Quantitative Biology

Authors and titles for February 2020

[201] arXiv:2002.03880 (cross-list from physics.bio-ph) [pdf, other]

Title: Resolving the degree of order in the bacterial chromosome using a statistical physics approach

Joris J.B. Messelink, Jacqueline Janssen, Muriel C.F. van Teeseling, Martin Thanbichler, Chase P. Broedersz

Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech); Genomics (q-bio.GN)

[202] arXiv:2002.03961 (cross-list from cond-mat.soft) [pdf, other]

Title: Shape and size changes of adherent elastic epithelia

Benjamin Loewe, Francesco Serafin, Suraj Shankar, Mark J. Bowick, M. Cristina Marchetti

Comments: 12 pages, 8 figures (including Appendix), published version including more calculations without changing results

Journal-ref: Soft Matter, 16, 5282-5293, 2020

Subjects: Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Tissues and Organs (q-bio.TO)

[203] arXiv:2002.04176 (cross-list from stat.AP) [pdf, other]

Title: Personalized acute stress classification from physiological signals with neural processes

Callum L. Stewart, Amos Folarin, Richard Dobson

Comments: 16 pages (inc. references), 5 figures, 3 tables

Subjects: Applications (stat.AP); Neurons and Cognition (q-bio.NC)

[204] arXiv:2002.04298 (cross-list from physics.bio-ph) [pdf, other]

Title: Normal epithelial and triple-negative breast cancer cells show the same invasion potential in rigid spatial confinement

Carlotta Ficorella, Rebeca Martinez Vasquez, Paul Heine, Eugenia Lepera, Jing Cao, Enrico Warmt, Roberto Osellame, Josef A. Käs

Comments: 32 pages, 10 figures

Journal-ref: New J. Phys. 21 (2019) 083016

Subjects: Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)

[205] arXiv:2002.04309 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: A unifying framework for mean-field theories of asymmetric kinetic Ising systems

Miguel Aguilera, S. Amin Moosavi, Hideaki Shimazaki

Journal-ref: Nature Communications 12, 1197 (2021)

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

[206] arXiv:2002.04358 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Dynamical persistence in resource-consumer models

Itay Dalmedigos, Guy Bunin

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

[207] arXiv:2002.04461 (cross-list from stat.ML) [pdf, other]

Title: TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics

Alexander Tong, Jessie Huang, Guy Wolf, David van Dijk, Smita Krishnaswamy

Comments: Presented at ICML 2020

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

[208] arXiv:2002.04473 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Translocation of links through a pore: effects of link complexity and size

Michele Caraglio, Enzo Orlandini, Stuart G Whittington

Comments: 15 pages, 7 figures

Subjects: Statistical Mechanics (cond-mat.stat-mech); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Computational Physics (physics.comp-ph); Biomolecules (q-bio.BM)

[209] arXiv:2002.04482 (cross-list from physics.soc-ph) [pdf, other]

Title: Network-Based Prediction of the 2019-nCoV Epidemic Outbreak in the Chinese Province Hubei

Bastian Prasse, Massimo A. Achterberg, Long Ma, Piet Van Mieghem

Comments: Ordering of cities in Table 1 has been corrected; Prediction considers more recent observations

Journal-ref: Applied Network Science, 5(1), pp.1-11 (2020)

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

[210] arXiv:2002.04500 (cross-list from eess.IV) [pdf, other]

Title: Artificial Intelligence Assistance Significantly Improves Gleason Grading of Prostate Biopsies by Pathologists

Wouter Bulten, Maschenka Balkenhol, Jean-Joël Awoumou Belinga, Américo Brilhante, Aslı Çakır, Xavier Farré, Katerina Geronatsiou, Vincent Molinié, Guilherme Pereira, Paromita Roy, Günter Saile, Paulo Salles, Ewout Schaafsma, Joëlle Tschui, Anne-Marie Vos, Hester van Boven, Robert Vink, Jeroen van der Laak, Christina Hulsbergen-van de Kaa, Geert Litjens

Comments: 21 pages, 5 figures

Journal-ref: Modern Pathology, Available online 5 August 2020

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

[211] arXiv:2002.04721 (cross-list from stat.ME) [pdf, other]

Title: A Method Expanding 2 by 2 Contingency Table by Obtaining Tendencies of Boolean Operators: Boolean Monte Carlo Method

Takuma Usuzaki, Minoru Shimoyama, Shuji Chiba, Naoko Mori, Shunji Mugikura

Comments: 9 pages, 1 figures

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

[212] arXiv:2002.04915 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Stem cell lineage survival as a noisy competition for niche access

Bernat Corominas-Murtra, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco van Rheenen, Edouard Hannezo

