
@article{fds318297,
Author = {Chen, J and Lu, J},
Title = {Analysis of the divideandconquer method for electronic
structure calculations},
Journal = {Mathematics of Computation},
Volume = {85},
Number = {302},
Pages = {29192938},
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 = {GaugeInvariant Frozen Gaussian Approximation Method for the
Schrödinger Equation with Periodic Potentials},
Journal = {SIAM Journal on Scientific Computing},
Volume = {38},
Number = {4},
Pages = {A2440A2463},
Year = {2016},
Month = {January},
url = {http://dx.doi.org/10.1137/15M1040384},
Doi = {10.1137/15M1040384},
Key = {fds320188}
}
%% 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 = {166180},
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 = {12},
Pages = {345362},
Year = {2016},
Month = {June},
url = {http://dx.doi.org/10.1007/s0020801513087},
Doi = {10.1007/s0020801513087},
Key = {fds318300}
}
%% Maggioni, Mauro
@article{fds320927,
Author = {Liao, W and Maggioni, M and Vigogna, S},
Title = {Learning adaptive multiscale approximations to data and
functions near lowdimensional sets},
Journal = {2016 IEEE Information Theory Workshop, ITW
2016},
Pages = {226230},
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 ddimensional 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 lowdimensional 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 = {388402},
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 = {HighDimensional 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 = {43164324},
Year = {2016},
Month = {September},
ISSN = {19391404},
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 lowsampled complexity for
intrinsically lowdimensional 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 stateoftheart 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 = {2016May},
Pages = {22992303},
Year = {2016},
Month = {May},
ISBN = {9781479999880},
ISSN = {15206149},
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 highlevel classiication output and the lowlevel
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
descriptorbased methods is problematic in the context of
drawings.},
Doi = {10.1109/ICASSP.2016.7472087},
Key = {fds317218}
}
@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},
Year = {2016},
Month = {March},
url = {http://dx.doi.org/10.1016/j.acha.2015.09.009},
Doi = {10.1016/j.acha.2015.09.009},
Key = {fds320928}
}
@article{fds314792,
Author = {Maggioni, M and Minsker, S and Strawn, N},
Title = {Multiscale dictionary learning: Nonasymptotic bounds and
robustness},
Journal = {Journal of machine learning research : JMLR},
Volume = {17},
Year = {2016},
Month = {January},
ISSN = {15324435},
url = {http://arxiv.org/abs/1401.5833},
Abstract = {© 2016 Mauro Maggioni, Stanislav Minsker, and Nate
Strawn.Highdimensional datasets are wellapproximated by
lowdimensional structures. Over the past decade, this
empirical observation motivated the investigation of
detection, measurement, and modeling techniques to exploit
these lowdimensional intrinsic structures, yielding
numerous implications for highdimensional statistics,
machine learning, and signal processing. Manifold learning
(where the lowdimensional structure is a manifold) and
dictionary learning (where the lowdimensional 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 recentlyintroduced Geometric
MultiResolution Analysis (GMRA) provides a robust,
computationally eficient, multiscale procedure for
simultaneously learning manifolds and dictionaries. In this
work, we prove nonasymptotic probabilistic bounds on the
approximation error of GMRA for a rich class of
datagenerating 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 lowdimensional
manifold, our results show that the approximation error of
the GMRA is completely independent of the ambient dimension.
Our work therefore establishes GMRA as a provably fast
algorithm for dictionary learning with approximation and
sparsity guarantees. We include several numerical
experiments confirming these theoretical results, and our
theoretical framework provides new tools for assessing the
behavior of manifold learning and dictionary learning
procedures on a large class of interesting
models.},
Key = {fds314792}
}
@inproceedings{MM:EEG,
Author = {E Causevic and R~R Coifman and R Isenhart and A Jacquin and E~R John and M Maggioni and L~S Prichep and F~J
Warner},
Title = {{QEEG}based classification with wavelet packets and
microstate features for triage applications in the
{ER}},
Year = {2005},
Key = {MM:EEG}
}
@misc{PathNIH2004,
Author = {GL Davis and Mauro Maggioni and FJ Warner and FB Geshwind and AC Coppi and RA DeVerse and RR Coifman},
Title = {Hyperspectral 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/TR1289},
Organization = {Dept. Comp. Sci., Yale University},
Institution = {Dept. Comp. Sci., Yale University},
Year = {2004},
Key = {CMTech}
}
%% Mattingly, Jonathan C.
