Quantitative Biology

Authors and titles for November 2020

[201] arXiv:2011.14118 [pdf, other]

Title: Risk assessment for airborne disease transmission by poly-pathogen aerosols

Freja Nordsiek, Eberhard Bodenschatz, Gholamhossein Bagheri

Comments: updated file with link to software on GitHub

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

[202] arXiv:2011.14241 [pdf, other]

Title: Computationally repurposed drugs and natural products against RNA dependent RNA polymerase as potential COVID-19 therapies

Sakshi Piplani, Puneet Singh, David A. Winkler, Nikolai Petrovsky

Comments: 38 pages plus supplementary, 11 figures

Subjects: Biomolecules (q-bio.BM)

[203] arXiv:2011.14255 [pdf, other]

Title: Optimal vaccination program for two infectious diseases with cross immunity

Yang Ye, Qingpeng Zhang, Zhidong Cao, Daniel Dajun Zeng

Comments: 5 pages, 3 figures

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

[204] arXiv:2011.14440 [pdf, other]

Title: Temporal assortment of cooperators in the spatial prisoner's dilemma

Tim Johnson, Oleg Smirnov

Comments: 16 pages; 5 figures

Subjects: Populations and Evolution (q-bio.PE); Computer Science and Game Theory (cs.GT); Social and Information Networks (cs.SI); Theoretical Economics (econ.TH); Applied Physics (physics.app-ph)

[205] arXiv:2011.14694 [pdf, other]

Title: Anchored-STFT and GNAA: An extension of STFT in conjunction with an adversarial data augmentation technique for the decoding of neural signals

Omair Ali, Muhammad Saif-ur-Rehman, Susanne Dyck, Tobias Glasmachers, Ioannis Iossifidis, Christian Klaes

Comments: 29 pages, 6 figures, 4 tables

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

[206] arXiv:2011.14731 [pdf, other]

Title: Spatiotemporal patterns of adaptation-induced slow oscillations in a whole-brain model of slow-wave sleep

Caglar Cakan, Cristiana Dimulescu, Liliia Khakimova, Daniela Obst, Agnes Flöel, Klaus Obermayer

Comments: For the simulations, the whole-brain neural mass modeling framework neurolib (this https URL) was used. Code for reproducing all figures can be found at this https URL

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

[207] arXiv:2011.14990 [pdf, other]

Title: Discovery of Multi-Level Network Differences Across Populations of Heterogeneous Connectomes

Vivek Gopalakrishnan, Jaewon Chung, Eric Bridgeford, Benjamin D. Pedigo, Jesús Arroyo, Lucy Upchurch, G. Allan Johnson, Nian Wang, Youngser Park, Carey E. Priebe, Joshua T. Vogelstein

Comments: 29 pages, 12 figures

Subjects: Neurons and Cognition (q-bio.NC); Methodology (stat.ME)

[208] arXiv:2011.00034 (cross-list from cs.RO) [pdf, other]

Title: Adaptive Semi-Supervised Intent Inferral to Control a Powered Hand Orthosis for Stroke

Jingxi Xu, Cassie Meeker, Ava Chen, Lauren Winterbottom, Michaela Fraser, Sangwoo Park, Lynne M. Weber, Mitchell Miya, Dawn Nilsen, Joel Stein, Matei Ciocarlie

Comments: 7 pages; Accepted to International Conference on Robotics and Automation (ICRA) 2022

Subjects: Robotics (cs.RO); Signal Processing (eess.SP); Neurons and Cognition (q-bio.NC)

[209] arXiv:2011.00121 (cross-list from eess.SP) [pdf, other]

Title: An Uncertainty Estimation Framework for Risk Assessment in Deep Learning-based Atrial Fibrillation Classification

James Belen, Sajad Mousavi, Alireza Shamsoshoara, Fatemeh Afghah

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

[210] arXiv:2011.00290 (cross-list from eess.SP) [pdf, other]

Title: Infectious Disease Transmission via Aerosol Propagation from a Molecular Communication Perspective: Shannon Meets Coronavirus

