Quantitative Biology

Authors and titles for July 2020

[301] arXiv:2007.05055 (cross-list from cs.LG) [pdf, other]

Title: SARS-CoV-2 virus RNA sequence classification and geographical analysis with convolutional neural networks approach

Selcuk Yazar

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

[302] arXiv:2007.05098 (cross-list from math.OC) [pdf, other]

Title: Optimal control of cytotoxic and antiangiogenic therapies on prostate cancer growth

Pierluigi Colli, Hector Gomez, Guillermo Lorenzo, Gabriela Marinoschi, Alessandro Reali, Elisabetta Rocca

Subjects: Optimization and Control (math.OC); Computational Engineering, Finance, and Science (cs.CE); Tissues and Organs (q-bio.TO)

[303] arXiv:2007.05114 (cross-list from stat.ME) [pdf, other]

Title: Analyzing the Effects of Observation Function Selection in Ensemble Kalman Filtering for Epidemic Models

Leah Mitchell, Andrea Arnold

Comments: 29 pages, 13 figures. This is the accepted manuscript of an article published in Mathematical Biosciences. The published journal article is available online at this https URL

Journal-ref: Mathematical Biosciences 339 (2021) 108655

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

[304] arXiv:2007.05351 (cross-list from cs.CV) [pdf, other]

Title: Are pathologist-defined labels reproducible? Comparison of the TUPAC16 mitotic figure dataset with an alternative set of labels

Christof A. Bertram, Mitko Veta, Christian Marzahl, Nikolas Stathonikos, Andreas Maier, Robert Klopfleisch, Marc Aubreville

Comments: 10 pages, submitted to LABELS@MICCAI 2020

Journal-ref: In: Cardoso J. et al. (eds) Interpretable and Annotation-Efficient Learning for Medical Image Computing. IMIMIC 2020, MIL3ID 2020, LABELS 2020. Lecture Notes in Computer Science, vol 12446. Springer, Cham

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

[305] arXiv:2007.05410 (cross-list from physics.bio-ph) [pdf, other]

Title: A Physics Modeling Study of SARS-CoV-2 Transport in Air

Luis A. Anchordoqui, James B. Dent, Thomas J. Weiler

Comments: 6 pages, 1 figure

Journal-ref: SciMedJ 2 (2020) 83-91

Subjects: Biological Physics (physics.bio-ph); Other Quantitative Biology (q-bio.OT)

[306] arXiv:2007.05424 (cross-list from stat.ME) [pdf, other]

Title: High heritability does not imply accurate prediction under the small additive effects hypothesis

Arthur Frouin (1), Claire Dandine-Roulland (1), Morgane Pierre-Jean (1), Jean-François Deleuze (1), Christophe Ambroise (2), Edith Le Floch (1) ((1) CNRGH, Institut Jacob, CEA - Université Paris-Saclay, (2) LaMME, Université Paris-Saclay, CNRS, Université d'Évry val d'Essonne)

Subjects: Methodology (stat.ME); Genomics (q-bio.GN)

[307] arXiv:2007.05496 (cross-list from physics.soc-ph) [pdf, other]

Title: In Response to COVID-19: Configuration Model of the Epidemic Spreading

Alexander I Nesterov, Pablo Héctor Mata Villafuerte, Gennady P Berman

Comments: 17 pages

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

[308] arXiv:2007.05672 (cross-list from physics.bio-ph) [pdf, other]

Title: A critical survey on the kinetic assays of DNA polymerase fidelity from a new theoretical perspective

Qiu-Shi Li, Yao-Gen Shu, Zhong-Can Ou-Yang, Ming Li

Comments: 13 pages, 14 figures

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

[309] arXiv:2007.05825 (cross-list from physics.soc-ph) [pdf, other]

Title: Safer working spaces at coronavirus time: A novel use of antibody tests

Patricio Foncea, Susana Mondschein, Ragheb Massouh

Comments: 24 pages, 6 figures, preliminary preprint

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

[310] arXiv:2007.06106 (cross-list from cs.LG) [pdf, other]

Title: Unsupervised Feature Selection for Tumor Profiles using Autoencoders and Kernel Methods

Martin Palazzo, Pierre Beauseroy, Patricio Yankilevich

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

[311] arXiv:2007.06252 (cross-list from cs.LG) [pdf, other]

Title: Intrinsic-Extrinsic Convolution and Pooling for Learning on 3D Protein Structures

Pedro Hermosilla, Marco Schäfer, Matěj Lang, Gloria Fackelmann, Pere Pau Vázquez, Barbora Kozlíková, Michael Krone, Tobias Ritschel, Timo Ropinski

Comments: International Conference on Learning Representations (ICLR) 2021

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

[312] arXiv:2007.06294 (cross-list from cs.CV) [pdf, other]

