Quantitative Biology

Authors and titles for December 2020

[201] arXiv:2012.02151 (cross-list from cs.LG) [pdf, other]

Title: Dr-COVID: Graph Neural Networks for SARS-CoV-2 Drug Repurposing

Siddhant Doshi, Sundeep Prabhakar Chepuri

Subjects: Machine Learning (cs.LG); Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)

[202] arXiv:2012.02296 (cross-list from cs.LG) [pdf, other]

Title: Generative Capacity of Probabilistic Protein Sequence Models

Francisco McGee, Quentin Novinger, Ronald M. Levy, Vincenzo Carnevale, Allan Haldane

Subjects: Machine Learning (cs.LG); Data Analysis, Statistics and Probability (physics.data-an); Quantitative Methods (q-bio.QM)

[203] arXiv:2012.02500 (cross-list from stat.AP) [pdf, other]

Title: A latent variable approach to account for correlated inputs in global sensitivity analysis with cases from pharmacological systems modelling

Nicola Melillo, Adam S. Darwich

Subjects: Applications (stat.AP); Quantitative Methods (q-bio.QM)

[204] arXiv:2012.02513 (cross-list from math.CO) [pdf, other]

Title: Complexity of fixed point counting problems in Boolean Networks

Florian Bridoux, Amélia Durbec, Kévin Perrot, Adrien Richard

Comments: 47 pages

Subjects: Combinatorics (math.CO); Computational Complexity (cs.CC); Discrete Mathematics (cs.DM); Molecular Networks (q-bio.MN)

[205] arXiv:2012.02552 (cross-list from physics.soc-ph) [pdf, other]

Title: Epidemic oscillations induced by social network control: the discontinuous case

Fabio Caccioli, Daniele De Martino

Comments: Comments are welcome

Subjects: Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

[206] arXiv:2012.02577 (cross-list from cs.CV) [pdf, other]

Title: Critical Evaluation of Deep Neural Networks for Wrist Fracture Detection

Abu Mohammed Raisuddin, Elias Vaattovaara, Mika Nevalainen, Marko Nikki, Elina Järvenpää, Kaisa Makkonen, Pekka Pinola, Tuula Palsio, Arttu Niemensivu, Osmo Tervonen, Aleksei Tiulpin

Subjects: Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Image and Video Processing (eess.IV); Quantitative Methods (q-bio.QM)

[207] arXiv:2012.02918 (cross-list from physics.bio-ph) [pdf, other]

Title: Precision of protein thermometry

Michael Vennettilli, Soutick Saha, Ushasi Roy, Andrew Mugler

Comments: 22 pages, 7 figures

Journal-ref: Phys. Rev. Lett. 127, 098102 (2021)

Subjects: Biological Physics (physics.bio-ph); Molecular Networks (q-bio.MN)

[208] arXiv:2012.03129 (cross-list from cs.CV) [pdf, other]

Title: Simultaneous Corn and Soybean Yield Prediction from Remote Sensing Data Using Deep Transfer Learning

Saeed Khaki, Hieu Pham, Lizhi Wang

Comments: 14 pages, 8 figures, 7 tables

Journal-ref: Scientific Reports, 11(1), 1-14 (2021)

Subjects: Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Image and Video Processing (eess.IV); Quantitative Methods (q-bio.QM); Applications (stat.AP)

[209] arXiv:2012.03227 (cross-list from math.PR) [pdf, other]

Title: An algebraic approach to product-form stationary distributions for some reaction networks

Beatriz Pascual-Escudero, Linard Hoessly

Comments: Accepted for publication in SIAM Journal on Applied Dynamical Systems

Subjects: Probability (math.PR); Algebraic Geometry (math.AG); Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)

[210] arXiv:2012.03280 (cross-list from physics.soc-ph) [pdf, other]

Title: Building surrogate temporal network data from observed backbones

Charley Presigny, Petter Holme, Alain Barrat

Journal-ref: Phys. Rev. E 103, 052304 (2021)

Subjects: Physics and Society (physics.soc-ph); Quantitative Methods (q-bio.QM)

[211] arXiv:2012.03303 (cross-list from physics.bio-ph) [pdf, other]

Title: A Tridomain Model for Potassium Clearance in Optic Nerve of Necturus

Yi Zhu, Shixin Xu, Robert S. Eisenberg, Huaxiong Huang

Comments: 35 pages, 13 figures

Subjects: Biological Physics (physics.bio-ph); Analysis of PDEs (math.AP); Neurons and Cognition (q-bio.NC)

