Quantitative Biology

Authors and titles for June 2020

[301] arXiv:2006.02552 (cross-list from physics.soc-ph) [pdf, other]

Title: Social distancing and epidemic resurgence in agent-based Susceptible-Infectious-Recovered models

Ruslan I. Mukhamadiarov, Shengfeng Deng, Shannon R. Serrao, Priyanka, Riya Nandi, Louie Hong Yao, Uwe C. Täuber (Virginia Tech)

Comments: 6 figures in main text, 4 more in supplementary materials; to appear in Scientific Reports

Journal-ref: Scientific Reports 11 (2021) 130

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

[302] arXiv:2006.02627 (cross-list from eess.IV) [pdf, other]

Title: Robust Automatic Whole Brain Extraction on Magnetic Resonance Imaging of Brain Tumor Patients using Dense-Vnet

Sara Ranjbar (1), Kyle W. Singleton (1), Lee Curtin (1), Cassandra R. Rickertsen (1), Lisa E. Paulson (1), Leland S. Hu (1,2), J. Ross Mitchell (3), Kristin R. Swanson (1) ((1) Mathematical NeuroOncology Lab, Precision Neurotherapeutics Innovation Program, Department of Neurological Surgery, Mayo Clinic, Phoenix, AZ, USA, (2) Department of Diagnostic Imaging and Interventional Radiology, Mayo Clinic, Phoenix, AZ, USA, (3) Department of Biostatistics and Bioinformatics, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA)

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

[303] arXiv:2006.02646 (cross-list from physics.soc-ph) [pdf, other]

Title: Spatio-temporal characteristics of dengue outbreaks

Saulo D. S. Reis, Lucas Böttcher, João P. da C. Nogueira, Geziel S. Sousa, Antonio S. Lima Neto, Hans J. Herrmann, José S. Andrade Jr

Comments: 25 pages, 8 figures

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

[304] arXiv:2006.02870 (cross-list from cs.SI) [pdf, other]

Title: The why, how, and when of representations for complex systems

Leo Torres, Ann S. Blevins, Danielle S. Bassett, Tina Eliassi-Rad

Comments: 50 pages, 18 figures

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

[305] arXiv:2006.02917 (cross-list from physics.geo-ph) [pdf, other]

Title: The effective mitigation of greenhouse gas emissions from rice paddies without compromising yield by early-season drainage

S. F. U. Islam, J. W. van Groenigen, L. S. Jensen, B. O. Sander, A. de Neergaard

Journal-ref: Science of the Total Environment, 2018: 612, 1329-1339

Subjects: Geophysics (physics.geo-ph); Quantitative Methods (q-bio.QM)

[306] arXiv:2006.02985 (cross-list from stat.CO) [pdf, other]

Title: Bayesian workflow for disease transmission modeling in Stan

Léo Grinsztajn, Elizaveta Semenova, Charles C. Margossian, Julien Riou

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

[307] arXiv:2006.02987 (cross-list from econ.EM) [pdf, other]

Title: Evaluating the Effectiveness of Regional Lockdown Policies in the Containment of Covid-19: Evidence from Pakistan

Hamza Umer, Muhammad Salar Khan

Comments: 28 pages, 3 figures (in the main text), 5 tables (in the main text)

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

[308] arXiv:2006.03157 (cross-list from physics.soc-ph) [pdf, other]

Title: Analytical and cellular automaton approach to a generalized SEIR model for infection spread in an open crowded space

Andrea Nava, Alessandro Papa, Marco Rossi, Domenico Giuliano

Comments: 14 pages, 9 figures

Journal-ref: Phys. Rev. Research 2, 043379 (2020)

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

[309] arXiv:2006.03226 (cross-list from cs.NE) [pdf, other]

Title: Brain-inspired global-local learning incorporated with neuromorphic computing

Yujie Wu, Rong Zhao, Jun Zhu, Feng Chen, Mingkun Xu, Guoqi Li, Sen Song, Lei Deng, Guanrui Wang, Hao Zheng, Jing Pei, Youhui Zhang, Mingguo Zhao, Luping Shi

