Quantitative Biology

Authors and titles for August 2020

[201] arXiv:2008.00520 (cross-list from cs.AI) [pdf, html, other]

Title: Bayesian Inference of Minimally Complex Models with Interactions of Arbitrary Order

Clélia de Mulatier, Matteo Marsili

Comments: 22 pages, 13 figures

Subjects: Artificial Intelligence (cs.AI); Statistics Theory (math.ST); Data Analysis, Statistics and Probability (physics.data-an); Quantitative Methods (q-bio.QM)

[202] arXiv:2008.00539 (cross-list from cs.LG) [pdf, other]

Title: An Investigation in Optimal Encoding of Protein Primary Sequence for Structure Prediction by Artificial Neural Networks

Aaron Hein, Casey Cole, Homayoun Valafar

Subjects: Machine Learning (cs.LG); Neural and Evolutionary Computing (cs.NE); Quantitative Methods (q-bio.QM)

[203] arXiv:2008.00559 (cross-list from stat.AP) [pdf, other]

Title: Vector quantisation and partitioning of COVID-19 temporal dynamics in the United States

Chris von Csefalvay

Comments: 13 pages, 5 figures

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

[204] arXiv:2008.00961 (cross-list from cs.AR) [pdf, other]

Title: Accelerating Genome Analysis: A Primer on an Ongoing Journey

Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie Kim, Saugata Ghose, Can Alkan, Onur Mutlu

Comments: This is an extended and updated version of a paper published in IEEE Micro, vol. 40, no. 5, pp. 65-75, 1 Sept.-Oct. 2020, this https URL

Journal-ref: IEEE Micro, Volume: 40, Issue: 5, Sept.-Oct. 1 2020

Subjects: Hardware Architecture (cs.AR); Genomics (q-bio.GN); Computation (stat.CO)

[205] arXiv:2008.01030 (cross-list from stat.AP) [pdf, other]

Title: Generalized additive models to capture the death rates in Canada COVID-19

Farzali Izadi

Comments: 19 pages

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

[206] arXiv:2008.01032 (cross-list from math.CO) [pdf, other]

Title: Combinatorial Geometry of Threshold-Linear Networks

Carina Curto, Christopher Langdon, Katherine Morrison

Comments: 24 pages, 16 figures

Subjects: Combinatorics (math.CO); Neurons and Cognition (q-bio.NC)

[207] arXiv:2008.01400 (cross-list from stat.ME) [pdf, other]

Title: A note on tools for prediction under uncertainty and identifiability of SIR-like dynamical systems for epidemiology

Chiara Piazzola, Lorenzo Tamellini, Raúl Tempone

Subjects: Methodology (stat.ME); Populations and Evolution (q-bio.PE)

[208] arXiv:2008.01625 (cross-list from physics.bio-ph) [pdf, other]

Title: Real-time observation of ligand-induced allosteric transitions in a PDZ domain

Olga Bozovic, Claudio Zanobini, Adnan Gulzar, Brankica Jankovic, David Buhrke, Matthias Post, Steffen Wolf, Gerhard Stock, Peter Hamm

Comments: This unedited earlier version of the manuscript may be downloaded for personal use only. Any other use requires prior permission of the author and the National Academy of Sciences USA. The final manuscript was published in Proceedings of the National Academy of Sciences USA 117, 26031-26039 (2020) and can be found under this https URL

Journal-ref: Proc. Natl. Acad. Sci. USA 117, 26031-26039 (2020)

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

[209] arXiv:2008.01690 (cross-list from physics.soc-ph) [pdf, other]

Title: A nucleation and growth model for COVID-19 epidemic in Japan

Yoshihiko Takase

Comments: 6 pages, 8 PDF figures

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

[210] arXiv:2008.01828 (cross-list from physics.soc-ph) [pdf, other]

Title: Understanding the Relationship between Social Distancing Policies, Traffic Volume, Air Quality, and the Prevalence of COVID-19 Outcomes in Urban Neighborhoods

Daniel L. Mendoza (1 and 2), Tabitha M. Benney (3), Rajive Ganguli (4), Rambabu Pothina (4), Benjamin Krick (3), Cheryl S. Pirozzi (5), Erik T. Crosman (6), Yue Zhang (7) ((1) Department of Atmospheric Sciences, University of Utah, Salt Lake City, Utah USA, (2) Department of City & Metropolitan Planning, University of Utah, Salt Lake City, Utah USA, (3) Department of Political Science, University of Utah, Salt Lake City, Utah USA, (4) Department of Mining Engineering, University of Utah, Salt Lake City, Utah USA, (5) Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, Utah USA, (6) Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas USA, (7) Division of Epidemiology, Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, Utah USA)

