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Mathematics Faculty: Publications since January 2016

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

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


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

@article{fds323823,
   Author = {Ying, R and Pan, J and Fox, K and Agarwal, PK},
   Title = {A simple efficient approximation algorithm for dynamic time
             warping},
   Journal = {GIS: Proceedings of the ACM International Symposium on
             Advances in Geographic Information Systems},
   Year = {2016},
   Month = {October},
   ISBN = {9781450345897},
   url = {http://dx.doi.org/10.1145/2996913.2996954},
   Abstract = {© 2016 ACM.Dynamic time warping (DTW) is a widely used
             curve similarity measure. We present a simple and efficient
             (1 + ∈)- approximation algorithm for DTW between a pair of
             point sequences, say, P and Q, each of which is sampled from
             a curve. We prove that the running time of the algorithm is
             O( κ2/∈ n log σ) for a pair of κ-packed curves with a
             total of n points, assuming that the spreads of P and Q are
             bounded by σ. The spread of a point set is the ratio of the
             maximum to the minimum pairwise distance, and a curve is
             called κ-packed if the length of its intersection with any
             disk of radius r is at most κr. Although an algorithm with
             similar asymptotic time complexity was presented in [1], our
             algorithm is considerably simpler and more efficient in
             practice. We have implemented our algorithm. Our experiments
             on both synthetic and real-world data sets show that it is
             an order of magnitude faster than the standard exact DP
             algorithm on point sequences of length 5; 000 or more while
             keeping the approximation error within 5-10%. We demonstrate
             the eficacy of our algorithm by using it in two applications
             computing the k most similar trajectories to a query
             trajectory, and running the iterative closest point method
             for a pair of trajectories. We show that we can achieve 8-12
             times speedup using our algorithm as a subroutine in these
             applications, without compromising much in
             accuracy.},
   Doi = {10.1145/2996913.2996954},
   Key = {fds323823}
}

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

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

@article{fds318111,
   Author = {Agarwal, PK and Kumar, N and Sintos, S and Suri, S},
   Title = {Range-max queries on uncertain data},
   Journal = {Proceedings of the ACM SIGACT-SIGMOD-SIGART Symposium on
             Principles of Database Systems},
   Volume = {26-June-01-July-2016},
   Pages = {465-476},
   Year = {2016},
   Month = {June},
   ISBN = {9781450341912},
   url = {http://dx.doi.org/10.1145/2902251.2902281},
   Abstract = {© 2016 ACM.Let P be a set of n uncertain points in 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
             d-dimensional query rectangle ρ, the expected maximum value
             or the most-likely maximum value in ρ can be computed
             quickly. The specific contributions of our paper include the
             following: (i) The first index of sub-quadratic size to
             achieve a sub-linear query time in any dimension d ≥ 1. It
             also provides a trade-off between query time and size of the
             index. (ii) A conditional lower bound for the most-likely
             range-max queries, based on the conjectured hardness of the
             set-intersection problem, which suggests that in the worst
             case the product (query time)2 x (index size) is
             Ω(n2/polylog(n)). (iii) A linear-size index for estimating
             the expected range-max 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 top-k values of the
             range-max.},
   Doi = {10.1145/2902251.2902281},
   Key = {fds318111}
}

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

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

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

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

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


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

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


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


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

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

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

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


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


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


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


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

@article{fds324089,
   Author = {Cornelis, B and Yang, H and Goodfriend, A and Ocon, N and Lu, J and Daubechies, I},
   Title = {Removal of Canvas Patterns in Digital Acquisitions of
             Paintings},
   Journal = {IEEE Transactions on Image Processing},
   Volume = {26},
   Number = {1},
   Pages = {160-171},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1109/TIP.2016.2621413},
   Abstract = {© 2016 IEEE.We address the removal of canvas artifacts from
             high-resolution digital photographs and X-ray images of
             paintings on canvas. Both imaging modalities are common
             investigative tools in art history and art conservation.
             Canvas artifacts manifest themselves very differently
             according to the acquisition modality; they can hamper the
             visual reading of the painting by art experts, for instance,
             in preparing a restoration campaign. Computer-aided canvas
             removal is desirable for restorers when the painting on
             canvas they are preparing to restore has acquired over the
             years a much more salient texture. We propose a new
             algorithm that combines a cartoon-texture decomposition
             method with adaptive multiscale thresholding in the
             frequency domain to isolate and suppress the canvas
             components. To illustrate the strength of the proposed
             method, we provide various examples, for acquisitions in
             both imaging modalities, for paintings with different types
             of canvas and from different periods. The proposed algorithm
             outperforms previous methods proposed for visual photographs
             such as morphological component analysis and Wiener
             filtering and it also works for the digital removal of
             canvas artifacts in X-ray images.},
   Doi = {10.1109/TIP.2016.2621413},
   Key = {fds324089}
}

