Quantitative Biology

Authors and titles for September 2020

[201] arXiv:2009.01091 (cross-list from cs.CY) [pdf, other]

Title: covid19.analytics: An R Package to Obtain, Analyze and Visualize Data from the Coronavirus Disease Pandemic

Marcelo Ponce, Amit Sandhel

Comments: Version with updates matching ver 2.1 of the this http URL package

Subjects: Computers and Society (cs.CY); Information Retrieval (cs.IR); Populations and Evolution (q-bio.PE)

[202] arXiv:2009.01140 (cross-list from physics.soc-ph) [pdf, other]

Title: Kinetic models for epidemic dynamics with social heterogeneity

G. Dimarco, B. Perthame, G. Toscani, M. Zanella

Subjects: Physics and Society (physics.soc-ph); Adaptation and Self-Organizing Systems (nlin.AO); Populations and Evolution (q-bio.PE)

[203] arXiv:2009.01379 (cross-list from eess.IV) [pdf, other]

Title: Soft thresholding schemes for multiple signal classification algorithm

Sebastian Acuña, Ida S. Opstad, Fred Godtliebsen, Balpreet Singh Ahluwalia, Krishna Agarwal

Comments: 15 pages, 5 figures

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

[204] arXiv:2009.01661 (cross-list from physics.bio-ph) [pdf, other]

Title: Radical pairs may play a role in xenon-induced general anesthesia

Jordan Smith, Hadi Zadeh Haghighi, Dennis Salahub, Christoph Simon

Comments: 17 pages, 10 figures

Journal-ref: Sci Rep 11, 6287 (2021)

Subjects: Biological Physics (physics.bio-ph); Neurons and Cognition (q-bio.NC); Quantum Physics (quant-ph)

[205] arXiv:2009.01780 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Topological phase transition in coupled rock-paper-scissor cycles

Johannes Knebel, Philipp M. Geiger, Erwin Frey

Journal-ref: Phys. Rev. Lett. 125, 258301 (2020)

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

[206] arXiv:2009.02307 (cross-list from stat.AP) [pdf, other]

Title: Adaptive preferential sampling in phylodynamics

Lorenzo Cappello, Julia A. Palacios

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

[207] arXiv:2009.02375 (cross-list from physics.soc-ph) [pdf, other]

Title: Quantifying Inaccuracies in Modeling COVID-19 Pandemic within a Continuous Time Picture

Ioan Baldea

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

[208] arXiv:2009.02526 (cross-list from cs.IR) [pdf, other]

Title: Vapur: A Search Engine to Find Related Protein-Compound Pairs in COVID-19 Literature

Abdullatif Köksal, Hilal Dönmez, Rıza Özçelik, Elif Ozkirimli, Arzucan Özgür

Comments: EMNLP 2020 - COVID-19 Workshop

Subjects: Information Retrieval (cs.IR); Machine Learning (cs.LG); Molecular Networks (q-bio.MN)

[209] arXiv:2009.02654 (cross-list from stat.AP) [pdf, other]

Title: Semi-parametric modeling of SARS-CoV-2 transmission using tests, cases, deaths, and seroprevalence data

Damon Bayer, Isaac Goldstein, Jonathan Fintzi, Keith Lumbard, Emily Ricotta, Sarah Warner, Lindsay M. Busch, Jeffrey R. Strich, Daniel S. Chertow, Daniel M. Parker, Bernadette Boden-Albala, Alissa Dratch, Richard Chhuon, Nichole Quick, Matthew Zahn, Volodymyr M. Minin

Comments: 53 pages, 33 pages of main text, including 7 figures

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

[210] arXiv:2009.02704 (cross-list from eess.IV) [pdf, other]

Title: Deep Learning for Automatic Spleen Length Measurement in Sickle Cell Disease Patients

Zhen Yuan, Esther Puyol-Anton, Haran Jogeesvaran, Catriona Reid, Baba Inusa, Andrew P. King

Comments: 9 pages, 2 figures

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

[211] arXiv:2009.02903 (cross-list from eess.IV) [pdf, other]

Title: Brain Tumor Survival Prediction using Radiomics Features

Sobia Yousaf, Syed Muhammad Anwar, Harish RaviPrakash, Ulas Bagci

Comments: Submitted to RNO Workshop at MICCAI 2020

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

[212] arXiv:2009.03068 (cross-list from cs.CL) [pdf, other]

Title: Uncovering the Corona Virus Map Using Deep Entities and Relationship Models

Kuldeep Singh, Puneet Singla, Ketan Sarode, Anurag Chandrakar, Chetan Nichkawde

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

[213] arXiv:2009.03168 (cross-list from physics.soc-ph) [pdf, other]