@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
pathdependent variables for efficiently estimating averages
that were not previously tractable.},
Key = {fds318322}
}
%% Miller, Ezra
@article{fds320533,
Author = {Berenstein, A and Braverman, M and Miller, E and Retakh, V and Weitsman,
J},
Title = {Andrei Zelevinsky, 1953–2013},
Journal = {Advances in Mathematics},
Volume = {300},
Pages = {14},
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, 19532013},
Journal = {Advances in Mathematics},
Volume = {299},
Pages = {601604},
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 = {13191332},
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 = {The annals of applied statistics},
Volume = {10},
Number = {1},
Pages = {198218},
Year = {2016},
Month = {January},
url = {http://arxiv.org/abs/1411.6652v1},
Abstract = {New representations of treestructured 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{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 = {115115},
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 = {288328},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.3150/15BEJ744},
Doi = {10.3150/15BEJ744},
Key = {fds323270}
}
@article{fds322049,
Author = {SnyderMackler, 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 GenomeWide Sequencing and LowCoverage Pedigree
Analysis from Noninvasively Collected Samples.},
Journal = {Genetics},
Volume = {203},
Number = {2},
Pages = {699714},
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 genomewide capture of
endogenous DNA from noninvasively collected samples, coupled
with a novel computational approach to reconstruct pedigree
links from the resulting lowcoverage data. We validated
both methods using fecal samples from 62 wild baboons,
including 48 from an independently constructed extended
pedigree. We enriched fecalderived DNA samples up to
40fold for endogenous baboon DNA and reconstructed
nearperfect pedigree relationships even with extremely
lowcoverage 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.tunglab.org/protocolsandsoftware.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 = {147},
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 dene a structured
Bayesian prior that encourages both elementwise and
columnwise shrinkage and leads to desirable behavior on
highdimensional data. In particular, our model puts a
structured prior on the joint factor loading matrix,
regularizing at three levels, which enables elementwise
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 parameterexpanded
expectationmaximization 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 highdimensional data sets, comparing results
against a number of stateofTheArt 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 observationand factorspecific
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, PR and Georgiev, S and Mukherjee, S and Patterson, NJ and Price, AL},
Title = {Fast PrincipalComponent Analysis Reveals Convergent
Evolution of ADH1B in Europe and East Asia.},
Journal = {The American Journal of Human Genetics},
Volume = {98},
Number = {3},
Pages = {456472},
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 PCbased
test for natural selection, we replicate previously known
selected loci and identify three new genomewide 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 = {156167},
Booktitle = {Proceedings of the VLDB Endowment},
Year = {2016},
Month = {January},
Abstract = {We describe Cümülön, a system aimed at helping users
develop and deploy matrixbased data analysis programs in a
public cloud. A key feature of Cümülön is its endtoend
support for the socalled spot instancesmachines 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 costbased 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 = {797824},
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{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 = {23042348},
Year = {2016},
Month = {December},
ISSN = {00103640},
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 = {439476},
Year = {2016},
Month = {September},
ISSN = {21940401},
url = {http://arxiv.org/abs/1406.2186},
Doi = {10.1007/s4007201500684},
Key = {fds316661}
}
@article{fds318326,
Author = {Nolen, JH and Roquejoffre, JM and Ryzhik, L},
Title = {Refined long time asymptotics for FisherKPP
fronts},
Year = {2016},
Key = {fds318326}
}
@article{fds316662,
Author = {Nolen, J and Roquejoffre, JM and Ryzhik, L},
Title = {Convergence to a single wave in the FisherKPP
equation},
Year = {2016},
url = {http://arxiv.org/abs/1604.02994},
Key = {fds316662}
}
@article{fds320462,
Author = {Hamel, F and Nolen, J and Roquejoffre, JM 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 = {465505},
Year = {2016},