Comments: 34 pages, 7 figures, 2 tables

Subjects: Physics and Society (physics.soc-ph); Computers and Society (cs.CY); General Economics (econ.GN); Populations and Evolution (q-bio.PE)

[211] arXiv:2008.01901 (cross-list from eess.SP) [pdf, other]

Title: Machine Learning and Feature Engineering for Predicting Pulse Status during Chest Compressions

Diya Sashidhar (1 and 3), Heemun Kwok (2 and 3), Jason Coult (3), Jen Blackwood (3), Peter Kudenchuck (3 and 4), Shiv Bhandari (3), Thomas Rea (3 and 5), J. Nathan Kutz (1 and 3) ((1) Department of Applied Mathematics, University of Washington (2) Department of Emergency Medicine, University of Washington, (3) Center for Progress in Resuscitation, (4) Heart Institute, University of Washington, (5) Harborview Medical Center, and General Internal Medicine, University of Washington)

Comments: 8 pages, 9 figures

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

[212] arXiv:2008.01937 (cross-list from cs.CL) [pdf, other]

Title: Antibody Watch: Text Mining Antibody Specificity from the Literature

Chun-Nan Hsu, Chia-Hui Chang, Thamolwan Poopradubsil, Amanda Lo, Karen A. William, Ko-Wei Lin, Anita Bandrowski, Ibrahim Burak Ozyurt, Jeffrey S. Grethe, Maryann E. Martone

Comments: 16 pages, 1 figures

Journal-ref: PLOS Computational Biology, 2021

Subjects: Computation and Language (cs.CL); Biomolecules (q-bio.BM)

[213] arXiv:2008.02068 (cross-list from physics.soc-ph) [pdf, other]

Title: COVID-19 in the United States: Trajectories and second surge behavior

Nick James, Max Menzies

Comments: Accepted manuscript. Extra appendices and resized figures compared to v1. Equal contribution

Journal-ref: Chaos 30, 091102 (2020)

Subjects: Physics and Society (physics.soc-ph); Data Analysis, Statistics and Probability (physics.data-an); Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)

[214] arXiv:2008.02072 (cross-list from eess.SP) [pdf, other]

Title: A Comparative study of Artificial Neural Networks Using Reinforcement learning and Multidimensional Bayesian Classification Using Parzen Density Estimation for Identification of GC-EIMS Spectra of Partially Methylated Alditol Acetates

Faramarz Valafar, Homayoun Valafar

Comments: 5 pages

Subjects: Signal Processing (eess.SP); Machine Learning (cs.LG); Neural and Evolutionary Computing (cs.NE); Biomolecules (q-bio.BM)

[215] arXiv:2008.02322 (cross-list from stat.AP) [pdf, other]

Title: Spatiotemporal dynamic of COVID-19 mortality in the city of Sao Paulo, Brazil: shifting the high risk from the best to the worst socio-economic conditions

Patricia Marques Moralejo Bermudi, Camila Lorenz, Breno Souza de Aguiar, Marcelo Antunes Failla, Ligia Vizeu Barrozo, Francisco Chiaravalloti-Neto

Comments: 22 pages, 6 figures, 2 tables, 3 supplementary materials

Subjects: Applications (stat.AP); Populations and Evolution (q-bio.PE)

[216] arXiv:2008.02353 (cross-list from physics.comp-ph) [pdf, other]

Title: Protein Conformational States: A First Principles Bayesian Method

David M. Rogers

Comments: 8 page article, 3 page SI, 4 figures

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

[217] arXiv:2008.02704 (cross-list from math.AP) [pdf, other]

Title: Some "counterintuitive" results in two species competition

Rana D. Parshad, Kwadwo Antwi-Fordjour, Eric M. Takyi

Comments: 21 pages, 27 figures

Journal-ref: SIAM Journal on Applied Mathematics 81(5):1847-1869, 2021

Subjects: Analysis of PDEs (math.AP); Dynamical Systems (math.DS); Populations and Evolution (q-bio.PE)

[218] arXiv:2008.02765 (cross-list from stat.AP) [pdf, other]