Comments: 21 pages 10 figures, (with appendix)

Journal-ref: Proceedings of the National Academy of Sciences (USA) 117 (29) 16969--16975 (2020)

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Tissues and Organs (q-bio.TO)

[213] arXiv:2002.04924 (cross-list from cs.NE) [pdf, other]

Title: Synaptic Integration of Spatiotemporal Features with a Dynamic Neuromorphic Processor

Mattias Nilsson, Foteini Liwicki, Fredrik Sandin

Comments: Copyright 2020 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works

Journal-ref: 2020 International Joint Conference on Neural Networks (IJCNN), 2020, pp. 1-7

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

[214] arXiv:2002.05048 (cross-list from stat.AP) [pdf, other]

Title: A powerful MAF-neutral allele-based test for case-control association studies

Marianne A. Jonker, Jakub Pecanka

Comments: 24 pages, 5 figures, includes Appendix

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

[215] arXiv:2002.05090 (cross-list from physics.soc-ph) [pdf, other]

Title: Predicting the speed of epidemics spreading on networks

Sam Moore, Tim Rogers

Journal-ref: Phys. Rev. Lett. 124, 068301, 2020

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

[216] arXiv:2002.05106 (cross-list from physics.soc-ph) [pdf, other]

Title: A novel route to cyclic dominance in voluntary social dilemmas

Hao Guo, Zhao Song, Sunčana Geček, Xuelong Li, Marko Jusup, Matjaz Perc, Yamir Moreno, Stefano Boccaletti, Zhen Wang

Comments: 9 pages, 6 figures, supplementary information

Journal-ref: J. R. Soc. Interface 17, 20190789 (2020)

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

[217] arXiv:2002.05487 (cross-list from eess.IV) [pdf, other]

Title: End-to-end semantic segmentation of personalized deep brain structures for non-invasive brain stimulation

Essam A. Rashed, Jose Gomez-Tames, Akimasa Hirata

Comments: To appear in Neural Networks

Journal-ref: Neural Networks 125, pp. 233-244, 2020

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

[218] arXiv:2002.05592 (cross-list from stat.ME) [pdf, other]

Title: On Contamination of Symbolic Datasets

Antony Pearson, Manuel E. Lladser

Comments: 18 pages, 4 figures, 1 table

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

[219] arXiv:2002.05623 (cross-list from physics.med-ph) [pdf, other]

Title: Speckle from branching vasculature: dependence on number density

Kevin J. Parker (1), Sedigheh S. Poul (2) ((1) University of Rochester, Department of Electrical and Computer Engineering, (2) University of Rochester, Department of Mechanical Engineering)

Comments: 23 pages, 10 figures

Journal-ref: J Med Imaging 7(2) p. 027001, 2020

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

[220] arXiv:2002.05627 (cross-list from physics.med-ph) [pdf, other]

Title: Fine-tuning the H-scan for visualizing types of tissue scatterers

Kevin J. Parker (1), Jihye Baek (1) ((1) Department of Electrical & Computer Engineering, University of Rochester)

Comments: 35 pages, 17 figures

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

[221] arXiv:2002.05692 (cross-list from eess.IV) [pdf, other]

Title: Neuromorphologicaly-preserving Volumetric data encoding using VQ-VAE

Petru-Daniel Tudosiu, Thomas Varsavsky, Richard Shaw, Mark Graham, Parashkev Nachev, Sebastien Ourselin, Carole H. Sudre, M. Jorge Cardoso

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

[222] arXiv:2002.05909 (cross-list from cs.LG) [pdf, other]

Title: Deep reconstruction of strange attractors from time series

William Gilpin

Comments: 9 pages, 6 figures, plus appendices

Journal-ref: NeurIPS (Neural Information Processing Systems) 2020

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

[223] arXiv:2002.06645 (cross-list from physics.soc-ph) [pdf, other]

Title: Heterogeneity in evolutionary games: an analysis of the risk perception

Marco A. Amaral, Marco A. Javarone

Comments: 7 pages, 5 figures

Journal-ref: Proc. R. Soc. A.47620200116 (2020)

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

[224] arXiv:2002.06680 (cross-list from physics.bio-ph) [pdf, other]

Title: Inferring the dynamics of underdamped stochastic systems

David B. Brückner, Pierre Ronceray, Chase P. Broedersz

Journal-ref: Phys. Rev. Lett. 125, 058103 (2020)

Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech); Cell Behavior (q-bio.CB); Quantitative Methods (q-bio.QM)

[225] arXiv:2002.06717 (cross-list from physics.bio-ph) [pdf, other]