url = {http://arxiv.org/abs/1211.6173},
Doi = {10.4171/JEMS/595},
Key = {fds320462}
}
@article{fds316609,
Author = {Nolen, J and Mourrat, JC},
Title = {Scaling limit of the corrector in stochastic
homogenization},
Journal = {The annals of applied probability : an official journal of
the Institute of Mathematical Statistics},
Publisher = {Institute of Mathematical Statistics (IMS)},
Year = {2016},
ISSN = {10505164},
url = {http://arxiv.org/abs/1502.07440},
Key = {fds316609}
}
%% 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{fds322709,
Author = {Kumar, S and Calderbank, R and Pfister, HD},
Title = {Beyond double transitivity: Capacityachieving cyclic codes
on erasure channels},
Journal = {2016 IEEE Information Theory Workshop, ITW
2016},
Pages = {241245},
Year = {2016},
Month = {October},
ISBN = {9781509010905},
url = {http://dx.doi.org/10.1109/ITW.2016.7606832},
Abstract = {© 2016 IEEE.Recently, sequences of errorcorrecting codes
with doublytransitive permutation groups were shown to
achieve capacity on erasure channels under symbolwise
maximum a posteriori (MAP) decoding. From this, it follows
that ReedMuller and primitive narrowsense BCH codes
achieve capacity in the same setting. In this article, we
extend this result to a large family of cyclic codes by
considering codes whose permutation groups satisfy a
condition weaker than double transitivity. The article
combines two simple technical contributions. First, we show
that the transition width of a monotone boolean function is
O(1/log k), where k is the size of the smallest orbit
induced by its symmetry group. The proof is based on
Talagrand's lower bound on influences for monotone boolean
functions. Second, we consider the extrinsic information
transfer (EXIT) function of an Fqlinear cyclic code whose
blocklength N divides qt1 and is coprime with q1. 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 qary 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 higherorder modulation},
Journal = {International Symposium on Turbo Codes and Iterative
Information Processing, ISTC},
Volume = {2016October},
Pages = {236240},
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, halfproduct codes, staircase codes, and
certain braided codes) for which the asymptotic performance
under iterative boundeddistance 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 higherorder
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 spatiallycoupled codes via optimized
irregular termination},
Journal = {International Symposium on Turbo Codes and Iterative
Information Processing, ISTC},
Volume = {2016October},
Pages = {3135},
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 rateloss
problem for spatiallycoupled LDPC (SCLDPC) codes on the
binary erasure channel. Although SCLDPC codes have good
noise thresholds under beliefpropagation (BP) decoding,
they also suffer a rateloss 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 singleletter upper bound on the feedback capacity of
unifilar finitestate channels},
Volume = {2016August},
Pages = {310314},
Year = {2016},
Month = {August},
ISBN = {9781509018062},
url = {http://dx.doi.org/10.1109/ISIT.2016.7541311},
Abstract = {© 2016 IEEE.A singleletter upper bound on the feedback
capacity of a unifilar finitestate 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 Qcontexts 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 = {Nearoptimal finitelength scaling for polar codes over
large alphabets},
Volume = {2016August},
Pages = {215219},
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 qary polar codes based on q by q
ReedSolomon polarization kernels. For transmission over a
qary erasure channel, they also derived a closedform
recursion for the erasure probability of each effective
channel. In this paper, we use that expression to analyze
the finitelength scaling of these codes on qary erasure
channel with erasure probability ϵ ⋯ (0, 1). Our primary
result is that, for any γ > 0 and δ > 0, there is a q0
such that, for all q ≥ q0, the fraction of effective
channels with erasure rate at most Nγ is at least 1  ϵ 
O(N1/2+δ), where N = qn is the blocklength. Since the gap
to the channel capacity 1  ϵ cannot vanish faster than
O(N1/2), this establishes nearoptimal finitelength
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 replicasymmetric prediction for compressed sensing with
Gaussian matrices is exact},
Volume = {2016August},
Pages = {665669},
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 meansquare 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 wellknown problem that has remained open
for over a decade.},
Doi = {10.1109/ISIT.2016.7541382},
Key = {fds322714}
}
@article{fds319310,