Max Schurwanz, Peter Adam Hoeher, Sunasheer Bhattacharjee, Martin Damrath, Lukas Stratmann, Falko Dressler

Comments: 7 pages, 4 figures, 1 table, submitted to IEEE Communications Magazine for the Feature Topic on "Nano-Networking for Nano-, Micro-, and Macro-Scale Applications"

Subjects: Signal Processing (eess.SP); Other Quantitative Biology (q-bio.OT)

[211] arXiv:2011.00293 (cross-list from math.OC) [pdf, other]

Title: Optimal control of diseases in prison populations through screening policies of new inmates

Pedro Gajardo, Victor Riquelme, Diego Vicencio

Comments: 28 pages, 4 figures

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

[212] arXiv:2011.00486 (cross-list from physics.bio-ph) [pdf, other]

Title: Mechanical Feedback in Regulating the Size of Growing Multicellular Spheroids

Alexander Erlich, Pierre Recho

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

[213] arXiv:2011.00511 (cross-list from cs.DS) [pdf, other]

Title: Best Match Graphs with Binary Trees

David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler

Subjects: Data Structures and Algorithms (cs.DS); Computational Complexity (cs.CC); Discrete Mathematics (cs.DM); Combinatorics (math.CO); Populations and Evolution (q-bio.PE)

[214] arXiv:2011.00790 (cross-list from math.OC) [pdf, other]

Title: On Control of Epidemics with Application to COVID-19

Chung-Han Hsieh

Comments: Submitted to the SIAM Journal on Control and Optimization

Journal-ref: IEEE Access, vol. 9, pp. 167948-167958, 2021

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

[215] arXiv:2011.00884 (cross-list from eess.SP) [pdf, other]

Title: Mobile Human Ad Hoc Networks: A Communication Engineering Viewpoint on Interhuman Airborne Pathogen Transmission

Fatih Gulec, Baris Atakan, Falko Dressler

Comments: 13 pages, 9 figures, to be published in Nano Communication Networks

Journal-ref: Nano Communication Networks, vol. 32-33, p. 100410, 2022

Subjects: Signal Processing (eess.SP); Social and Information Networks (cs.SI); Other Quantitative Biology (q-bio.OT)

[216] arXiv:2011.01131 (cross-list from physics.bio-ph) [pdf, other]

Title: Mechanical behavior of multi-cellular spheroids under osmotic compression

Monika Dolega, Giuseppe Zurlo, Magali Le Goff, Magdalena Greda, Claude Verdier, Jean-François Joanny, Giovanni Cappello, Pierre Recho

Subjects: Biological Physics (physics.bio-ph); Materials Science (cond-mat.mtrl-sci); Tissues and Organs (q-bio.TO)

[217] arXiv:2011.01355 (cross-list from cs.LG) [pdf, other]

Title: Patch2Self: Denoising Diffusion MRI with Self-Supervised Learning

Shreyas Fadnavis, Joshua Batson, Eleftherios Garyfallidis

Journal-ref: Thirty-fourth Conference on Neural Information Processing Systems, 2020

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

[218] arXiv:2011.01689 (cross-list from physics.med-ph) [pdf, other]

Title: Improved unsupervised physics-informed deep learning for intravoxel incoherent motion modeling and evaluation in pancreatic cancer patients

Misha P.T. Kaandorp, Sebastiano Barbieri, Remy Klaassen, Hanneke W.M. van Laarhoven, Hans Crezee, Peter T. While, Aart J. Nederveen, Oliver J. Gurney-Champion

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

[219] arXiv:2011.01786 (cross-list from physics.soc-ph) [pdf, other]

Title: The evolution of punishing institutions

Mohammad Salahshour

Comments: 36 pages, 18 figures

Journal-ref: Plos one 16.8 (2021): e0254860

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

[220] arXiv:2011.01921 (cross-list from cs.LG) [pdf, other]