Comments: 5 figures, 6 tables

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

[310] arXiv:2006.03278 (cross-list from physics.soc-ph) [pdf, other]

Title: Type reproduction number for epidemic models on heterogeneous networks

Satoru Morita

Comments: 4 pages, 1 fingure

Journal-ref: Physica A, 587, 126514 (2022)

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

[311] arXiv:2006.03402 (cross-list from physics.bio-ph) [pdf, other]

Title: The activity of native vacuolar proton-ATPase in an oscillating electric field -- demystifying an apparent effect of music on a biomolecule

Pal Petrovszki, Krisztina Sebok-Nagy, Tibor Pali

Comments: in extenso paper, version 3, same results but improved arguments, 25 pages with supplementary part, 4 figures, 1 table in main body, 2 tables in supplementary

Journal-ref: https://www.frontiersin.org/articles/10.3389/fmolb.2021.772167/full

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

[312] arXiv:2006.03476 (cross-list from physics.med-ph) [pdf, other]

Title: COVID-19 diagnosis by routine blood tests using machine learning

Matjaž Kukar, Gregor Gunčar, Tomaž Vovko, Simon Podnar, Peter Černelč, Miran Brvar, Mateja Zalaznik, Mateja Notar, Sašo Moškon, Marko Notar

Comments: 11 pages, 4 figures, 2 tables

Subjects: Medical Physics (physics.med-ph); Machine Learning (cs.LG); Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)

[313] arXiv:2006.03622 (cross-list from cs.CV) [pdf, other]

Title: Data Augmentation using Generative Adversarial Networks (GANs) for GAN-based Detection of Pneumonia and COVID-19 in Chest X-ray Images

Saman Motamed, Patrik Rogalla, Farzad Khalvati

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

[314] arXiv:2006.03672 (cross-list from physics.soc-ph) [pdf, other]

Title: Planning of School Teaching during COVID-19

Alberto Gandolfi

Comments: 14 page, 2 figures

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

[315] arXiv:2006.03702 (cross-list from stat.AP) [pdf, other]

Title: Histopathological imaging features- versus molecular measurements-based cancer prognosis modeling

Sanguo Zhang, Yu Fan, Tingyan Zhong, Shuangge Ma

Subjects: Applications (stat.AP); Image and Video Processing (eess.IV); Quantitative Methods (q-bio.QM)

[316] arXiv:2006.03742 (cross-list from eess.IV) [pdf, other]

Title: AV-Net: Deep learning for fully automated artery-vein classification in optical coherence tomography angiography

Minhaj Alam, David Le, Taeyoon Son, Jennifer I. Lim, Xincheng Yao

Subjects: Image and Video Processing (eess.IV); Quantitative Methods (q-bio.QM)

[317] arXiv:2006.03775 (cross-list from nlin.PS) [pdf, other]

Title: Localized Signaling Compartments in 2-D Coupled by a Bulk Diffusion Field: Quorum Sensing and Synchronous Oscillations in the Well-Mixed Limit

Sarafa A. Iyaniwura, Michael J. Ward

Comments: 25 pages, 68 figures

Subjects: Pattern Formation and Solitons (nlin.PS); Cell Behavior (q-bio.CB)

[318] arXiv:2006.03893 (cross-list from physics.soc-ph) [pdf, other]

Title: Evolution of Cooperation in the Presence of Higher-Order Interactions: from Networks to Hypergraphs

Giulio Burgio, Joan T. Matamalas, Sergio Gómez, Alex Arenas

Comments: 24 pages, 11 figures

Journal-ref: Entropy 22 (2020) 744

Subjects: Physics and Society (physics.soc-ph); Computer Science and Game Theory (cs.GT); Social and Information Networks (cs.SI); Adaptation and Self-Organizing Systems (nlin.AO); Populations and Evolution (q-bio.PE)

[319] arXiv:2006.03961 (cross-list from math.DS) [pdf, other]

Title: Analytical Mechanics Allows Novel Vistas on Mathematical Epidemic Dynamics Modelling