[212] arXiv:2012.03378 (cross-list from cs.AI) [pdf, other]

Title: Brain Co-Processors: Using AI to Restore and Augment Brain Function

Rajesh P. N. Rao

Comments: arXiv admin note: text overlap with arXiv:1811.11876

Subjects: Artificial Intelligence (cs.AI); Neural and Evolutionary Computing (cs.NE); Adaptation and Self-Organizing Systems (nlin.AO); Neurons and Cognition (q-bio.NC)

[213] arXiv:2012.03460 (cross-list from cs.LG) [pdf, other]

Title: Reprogramming Language Models for Molecular Representation Learning

Ria Vinod, Pin-Yu Chen, Payel Das

Comments: 6 pages, 5 tables, accepted at Learning Meaningful Representations of Life @ NeurIPS 2020, Women in Machine Learning @ NeurIPS 2020. 8 pages, LaTeX; typos corrected, references added

Subjects: Machine Learning (cs.LG); Molecular Networks (q-bio.MN)

[214] arXiv:2012.03849 (cross-list from cs.CV) [pdf, other]

Title: Correct block-design experiments mitigate temporal correlation bias in EEG classification

Simone Palazzo, Concetto Spampinato, Joseph Schmidt, Isaak Kavasidis, Daniela Giordano, Mubarak Shah

Subjects: Computer Vision and Pattern Recognition (cs.CV); Neurons and Cognition (q-bio.NC)

[215] arXiv:2012.03993 (cross-list from physics.comp-ph) [pdf, other]

Title: Poroelasticity as a Model of Soft Tissue Structure: Hydraulic Permeability Inference for Magnetic Resonance Elastography in Silico

Damian R Sowinski, Matthew DJ McGarry, Elijah Van Houten, Scott Gordon-Wylie, John Weaver, Keith D Paulsen

Comments: 14 pages, 12 figures

Subjects: Computational Physics (physics.comp-ph); Biological Physics (physics.bio-ph); Medical Physics (physics.med-ph); Quantitative Methods (q-bio.QM)

[216] arXiv:2012.04035 (cross-list from cs.LG) [pdf, other]

Title: ATOM3D: Tasks On Molecules in Three Dimensions

Raphael J.L. Townshend, Martin Vögele, Patricia Suriana, Alexander Derry, Alexander Powers, Yianni Laloudakis, Sidhika Balachandar, Bowen Jing, Brandon Anderson, Stephan Eismann, Risi Kondor, Russ B. Altman, Ron O. Dror

Comments: NeurIPS 2021 Datasets and Benchmarks Track

Subjects: Machine Learning (cs.LG); Biological Physics (physics.bio-ph); Computational Physics (physics.comp-ph); Biomolecules (q-bio.BM)

[217] arXiv:2012.04171 (cross-list from cs.LG) [pdf, other]

Title: Sparse encoding for more-interpretable feature-selecting representations in probabilistic matrix factorization

Joshua C. Chang, Patrick Fletcher, Jungmin Han, Ted L. Chang, Shashaank Vattikuti, Bart Desmet, Ayah Zirikly, Carson C. Chow

Comments: Fixed typo in Eq 2

Subjects: Machine Learning (cs.LG); Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)

[218] arXiv:2012.04214 (cross-list from physics.bio-ph) [pdf, other]

Title: Noise-induced acceleration of single molecule kinesin-1

Takayuki Ariga, Keito Tateishi, Michio Tomishige, Daisuke Mizuno

Comments: 6 pages for the main text and 18 pages for the Supplemental Material

Subjects: Biological Physics (physics.bio-ph); Biomolecules (q-bio.BM)

[219] arXiv:2012.04728 (cross-list from cs.LG) [pdf, other]

Title: Neural Mechanics: Symmetry and Broken Conservation Laws in Deep Learning Dynamics

Daniel Kunin, Javier Sagastuy-Brena, Surya Ganguli, Daniel L.K. Yamins, Hidenori Tanaka

Comments: 30 pages, 17 figures, ICLR 2021

Subjects: Machine Learning (cs.LG); Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Neurons and Cognition (q-bio.NC); Machine Learning (stat.ML)

[220] arXiv:2012.04747 (cross-list from cs.LG) [pdf, other]

Title: STELAR: Spatio-temporal Tensor Factorization with Latent Epidemiological Regularization

Nikos Kargas, Cheng Qian, Nicholas D. Sidiropoulos, Cao Xiao, Lucas M. Glass, Jimeng Sun

Comments: AAAI 2021

Subjects: Machine Learning (cs.LG); Populations and Evolution (q-bio.PE)