Title: Optimizing Molecules using Efficient Queries from Property Evaluations

Samuel Hoffman, Vijil Chenthamarakshan, Kahini Wadhawan, Pin-Yu Chen, Payel Das

Comments: Preprint version to be published at Nature Machine Intelligence; Github: this https URL

Journal-ref: Nat Mach Intell 4, 21-31 (2022)

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

[221] arXiv:2011.02032 (cross-list from physics.soc-ph) [pdf, other]

Title: COVID-19 Epidemic in Mumbai: Projections, full economic opening, and containment zones versus contact tracing and testing: An Update

Prahladh Harsha, Sandeep Juneja, Daksh Mittal, Ramprasad Saptharishi

Comments: 36 pages

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

[222] arXiv:2011.02145 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: First-passage processes and the target-based accumulation of resources

Paul C Bressloff

Comments: 16 pages, 17 figures. arXiv admin note: substantial text overlap with arXiv:2008.06748

Journal-ref: Phys. Rev. E 103, 012101 (2021)

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

[223] arXiv:2011.02174 (cross-list from cond-mat.soft) [pdf, other]

Title: The fluid dynamics of collective vortex structures of plant-animal worms

George T. Fortune, Alan Worley, Ana B. Sendova-Franks, Nigel R. Franks, Kyriacos C. Leptos, Eric Lauga, Raymond E. Goldstein

Comments: 28 pages, 9 figures; Supplementary Videos available at website of REG

Journal-ref: J. Fluid Mech. 914 (2021) A20

Subjects: Soft Condensed Matter (cond-mat.soft); Fluid Dynamics (physics.flu-dyn); Quantitative Methods (q-bio.QM)

[224] arXiv:2011.02444 (cross-list from cond-mat.stat-mech) [pdf, html, other]

Title: Scaling study of diffusion in dynamic crowded spaces

H. Bendekgey, G. Huber, D. Yllanes

Comments: Version accepted for publication in J. Phys. A. 13 pages, 7 figures

Journal-ref: J. Phys. A: Math. Theor. 57 445207 (2024)

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

[225] arXiv:2011.02791 (cross-list from physics.bio-ph) [pdf, other]

Title: A geometry-based relaxation algorithm for equilibrating a trivalent polygonal network in two dimensions and its implications

Kai Xu

Journal-ref: Philosophical Magazine, 2021, 101(14): 1632-1653

Subjects: Biological Physics (physics.bio-ph); Adaptation and Self-Organizing Systems (nlin.AO); Cell Behavior (q-bio.CB)

[226] arXiv:2011.02971 (cross-list from physics.bio-ph) [pdf, other]

Title: Drug design principles from electric field calculations: understanding SARS-CoV-2 main protease interaction with X77 non-covalent inhibitor

Valerie Vaissier Welborn

Comments: 7 pages, 8 figures

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

[227] arXiv:2011.02977 (cross-list from physics.data-an) [pdf, other]

Title: Serial Electron Diffraction Data Processing with diffractem and CrystFEL

Robert Bücker, Pascal Hogan-Lamarre, R. J. Dwayne Miller

Comments: 21 pages, 9 figures

Subjects: Data Analysis, Statistics and Probability (physics.data-an); Biomolecules (q-bio.BM)

[228] arXiv:2011.03089 (cross-list from cs.LG) [pdf, other]

Title: Mining Functionally Related Genes with Semi-Supervised Learning

Kaiyu Shen, Razvan Bunescu, Sarah E. Wyatt

Comments: Submitted for publication in 2014

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

[229] arXiv:2011.03123 (cross-list from cs.IR) [pdf, other]

Title: PubSqueezer: A Text-Mining Web Tool to Transform Unstructured Documents into Structured Data

Alberto Calderone

Subjects: Information Retrieval (cs.IR); Computation and Language (cs.CL); Quantitative Methods (q-bio.QM)

[230] arXiv:2011.03263 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Hybrid-type synchronization transitions: where marginal coherence, scale-free avalanches, and bistability live together

Victor Buendía, Pablo Villegas, Raffaella Burioni, Miguel A. Muñoz

Comments: 7 pages, 4 figures, and Supplementary Information. Accepted to be published in PRR