Paul Steinmann

Journal-ref: Math. Mech. Compl. Sys. 8 (2020) 321-343

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

[320] arXiv:2006.03965 (cross-list from cs.CL) [pdf, other]

Title: Generative Adversarial Phonology: Modeling unsupervised phonetic and phonological learning with neural networks

Gašper Beguš

Comments: Provisionally accepted in Frontiers in Artificial Intelligence

Journal-ref: Frontiers in Artificial Intelligence 2020

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

[321] arXiv:2006.04018 (cross-list from physics.soc-ph) [pdf, other]

Title: Projecting and comparing non-pharmaceutical interventions to contain COVID-19 in major economies

Jingjing He, Xuefei Guan, Xiaochang Duan, Tian Shen, Jing Lin

Comments: The results in this study projects the pandemic will end in one half to one year, which apparently is meaningless. Therefore, it is considered not accurate. To avoid unnecessary ambiguity, the authors would like to withdraw this draft. Thank you

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

[322] arXiv:2006.04039 (cross-list from math.DS) [pdf, other]

Title: Simulating brain rhythms using an ODE with stochastically varying coefficients

Benjamin Ambrosio, Lai-Sang Young

Subjects: Dynamical Systems (math.DS); Adaptation and Self-Organizing Systems (nlin.AO); Neurons and Cognition (q-bio.NC)

[323] arXiv:2006.04141 (cross-list from stat.AP) [pdf, other]

Title: Where Bayes tweaks Gauss: Conditionally Gaussian priors for stable multi-dipole estimation

Alessandro Viani, Gianvittorio Luria, Harald Bornfleth, Alberto Sorrentino

Comments: 23 pages, 8 figures

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

[324] arXiv:2006.04519 (cross-list from physics.bio-ph) [pdf, other]

Title: A minimal model for structure, dynamics, and tension of monolayered cell colonies

Debarati Sarkar, Gerhard Gompper, Jens Elgeti

Journal-ref: Commun. Phys. 4, 36 (2021)

Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Cell Behavior (q-bio.CB)

[325] arXiv:2006.04720 (cross-list from cs.NE) [pdf, other]

Title: Host-Pathongen Co-evolution Inspired Algorithm Enables Robust GAN Training

Andrei Kucharavy (1), El Mahdi El Mhamdi (1), Rachid Guerraoui (1) ((1) Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland)

Comments: 8 pages, 10 figures

Subjects: Neural and Evolutionary Computing (cs.NE); Machine Learning (cs.LG); Populations and Evolution (q-bio.PE); Machine Learning (stat.ML)

[326] arXiv:2006.04748 (cross-list from cs.CY) [pdf, other]

Title: Serverless on FHIR: Deploying machine learning models for healthcare on the cloud

Bell Raj Eapen, Kamran Sartipi, Norm Archer

Comments: 10 pages, 1 figure

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

[327] arXiv:2006.04765 (cross-list from cs.NE) [pdf, other]

Title: An Astrocyte-Modulated Neuromorphic Central Pattern Generator for Hexapod Robot Locomotion on Intel's Loihi

Ioannis Polykretis, Konstantinos P. Michmizos

Comments: 8 pages, 7 figures, International Conference on Neuromorphic Systems (ICONS) 2020

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

[328] arXiv:2006.05002 (cross-list from stat.AP) [pdf, other]

Title: Determination and estimation of optimal quarantine duration for infectious diseases with application to data analysis of COVID-19

Ruoyu Wang, Qihua Wang

Journal-ref: biometrics,2022

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

[329] arXiv:2006.05113 (cross-list from cs.CL) [pdf, other]

Title: Human brain activity for machine attention

Lukas Muttenthaler, Nora Hollenstein, Maria Barrett

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

[330] arXiv:2006.05175 (cross-list from cs.HC) [pdf, other]

Title: Visual cohort comparison for spatial single-cell omics-data

Antonios Somarakis, Marieke E. Ijsselsteijn, Sietse J. Luk, Boyd Kenkhuis, Noel F.C.C. de Miranda, Boudewijn P.F. Lelieveldt, Thomas Höllt