Title: Static adhesion hysteresis in elastic structures

Edvin Memet, Feodor Hilitski, Zvonimir Dogic, L. Mahadevan

Comments: 7 pages, 4 figures. Soft Matter, (2021)

Subjects: Biological Physics (physics.bio-ph); Materials Science (cond-mat.mtrl-sci); Soft Condensed Matter (cond-mat.soft); Applied Physics (physics.app-ph); Subcellular Processes (q-bio.SC)

[226] arXiv:2002.06816 (cross-list from cs.CV) [pdf, html, other]

Title: On the Similarity of Deep Learning Representations Across Didactic and Adversarial Examples

Pk Douglas, Farzad Vasheghani Farahani

Comments: 2 figures

Journal-ref: Med NeurIPS 2019

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

[227] arXiv:2002.06926 (cross-list from physics.soc-ph) [pdf, other]

Title: Virus spread and voter model on random graphs with multiple type nodes

Ágnes Backhausz, Edit Bognár

Comments: 27 pages

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

[228] arXiv:2002.07096 (cross-list from physics.med-ph) [pdf, other]

Title: Visual Data Analysis and Simulation Prediction for COVID-19

Baoquan Chen, Mingyi Shi, Xingyu Ni, Liangwang Ruan, Hongda Jiang, Heyuan Yao, Mengdi Wang, Zhenhua Song, Qiang Zhou, Tong Ge

Comments: 19 pages, 21 figures, revised English version and originally Chinese version

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

[229] arXiv:2002.07377 (cross-list from physics.bio-ph) [pdf, other]

Title: High spatially sensitive quantitative phase imaging assisted with deep neural network for classification of human spermatozoa under stressed condition

Ankit Butola, Daria Popova, Dilip K Prasad, Azeem Ahmad, Anowarul Habib, Jean Claude Tinguely, Purusotam Basnet, Ganesh Acharya, Paramasivam Senthilkumaran, Dalip Singh Mehta, Balpreet Singh Ahluwalia

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

[230] arXiv:2002.07534 (cross-list from cs.RO) [pdf, other]

Title: A Spiking Neural Network Emulating the Structure of the Oculomotor System Requires No Learning to Control a Biomimetic Robotic Head

Praveenram Balachandar, Konstantinos P. Michmizos

Comments: 6 pages, 3 figures, IEEE International Conference on Biomedical Robotics and Biomechatronics (BioRob) 2020

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

[231] arXiv:2002.07541 (cross-list from cs.RO) [pdf, other]

Title: Machine Learning for Motor Learning: EEG-based Continuous Assessment of Cognitive Engagement for Adaptive Rehabilitation Robots

Neelesh Kumar, Konstantinos P. Michmizos

Comments: 6 pages, 6 figures, 1 table

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

[232] arXiv:2002.07542 (cross-list from math.AP) [pdf, other]

Title: Equilibrium and sensitivity analysis of a spatio-temporal host-vector epidemic model

Olivier Martin (BIOSP), Yasmil Fernandez-Diclo, Jerome Coville (BIOSP), Samuel Soubeyrand (BIOSP)

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

[233] arXiv:2002.07681 (cross-list from cs.LG) [pdf, other]

Title: Deep Neural Networks for the Correction of Mie Scattering in Fourier-Transformed Infrared Spectra of Biological Samples

Arne P. Raulf, Joshua Butke, Lukas Menzen, Claus Küpper, Frederik Großerueschkamp, Klaus Gerwert, Axel Mosig

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

[234] arXiv:2002.08104 (cross-list from cs.LG) [pdf, other]

Title: Analyzing Neural Networks Based on Random Graphs

Romuald A. Janik, Aleksandra Nowak

Comments: Added new results and discussion

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

[235] arXiv:2002.08132 (cross-list from math.DS) [pdf, other]

Title: How to generate species with positive concentrations for all positive times?

Seyed Mahdi Shavarani, János Tóth, Béla Vizvári

Comments: 19 pages, 7 figures

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

[236] arXiv:2002.08138 (cross-list from physics.bio-ph) [pdf, other]

Title: Bayesian gradient sensing in the presence of rotational diffusion

Maja Novak, Benjamin M. Friedrich

Comments: 11 pages + 5 pages appendix, 2 color figures

Subjects: Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)

[237] arXiv:2002.08354 (cross-list from cs.RO) [pdf, other]

Title: Deep Learning of Movement Intent and Reaction Time for EEG-informed Adaptation of Rehabilitation Robots

Neelesh Kumar, Konstantinos P. Michmizos

Comments: 6 pages, 3 figures, 3 tables. arXiv admin note: text overlap with arXiv:2002.07541

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

[238] arXiv:2002.08363 (cross-list from cs.SE) [pdf, other]