Title: Quantifying uncertainty and dynamical changes in multi-species fishing mortality rates, catches and biomass by combining state-space and mechanistic multi-species models

Michael A. Spence, Robert B. Thorpe, Paul G. Blackwell, Finlay Scott, Richard Southwell, Julia L. Blanchard

Comments: 35 pages 6 figures. To view Supplementary material and Simulation study, please download and extract the zipped source file listed under "Other formats"

Subjects: Applications (stat.AP); Populations and Evolution (q-bio.PE)

[219] arXiv:2008.02907 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Critical patch size reduction by heterogeneous diffusion

M. A. F. dos Santos, V. Dornelas, E. H. Colombo, C. Anteneodo

Comments: 7 pages, 5 figures

Journal-ref: Phys. Rev. E 102, 042139 (2020)

Subjects: Statistical Mechanics (cond-mat.stat-mech); Populations and Evolution (q-bio.PE)

[220] arXiv:2008.02961 (cross-list from cs.LG) [pdf, other]

Title: From Connectomic to Task-evoked Fingerprints: Individualized Prediction of Task Contrasts from Resting-state Functional Connectivity

Gia H. Ngo, Meenakshi Khosla, Keith Jamison, Amy Kuceyeski, Mert R. Sabuncu

Comments: Accepted to MICCAI 2020

Subjects: Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC); Machine Learning (stat.ML)

[221] arXiv:2008.03283 (cross-list from econ.GN) [pdf, other]

Title: COVID-19: What If Immunity Wanes?

M. Alper Çenesiz, Luís Guimarães

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

[222] arXiv:2008.03433 (cross-list from cs.LG) [pdf, other]

Title: GPU-Accelerated Primal Learning for Extremely Fast Large-Scale Classification

John T. Halloran, David M. Rocke

Comments: 34th Conference on Neural Information Processing Systems (NeurIPS 2020), Vancouver, Canada

Subjects: Machine Learning (cs.LG); Distributed, Parallel, and Cluster Computing (cs.DC); Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)

[223] arXiv:2008.03519 (cross-list from cs.AI) [pdf, other]

Title: Learning abstract structure for drawing by efficient motor program induction

Lucas Y. Tian, Kevin Ellis, Marta Kryven, Joshua B. Tenenbaum

Subjects: Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)

[224] arXiv:2008.03537 (cross-list from physics.med-ph) [pdf, other]

Title: Photodynamic therapy of 4T1 tumors in NOD-SCID mice

Georgios Kareliotis, Stavros Xanthopoulos, Eleni Drakaki, Maria Papachristou, Ioannis Datseris, Penelope Bouziotis, Mersini Makropoulou

Comments: 14 pages, 6 figures

Subjects: Medical Physics (physics.med-ph); Tissues and Organs (q-bio.TO)

[225] arXiv:2008.03646 (cross-list from cs.CV) [pdf, other]

Title: Augmenting Molecular Images with Vector Representations as a Featurization Technique for Drug Classification

Daniel de Marchi, Amarjit Budhiraja

Journal-ref: ICASSP 2020 - 2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)

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

[226] arXiv:2008.03869 (cross-list from stat.ML) [pdf, other]

Title: Individualized Prediction of COVID-19 Adverse outcomes with MLHO

Hossein Estiri, Zachary H. Strasser, Shawn N. Murphy

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

[227] arXiv:2008.03978 (cross-list from physics.bio-ph) [pdf, other]

Title: Learning the dynamics of cell-cell interactions in confined cell migration

David B. Brückner, Nicolas Arlt, Alexandra Fink, Pierre Ronceray, Joachim O. Rädler, Chase P. Broedersz

Journal-ref: Proc. Natl. Acad. Sci. USA 118 (2021) e2016602118

Subjects: Biological Physics (physics.bio-ph); Statistical Mechanics (cond-mat.stat-mech); Cell Behavior (q-bio.CB)

[228] arXiv:2008.04208 (cross-list from cs.NE) [pdf, other]

Title: Working Memory for Online Memory Binding Tasks: A Hybrid Model

Seyed Mohammad Mahdi Heidarpoor Yazdi, Abdolhossein Abbassian

Comments: 23 pages, 17 figures

Subjects: Neural and Evolutionary Computing (cs.NE); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)

[229] arXiv:2008.04215 (cross-list from cs.SI) [pdf, other]