Title: Seeing eye-to-eye? A comparison of object recognition performance in humans and deep convolutional neural networks under image manipulation

Leonard E. van Dyck, Walter R. Gruber

Comments: 19 pages, 7 figures, 3 tables

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

[313] arXiv:2007.06383 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Ginzburg-Landau amplitude equation for nonlinear nonlocal models

Stefano Garlaschi, Deepak Gupta, Amos Maritan, Sandro Azaele

Comments: 14 pages including appendices

Journal-ref: Phys. Rev. E 103, 022210 (2021)

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

[314] arXiv:2007.06407 (cross-list from cs.NE) [pdf, other]

Title: Deep Cross-Subject Mapping of Neural Activity

Marko Angjelichinoski, Bijan Pesaran, Vahid Tarokh

Comments: More details on hyper-parameter tuning and some additional results

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

[315] arXiv:2007.06442 (cross-list from physics.soc-ph) [pdf, other]

Title: Modeling a Cognitive Transition at the Origin of Cultural Evolution using Autocatalytic Networks

Liane Gabora, Mike Steel

Comments: 46 pages; 7 figures; accepted for publication (but not yet published) in Cognitive Science

Subjects: Physics and Society (physics.soc-ph); Neurons and Cognition (q-bio.NC)

[316] arXiv:2007.06541 (cross-list from stat.ME) [pdf, other]

Title: Bayesian Modeling of COVID-19 Positivity Rate -- the Indiana experience

Ben Boukai, Jiayue Wang

Comments: 13 pages, 7 figures and 2 tables. The numerical results provided were obtained via an updatable R Markdown document

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

[317] arXiv:2007.06697 (cross-list from math.PR) [pdf, other]

Title: Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods

Max Hill, Brandon Legried, Sebastien Roch

Comments: 35 pages, 1 figure

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

[318] arXiv:2007.06706 (cross-list from cs.CV) [pdf, other]

Title: Domain Adaptation for Robust Workload Level Alignment Between Sessions and Subjects using fNIRS

Boyang Lyu, Thao Pham, Giles Blaney, Zachary Haga, Angelo Sassaroli, Sergio Fantini, Shuchin Aeron

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

[319] arXiv:2007.06733 (cross-list from physics.bio-ph) [pdf, other]

Title: Kinetic energy flows in activated dynamics of biomolecules

Huiyu Li, Ao Ma

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

[320] arXiv:2007.06971 (cross-list from stat.AP) [pdf, other]

Title: Use of Machine Learning and Artificial Intelligence to predict SARS-CoV-2 infection from Full Blood Counts in a population

Abhirup Banerjee, Surajit Ray, Bart Vorselaars, Joanne Kitson, Michail Mamalakis, Simonne Weeks, Mark Baker, Louise S. Mackenzie

Journal-ref: International Immunopharmacology, Volume 86,2020,106705,

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

[321] arXiv:2007.07156 (cross-list from physics.soc-ph) [pdf, other]

Title: Characterizing the spread of CoViD-19

Dean Karlen

Comments: 17 pages, 10 figures. Submitted to Statistical Methods in Medical Research

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

[322] arXiv:2007.07310 (cross-list from physics.soc-ph) [pdf, other]

Title: A fractal viewpoint to COVID-19 infection

Oscar Sotolongo-Costa, José Weberszpil, Oscar Sotolongo-Grau

Comments: 16 pages, 8 figures. To be submitted for publicantion

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

[323] arXiv:2007.07426 (cross-list from stat.ME) [pdf, other]

Title: A simple correction for COVID-19 sampling bias

Daniel Andrés Díaz-Pachón, J Sunil Rao

Comments: 14 pages. Title changed. The whole Section 7 with information from Lombardy, Italy, was added (another real dataset). Some typos were corrected. In spite of several lengthy additions, no substantial changes were done to the paper. The goal of the additions was more to clarify than to correct

Journal-ref: Journal of Theoretical Biology Journal of Theoretical Biology, Volume 512, 7 March 2021, 110556

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

[324] arXiv:2007.07471 (cross-list from stat.AP) [pdf, other]

Title: Predication of Inflection Point and Outbreak Size of COVID-19 in New Epicentres

Qibin Duan, Jinran Wu, Gaojun Wu, You-Gan Wang

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

[325] arXiv:2007.07510 (cross-list from cond-mat.soft) [pdf, other]

Title: The mechanics and thermodynamics of tubule formation in biological membranes

Arijit Mahapatra, Can Uysalel, Padmini Rangamani (University of California San Diego)

Comments: Arijit Mahapatra and Can Uysalel contributed equally, Padmini Rangamani is the corresponding author, 21 pages, 4 figures

Subjects: Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Subcellular Processes (q-bio.SC)