Author = {Hager, C and Pfister, HD and Graell I Amat and A and Brannstrom,
F},
Title = {Deterministic and ensemblebased spatiallycoupled product
codes},
Volume = {2016August},
Pages = {21142118},
Year = {2016},
Month = {August},
ISBN = {9781509018062},
url = {http://dx.doi.org/10.1109/ISIT.2016.7541672},
Abstract = {© 2016 IEEE.Several authors have proposed spatiallycoupled
(or convolutionallike) 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
blockwise 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 spatiallycoupled 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 = {Reedmuller codes achieve capacity on the quantum erasure
channel},
Volume = {2016August},
Pages = {17501754},
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 errorcorrecting codes called stabilizer codes is
known to contain capacityachieving sequences for the
quantum erasure channel, but no efficient method is known to
construct these sequences. In this article, we explicitly
describe a capacityachieving code sequence for the quantum
erasure channel. In particular, we show that
CalderbankShorSteane (CSS) stabilizer codes constructed
from selforthogonal binary linear codes are
capacityachieving on the quantum erasure channel if the
binary linear codes are capacityachieving on the binary
erasure channel. Recently, ReedMuller codes were shown to
achieve capacity on classical erasure channels. Using this,
we show that CSS codes constructed from binary ReedMuller
codes achieve the capacity of the quantum erasure channel.
The capacityachieving 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 bitMAP and blockMAP decoding thresholds of
reedmuller codes on BMS channels},
Volume = {2016August},
Pages = {17551759},
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
capacityachieving is a longstanding 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
doublytransitive permutation groups, achieves capacity on
the memoryless erasure channel under bitMAP decoding. Thus,
a natural question is what happens under blockMAP decoding.
In [1], [2], by exploiting further symmetries of the code,
the bitMAP 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
bitMAP threshold to blockMAP 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 bitMAP error probability decays
as Nδ, for some δ > 0. Then, the blockMAP 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 capacityachieving 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.,
nonensemblebased) codes in the waterfall and error floor
region. The analysis directly applies to several FEC classes
proposed for highspeed 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 = {ReedMuller codes achieve capacity on erasure
channels},
Journal = {Proceedings of the Annual ACM Symposium on Theory of
Computing},
Volume = {1921June2016},
Pages = {658669},
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 nearoptimal performance. An important consequence
of this result is that a sequence of ReedMuller 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 affineinvariant codes and, thus, to all
extended primitive narrowsense BCH codes. This is used to
resolve, in the affirmative, the existence question for
capacityachieving 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 = {Spatiallycoupled codes for writeonce memories},
Journal = {2015 53rd Annual Allerton Conference on Communication,
Control, and Computing, Allerton 2015},
Pages = {125131},
Year = {2016},
Month = {April},
ISBN = {9781509018239},
url = {http://dx.doi.org/10.1109/ALLERTON.2015.7446994},
Abstract = {© 2015 IEEE.The focus of this article is on lowcomplexity
capacityachieving coding schemes for writeonce memory
(WOM) systems. The construction is based on
spatiallycoupled 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 GelfandPinsker 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
2write WOM system with lowcomplexity messagepassing
encoding and decoding algorithms.},
Doi = {10.1109/ALLERTON.2015.7446994},
Key = {fds322716}
}
@article{fds322717,
Author = {Lian, M and Pfister, HD},
Title = {Beliefpropagation reconstruction for compressed sensing:
Quantization vs. Gaussian approximation},
Journal = {2015 53rd Annual Allerton Conference on Communication,
Control, and Computing, Allerton 2015},
Pages = {11061113},
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
beliefpropagation (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 = {ReedMuller codes achieve capacity on erasure
channels.},
Journal = {STOC},
Pages = {658669},
Publisher = {ACM},
Editor = {Wichs, D and Mansour, Y},
Year = {2016},
ISBN = {9781450341325},
url = {http://dx.doi.org/10.1145/2897518.2897584},
Doi = {10.1145/2897518.2897584},
Key = {fds323532}
}
%% Pierce, Lillian B.