Title: STAN: Spatio-Temporal Attention Network for Pandemic Prediction Using Real World Evidence

Junyi Gao, Rakshith Sharma, Cheng Qian, Lucas M. Glass, Jeffrey Spaeder, Justin Romberg, Jimeng Sun, Cao Xiao

Subjects: Social and Information Networks (cs.SI); Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

[230] arXiv:2008.04218 (cross-list from eess.SP) [pdf, other]

Title: Viral Aerosol Concentration Characterization and Detection in Bounded Environments

Osama Amin, Hayssam Dahrouj, Nojood Almayouf, Tareq Y. Al-Naffouri, Basem Shihada, Mohamed-Slim Alouini

Comments: 29 pages, submitted to IEEE Transactions on Molecular, Biological, and Multi-Scale Communications for the special issue "Molecular Communications for Diagnostics and Therapeutic Development of Infectious Diseases"

Subjects: Signal Processing (eess.SP); Information Theory (cs.IT); Molecular Networks (q-bio.MN)

[231] arXiv:2008.04757 (cross-list from cs.CV) [pdf, other]

Title: Transfer Learning for Protein Structure Classification at Low Resolution

Alexander Hudson, Shaogang Gong

Comments: 9 pages excluding references and appendices

Subjects: Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Biomolecules (q-bio.BM)

[232] arXiv:2008.04870 (cross-list from physics.bio-ph) [pdf, other]

Title: Neuroprotective Immunity by Essential Nutrient "Choline" for the Prevention of SARS CoV2 Infections: An in Silico Study by Molecular Dynamics Approach

Papia Chowdhury, Pustak Pathak

Comments: Role cf choline in reducing the effect of Prenatal COVID infection is studied

Journal-ref: Chemical Physics Letters 761 (2020) 138057

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

[233] arXiv:2008.04939 (cross-list from physics.med-ph) [pdf, other]

Title: Microstructure with Diffusion MRI: What Scale We Are Sensitive to?

Valerij G. Kiselev

Comments: Review with 7 figures

Subjects: Medical Physics (physics.med-ph); Tissues and Organs (q-bio.TO)

[234] arXiv:2008.05217 (cross-list from eess.IV) [pdf, other]

Title: Large-Scale Analysis of Iliopsoas Muscle Volumes in the UK Biobank

Julie Fitzpatrick, Nicolas Basty, Madeleine Cule, Yi Liu, Jimmy D. Bell, E. Louise Thomas, Brandon Whitcher

Comments: Julie Fitzpatrick and Nicolas Basty are joint first authors

Journal-ref: Scientific Reports 10 (1), 1-10, 2020

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

[235] arXiv:2008.05332 (cross-list from eess.IV) [pdf, other]

Title: Renal Cell Carcinoma Detection and Subtyping with Minimal Point-Based Annotation in Whole-Slide Images

Zeyu Gao, Pargorn Puttapirat, Jiangbo Shi, Chen Li

Comments: 10 pages, 5 figure, 3 tables, accepted at MICCAI 2020

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

[236] arXiv:2008.05410 (cross-list from math.PR) [pdf, other]

Title: Darwinian evolution as Brownian motion on the simplex: A geometric perspective on stochastic replicator dynamics

Tobias Lehmann

Subjects: Probability (math.PR); Populations and Evolution (q-bio.PE)

[237] arXiv:2008.05560 (cross-list from math.CO) [pdf, other]

Title: A path-deformation framework for determining weighted genome rearrangement distance

Sangeeta Bhatia, Attila Egri-Nagy, Stuart Serdoz, Cheryl E. Praeger, Volker Gebhardt, Andrew Francis

Comments: 15 pages, 4 figures. To appear in Frontiers in Genetics: Evolution and Population Genetics, in a special issue on Algebraic and Geometric Phylogenetics

Subjects: Combinatorics (math.CO); Populations and Evolution (q-bio.PE)

[238] arXiv:2008.05608 (cross-list from physics.bio-ph) [pdf, other]

Title: Design principles for the glycoprotein quality control pathway

Aidan I Brown, Elena F Koslover

Comments: 22 pages, 8 figures

Subjects: Biological Physics (physics.bio-ph); Subcellular Processes (q-bio.SC)

[239] arXiv:2008.05644 (cross-list from cs.CY) [pdf, other]