[326] arXiv:2007.07583 (cross-list from math.PR) [pdf, other]

Title: Stochastic and deterministic SIS patch model

T. Yeo

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

[327] arXiv:2007.08047 (cross-list from stat.AP) [pdf, other]

Title: Heterogeneity Learning for SIRS model: an Application to the COVID-19

Guanyu Hu, Junxian Geng

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

[328] arXiv:2007.08236 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Box-scaling as a proxy of finite-size correlations

Daniel A. Martin, Tiago L. Ribeiro, Sergio A. Cannas, Tomas S. Grigera, Dietmar Plenz, Dante R. Chialvo

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Neurons and Cognition (q-bio.NC)

[329] arXiv:2007.08855 (cross-list from cs.NE) [pdf, other]

Title: A Biologically Plausible Audio-Visual Integration Model for Continual Learning

Wenjie Chen, Fengtong Du, Ye Wang, Lihong Cao

Comments: Accepted by 2021 International Joint Conference on Neural Networks

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

[330] arXiv:2007.08925 (cross-list from eess.SY) [pdf, other]

Title: Initialization of a Disease Transmission Model

Håkan Runvik, Alexander Medvedev, Robin Eriksson, Stefan Engblom

Comments: 7 pages, 8 figures

Subjects: Systems and Control (eess.SY); Populations and Evolution (q-bio.PE)

[331] arXiv:2007.09066 (cross-list from physics.bio-ph) [pdf, other]

Title: Effect of Cholesterol vs. Ergosterol on DPPC Bilayer Properties: Insights from Atomistic Simulations

Azadeh Alavizargar, Fabian Keller, R. Wedlich-Söldner, Andreas Heuer

Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Subcellular Processes (q-bio.SC)

[332] arXiv:2007.09085 (cross-list from cs.CR) [pdf, other]

Title: Preservation of DNA Privacy During the Large Scale Detection of COVID-19

Marcel Hollenstein, David Naccache, Peter B. Rønne, Peter Y A Ryan, Robert Weil, Ofer Yifrach-Stav

Comments: 10 pages, 1 figure

Subjects: Cryptography and Security (cs.CR); Quantitative Methods (q-bio.QM)

[333] arXiv:2007.09114 (cross-list from cs.LG) [pdf, other]

Title: SBI -- A toolkit for simulation-based inference

Alvaro Tejero-Cantero (1), Jan Boelts (1), Michael Deistler (1), Jan-Matthis Lueckmann (1), Conor Durkan (2), Pedro J. Gonçalves (1, 3), David S. Greenberg (1, 4), Jakob H. Macke (1, 5, 6) ((1) Computational Neuroengineering, Department of Electrical and Computer Engineering, Technical University of Munich, (2) School of Informatics, University of Edinburgh, (3) Neural Systems Analysis, Center of Advanced European Studies and Research (caesar), Bonn, (4) Model-Driven Machine Learning, Centre for Materials and Coastal Research, Helmholtz-Zentrum Geesthacht, (5) Machine Learning in Science, University of Tübingen, (6) Empirical Inference, Max Planck Institute for Intelligent Systems, Tübingen)

Comments: Alvaro Tejero-Cantero, Jan Boelts, Michael Deistler, Jan-Matthis Lueckmann and Conor Durkan contributed equally in shared first authorship. This manuscript has been submitted for consideration to the Journal of Open Source Software (JOSS). 4 pages, no figures; v2: added link to sbi home

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

[334] arXiv:2007.09171 (cross-list from cs.IT) [pdf, other]

Title: Compressed sensing-based SARS-CoV-2 pool testing

Hendrik Bernd Petersen, Bubacarr Bah, Peter Jung

Comments: 12 Pages, 3 Figure

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

[335] arXiv:2007.09260 (cross-list from eess.IV) [pdf, other]

Title: Visual Explanation for Identification of the Brain Bases for Dyslexia on fMRI Data

Laura Tomaz Da Silva, Nathalia Bianchini Esper, Duncan D. Ruiz, Felipe Meneguzzi, Augusto Buchweitz

Comments: 19 pages, 7 Figures, submitted to Journal of Visualization

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

[336] arXiv:2007.09334 (cross-list from cs.LG) [pdf, other]

Title: Deep Learning of High-Order Interactions for Protein Interface Prediction

Yi Liu, Hao Yuan, Lei Cai, Shuiwang Ji

Comments: 10 pages, 3 figures, 4 tables. KDD2020

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

[337] arXiv:2007.09341 (cross-list from cs.HC) [pdf, other]

Title: Applications of brain imaging methods in driving behaviour research

Milad Haghani, Michiel C. J. Bliemer, Bilal Farooq, Inhi Kim, Zhibin Li, Cheol Oh, Zahra Shahhoseini, Hamish MacDougall