Title: Effect of lockdown interventions to control the COVID-19 epidemic in India

Ankit Sharma, Shreyash Arya, Shashee Kumari, Arnab Chatterjee

Comments: 21 pages, 9 figures

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

[214] arXiv:2009.03587 (cross-list from cs.AI) [pdf, other]

Title: TaBooN -- Boolean Network Synthesis Based on Tabu Search

Sara Sadat Aghamiri, Franck Delaplace

Subjects: Artificial Intelligence (cs.AI); Computational Engineering, Finance, and Science (cs.CE); Molecular Networks (q-bio.MN)

[215] arXiv:2009.03608 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Intermittency as metastability: a predictive approach to evolution in disordered environments

Matteo Smerlak

Comments: Extension of arXiv:1912.05890

Journal-ref: Europhysics Letters 134 (2), 28002, 2021

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

[216] arXiv:2009.03649 (cross-list from physics.soc-ph) [pdf, other]

Title: The Role of Asymptomatic Individuals in the COVID-19 Pandemic via Complex Networks

Leonardo Stella, Alejandro Pinel Martínez, Dario Bauso, Patrizio Colaneri

Comments: 38 pages, journal

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

[217] arXiv:2009.04034 (cross-list from physics.data-an) [pdf, other]

Title: Long-timescale predictions from short-trajectory data: A benchmark analysis of the trp-cage miniprotein

John Strahan, Adam Antoszewski, Chatipat Lorpaiboon, Bodhi P. Vani, Jonathan Weare, Aaron R. Dinner

Comments: 61 pages, 17 figures

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

[218] arXiv:2009.04098 (cross-list from eess.SY) [pdf, other]

Title: Robustness of networked systems to unintended interactions with application to engineered genetic circuits

Yili Qian, Domitilla Del Vecchio

Subjects: Systems and Control (eess.SY); Molecular Networks (q-bio.MN)

[219] arXiv:2009.04524 (cross-list from cs.LG) [pdf, other]

Title: Interpreting Deep Glucose Predictive Models for Diabetic People Using RETAIN

Maxime De Bois, Mounîm A. El Yacoubi, Mehdi Ammi

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

[220] arXiv:2009.04647 (cross-list from cs.LG) [pdf, other]

Title: COVID-19 Pandemic Cyclic Lockdown Optimization Using Reinforcement Learning

Mauricio Arango, Lyudmil Pelov

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

[221] arXiv:2009.04765 (cross-list from cs.CL) [pdf, other]

Title: Brain2Word: Decoding Brain Activity for Language Generation

Nicolas Affolter, Beni Egressy, Damian Pascual, Roger Wattenhofer

Comments: Preprint. Work in progress

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

[222] arXiv:2009.04966 (cross-list from eess.SP) [pdf, other]

Title: Duality between Coronavirus Transmission and Air-based Macroscopic Molecular Communication

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

Comments: 9 pages, 6 figures, submitted to IEEE Transactions on Molecular, Biological, and Multi-Scale Communications for the special issue "Section II: Molecular Communications for Diagnostics and Therapeutic Development of Infectious Diseases"

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

[223] arXiv:2009.05277 (cross-list from cs.CV) [pdf, other]

Title: AFP-SRC: Identification of Antifreeze Proteins Using Sparse Representation Classifier

Shujaat Khan, Muhammad Usman, Abdul Wahab

Comments: This preprint has not undergone any post-submission improvements or corrections. The Version of Record of this article is published in Neural Computing and Applications, and is available online at this https URL

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

[224] arXiv:2009.05327 (cross-list from physics.soc-ph) [pdf, other]

Title: Coupled effects of epidemic information and risk awareness on contagion

Wen-Juan Xu, Chen-Yang Zhong, Hui-Fen Ye, Rong-Da Chen, Tian Qiu, Fei Ren, Li-Xin Zhong

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

[225] arXiv:2009.05354 (cross-list from physics.soc-ph) [pdf, other]

Title: The emergence of segregation: from observable markers to group specific norms

Juan Ozaita, Andrea Baronchelli, Angel Sánchez

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

[226] arXiv:2009.05359 (cross-list from cs.NE) [pdf, other]

Title: Activation Relaxation: A Local Dynamical Approximation to Backpropagation in the Brain

Beren Millidge, Alexander Tschantz, Anil K Seth, Christopher L Buckley

Comments: initial upload; revised version (updated abstract, related work) 28-09-20; 05/10/20: revised for ICLR submission; 10/10/20: minor revisions

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

[227] arXiv:2009.06076 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Stochastic Turing pattern formation in a model with active and passive transport