Title: A Deep Learning Approach for COVID-19 Trend Prediction

Tong Yang, Long Sha, Justin Li, Pengyu Hong

Comments: 7 pages, 11 figures, accepted by KDD 2020 epiDAMIK workshop

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

[240] arXiv:2008.05661 (cross-list from physics.soc-ph) [pdf, other]

Title: Why are U.S. Parties So Polarized? A "Satisficing" Dynamical Model

Vicky Chuqiao Yang, Daniel M. Abrams, Georgia Kernell, Adilson E. Motter

Comments: 13 pages, 5 figures

Journal-ref: SIAM Review, 2020, 62(3), 646-657

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

[241] arXiv:2008.05973 (cross-list from physics.bio-ph) [pdf, other]

Title: Requirements for DNA-bridging proteins to act as topological barriers of the bacterial genome

Marc Joyeux, Ivan Junier

Comments: Accepted for publication in the Biophysical Journal

Journal-ref: Biophysical Journal 119 (2020) 1215-1225

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

[242] arXiv:2008.05979 (cross-list from physics.soc-ph) [pdf, other]

Title: An epidemiological model with voluntary quarantine strategies governed by evolutionary game dynamics

Marco A. Amaral, Marcelo M. de Oliveira, Marco A. Javarone

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

[243] arXiv:2008.06142 (cross-list from eess.IV) [pdf, other]

Title: Landmark detection in Cardiac Magnetic Resonance Imaging Using A Convolutional Neural Network

Hui Xue, Jessica Artico, Marianna Fontana, James C Moon, Rhodri H Davies, Peter Kellman

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

[244] arXiv:2008.06151 (cross-list from eess.IV) [pdf, other]

Title: Interpretation of Brain Morphology in Association to Alzheimer's Disease Dementia Classification Using Graph Convolutional Networks on Triangulated Meshes

Emanuel A. Azcona, Pierre Besson, Yunan Wu, Arjun Punjabi, Adam Martersteck, Amil Dravid, Todd B. Parrish, S. Kathleen Bandt, Aggelos K. Katsaggelos

Comments: Accepted for the Shape in Medical Imaging (ShapeMI) workshop at MICCAI International Conference 2020

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

[245] arXiv:2008.06193 (cross-list from physics.soc-ph) [pdf, other]

Title: Risk mapping for COVID-19 outbreaks in Australia using mobility data

Cameron Zachreson, Lewis Mitchell, Michael J. Lydeamore, Nicolas Rebuli, Martin Tomko, Nicholas Geard

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

[246] arXiv:2008.06332 (cross-list from eess.IV) [pdf, other]

Title: Integrating uncertainty in deep neural networks for MRI based stroke analysis

Lisa Herzog, Elvis Murina, Oliver Dürr, Susanne Wegener, Beate Sick

Comments: 21 pages, 13 figures

Journal-ref: Medical Image Analysis (2020): 101790

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

[247] arXiv:2008.06335 (cross-list from cs.SI) [pdf, other]

Title: Exo-SIR: An Epidemiological Model to Analyze the Impact of Exogenous Infection of COVID-19 in India

Nirmal Kumar Sivaraman, Manas Gaur, Shivansh Baijal, Ch V Radha Sai Rupesh, Sakthi Balan Muthiah, Amit Sheth

Comments: 9 pages, 9 figures, Accepted at ACM KDD'20 Health Day (AI for COVID)

Subjects: Social and Information Networks (cs.SI); Computers and Society (cs.CY); Populations and Evolution (q-bio.PE)

[248] arXiv:2008.06608 (cross-list from physics.bio-ph) [pdf, other]

Title: Challenging Eukaryogenesis: The Story of the Eukaryotic Ancestor

Monica Vidaurri

Comments: 3 figures, 13 pages (including ~3.5 pages of references)

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

[249] arXiv:2008.06748 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Target competition for resources under diffusive search-and-capture

Paul C. Bressloff

Comments: 21 pages, 3 figures. (This is an updated version of previous submission that focuses on 3D search processes. The example of concentric spheres is now developed in a separate paper.)

Subjects: Statistical Mechanics (cond-mat.stat-mech); Subcellular Processes (q-bio.SC)

[250] arXiv:2008.06863 (cross-list from physics.soc-ph) [pdf, other]

Title: Discontinuous transitions of social distancing in SIR model

R. Arazi, A. Feigel

Comments: version 2, 3 figures added, introduction/model explanation are extended, no change of results

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