Publications

Herreros, D; Lederman, Roy R; Krieger, J; Jiménez-Moreno, A; Martínez, M; Myška, D; Strelak, D; Filipovic, J; Bahar, I; Carazo, J M; Sanchez, C O S

Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials Journal Article

IUCrJ, 8 (6), 2021, ISSN: 2052-2525, (Number: 6 Publisher: International Union of Crystallography).

Abstract | Links | BibTeX | Tags: cryo-EM, heterogeneity, Zernike

Calero, David Herreros; Lederman, Roy R; Krieger, James; Myška, David; Strelak, David; Filipovic, Jiri; Bahar, Ivet; Carazo, Jose Maria; Sorzano, Carlos Oscar

Continuous heterogeneity analysis of CryoEM images through Zernike polynomials and spherical harmonics Journal Article

Microscopy and Microanalysis, 27 (S1), pp. 1680–1682, 2021, ISSN: 1431-9276, 1435-8115, (Publisher: Cambridge University Press).

Abstract | Links | BibTeX | Tags: cryo-EM, heterogeneity, Zernike

Brofos, James; Lederman, Roy R

Evaluating the Implicit Midpoint Integrator for Riemannian Hamiltonian Monte Carlo Inproceedings

International Conference on Machine Learning, pp. 1072–1081, PMLR, 2021, (ISSN: 2640-3498).

Links | BibTeX | Tags: HMC, Manifolds, MCMC, Numerical Analysis

Brofos, James A; Brubaker, Marcus A; Lederman, Roy R

Manifold Density Estimation via Generalized Dequantization Technical Report

2021, (arXiv: 2102.07143).

Abstract | Links | BibTeX | Tags: Algorithms, Computer Science - Machine Learning, Density estimation, Manifolds, Statistics - Machine Learning

Fan, Zhou; Lederman, Roy R; Sun, Yi; Wang, Tianhao; Xu, Sheng

Maximum likelihood for high-noise group orbit estimation and single-particle cryo-EM Technical Report

2021, (arXiv: 2107.01305).

Abstract | Links | BibTeX | Tags: Computer Science - Information Theory, Mathematics - Optimization and Control, Mathematics - Statistics Theory

Brofos, James A; Lederman, Roy R

Magnetic Manifold Hamiltonian Monte Carlo Technical Report

2020, (arXiv: 2010.07753).

Abstract | Links | BibTeX | Tags: Algorithms, Computer Science - Machine Learning, HMC, Manifolds, MCMC, Statistics - Machine Learning

Katz, Ori; Lederman, Roy R; Talmon, Ronen

Spectral Flow on the Manifold of SPD Matrices for Multimodal Data Processing Technical Report

2020, (arXiv: 2009.08062).

Abstract | Links | BibTeX | Tags: Common variable, Computer Science - Machine Learning, Manifold Learning, Multi-view, multimodal, SPD Matrices, Statistics - Machine Learning

Lederman, Roy R; Andén, Joakim; Singer, Amit

Hyper-molecules: on the representation and recovery of dynamical structures for applications in flexible macro-molecules in cryo-EM Journal Article

Inverse Problems, 36 (4), pp. 044005, 2020, ISSN: 0266-5611, 1361-6420.

Links | BibTeX | Tags: cryo-EM, heterogeneity, HyperMolecules, MCMC, Variational inference

Lederman, Roy R; Singer, Amit

A representation theory perspective on simultaneous alignment and classification Journal Article

Applied and Computational Harmonic Analysis, 49 (3), pp. 1001–1024, 2020, ISSN: 1063-5203.

Abstract | Links | BibTeX | Tags: Algorithms, Alignment, Classification, cryo-EM, Graph-cut, heterogeneity, Heterogeneous multireference alignment, Representation Theory, Rotation group, SDP, Synchronization

Bandeira, Afonso S; Chen, Yutong; Lederman, Roy R; Singer, Amit

Non-unique games over compact groups and orientation estimation in cryo-EM Journal Article

Inverse Problems, 36 (6), pp. 064002, 2020, ISSN: 0266-5611, 1361-6420.

Links | BibTeX | Tags: Algorithms, cryo-EM, Non-unique games, Representation Theory

Brofos, James A; Lederman, Roy R

Non-Canonical Hamiltonian Monte Carlo Technical Report

2020, (arXiv: 2008.08191).