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

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

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

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

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

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

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

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


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

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


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

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

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

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

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

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

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

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

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

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

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

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

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


%% 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 = {82-107},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1016/j.aam.2017.01.002},
   Doi = {10.1016/j.aam.2017.01.002},
   Key = {fds323833}
}

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

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

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

@article{fds243415,
   Author = {Durrett, R and Foo, J and Leder, K},
   Title = {Spatial Moran models, II: cancer initiation in spatially
             structured tissue},
   Journal = {Journal of Mathematical Biology},
   Volume = {72},
   Number = {5},
   Pages = {1369-1400},
   Year = {2016},
   Month = {April},
   ISSN = {0303-6812},
   url = {http://dx.doi.org/10.1007/s00285-015-0912-1},
   Doi = {10.1007/s00285-015-0912-1},
   Key = {fds243415}
}


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

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

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

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


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


%% Hahn, Heekyoung   
@article{fds320417,
   Author = {Hahn, H},
   Title = {On classical groups detected by the triple tensor products
             and the Littlewood-Richardson semigroup},
   Journal = {Reserch in Number Theory},
   Volume = {2},
   Number = {1},
   Pages = {1-12},
   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 = {5061-5069},
   Year = {2016},
   Month = {May},
   url = {http://dx.doi.org/10.1090/proc/13134},
   Doi = {10.1090/proc/13134},
   Key = {fds320109}
}

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

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


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

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

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

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

@article{fds320425,
   Author = {Hain, R},
   Title = {Deligne-Beilinson Cohomology of Affine Groups},
   Year = {2016},
   url = {http://arxiv.org/abs/1507.03144},
   Abstract = {The goal of this paper is to develop the theory of
             Deligne-Beilinson cohomology of affine groups with a mixed
             Hodge structure. The motivation comes from Hodge theory and
             the study of motives, where such groups appear. Several of
             Francis Brown's period computations (arXiv:1407.5167) are
             interpreted as elements of the DB cohomology of the relative
             unipotent completion of $SL_2(Z)$ and their cup products.
             The results in this paper are used in arXiv:1403.6443 where
             they are used to prove that Pollack's quadratic relations
             are motivic.},
   Key = {fds320425}
}


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

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

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


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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

@article{fds320670,
   Author = {W. Cong and J.-G. Liu},
   Title = {Uniform $L^\infty$ boundedness for a degenerate
             parabolic-parabolic Keller-Segel model},
   Journal = {Discrete and Continuous Dynamical Systems - Series
             B},
   Volume = {22},
   Pages = {307-338},
   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 = {35-60},
   Year = {2017},
   Key = {fds320659}
}

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

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

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

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

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

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

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

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

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

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

@article{fds320652,
   Author = {J. Chen and J.-G. Liu and Z. Zhou},
   Title = {On a Schrodinger-Landau-Lifshitz system: Variational struc-
             ture and numerical methods},
   Journal = {Multiscale Modeling and Simulation},
   Volume = {14},
   Pages = {1463-1487},
   Year = {2016},
   Key = {fds320652}
}

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

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

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

@article{fds320738,
   Author = {H. Huang and J.-G. Liu},
   Title = {Error estimate of a random particle blob method for the
             Keller-Segel 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{fds300225,
   Author = {J.-G. Liu and J. Wang},
   Title = {Refined hyper-contractivity and uniqueness for the
             Keller-Segel equations},
   Journal = {Applied Math Letter},
   Volume = {52},
   Pages = {212-219},
   Year = {2016},
   Key = {fds300225}
}