[221] arXiv:2012.04819 (cross-list from math.OC) [pdf, other]

Title: Stability analysis and optimal control of a fractional HIV-AIDS epidemic model with memory and general incidence rate

Adnane Boukhouima, El Mehdi Lotfi, Marouane Mahrouf, Silverio Rosa, Delfim F. M. Torres, Noura Yousfi

Comments: This is a preprint of a paper whose final and definite form is with 'The European Physical Journal Plus', E-ISSN 2190-5444. Submitted: 02-Feb-2020 / Revised: 20-Oct-2020 and 24-Nov-2020 / Accepted: 08-Dec-2020

Journal-ref: Eur. Phys. J. Plus 136 (2021), Art. 103, 20 pp

Subjects: Optimization and Control (math.OC); Populations and Evolution (q-bio.PE)

[222] arXiv:2012.04860 (cross-list from physics.bio-ph) [pdf, other]

Title: A Linear Reciprocal Relationship Between Robustness and Plasticity in Homeostatic Biological Networks

Tetsuhiro S. Hatakeyama, Kunihiko Kaneko

Comments: 5 pages, 4 figures

Subjects: Biological Physics (physics.bio-ph); Adaptation and Self-Organizing Systems (nlin.AO); Subcellular Processes (q-bio.SC)

[223] arXiv:2012.05194 (cross-list from physics.soc-ph) [pdf, other]

Title: A simplified estimate of the Effective Reproduction Number $R_t$ using its relation with the doubling time and application to Italian COVID-19 data

Gianluca Bonifazi, Luca Lista, Dario Menasce, Mauro Mezzetto, Daniele Pedrini, Roberto Spighi, Antonio Zoccoli

Journal-ref: The European Physical Journal Plus, 136(4), 1-14, April 11th 2021

Subjects: Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

[224] arXiv:2012.05285 (cross-list from math.ST) [pdf, other]

Title: Testing for genetic interactions in complex disease with distance correlation

Fernando Castro-Prado, Javier Costas, Dominic Edelmann, Wenceslao González-Manteiga, David R. Penas

Comments: 15 pages with 3 figures, plus a 10-page supplement. This document supersedes a much older version of the manuscript, in which we used other theoretical and computational approaches. Simulations, real data analyses and the writing of the paper have also been improved

Subjects: Statistics Theory (math.ST); Genomics (q-bio.GN); Applications (stat.AP)

[225] arXiv:2012.05301 (cross-list from stat.ME) [pdf, other]

Title: What Were They Thinking? Pharmacologic priors implicit in a choice of 3+3 dose-escalation design

David C. Norris

Comments: 5 pages, 3 figures, 1 table, 13 references with added hyperlinks. Version 2 restores to the exhibit on page 2 a DCG clause which v1 had mistakenly cropped; additionally, footnote 6 is expanded and a few minor typographical or grammatical improvements are made

Subjects: Methodology (stat.ME); Quantitative Methods (q-bio.QM); Applications (stat.AP)

[226] arXiv:2012.05377 (cross-list from physics.flu-dyn) [pdf, other]

Title: Pump efficacy in a fluid-structure interaction model of a chain of contracting lymphangions

Hallie Elich, Aaron Barrett, Varun Shankar, Aaron L. Fogelson

Comments: Main text: 30 pages, 14 figures, 3 tables. Accepted to Biomechanics and Modeling in Mechanobiology. Supplementary Information: 16 pages, 5 figures, 1 table

Subjects: Fluid Dynamics (physics.flu-dyn); Dynamical Systems (math.DS); Tissues and Organs (q-bio.TO)

[227] arXiv:2012.05549 (cross-list from cs.LG) [pdf, other]

Title: Categorical Perception: A Groundwork for Deep Learning

Laurent Bonnasse-Gahot, Jean-Pierre Nadal

Journal-ref: Neural Computation 2021

Subjects: Machine Learning (cs.LG); Information Theory (cs.IT); Neurons and Cognition (q-bio.NC)

[228] arXiv:2012.05965 (cross-list from cs.GL) [pdf, other]

Title: Analog Computation and Representation

Corey J. Maley

Comments: To be published in British Journal for the Philosophy of Science

Subjects: General Literature (cs.GL); Neurons and Cognition (q-bio.NC)

[229] arXiv:2012.06033 (cross-list from math.DS) [pdf, other]