Comments: 11 pages, 10 figures, 2 tables. Revised based on IEEE VIS 2020 reviewers comments. ACM 2012 CCS - Human-centered computing, Visualization, Visualization application domains, Visual analytics. Binary of the presented tool is available is our repository: this https URL

Journal-ref: Presented in IEEE Vis 2020. Published in IEEE Transactions on Visualization and Computer Graphics (TVCG)

Subjects: Human-Computer Interaction (cs.HC); Genomics (q-bio.GN)

[331] arXiv:2006.05176 (cross-list from cs.SI) [pdf, other]

Title: Explainable Classification of Brain Networks via Contrast Subgraphs

Tommaso Lanciano, Francesco Bonchi, Aristides Gionis

Comments: To be published at KDD 2020

Subjects: Social and Information Networks (cs.SI); Neurons and Cognition (q-bio.NC)

[332] arXiv:2006.05467 (cross-list from cs.LG) [pdf, other]

Title: Pruning neural networks without any data by iteratively conserving synaptic flow

Hidenori Tanaka, Daniel Kunin, Daniel L. K. Yamins, Surya Ganguli

Comments: NeurIPS 2020, 18 pages, 10 figures

Journal-ref: Advances in Neural Information Processing Systems 2020

Subjects: Machine Learning (cs.LG); Disordered Systems and Neural Networks (cond-mat.dis-nn); Computer Vision and Pattern Recognition (cs.CV); Neurons and Cognition (q-bio.NC); Machine Learning (stat.ML)

[333] arXiv:2006.05509 (cross-list from eess.IV) [pdf, other]

Title: Can artificial intelligence (AI) be used to accurately detect tuberculosis (TB) from chest X-rays? An evaluation of five AI products for TB screening and triaging in a high TB burden setting

Zhi Zhen Qin, Shahriar Ahmed, Mohammad Shahnewaz Sarker, Kishor Paul, Ahammad Shafiq Sikder Adel, Tasneem Naheyan, Rachael Barrett, Sayera Banu, Jacob Creswell

Comments: 43 pages, 3 Tables 3 Figures

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

[334] arXiv:2006.05581 (cross-list from stat.ME) [pdf, other]

Title: Semiparametric Bayesian Inference for the Transmission Dynamics of COVID-19 with a State-Space Model

Tianjian Zhou, Yuan Ji

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

[335] arXiv:2006.05634 (cross-list from physics.app-ph) [pdf, other]

Title: Chemical-Grafting of Graphene Oxide Quantum Dots for Enhanced Electrochemical Analysis of Aromatics

Albina Mikhraliieva, Volodymyr Zaitsev, Oleg Tkachenko, Michael Nazarkovsky, Edilson V. Benvenutti

Comments: 29 pages, 3 tables, 15 figures

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

[336] arXiv:2006.05733 (cross-list from math.OC) [pdf, other]

Title: Optimal immunity control by social distancing for the SIR epidemic model

Pierre-Alexandre Bliman (MAMBA, LJLL), Michel Duprez (CEREMADE), Yannick Privat (IRMA, TONUS), Nicolas Vauchelet (LAGA)

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

[337] arXiv:2006.05937 (cross-list from physics.soc-ph) [pdf, other]

Title: Aging and equilibration in bistable contagion dynamics

Paul Richter, Malte Henkel, Lucas Böttcher

Comments: 10 pages, 6 figures

Journal-ref: Phys. Rev. E 102, 042308 (2020)

Subjects: Physics and Society (physics.soc-ph); Statistical Mechanics (cond-mat.stat-mech); Populations and Evolution (q-bio.PE)

[338] arXiv:2006.05943 (cross-list from cond-mat.soft) [pdf, other]

Title: Soft macromolecular confinement

Subhadip Biswas, Buddhapriya Chakrabarti

Comments: 20 pages, 18 figures

Subjects: Soft Condensed Matter (cond-mat.soft); Materials Science (cond-mat.mtrl-sci); Statistical Mechanics (cond-mat.stat-mech); Biomolecules (q-bio.BM)

[339] arXiv:2006.06039 (cross-list from physics.soc-ph) [pdf, other]

Title: Activity-based contact network scaling and epidemic propagation in metropolitan areas