Title: Pline: automatic generation of modern web interfaces for command-line programs

Andres Veidenberg, Ari Löytynoja

Subjects: Software Engineering (cs.SE); Quantitative Methods (q-bio.QM)

[239] arXiv:2002.08658 (cross-list from math.PR) [pdf, other]

Title: Ancestral lines under recombination

Ellen Baake, Michael Baake

Comments: to appear in: Probabilistic Structures in Evolution, E. Baake and A. Wakolbinger (eds.), EMS Publishing House, Zurich

Journal-ref: in: Probabilistic Structures in Evolution (E. Baake, A. Wakolbinger, eds.), EMS Press, Berlin, 2021, pp. 365-382

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

[240] arXiv:2002.08820 (cross-list from eess.IV) [pdf, other]

Title: Deep Learning Estimation of Multi-Tissue Constrained Spherical Deconvolution with Limited Single Shell DW-MRI

Vishwesh Nath, Sudhir K. Pathak, Kurt G. Schilling, Walt Schneider, Bennett A. Landman

Comments: 10 pages, 7 figures

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

[241] arXiv:2002.09032 (cross-list from stat.ME) [pdf, other]

Title: Knockoff Boosted Tree for Model-Free Variable Selection

Tao Jiang, Yuanyuan Li, Alison A. Motsinger-Reif

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

[242] arXiv:2002.09117 (cross-list from nlin.AO) [pdf, other]

Title: Synaptic balance due to homeostatically self-organized quasicritical dynamics

Mauricio Girardi-Schappo, Ludmila Brochini, Ariadne A. Costa, Tawan T. A. Carvalho, Osame Kinouchi

Comments: 18 pages, 4 figures

Journal-ref: Phys. Rev. Research 2, 012042(R) (2020)

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

[243] arXiv:2002.09199 (cross-list from physics.soc-ph) [pdf, other]

Title: Scaling features in the spreading of COVID-19

Ming Li, Jie Chen, Youjin Deng

Comments: 7 pages, 5 figures

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

[244] arXiv:2002.09283 (cross-list from cs.DL) [pdf, other]

Title: MODMA dataset: a Multi-modal Open Dataset for Mental-disorder Analysis

Hanshu Cai, Yiwen Gao, Shuting Sun, Na Li, Fuze Tian, Han Xiao, Jianxiu Li, Zhengwu Yang, Xiaowei Li, Qinglin Zhao, Zhenyu Liu, Zhijun Yao, Minqiang Yang, Hong Peng, Jing Zhu, Xiaowei Zhang, Guoping Gao, Fang Zheng, Rui Li, Zhihua Guo, Rong Ma, Jing Yang, Lan Zhang, Xiping Hu, Yumin Li, Bin Hu

Journal-ref: Sci Data 9, 178 (2022)

Subjects: Digital Libraries (cs.DL); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)

[245] arXiv:2002.09325 (cross-list from physics.bio-ph) [pdf, other]

Title: Stochastic model of T Cell repolarization during target elimination (I)

Ivan Hornak, Heiko Rieger

Comments: Suplemental videos can be found at this http URL

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

[246] arXiv:2002.09626 (cross-list from eess.SY) [pdf, other]

Title: Feedback Identification of conductance-based models

Thiago B. Burghi, Maarten Schoukens, Rodolphe Sepulchre

Journal-ref: Automatica; 2021. Vol 123. Article 109297

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

[247] arXiv:2002.09711 (cross-list from physics.bio-ph) [pdf, other]

Title: Robotic modeling of snake traversing large, smooth obstacles reveals stability benefits of body compliance

Qiyuan Fu, Chen Li

Journal-ref: Royal Society Open Science (2020), 7, 191192

Subjects: Biological Physics (physics.bio-ph); Systems and Control (eess.SY); Quantitative Methods (q-bio.QM)

[248] arXiv:2002.10284 (cross-list from cs.CL) [pdf, other]

Title: Word Embeddings Inherently Recover the Conceptual Organization of the Human Mind

Victor Swift

Comments: 12 pages, 4 figures

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

[249] arXiv:2002.10378 (cross-list from cs.LG) [pdf, other]

Title: Contrastive Similarity Matching for Supervised Learning

Shanshan Qin, Nayantara Mudur, Cengiz Pehlevan

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

[250] arXiv:2002.10498 (cross-list from cs.DM) [pdf, other]

Title: Genome assembly, from practice to theory: safe, complete and linear-time

Massimo Cairo, Romeo Rizzi, Alexandru I. Tomescu, Elia C. Zirondelli

Subjects: Discrete Mathematics (cs.DM); Combinatorics (math.CO); Genomics (q-bio.GN)