@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 zerodensity 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,
powersaving 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 multidimensional short mixed character
sums},
Journal = {Journal of Number Theory},
Volume = {163},
Pages = {172210},
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 stoppingtime 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 onedimensional 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 vectorvalued variant of the CarlesonHunt
theorem.},
Key = {fds320661}
}
%% Randles, Amanda
@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 = {2016October},
Pages = {34293432},
Year = {2016},
Month = {October},
ISBN = {9781457702204},
url = {http://dx.doi.org/10.1109/EMBC.2016.7591465},
Abstract = {© 2016 IEEE.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
patientspecific 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 coarctationinduced 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{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 = {374383},
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 colocalized
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
concentrationdependent 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 coimplicated in many of the brain's
functions. In this paper, we develop a novel voltammetric
method for simultaneous realtime 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 = {22552273},
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 = {121132},
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 = {494494},
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{fds320189,
Author = {Robles, C},
Title = {Classification of horizontal s},
Journal = {Compositio Mathematica},
Volume = {152},
Number = {05},
Pages = {918954},
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 = {725758},
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 BorelSerre
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 BorelSerre
compactification of a Hermitian locally symmetric space as a
tool to study perverse sheaves on the BailyBorel
compactification, a projective algebraic variety. We sketch
why the decomposition theorem holds for the natural map
between the reductive BorelSerre and the BailyBorel
compactifications. We demonstrate how to calculate
extensions of simple perverse sheaves on the reductive
BorelSerre compactification and illustrate with the example
of Sp(4,R).},
Key = {fds320662}
}
@article{fds320773,
Author = {Saper, L},
Title = {ℒmodules and microsupport},
Journal = {Annals of Mathematics},
Year = {2017},
Key = {fds320773}
}
%% Sapiro, Guillermo
@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 Followup to Improve Quality of Screening for
Autism.},
Journal = {The Journal of Pediatrics},
Year = {2017},
Month = {February},
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 Followup
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 χ(2) 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 tabletbased digital version
of the Modified Checklist for Autism in Toddlers  Revised
with Followup 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{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 fieldofview
retinal optical coherence tomography volumes.},
Journal = {Biomedical Optics Express},
Volume = {7},
Number = {12},
Pages = {48274846},
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 fieldofview (FOV) retinal optical
coherence tomography (OCT) volumes. A popular strategy for
reducing motion artifacts is to capture two orthogonally
oriented volumetric scans. However, due to larger volume
sizes, longer acquisition times, and corresponding larger
motion artifacts, the registration of wide FOV scans remains
a challenging problem. In particular, gaps in data
acquisition due to eye motion, such as saccades, can be
significant and their modeling becomes critical for
successful registration. In this article, we develop a
complete computational pipeline for the automatic motion
correction and accurate registration of wide FOV
orthogonally scanned OCT images of the human retina. The
proposed framework utilizes the retinal boundary
segmentation as a guide for registration and requires only a
minimal transformation of the acquired data to produce a
successful registration. It includes saccade detection and
correction, a custom version of the optical flow algorithm
for dense lateral registration and a linear optimization
approach for axial registration. Utilizing a wide FOV swept
source OCT system, we acquired retinal volumes of 12
subjects and we provide qualitative and quantitative
experimental results to validate the stateoftheart
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 MultiImage Alignment},
Journal = {IEEE Transactions on Signal Processing},
Volume = {64},
Number = {21},
Pages = {57075722},