Hyunjoong Kim, Paul C. Bressloff

Comments: 26 pages, 8 figures

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

[228] arXiv:2009.06095 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Directional search-and-capture model of cytoneme-based morphogenesis

Paul C Bressloff

Comments: 20 pages, 11 figures

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

[229] arXiv:2009.06307 (cross-list from physics.soc-ph) [pdf, other]

Title: Ranking influential nodes in networks from partial information

Silvia Bartolucci, Fabio Caccioli, Francesco Caravelli, Pierpaolo Vivo

Comments: 13 pages, 7 figures. Significant changes in title and content (references added, more data sets analyzed, effect of network sparsity studied in more detail)

Journal-ref: Phys. Rev. Research 5, 033123 (2023)

Subjects: Physics and Society (physics.soc-ph); Statistical Mechanics (cond-mat.stat-mech); Other Quantitative Biology (q-bio.OT)

[230] arXiv:2009.06499 (cross-list from astro-ph.EP) [pdf, other]

Title: Phosphine on Venus Cannot be Explained by Conventional Processes

William Bains, Janusz J. Petkowski, Sara Seager, Sukrit Ranjan, Clara Sousa-Silva, Paul B. Rimmer, Zhuchang Zhan, Jane S. Greaves, Anita M. S. Richards

Comments: v2 is in press in Astrobiology, Special Collection: Venus; v2 also expands on the potential of phosphides from the deep mantle volcanism as a source of PH3 (as suggested by Truong and Lunine 2021: this https URL) and shows the volcanic source of PH3 to be unlikely

Subjects: Earth and Planetary Astrophysics (astro-ph.EP); Chemical Physics (physics.chem-ph); Other Quantitative Biology (q-bio.OT)

[231] arXiv:2009.06745 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Escape from an attractor generated by recurrent exit

Lou Zonca, David Holcman

Comments: 3 figures

Journal-ref: Phys. Rev. Research 3, 023115 (2021)

Subjects: Statistical Mechanics (cond-mat.stat-mech); Probability (math.PR); Chaotic Dynamics (nlin.CD); Cell Behavior (q-bio.CB)

[232] arXiv:2009.06808 (cross-list from cs.NE) [pdf, other]

Title: Optimality of short-term synaptic plasticity in modelling certain dynamic environments

Timoleon Moraitis, Abu Sebastian, Evangelos Eleftheriou (IBM Research - Zurich)

Comments: Main paper: 12 pages, 4 figures. Supplementary Information: 13 pages, 4 figures

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

[233] arXiv:2009.06829 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Universal relation between instantaneous diffusivity and radius of gyration of proteins in aqueous solution

Eiji Yamamoto, Takuma Akimoto, Ayori Mitsutake, Ralf Metzler

Journal-ref: Phys. Rev. Lett. 126, 128101 (2021)

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

[234] arXiv:2009.06919 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Hierarchical Coarse-grained Approach to the Duration-dependent Spreading Dynamics in Complex Networks

Jin-Fu Chen, Yi-Mu Du, Hui Dong, Chang-Pu Sun

Comments: 19 pages, 5 figures

Journal-ref: J. Phys. Complex. 2 02LT01 (2021)

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

[235] arXiv:2009.07250 (cross-list from cs.CV) [pdf, other]

Title: PointIso: Point Cloud Based Deep Learning Model for Detecting Arbitrary-Precision Peptide Features in LC-MS Map through Attention Based Segmentation

Fatema Tuz Zohora, M Ziaur Rahman, Ngoc Hieu Tran, Lei Xin, Baozhen Shan, Ming Li

Comments: 16 pages (main text) with 10 figures, then supplementary material of about 5 pages. preprint of journal submission

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

[236] arXiv:2009.07692 (cross-list from cs.AR) [pdf, other]

Title: GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis

Damla Senol Cali, Gurpreet S. Kalsi, Zülal Bingöl, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gomez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu

Comments: To appear in MICRO 2020

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

[237] arXiv:2009.07791 (cross-list from physics.soc-ph) [pdf, other]

Title: Dynamics of heuristics selection for cooperative behaviour

Felipe Maciel Cardoso, Carlos Gracia-Lazaro, Yamir Moreno

Comments: 22 pages and 23 figures, including the supplementary information. Submitted for publication

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

[238] arXiv:2009.08111 (cross-list from cs.AI) [pdf, other]

Title: Reward Maximisation through Discrete Active Inference

Lancelot Da Costa, Noor Sajid, Thomas Parr, Karl Friston, Ryan Smith

Comments: 18 pages, 3 figures (main text); 37 pages including references and appendix

Subjects: Artificial Intelligence (cs.AI); Optimization and Control (math.OC); Neurons and Cognition (q-bio.NC)