Journal-ref: Phys. Rev. Research 3, 023224 (2021)

Subjects: Statistical Mechanics (cond-mat.stat-mech); Disordered Systems and Neural Networks (cond-mat.dis-nn); Adaptation and Self-Organizing Systems (nlin.AO); Neurons and Cognition (q-bio.NC)

[231] arXiv:2011.03296 (cross-list from physics.optics) [pdf, other]

Title: Localization microscopy: a review of the progress in methods and applications

Jack W Shepherd, Mark C Leake

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

[232] arXiv:2011.03380 (cross-list from physics.soc-ph) [pdf, other]

Title: Outbreak diversity in epidemic waves propagating through distinct geographical scales

Guilherme S. Costa, Wesley Cota, Silvio C. Ferreira

Comments: 13 pages, 7 figures, accepted for publication in Phys. Rev. Res. (2020). Supplementary figures and movies available as ancillary files

Journal-ref: Phys. Rev. Research 2, 043306 (2020)

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

[233] arXiv:2011.03544 (cross-list from eess.SP) [pdf, other]

Title: Machine learning applications to DNA subsequence and restriction site analysis

Ethan J. Moyer (1), Anup Das (PhD) (2) ((1) School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania, USA, (2) College of Engineering, Drexel University, Philadelphia, Pennsylvania, USA)

Comments: 6 pages, 8 Figures. Accepted to 2020 IEEE Signal Processing in Medicine and Biology Symposium, Temple University, Philadelphia, PA

Subjects: Signal Processing (eess.SP); Machine Learning (cs.LG); Genomics (q-bio.GN)

[234] arXiv:2011.03638 (cross-list from physics.bio-ph) [pdf, other]

Title: Profile likelihood analysis for a stochastic model of diffusion in heterogeneous media

Matthew J Simpson, Alexander P Browning, Christopher Drovandi, Elliot J Carr, Oliver J Maclaren, Ruth E Baker

Comments: 41 pages, 11 figures

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

[235] arXiv:2011.04312 (cross-list from cs.LG) [pdf, other]

Title: Nanopore Base Calling on the Edge

Peter Perešíni, Vladimír Boža, Broňa Brejová, Tomáš Vinař

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

[236] arXiv:2011.04441 (cross-list from eess.SY) [pdf, other]

Title: Neuromorphic Control

Luka Ribar, Rodolphe Sepulchre

Journal-ref: IEEE Control Systems Magazine, vol. 41, no. 6, pp. 34-63, Dec. 2021

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

[237] arXiv:2011.04526 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Computational methods and fast hybrid stochastic simulations for triangulation sensing and identifying principles of cell navigation in the brain

Ulrich Dobramysl, David Holcman

Comments: 52 pages, 26 figures

Subjects: Statistical Mechanics (cond-mat.stat-mech); Analysis of PDEs (math.AP); Cell Behavior (q-bio.CB)

[238] arXiv:2011.04565 (cross-list from math.CO) [pdf, other]

Title: Nondegenerate Neural Codes and Obstructions to Closed-Convexity

Patrick Chan, Katherine Johnston, Joseph Lent, Alexander Ruys de Perez, Anne Shiu

Comments: Added Corollary 4.14 and updated Remark 4.28

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

[239] arXiv:2011.04614 (cross-list from cond-mat.soft) [pdf, other]

Title: Turing's diffusive threshold in random reaction-diffusion systems

Pierre A. Haas, Raymond E. Goldstein

Comments: 6 pages, 4 figures; 5 pages of Supplemental Material; revised, expanded, and updated version

Journal-ref: Phys. Rev. Lett. 126, 238101 (2021)

Subjects: Soft Condensed Matter (cond-mat.soft); Pattern Formation and Solitons (nlin.PS); Populations and Evolution (q-bio.PE)

[240] arXiv:2011.04636 (cross-list from math.OC) [pdf, other]