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

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

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

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

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

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

@article{fds325467,
   Author = {Cornelis, B and Yang, H and Goodfriend, A and Ocon, N and Lu, J and Daubechies, I},
   Title = {Removal of Canvas Patterns in Digital Acquisitions of
             Paintings},
   Journal = {IEEE Transactions on Image Processing},
   Volume = {26},
   Number = {1},
   Pages = {160-171},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1109/TIP.2016.2621413},
   Doi = {10.1109/TIP.2016.2621413},
   Key = {fds325467}
}

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

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

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

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

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

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

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

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

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

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

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


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

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


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

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

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

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

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

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

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

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


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

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

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


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

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

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

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


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


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

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

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

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

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


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


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

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

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

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

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

@article{fds316609,
   Author = {Nolen, J and Mourrat, J-C},
   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 = {1050-5164},
   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{fds324463,
   Author = {Sabag, O and Permuter, HH and Pfister, HD},
   Title = {A Single-Letter Upper Bound on the Feedback Capacity of
             Unifilar Finite-State Channels},
   Journal = {IEEE Transactions on Information Theory},
   Volume = {63},
   Number = {3},
   Pages = {1392-1409},
   Year = {2017},
   Month = {March},
   url = {http://dx.doi.org/10.1109/TIT.2016.2636851},
   Abstract = {© 1963-2012 IEEE.An upper bound on the feedback capacity of
             unifilar finite-state channels (FSCs) is derived. A new
             technique, called the Q-context mapping, is based on a
             construction of a directed graph that is used for a
             sequential quantization of the receiver's output sequences
             to a finite set of contexts. For any choice of Q-graph, the
             feedback capacity is bounded by a single-letter expression,
             Cfb ≤ sup I (X, S; Y|Q), where the supremum is over p(x|s,
             q) and the distribution of (S, Q) is their stationary
             distribution. It is shown that the bound is tight for all
             unifilar FSCs, where feedback capacity is known: channels
             where the state is a function of the outputs, the trapdoor
             channel, Ising channels, the no-consecutive-ones
             input-constrained erasure channel, and the memoryless
             channel. Its efficiency is also demonstrated by deriving a
             new capacity result for the dicode erasure channel; the
             upper bound is obtained directly from the above-mentioned
             expression and its tightness is concluded with a general
             sufficient condition on the optimality of the upper bound.
             This sufficient condition is based on a fixed point
             principle of the BCJR equation and, indeed, formulated as a
             simple lower bound on feedback capacity of unifilar FSCs for
             arbitrary Q-graphs. This upper bound indicates that a
             single-letter expression might exist for the capacity of
             finite-state channels with or without feedback based on a
             construction of auxiliary random variable with specified
             structure, such as the Q-graph, and not with i.i.d
             distribution. The upper bound also serves as a non-trivial
             bound on the capacity of channels without feedback, a
             problem that is still open.},
   Doi = {10.1109/TIT.2016.2636851},
   Key = {fds324463}
}

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

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

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

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

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

@article{fds322713,
   Author = {Pfister, HD and Urbanke, R},
   Title = {Near-optimal finite-length scaling for polar codes over
             large alphabets},
   Volume = {2016-August},
   Pages = {215-219},
   Year = {2016},
   Month = {August},
   ISBN = {9781509018062},
   url = {http://dx.doi.org/10.1109/ISIT.2016.7541292},
   Abstract = {© 2016 IEEE.For any prime power q, Mori and Tanaka
             introduced a family of q-ary polar codes based on q by q
             Reed-Solomon polarization kernels. For transmission over a
             q-ary erasure channel, they also derived a closed-form
             recursion for the erasure probability of each effective
             channel. In this paper, we use that expression to analyze
             the finite-length scaling of these codes on q-ary erasure
             channel with erasure probability ϵ ⋯ (0, 1). Our primary
             result is that, for any γ > 0 and δ > 0, there is a q0
             such that, for all q ≥ q0, the fraction of effective
             channels with erasure rate at most N-γ is at least 1 - ϵ -
             O(N-1/2+δ), where N = qn is the blocklength. Since the gap
             to the channel capacity 1 - ϵ cannot vanish faster than
             O(N-1/2), this establishes near-optimal finite-length
             scaling for this family of codes. Our approach can be seen
             as an extension of a similar analysis for binary polar codes
             by Mondelli, Hassani, and Urbanke.},
   Doi = {10.1109/ISIT.2016.7541292},
   Key = {fds322713}
}