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 = {DissimilarityBased Sparse Subset Selection.},
Journal = {IEEE Transactions on Pattern Analysis and Machine
Intelligence},
Volume = {38},
Number = {11},
Pages = {21822197},
Year = {2016},
Month = {November},
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 rowsparsity regularized trace
minimization problem. Since the proposed formulation is, in
general, NPhard, we consider a convex relaxation. The
solution of our optimization finds representatives and the
assignment of each element of the target set to each
representative, hence, obtaining a clustering. We analyze
the solution of our proposed optimization as a function of
the regularization parameter. We show that when the two sets
jointly partition into multiple groups, our algorithm finds
representatives from all groups and reveals clustering of
the sets. In addition, we show that the proposed framework
can effectively deal with outliers. Our algorithm works with
arbitrary dissimilarities, which can be asymmetric or
violate the triangle inequality. To efficiently implement
our algorithm, we consider an Alternating Direction Method
of Multipliers (ADMM) framework, which results in quadratic
complexity in the problem size. We show that the ADMM
implementation allows to parallelize the algorithm, hence
further reducing the computational time. Finally, by
experiments on realworld datasets, we show that our
proposed algorithm improves the state of the art on the two
problems of scene categorization using representative images
and timeseries modeling and segmentation using
representative models.},
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 = {2016September},
Year = {2016},
Month = {September},
ISBN = {9781509021031},
url = {http://dx.doi.org/10.1109/SAM.2016.7569685},
Abstract = {© 2016 IEEE.The interest in problems related to graph
inference has been increasing significantly during the last
decade. However, the vast majority of the problems addressed
are either static, or systems where changes in one node are
immediately reflected in other nodes. In this paper we
address the problem of mobility graph estimation, when the
available dataset has an asynchronous and timevariant
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 = {34443457},
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 shortgraph fourier transform via personalized pagerank
vectors},
Journal = {IEEE International Conference on Acoustics Speech and Signal
Processing},
Volume = {2016May},
Pages = {48064810},
Year = {2016},
Month = {May},
ISBN = {9781479999880},
url = {http://dx.doi.org/10.1109/ICASSP.2016.7472590},
Abstract = {© 2016 IEEE.The shorttime 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 realworld 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 = {22692283},
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 = {18441853},
Year = {2016},
Month = {April},
url = {http://dx.doi.org/10.1109/TSP.2015.2505661},
Doi = {10.1109/TSP.2015.2505661},
Key = {fds322678}
}
@article{fds322679,
Author = {Huang, J and Qiu, Q and Calderbank, R and Sapiro,
G},
Title = {Geometryaware deep transform},
Journal = {Proceedings / IEEE International Conference on Computer
Vision. IEEE International Conference on Computer
Vision},
Volume = {1118December2015},
Pages = {41394147},
Year = {2016},
Month = {February},
ISBN = {9781467383912},
url = {http://dx.doi.org/10.1109/ICCV.2015.471},
Abstract = {© 2015 IEEE.Many recent efforts have been devoted to
designing sophisticated deep learning structures, obtaining
revolutionary results on benchmark datasets. The success of
these deep learning methods mostly relies on an enormous
volume of labeled training samples to learn a huge number of
parameters in a network, therefore, understanding the
generalization ability of a learned deep network cannot be
overlooked, especially when restricted to a small training
set, which is the case for many applications. In this paper,
we propose a novel deep learning objective formulation that
unifies both the classification and metric learning
criteria. We then introduce a geometryaware deep transform
to enable a nonlinear discriminative and robust feature
transform, which shows competitive performance on small
training sets for both synthetic and realworld data. We
further support the proposed framework with a formal
(K)robustness analysis.},
Doi = {10.1109/ICCV.2015.471},
Key = {fds322679}
}
@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 parentreport interview for assessing
psychopathology, including anxiety disorders, in 2 to 5 year
old children. In this paper, we apply machinelearning tools
to already collected PAPA data from two large community
studies to identify subsets of PAPA items that could be
developed into an efficient, reliable, and valid screening
tool to assess a young child's risk for an anxiety disorder.