Title: Low-Order Nonlinear Animal Model of Glucose Dynamics for a Bihormonal Intraperitoneal Artificial Pancreas

Claudia Lopez-Zazueta, Øyvind Stavdahl, Anders Lyngvi Fougner

Journal-ref: IEEE Transactions on Biomedical Engineering 2021

Subjects: Optimization and Control (math.OC); Other Quantitative Biology (q-bio.OT)

[241] arXiv:2011.04798 (cross-list from stat.ML) [pdf, other]

Title: Learning identifiable and interpretable latent models of high-dimensional neural activity using pi-VAE

Ding Zhou, Xue-Xin Wei

Journal-ref: NeurIPS 2020

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

[242] arXiv:2011.04802 (cross-list from cs.LG) [pdf, other]

Title: Sparse Longitudinal Representations of Electronic Health Record Data for the Early Detection of Chronic Kidney Disease in Diabetic Patients

Jinghe Zhang, Kamran Kowsari, Mehdi Boukhechba, James Harrison, Jennifer Lobo, Laura Barnes

Comments: Accepted in IEEE BIBM 2020

Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)

[243] arXiv:2011.04832 (cross-list from cs.LG) [pdf, other]

Title: Adaptive Learning of Rank-One Models for Efficient Pairwise Sequence Alignment

Govinda M. Kamath, Tavor Z. Baharav, Ilan Shomorony

Comments: NeurIPS 2020

Subjects: Machine Learning (cs.LG); Information Theory (cs.IT); Genomics (q-bio.GN); Machine Learning (stat.ML)

[244] arXiv:2011.05013 (cross-list from cs.LG) [pdf, other]

Title: A step towards neural genome assembly

Lovro Vrček, Petar Veličković, Mile Šikić

Comments: NeurIPS 2020 Learning Meets Combinatorial Algorithms Workshop. 5 pages, 1 figure

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

[245] arXiv:2011.05154 (cross-list from physics.bio-ph) [pdf, other]

Title: Molecular Communication Theoretical Modeling and Analysis of SARS-CoV2 Transmission in Human Respiratory System

Caglar Koca, Meltem Civas, Selin M. Sahin, Onder Ergonul, Ozgur B. Akan

Comments: IEEE Transactions on Molecular, Biological, and Multi-Scale Communications

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

[246] arXiv:2011.05292 (cross-list from eess.SY) [pdf, other]

Title: A Stochastic Optimal Control Model with Internal Feedback and Velocity Tracking for Saccades

Varsha V, Aditya Murthy, Radhakant Padhi

Comments: 10 pages, 10 figures

Subjects: Systems and Control (eess.SY); Neurons and Cognition (q-bio.NC)

[247] arXiv:2011.05342 (cross-list from physics.bio-ph) [pdf, other]

Title: Extreme antagonism arising from gene-environment interactions

Thomas P. Wytock, Manjing Zhan, Adrian Jinich, Aretha Fiebig, Sean Crosson, Adilson E. Motter

Comments: 34 pages, 8 figures, 10 tables. Published in Biophysical Journal

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

[248] arXiv:2011.05410 (cross-list from eess.IV) [pdf, other]

Title: Glioma Classification Using Multimodal Radiology and Histology Data

Azam Hamidinekoo, Tomasz Pieciak, Maryam Afzali, Otar Akanyeti, Yinyin Yuan

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

[249] arXiv:2011.05694 (cross-list from physics.med-ph) [pdf, other]

Title: Reverberant Elastography for the Elastic Characterization of Anisotropic Tissues

Luis A. Aleman-Castaneda, Fernando Zvietcovich, Kevin J. Parker

Comments: 12 pages, 14 figures

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

[250] arXiv:2011.06301 (cross-list from cs.LG) [pdf, other]

Title: Learning Inter-Modal Correspondence and Phenotypes from Multi-Modal Electronic Health Records

Kejing Yin, William K. Cheung, Benjamin C. M. Fung, Jonathan Poon

Comments: Accepted by IEEE Transactions on Knowledge and Data Engineering (TKDE)

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