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

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

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

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

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

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

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

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

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


%% Pierce, Lillian B.   
@article{fds320660,
   Author = {Ellenberg, J and Pierce, LB and Wood, MM},
   Title = {On $\ell$-torsion in class groups of number
             fields},
   Journal = {arXiv:1606.06103 [math]},
   Year = {2016},
   Month = {June},
   Abstract = {For each integer $\ell \geq 1$, we prove an unconditional
             upper bound on the size of the $\ell$-torsion subgroup of
             the class group, which holds for all but a zero-density set
             of field extensions of $\mathbb{Q}$ of degree $d$, for any
             fixed $d \in \{2,3,4,5\}$ (with the additional restriction
             in the case $d=4$ that the field be non-$D_4$). For
             sufficiently large $\ell$ (specified explicitly), these
             results are as strong as a previously known bound that is
             conditional on GRH. As part of our argument, we develop a
             probabilistic "Chebyshev sieve," and give uniform,
             power-saving error terms for the asymptotics of quartic
             (non-$D_4$) and quintic fields with chosen splitting types
             at a finite set of primes.},
   Key = {fds320660}
}

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

@article{fds320661,
   Author = {Guo, S and Pierce, LB and Roos, J and Yung, P},
   Title = {Polynomial Carleson operators along monomial curves in the
             plane},
   Journal = {arXiv:1605.05812 [math]},
   Year = {2016},
   Month = {May},
   Abstract = {We prove $L^p$ bounds for partial polynomial Carleson
             operators along monomial curves $(t,t^m)$ in the plane
             $\mathbb{R}^2$ with a phase polynomial consisting of a
             single monomial. These operators are "partial" in the sense
             that we consider linearizing stopping-time functions that
             depend on only one of the two ambient variables. A
             motivation for studying these partial operators is the
             curious feature that, despite their apparent limitations,
             for certain combinations of curve and phase, $L^2$ bounds
             for partial operators along curves imply the full strength
             of the $L^2$ bound for a one-dimensional Carleson operator,
             and for a quadratic Carleson operator. Our methods, which
             can at present only treat certain combinations of curves and
             phases, in some cases adapt a $TT^*$ method to treat phases
             involving fractional monomials, and in other cases use a
             known vector-valued variant of the Carleson-Hunt
             theorem.},
   Key = {fds320661}
}


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


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


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

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

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

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

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

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

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

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


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

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


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

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


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

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

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

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

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

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

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

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

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

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

@article{fds322679,
   Author = {Huang, J and Qiu, Q and Calderbank, R and Sapiro,
             G},
   Title = {Geometry-aware deep transform},
   Journal = {Proceedings / IEEE International Conference on Computer
             Vision. IEEE International Conference on Computer
             Vision},
   Volume = {11-18-December-2015},
   Pages = {4139-4147},
   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 geometry-aware deep transform
             to enable a non-linear discriminative and robust feature
             transform, which shows competitive performance on small
             training sets for both synthetic and real-world 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 parent-report interview for assessing
             psychopathology, including anxiety disorders, in 2 to 5 year
             old children. In this paper, we apply machine-learning tools
             to already collected PAPA data from two large community
             studies to identify sub-sets of PAPA items that could be
             developed into an efficient, reliable, and valid screening
             tool to assess a young child's risk for an anxiety disorder.
             Using machine learning, we were able to decrease by an order
             of magnitude the number of items needed to identify a child
             who is at risk for an anxiety disorder with an accuracy of
             over 96% for both generalized anxiety disorder (GAD) and
             separation anxiety disorder (SAD). Additionally, rather than
             considering GAD or SAD as discrete/binary entities, we
             present a continuous risk score representing the child's
             risk of meeting criteria for GAD or SAD. Identification of a
             short question-set that assesses risk for an anxiety
             disorder could be a first step toward development and
             validation of a relatively short screening tool feasible for
             use in pediatric clinics and daycare/preschool
             settings.},
   Doi = {10.1371/journal.pone.0165524},
   Key = {fds322213}
}