Title: Autocatalytic systems and recombination: a reaction network perspective

Gheorghe Craciun, Abhishek Deshpande, Badal Joshi, Polly Y. Yu

Comments: 24 pages, 6 figures

Subjects: Dynamical Systems (math.DS); Molecular Networks (q-bio.MN)

[230] arXiv:2012.06075 (cross-list from eess.SP) [pdf, other]

Title: An algorithm for onset detection of linguistic segments in continuous electroencephalogram signals

Tonatiuh Hernández-Del-Toro, Carlos A. Reyes-García

Journal-ref: Proceedings of the 11th Models and Analysis of Vocal Emissions for Biomedical Applications (MAVEBA), pages 249-252, Florence, Italy, 2019. Firenze University Press

Subjects: Signal Processing (eess.SP); Computation and Language (cs.CL); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)

[231] arXiv:2012.06104 (cross-list from cs.LG) [pdf, other]

Title: A Review of Hidden Markov Models and Recurrent Neural Networks for Event Detection and Localization in Biomedical Signals

Yassin Khalifa, Danilo Mandic, Ervin Sejdić

Journal-ref: Yassin Khalifa, Danilo Mandic, and Ervin Sejdi\'c. "A review of Hidden Markov models and Recurrent Neural Networks for event detection and localization in biomedical signals." Information Fusion, Volume 69, 52-72 (2021)

Subjects: Machine Learning (cs.LG); Signal Processing (eess.SP); Quantitative Methods (q-bio.QM)

[232] arXiv:2012.06127 (cross-list from physics.bio-ph) [pdf, other]

Title: Searching for sequence features that control DNA flexibility

Yaojun Zhang, Aakash Basu, Taekjip Ha, William Bialek

Subjects: Biological Physics (physics.bio-ph); Biomolecules (q-bio.BM); Quantitative Methods (q-bio.QM)

[233] arXiv:2012.06240 (cross-list from cs.IT) [pdf, other]

Title: Soft Compression for Lossless Image Coding

Gangtao Xin, Pingyi Fan

Subjects: Information Theory (cs.IT); Artificial Intelligence (cs.AI); Image and Video Processing (eess.IV); Quantitative Methods (q-bio.QM)

[234] arXiv:2012.06383 (cross-list from physics.bio-ph) [pdf, other]

Title: Power-law multi-wave model for COVID-19 propagation in countries with nonuniform population density

P.S. Grinchuk, S.P. Fisenko

Comments: The forecast was published for the first time on June 01, 2020 (this https URL)

Subjects: Biological Physics (physics.bio-ph); Populations and Evolution (q-bio.PE)

[235] arXiv:2012.06391 (cross-list from cs.LG) [pdf, other]

Title: Learning physically consistent mathematical models from data using group sparsity

Suryanarayana Maddu, Bevan L. Cheeseman, Christian L. Müller, Ivo F. Sbalzarini

Journal-ref: Phys. Rev. E 103, 042310 (2021)

Subjects: Machine Learning (cs.LG); Quantitative Methods (q-bio.QM); Applications (stat.AP)

[236] arXiv:2012.06564 (cross-list from stat.ML) [pdf, other]

Title: Glucose values prediction five years ahead with a new framework of missing responses in reproducing kernel Hilbert spaces, and the use of continuous glucose monitoring technology

Marcos Matabuena, Paulo Félix, Carlos Meijide-Garcia, Francisco Gude

Subjects: Machine Learning (stat.ML); Machine Learning (cs.LG); Quantitative Methods (q-bio.QM); Applications (stat.AP); Methodology (stat.ME)

[237] arXiv:2012.06720 (cross-list from math.OC) [pdf, other]

Title: Low-Order Model of Biological Neural Networks

Huachuan Wang, James Ting-Ho Lo

Subjects: Optimization and Control (math.OC); Neural and Evolutionary Computing (cs.NE); Neurons and Cognition (q-bio.NC)

[238] arXiv:2012.07354 (cross-list from cs.DS) [pdf, other]

Title: Reflections on kernelizing and computing unrooted agreement forests

Rim van Wersch, Steven Kelk, Simone Linz, Georgios Stamoulis

Comments: Updated version. New figures and analysis. Accepted for journal publication

Subjects: Data Structures and Algorithms (cs.DS); Populations and Evolution (q-bio.PE)

[239] arXiv:2012.07397 (cross-list from stat.ML) [pdf, other]

Title: Molecular graph generation with Graph Neural Networks

Pietro Bongini, Monica Bianchini, Franco Scarselli

Comments: 20 pages, 4 figures (2 figures are composed of double images, for a total of 6 images)