Using machine learning, we were able to decrease by an order
of magnitude the number of items needed to identify a child
who is at risk for an anxiety disorder with an accuracy of
over 96% for both generalized anxiety disorder (GAD) and
separation anxiety disorder (SAD). Additionally, rather than
considering GAD or SAD as discrete/binary entities, we
present a continuous risk score representing the child's
risk of meeting criteria for GAD or SAD. Identification of a
short questionset 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 = {Synthesisbased lowcost gaze analysis},
Journal = {Communications in Computer and Information
Science},
Volume = {618},
Pages = {95100},
Year = {2016},
Month = {January},
ISBN = {9783319405414},
url = {http://dx.doi.org/10.1007/9783319405421_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
lowcost 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 lowcost, scalable and real time analysis of
human gaze using this RealSense camera. We exploit the
direct measurement of eye surface geometry captured by the
RGBD camera, and perform gaze estimation through novel
synthesisbased 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 RGBD eye image, we first repeat the same
synthesis process. For each synthesized image, we estimate
the gaze from our gaze regression model, and factorout the
associated camera/head motion. In this way, we obtain
multiple gaze estimations for each RGBD eye image, and the
consensus is adopted. We show that this synthesisbased
training and testing significantly improves the precision in
gaze estimation, opening the door to true lowcost
solutions.},
Doi = {10.1007/9783319405421_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 = {6073},
Year = {2016},
Month = {January},
url = {http://dx.doi.org/10.1109/tpami.2015.2424894},
Abstract = {Graph matchingaligning a pair of graphs to minimize their
edge disagreementshas received widespread attention from
both theoretical and applied communities over the past
several decades, including combinatorics, computer vision,
and connectomics. Its attention can be partially attributed
to its computational difficulty. Although many heuristics
have previously been proposed in the literature to
approximately solve graph matching, very few have any
theoretical support for their performance. A common
technique is to relax the discrete problem to a continuous
problem, therefore enabling practitioners to bring
gradientdescenttype 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 = {119129},
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 ...},
Key = {fds323466}
}
%% Stern, Mark A.
@article{fds317670,
Author = {Sergey A. Cherkis and Andres LarrainHubach and Mark
Stern},
Title = {Instantons on multiTaubNUT Spaces I: Asymptotic Form and
Index Theorem},
Journal = {arXiv:1608.00018},
Year = {2016},
Month = {August},
Abstract = {We study finite action antiselfdual YangMills connections
on the multiTaubNUT 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 multiTaubNUT spaces and exploring it in
detail.},
Key = {fds317670}
}
%% TurnageButterbaugh, Caroline
@book{fds320234,
Author = {Mackall, B and Miller, SJ and Rapti, C and TurnageButterbaugh, C and Winsor, K},
Title = {Some Results in the Theory of Lowlying Zeros},
Booktitle = {Families of Automorphic Forms and the Trace
Formula},
Publisher = {Springer},
Year = {2016},
Month = {September},
ISBN = {3319414240},
Abstract = {Featuring the work of twentythree internationallyrecognized
experts, this volume explores the trace formula, spectra of
locally symmetric spaces, padic families, and other recent
techniques from harmonic analysis and representation
...},
Key = {fds320234}
}
@article{fds318339,
Author = {Bui, HM and Heap, WP and TurnageButterbaugh, CL},
Title = {GAPS BETWEEN ZEROS OF DEDEKIND ZETAFUNCTIONS OF QUADRATIC
NUMBER FIELDS. II},
Journal = {Quarterly Journal of Mathematics},
Volume = {67},
Number = {3},
Pages = {467482},
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 TurnageButterbaugh,
C},
Title = {From Quantum Systems to LFunctions: Pair Correlation
Statistics and Beyond},
Pages = {123171},
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 TurnageButterbaugh, 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{fds320428,
Author = {Komineas, S and Shipman, SP and Venakides, S},
Title = {Lossless polariton solitons},
Journal = {Physica D: Nonlinear Phenomena},
Volume = {316},
Pages = {4356},
Year = {2016},
Month = {February},
url = {http://dx.doi.org/10.1016/j.physd.2015.10.018},
Abstract = {© 2015 Elsevier B.V. All rights reserved.Photons and
excitons in a semiconductor microcavity interact to form
excitonpolariton condensates. These are governed by a
nonlinear quantummechanical system involving exciton and
photon wavefunctions. We calculate all nontraveling
harmonic soliton solutions for the onedimensional lossless
system. There are two frequency bands of bright solitons
when the interexciton 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 farfield 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}
}
%% Witelski, Thomas P.