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

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


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


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


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

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

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

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


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


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

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

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

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

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


%% Yang, Haizhao   
@article{fds311606,
   Author = {Cornelis, B and Yang, H and Goodfriend, A and Ocon, N and Lu, J and Daubechies, I},
   Title = {Removal of Canvas Patterns in Digital Acquisitions of
             Paintings},
   Journal = {IEEE Transactions on Image Processing},
   Volume = {26},
   Number = {1},
   Pages = {160-171},
   Publisher = {Institute of Electrical and Electronics Engineers
             (IEEE)},
   Year = {2017},
   Month = {January},
   ISSN = {1941-0042},
   url = {http://hdl.handle.net/10161/11650 Duke open
             access},
   Abstract = {© 2016 IEEE.We address the removal of canvas artifacts from
             high-resolution digital photographs and X-ray images of
             paintings on canvas. Both imaging modalities are common
             investigative tools in art history and art conservation.
             Canvas artifacts manifest themselves very differently
             according to the acquisition modality; they can hamper the
             visual reading of the painting by art experts, for instance,
             in preparing a restoration campaign. Computer-aided canvas
             removal is desirable for restorers when the painting on
             canvas they are preparing to restore has acquired over the
             years a much more salient texture. We propose a new
             algorithm that combines a cartoon-texture decomposition
             method with adaptive multiscale thresholding in the
             frequency domain to isolate and suppress the canvas
             components. To illustrate the strength of the proposed
             method, we provide various examples, for acquisitions in
             both imaging modalities, for paintings with different types
             of canvas and from different periods. The proposed algorithm
             outperforms previous methods proposed for visual photographs
             such as morphological component analysis and Wiener
             filtering and it also works for the digital removal of
             canvas artifacts in X-ray images.},
   Doi = {10.1109/TIP.2016.2621413},
   Key = {fds311606}
}

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

@article{fds315394,
   Author = {Li, Y and Yang, H},
   Title = {Interpolative Butterfly Factorization},
   Year = {2016},
   Month = {May},
   url = {http://arxiv.org/abs/1605.03616},
   Key = {fds315394}
}

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

@article{fds312767,
   Author = {Lu, J and Yang, H},
   Title = {Preconditioning orbital minimization method for planewave
             discretization},
   Year = {2016},
   Month = {March},
   url = {http://hdl.handle.net/10161/11833 Duke open
             access},
   Abstract = {We present an efficient preconditioner for the orbital
             minimization method when the Hamiltonian is discretized
             using planewaves (i.e., pseudospectral method). This novel
             preconditioner is based on an approximate Fermi operator
             projection by pole expansion, combined with the sparsifying
             preconditioner to efficiently evaluate the pole expansion
             for a wide range of Hamiltonian operators. Numerical results
             validate the performance of the new preconditioner for the
             orbital minimization method, in particular, the iteration
             number is reduced to $O(1)$ and often only a few iterations
             are enough for convergence.},
   Key = {fds312767}
}

@article{fds311605,
   Author = {Li, Y and Yang, H and Ying, L},
   Title = {Multidimensional Butterfly Factorization},
   Journal = {Applied and Computational Harmonic Analysis},
   Publisher = {Elsevier},
   Year = {2016},
   Month = {February},
   ISSN = {1096-603X},
   url = {http://hdl.handle.net/10161/11651 Duke open
             access},
   Key = {fds311605}
}


%% 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 = {1-23},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1007/s10915-017-0356-4},
   Abstract = {© 2017 Springer Science+Business Media New YorkIn this
             paper, we investigate numerical approximations of the scalar
             conservation law with the Caputo derivative, which
             introduces the memory effect. We construct the first order
             and the second order explicit upwind schemes for such
             equations, which are shown to be conditionally (Formula
             presented.) contracting and TVD. However, the Caputo
             derivative leads to the modified CFL-type stability
             condition, (Formula presented.), where (Formula presented.)
             is the fractional exponent in the derivative. When (Formula
             presented.) is small, such strong constraint makes the
             numerical implementation extremely impractical. We have then
             proposed the implicit upwind scheme to overcome this issue,
             which is proved to be unconditionally (Formula presented.)
             contracting and TVD. Various numerical tests are presented
             to validate the properties of the methods and provide more
             numerical evidence in interpreting the memory effect in
             conservation laws.},
   Doi = {10.1007/s10915-017-0356-4},
   Key = {fds323230}
}

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

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

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

 

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