Journal-ref: Neurocomputing 2021

Subjects: Machine Learning (stat.ML); Machine Learning (cs.LG); Biomolecules (q-bio.BM)

[240] arXiv:2012.07596 (cross-list from cs.LG) [pdf, other]

Title: Biomechanical modelling of brain atrophy through deep learning

Mariana da Silva, Kara Garcia, Carole H. Sudre, Cher Bass, M. Jorge Cardoso, Emma Robinson

Comments: Submitted to Medical Imaging Meets NeurIPS 2020

Subjects: Machine Learning (cs.LG); Computer Vision and Pattern Recognition (cs.CV); Image and Video Processing (eess.IV); Tissues and Organs (q-bio.TO); Machine Learning (stat.ML)

[241] arXiv:2012.07601 (cross-list from physics.soc-ph) [pdf, other]

Title: A case for location based contact tracing

Atul Pokharel (1), Robert Soulé (2), Avi Silberschatz (2) ((1) New York University, (2) Yale University)

Comments: 14 pages, 7 figures, submitted to Healthcare Management Science

Subjects: Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE); Applications (stat.AP)

[242] arXiv:2012.07640 (cross-list from cs.LG) [pdf, other]

Title: A Comparative Analysis of the Ensemble Methods for Drug Design

Rifkat Davronova, Fatima Adilovab

Comments: 11 pages, 2 figures, 7 tables

Subjects: Machine Learning (cs.LG); Information Theory (cs.IT); Quantitative Methods (q-bio.QM)

[243] arXiv:2012.07669 (cross-list from econ.GN) [pdf, other]

Title: The structure of multiplex networks predicts play in economic games and real-world cooperation

Curtis Atkisson, Monique Borgerhoff Mulder

Subjects: General Economics (econ.GN); Populations and Evolution (q-bio.PE)

[244] arXiv:2012.07770 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Construction of stochastic hybrid path integrals using "quantum-mechanical'' operators

Paul C. Bressloff

Comments: 32 pages, 2 figures

Subjects: Statistical Mechanics (cond-mat.stat-mech); Quantitative Methods (q-bio.QM)

[245] arXiv:2012.08655 (cross-list from eess.IV) [pdf, other]

Title: CUDA-Optimized real-time rendering of a Foveated Visual System

Elian Malkin, Arturo Deza, Tomaso Poggio

Comments: 16 pages, 13 figures, presented at the Shared Visual Representations in Human and Machine Intelligence Workshop (SVRHM NeurIPS 2020)

Subjects: Image and Video Processing (eess.IV); Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)

[246] arXiv:2012.08925 (cross-list from cs.SI) [pdf, other]

Title: Analysing the Social Spread of Behaviour: Integrating Complex Contagions into Network Based Diffusions

Josh A. Firth, Gregory F. Albery, Kristina B. Beck, Ivan Jarić, Lewis G. Spurgin, Ben C. Sheldon, Will Hoppitt

Subjects: Social and Information Networks (cs.SI); Quantitative Methods (q-bio.QM)

[247] arXiv:2012.09267 (cross-list from eess.SP) [pdf, other]

Title: Reduction in the complexity of 1D 1H-NMR spectra by the use of Frequency to Information Transformation

Homayoun Valafar, Faramarz Valafar

Comments: 21 pages

Subjects: Signal Processing (eess.SP); Computer Vision and Pattern Recognition (cs.CV); Biomolecules (q-bio.BM)

[248] arXiv:2012.09457 (cross-list from physics.soc-ph) [pdf, other]

Title: Cooperative coinfection dynamics on clustered networks

Peter Mann, Anne Smith, John Mitchell, Simon Dobson

Comments: 9 page, 5 figures

Journal-ref: Phys. Rev. E 103, 042307 (2021)

Subjects: Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

[249] arXiv:2012.09575 (cross-list from cs.LG) [pdf, other]

Title: Task Uncertainty Loss Reduce Negative Transfer in Asymmetric Multi-task Feature Learning

Rafael Peres da Silva, Chayaporn Suphavilai, Niranjan Nagarajan

Comments: Accepted in AAAI 2021 Student Abstract and Poster Program

Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Genomics (q-bio.GN)

[250] arXiv:2012.09763 (cross-list from physics.med-ph) [pdf, other]

Title: Influence of Rotator Cuff Integrity on Loading and Kinematics Before and After Reverse Shoulder Arthroplasty

Fabien Péan, Philippe Favre, Orcun Goksel

Comments: 8 pages, 5 figures

Subjects: Medical Physics (physics.med-ph); Quantitative Methods (q-bio.QM)