@article{fds320453,
Author = {Ji, H and Witelski, TP},
Title = {Finitetime thin film rupture driven by modified evaporative
loss},
Journal = {Physica D: Nonlinear Phenomena},
Volume = {342},
Pages = {115},
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
nonsmooth system},
Journal = {International Journal of NonLinear Mechanics},
Volume = {81},
Pages = {5564},
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 = {3659},
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 = {126132},
Year = {2016},
Month = {May},
ISSN = {09277757},
url = {http://dx.doi.org/10.1016/j.colsurfa.2016.02.026},
Doi = {10.1016/j.colsurfa.2016.02.026},
Key = {fds317250}
}
%% Yang, Haizhao
@article{fds311604,
Author = {Yang, H},
Title = {Statistical analysis of synchrosqueezed transforms},
Journal = {Applied and Computational Harmonic Analysis},
Publisher = {Elsevier},
Year = {2017},
Month = {January},
ISSN = {1096603X},
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 = {194210},
Publisher = {Elsevier},
Editor = {Bhattacharya, K},
Year = {2016},
Month = {April},
ISSN = {00225096},
url = {http://hdl.handle.net/10161/11296 Duke open
access},
Abstract = {© 2016 Elsevier Ltd. All rights reserved.We develop a
variational optimization method for crystal analysis in
atomic resolution images, which uses information from a 2D
synchrosqueezed transform (SST) as input. The
synchrosqueezed transform is applied to extract initial
information from atomic crystal images: crystal defects,
rotations and the gradient of elastic deformation. The
deformation gradient estimate is then improved outside the
identified defect region via a variational approach, to
obtain more robust results agreeing better with the physical
constraints. The variational model is optimized by a
nonlinear projected conjugate gradient method. Both examples
of images from computer simulations and imaging experiments
are analyzed, with results demonstrating the effectiveness
of the proposed method.},
Doi = {10.1016/j.jmps.2016.01.002},
Key = {fds303562}
}
%% Zhou, Zhennan
@article{fds323230,
Author = {Liu, JG and Ma, Z and Zhou, Z},
Title = {Explicit and Implicit TVD Schemes for Conservation Laws with
Caputo Derivatives},
Journal = {Journal of Scientific Computing},
Pages = {123},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1007/s1091501703564},
Abstract = {© 2017 Springer Science+Business Media New YorkIn this
paper, we investigate numerical approximations of the scalar
conservation law with the Caputo derivative, which
introduces the memory effect. We construct the first order
and the second order explicit upwind schemes for such
equations, which are shown to be conditionally (Formula
presented.) contracting and TVD. However, the Caputo
derivative leads to the modified CFLtype 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/s1091501703564},
Key = {fds323230}
}
@article{fds318345,
Author = {Ma, Z and Zhang, Y and Zhou, Z},
Title = {An improved semiLagrangian time splitting spectral method
for the semiclassical Schrödinger equation with vector
potentials using NUFFT},
Journal = {Applied Numerical Mathematics},
Volume = {111},
Pages = {144159},
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 timedependent selfconsistent
field system: Analysis and computation},
Journal = {Kinetic and Related Models},
Volume = {10},
Number = {1},
Pages = {263298},
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, JG and Zhou, Z},
Title = {On a SchrödingerLandauLifshitz System: Variational
Structure and Numerical Methods},
Journal = {Multiscale Modeling & Simulation},
Volume = {14},
Number = {4},
Pages = {14631487},
Year = {2016},
Month = {January},
url = {http://dx.doi.org/10.1137/16M106947X},
Doi = {10.1137/16M106947X},
Key = {fds322468}
}