Nishant Kumar, Jimi B. Oke, Bat-hen Nahmias-Biran

Comments: 19 pages, 9 figures

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

[340] arXiv:2006.06100 (cross-list from math.DS) [pdf, other]

Title: Models for plasma kinetics during simultaneous therapeutic plasma exchange and extracorporeal membrane oxygenation

Charles Puelz, Zach Danial, Jon Marinaro, Jay S. Raval, Boyce E. Griffith, Charles S. Peskin

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

[341] arXiv:2006.06104 (cross-list from physics.bio-ph) [pdf, other]

Title: The nuclear pore complex as an entropic gate: theory and simulation

Mike Castellano, Steffen Wolf, Thorsten Koslowski

Comments: This document is the unedited version of a manuscript that has been submitted to a scientific journal for consideration as publication and may be downloaded for personal use only

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

[342] arXiv:2006.06249 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Control of tumour growth distributions through kinetic methods

L. Preziosi, G. Toscani, M. Zanella

Subjects: Statistical Mechanics (cond-mat.stat-mech); Optimization and Control (math.OC); Adaptation and Self-Organizing Systems (nlin.AO); Biological Physics (physics.bio-ph); Quantitative Methods (q-bio.QM)

[343] arXiv:2006.06404 (cross-list from physics.soc-ph) [pdf, other]

Title: A model for the spread of an epidemic from local to global: A case study of COVID-19 in India

Buddhananda Banerjee, Pradumn Kumar Pandey, Bibhas Adhikari

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

[344] arXiv:2006.06409 (cross-list from physics.soc-ph) [pdf, other]

Title: Cyclical lock-down and the economic activity along the pandemic of COVID-19

Fernando E. Cornes, Guillermo A. Frank, Claudio O. Dorso

Comments: 7 pages, 13 figures

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

[345] arXiv:2006.06410 (cross-list from physics.soc-ph) [pdf, other]

Title: Long-Term Care Facilities as a Risk Factor for Death Due to COVID-19

Neil Gandal, Matan Yonas, Michal Feldman, Ady Pauzner, Avraham Tabbach

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

[346] arXiv:2006.06435 (cross-list from cs.CE) [pdf, other]

Title: The Computational Patient has Diabetes and a COVID

Pietro Barbiero, Pietro Lió

Comments: 37 pages

Subjects: Computational Engineering, Finance, and Science (cs.CE); Quantitative Methods (q-bio.QM)

[347] arXiv:2006.06497 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: A new inference approach for training shallow and deep generalized linear models of noisy interacting neurons

Gabriel Mahuas, Giulio Isacchini, Olivier Marre, Ulisse Ferrari, Thierry Mora

Comments: Final submission

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

[348] arXiv:2006.06503 (cross-list from physics.bio-ph) [pdf, other]

Title: Insights from Graph Theory on the Morphologies of Actomyosin Networks with Multilinkers

Yossi Eliaz, Francois Nedelec, Greg Morrison, Herbert Levine, Margaret S. Cheung

Comments: 10 figures

Journal-ref: Phys. Rev. E 102, 062420 (2020)

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

[349] arXiv:2006.06530 (cross-list from physics.soc-ph) [pdf, other]

Title: Age-structured estimation of COVID-19 ICU demand from low quality data

Rodrigo Veiga, Rodrigo Murta, Renato Vicente

Comments: 6 pages, 3 figures, 4 tables. Code available at this https URL

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

[350] arXiv:2006.06580 (cross-list from cs.GT) [pdf, other]

Title: Online Learning in Iterated Prisoner's Dilemma to Mimic Human Behavior

Baihan Lin, Djallel Bouneffouf, Guillermo Cecchi

Comments: Proceeding of PRICAI 2022. To the best of our knowledge, this is the first attempt to explore the full spectrum of reinforcement learning agents (multi-armed bandits, contextual bandits and reinforcement learning) in the sequential social dilemma. Codes at this https URL

Subjects: Computer Science and Game Theory (cs.GT); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Multiagent Systems (cs.MA); Neurons and Cognition (q-bio.NC)