Subjects: Human-Computer Interaction (cs.HC); Neurons and Cognition (q-bio.NC)

[338] arXiv:2007.09417 (cross-list from stat.AP) [pdf, other]

Title: Modeling a Nonlinear Biophysical Trend Followed by Long-Memory Equilibrium with Unknown Change Point

Wenyu Zhang, Maryclare Griffin, David S. Matteson

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

[339] arXiv:2007.09469 (cross-list from cs.AI) [pdf, other]

Title: ESCELL: Emergent Symbolic Cellular Language

Aritra Chowdhury, James R. Kubricht, Anup Sood, Peter Tu, Alberto Santamaria-Pang

Comments: IEEE International Symposium on Biomedical Imaging (IEEE ISBI 2020)

Journal-ref: 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), Iowa City, IA, USA, 2020, pp. 1604-1607

Subjects: Artificial Intelligence (cs.AI); Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Cell Behavior (q-bio.CB)

[340] arXiv:2007.09471 (cross-list from eess.IV) [pdf, other]

Title: Automated Phenotyping via Cell Auto Training (CAT) on the Cell DIVE Platform

Alberto Santamaria-Pang, Anup Sood, Dan Meyer, Aritra Chowdhury, Fiona Ginty

Comments: 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Journal-ref: 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), San Diego, CA, USA, 2019, pp. 2750-2756

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

[341] arXiv:2007.09524 (cross-list from stat.ML) [pdf, other]

Title: A Manifold Proximal Linear Method for Sparse Spectral Clustering with Application to Single-Cell RNA Sequencing Data Analysis

Zhongruo Wang, Bingyuan Liu, Shixiang Chen, Shiqian Ma, Lingzhou Xue, Hongyu Zhao

Subjects: Machine Learning (stat.ML); Machine Learning (cs.LG); Optimization and Control (math.OC); Genomics (q-bio.GN)

[342] arXiv:2007.09607 (cross-list from physics.med-ph) [pdf, other]

Title: Optimal COVID-19 infection spread under low temperature, dry air, and low UV radiation

Eitan Asher, Yosef Ashkenazy, Shlomo Havlin, Alon Sela

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

[343] arXiv:2007.09640 (cross-list from cs.DS) [pdf, other]

Title: Exploitation of Multiple Replenishing Resources with Uncertainty

Amos Korman, Yuval Emek, Simon Collet, Aya Goldshtein, Yossi Yovel

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

[344] arXiv:2007.09701 (cross-list from math.PR) [pdf, other]

Title: Combinatorial and stochastic properties of ranked tree-child networks

François Bienvenu, Amaury Lambert, Mike Steel

Journal-ref: Random Structures & Algorithms, 60(4):653-689 (2022)

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

[345] arXiv:2007.09743 (cross-list from physics.soc-ph) [pdf, other]

Title: A framework to evaluate whether to pool or separate behaviors in a multilayer network

Annemarie van der Marel (1), Sanjay Prasher (1), Chelsea Carminito (1), Claire O'Connell (1), Alexa Phillips (1), Bryan M. Kluever (2), Elizabeth A. Hobson (1) ((1) Department of Biological Sciences, University of Cincinnati, Ohio USA, (2) United States Department of Agriculture, Wildlife Services, National Wildlife Research Center, Florida Field Station, USA)

Comments: accepted for Current Zoology

Journal-ref: Current Zoology, 2021

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

[346] arXiv:2007.09755 (cross-list from stat.AP) [pdf, other]

Title: COVID-19 Data Analysis and Forecasting: Algeria and the World

Sami Belkacem

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

[347] arXiv:2007.10130 (cross-list from cond-mat.soft) [pdf, other]

Title: Network permeability changes according to a quadratic power law upon removal of a single edge

S. Lange, B.M. Friedrich

Comments: 6 pages, 3 figures

Subjects: Soft Condensed Matter (cond-mat.soft); Fluid Dynamics (physics.flu-dyn); Tissues and Organs (q-bio.TO)

[348] arXiv:2007.10188 (cross-list from math.DS) [pdf, other]

Title: Random perturbations of an eco-epidemiological model

Lopo F. de Jesus, César M. Silva, Helder Vilarinho

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

[349] arXiv:2007.10263 (cross-list from cs.LG) [pdf, other]

Title: A Hierarchical Approach to Scaling Batch Active Search Over Structured Data

Vivek Myers, Peyton Greenside

Comments: Presented at the 2020 ICML Workshop on Real World Experiment Design and Active Learning

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

[350] arXiv:2007.10279 (cross-list from math.DS) [pdf, other]

Title: Dynamics of a discrete eco-epidemiological model with disease in the prey

Lopo F. de Jesus, César M. Silva, Helder Vilarinho

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