Abstract | Links | BibTeX | Tags: Algorithms, Computer Science - Machine Learning, HMC, MCMC, Statistics - Machine Learning

Brofos, James A; Shu, Rui; Lederman, Roy R

A Bias-Variance Decomposition for Bayesian Deep Learning Inproceedings

pp. 14, 2019.

Abstract | BibTeX | Tags: Bayesian Deep Learning, Bayesian Inference, Deep Learning

Lederman, Roy R; Steinerberger, S

Extreme Values of the Fiedler Vector on Trees Technical Report

2019, (arXiv: 1912.08327).

Abstract | Links | BibTeX | Tags: Computer Science - Discrete Mathematics, Graph Theory, Mathematics - Combinatorics, Mathematics - Spectral Theory

Shnitzer, Tal; Lederman, Roy R; Liu, Gi-Ren; Talmon, Ronen; Wu, Hau-Tieng

Diffusion operators for multimodal data analysis Incollection

Handbook of Numerical Analysis, 20 , pp. 1–39, Elsevier, 2019, ISBN: 978-0-444-64140-3.

Links | BibTeX | Tags: Alternating Diffusion, BookChapter, Common variable, diffusion maps, Manifold Learning, Multi-view, multimodal, Multimodal data, Sensor fusion, Shape differences

Lederman, Roy R; Talmon, Ronen

Learning the geometry of common latent variables using alternating-diffusion Journal Article

Applied and Computational Harmonic Analysis, 44 (3), pp. 509–536, 2018, ISSN: 1063-5203.

Abstract | Links | BibTeX | Tags: Algorithms, Alternating Diffusion, Alternating-diffusion, Common variable, diffusion maps, Diffusion-maps, Multi-view, multimodal, Multimodal analysis

Aldroubi, Akram; Huang, Longxiu; Krishtal, Ilya; Ledeczi, Akos; Lederman, Roy R; Volgyesi, Peter

Dynamical sampling with additive random noise Technical Report

(arXiv:1807.10866 [math]), 2018, (arXiv: 1807.10866).

Abstract | Links | BibTeX | Tags: Mathematics - Numerical Analysis

Shaham, Uri; Lederman, Roy R

Learning by coincidence: Siamese networks and common variable learning Journal Article

Pattern Recognition, 74 , pp. 52–63, 2018, ISSN: 00313203.

Links | BibTeX | Tags: Common variable, Deep Learning, Multi-view, multimodal, Siamese networks

Boumal, N; Bendory, T; Lederman, Roy R; Singer, A

Heterogeneous multireference alignment: A single pass approach Inproceedings

2018 52nd Annual Conference on Information Sciences and Systems (CISS), pp. 1–6, 2018.

Abstract | Links | BibTeX | Tags: bispectrum, concave programming, cryo-EM, cyclic shifts, Discrete Fourier transforms, estimation theory, expectation-maximization, Gaussian mixture models, heterogeneity, heterogeneous MRA, Heterogeneous multireference alignment, Multireference alignment, Noise measurement, non-convex optimization, nonconvex optimization problem, Optimization, Reliability, signal estimation, signal processing, Signal resolution, Signal to noise ratio, single pass approach, Standards

Lederman, Roy R

Numerical Algorithms for the Computation of Generalized Prolate Spheroidal Functions Technical Report

2017.

Abstract | Links | BibTeX | Tags: Algorithms, cryo-EM, Fourier Transform, Numerical Analysis, Prolate, Slepian, Software

Lederman, Roy R; Steinerberger, Stefan

Lower Bounds for Truncated Fourier and Laplace Transforms Journal Article

Integral Equations and Operator Theory, 87 (4), pp. 529–543, 2017, ISSN: 0378-620X, 1420-8989.

Links | BibTeX | Tags: Fourier Transform, Laplace Transform

Lederman, Roy R; Singer, Amit

Continuously heterogeneous hyper-objects in cryo-EM and 3-Đ movies of many temporal dimensions Technical Report

(arXiv:1704.02899 [cs]), 2017, (arXiv: 1704.02899).

Abstract | Links | BibTeX | Tags: Computer Science - Computer Vision and Pattern Recognition, cryo-EM, heterogeneity, HyperMolecules

Stanton, Kelly P; Jin, Jiaqi; Lederman, Roy R; Weissman, Sherman M; Kluger, Yuval

Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling Journal Article

Nucleic Acids Research, 45 (21), pp. e173–e173, 2017, ISSN: 0305-1048, (Publisher: Oxford Academic).