[239] arXiv:2009.08371 (cross-list from cs.CV) [pdf, other]

Title: Microtubule Tracking in Electron Microscopy Volumes

Nils Eckstein, Julia Buhmann, Matthew Cook, Jan Funke

Comments: Accepted at MICCAI 2020

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

[240] arXiv:2009.08373 (cross-list from cs.AI) [pdf, other]

Title: Modeling human visual search: A combined Bayesian searcher and saliency map approach for eye movement guidance in natural scenes

M. Sclar, G. Bujia, S. Vita, G. Solovey, J. E. Kamienkowski

Subjects: Artificial Intelligence (cs.AI); Computer Vision and Pattern Recognition (cs.CV); Neurons and Cognition (q-bio.NC)

[241] arXiv:2009.08515 (cross-list from math.PR) [pdf, other]

Title: A computational framework for evaluating the role of mobility on the propagation of epidemics on point processes

François Baccelli, Nithin Ramesan

Comments: post-revision, JMB

Subjects: Probability (math.PR); Social and Information Networks (cs.SI); Quantitative Methods (q-bio.QM)

[242] arXiv:2009.08664 (cross-list from eess.IV) [pdf, other]

Title: An Analysis by Synthesis Method that Allows Accurate Spatial Modeling of Thickness of Cortical Bone from Clinical QCT

Stefan Reinhold, Timo Damm, Sebastian Büsse, Stanislav N. Gorb, Claus-C. Glüer, Reinhard Koch

Comments: Accepted for publication in MICCAI 2020 conference

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

[243] arXiv:2009.08866 (cross-list from quant-ph) [pdf, other]

Title: ACSS-q: Algorithmic complexity for short strings via quantum accelerated approach

Aritra Sarkar, Koen Bertels

Comments: 8 pages

Subjects: Quantum Physics (quant-ph); Computational Complexity (cs.CC); Emerging Technologies (cs.ET); Formal Languages and Automata Theory (cs.FL); Quantitative Methods (q-bio.QM)

[244] arXiv:2009.08872 (cross-list from physics.soc-ph) [pdf, other]

Title: Economy Versus Disease Spread: Reopening Mechanisms for COVID 19

John Augustine, Khalid Hourani, Anisur Rahaman Molla, Gopal Pandurangan, Adi Pasic

Comments: 16 pages, 3 figures, 3 tables

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

[245] arXiv:2009.08889 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Large Deviations Approach to Random Recurrent Neuronal Networks: Parameter Inference and Fluctuation-Induced Transitions

Alexander van Meegen, Tobias Kühn, Moritz Helias

Comments: Extension to multiple populations

Journal-ref: Phys. Rev. Lett. 127, 158302 (2021)

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

[246] arXiv:2009.08917 (cross-list from eess.IV) [pdf, other]

Title: Predicting molecular phenotypes from histopathology images: a transcriptome-wide expression-morphology analysis in breast cancer

Yinxi Wang, Kimmo Kartasalo, Masi Valkonen, Christer Larsson, Pekka Ruusuvuori, Johan Hartman, Mattias Rantalainen

Comments: 42 pages, 6 figures

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

[247] arXiv:2009.09081 (cross-list from cs.ET) [pdf, other]

Title: Closed-loop spiking control on a neuromorphic processor implemented on the iCub

Jingyue Zhao, Nicoletta Risi, Marco Monforte, Chiara Bartolozzi, Giacomo Indiveri, Elisa Donati

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

[248] arXiv:2009.09418 (cross-list from math.PR) [pdf, other]

Title: $\Lambda$-coalescents arising in populations with dormancy

Fernando Cordero, Adrián González Casanova, Jason Schweinsberg, Maite Wilke-Berenguer

Comments: 35 pages

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

[249] arXiv:2009.09514 (cross-list from physics.soc-ph) [pdf, other]

Title: Early Indicators of COVID-19 Spread Risk Using Digital Trace Data of Population Activities

Xinyu Gao, Chao Fan, Yang Yang, Sanghyeon Lee, Qingchun Li, Mikel Maron, Ali Mostafavi

Comments: 12 pages, 8 figures

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

[250] arXiv:2009.09648 (cross-list from physics.soc-ph) [pdf, other]

Title: Measuring the effect of Non-Pharmaceutical Interventions (NPIs) on mobility during the COVID-19 pandemic using global mobility data

Berber T Snoeijer, Mariska Burger, Shaoxiong Sun, Richard JB Dobson, Amos A Folarin

Comments: 16 pages, 6 figures

Subjects: Physics and Society (physics.soc-ph); Social and Information Networks (cs.SI); Quantitative Methods (q-bio.QM)