Abstract | Links | BibTeX | Tags: DNA sequencing, Sequencing, Software

Aldroubi, Akram; Huang, L; Krishtal, I; Lederman, Roy R

Dynamical sampling with random noise Inproceedings

2017 International Conference on Sampling Theory and Applications (SampTA), pp. 409–412, 2017.

Abstract | Links | BibTeX | Tags: Dynamical Sampling, evolution operator, signal reconstruction, signal recovery, signal sampling

Lederman, Roy R; Singer, Amit

A Representation Theory Perspective on Simultaneous Alignment and Classification Technical Report

(arXiv:1607.03464 [cs, math]), 2016, (arXiv: 1607.03464).

Abstract | Links | BibTeX | Tags: Algorithms, Computer Science - Computer Vision and Pattern Recognition, cryo-EM, Mathematics - Optimization and Control, Representation Theory

Lederman, Roy R; Steinerberger, Stefan

Stability Estimates for Truncated Fourier and Laplace Transforms Technical Report

(arXiv:1605.03866), 2016.

Abstract | Links | BibTeX | Tags: Laplace Transform

Lederman, Roy R; Rokhlin, V

On the Analytical and Numerical Properties of the Truncated Laplace Transform. Part II Journal Article

SIAM Journal on Numerical Analysis, 54 (2), pp. 665–687, 2016, ISSN: 0036-1429, 1095-7170.

Links | BibTeX | Tags: Algorithms, Laplace Transform, Numerical Analysis

Shaham, Uri; Lederman, Roy R

Common Variable Learning and Invariant Representation Learning using Siamese Neural Networks Technical Report

2015.

Abstract | Links | BibTeX | Tags: Common variable, Deep Learning, Multi-view

Lederman, Roy R; Talmon, Ronen; Wu, Hau-tieng; Lo, Yu-Lun; Coifman, Ronald R

Alternating diffusion for common manifold learning with application to sleep stage assessment Inproceedings

2015 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), pp. 5758–5762, 2015, (ISSN: 2379-190X).

Abstract | Links | BibTeX | Tags: Alternating Diffusion, Common variable, diffusion maps, Kernel, learning (artificial intelligence), Manifolds, multimodal, multimodal respiratory signals, multimodal signal processing, Physiology, Sensitivity, Sensor phenomena and characterization, signal processing, sleep, sleep stage assessment, standard manifold learning method, time series

Lederman, Roy R; Rokhlin, V

On the Analytical and Numerical Properties of the Truncated Laplace Transform I. Journal Article

SIAM Journal on Numerical Analysis, 53 (3), pp. 1214–1235, 2015, ISSN: 0036-1429, 1095-7170.

Links | BibTeX | Tags: Algorithms, Laplace Transform, Numerical Analysis

Lederman, Roy R; Talmon, Ronen

Common Manifold Learning Using Alternating-Diffusion Technical Report

Yale CS (YALEU/DCS/TR-1497), 2014.

Links | BibTeX | Tags: AD, Algorithms, Alternating Diffusion, Manifold Learning

Lederman, Roy R

On the Analytical and Numerical Properties of the Truncated Laplace Transform PhD Thesis

Yale University, 2014, (YALEU/DCS/TR-1490).

BibTeX | Tags: Algorithms, Laplace Transform, Numerical Analysis

Lederman, Roy R

A random-permutations-based approach to fast read alignment Journal Article

BMC Bioinformatics, 14 (5), pp. S8, 2013, ISSN: 1471-2105.

Abstract | Links | BibTeX | Tags: Algorithm, DNA sequencing, Fast algorithms, Neighbor Search, Random Permutation, Reference Genome, Reference Library, Search Problem

Lederman, Roy R

A Note about the Resolution-Length Characteristics of DNA Technical Report

Yale CS (YALEU/DCS/TR-1473), 2013.

BibTeX | Tags: Sequence Alignment, Sequencing

Lederman, Roy R

A permutations-based algorithm for fast alignment of long paired-end reads Technical Report

Yale CS (YALEU/DCS/TR-1474), 2013.

BibTeX | Tags: Algorithms, DNA sequencing, Fast algorithms, Randomized algorithms, Sequencing

Lederman, Roy R

Building approximate overlap graphs for DNA assembly using random-permutations-based search Technical Report

Yale CS (YALEU/DCS/TR-1470), 2012.

BibTeX | Tags: DNA sequencing, Sequencing

Lederman, Roy R

Homopolymer Length Filters Technical Report

Yale CS (YALEU/DCS/TR-1465), 2012.

BibTeX | Tags: Algorithms, DNA sequencing, Sequence Alignment, Sequencing