Quantitative Biology

Authors and titles for July 2020

[251] arXiv:2007.16012 [pdf, other]

Title: BERT Learns (and Teaches) Chemistry

Josh Payne, Mario Srouji, Dian Ang Yap, Vineet Kosaraju

Comments: 10 pages, 5 figures

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

[252] arXiv:2007.16018 [pdf, other]

Title: Quantifying dynamical high-order interdependencies from the O-information: an application to neural spiking dynamics

Sebastiano Stramaglia, Tomas Scagliarini, Bryan C. Daniels, Daniele Marinazzo

Subjects: Neurons and Cognition (q-bio.NC)

[253] arXiv:2007.16069 [pdf, other]

Title: Exact closed-form solution of a modified SIR model

Angel Ballesteros, Alfonso Blasco, Ivan Gutierrez-Sagredo

Comments: 17 pages. New section added

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

[254] arXiv:2007.16121 [pdf, other]

Title: Reweighting of Binaural Localization Cues Induced by Lateralization Training

Maike Klingel (1, 2 and 3), Norbert Kopco (3), Bernhard Laback (1) ((1) Acoustics Research Institute, Austrian Academy of Sciences, (2) Department of Cognition, Emotion, and Methods in Psychology, Faculty of Psychology, University of Vienna, (3) Institute of Computer Science, Faculty of Science, P. J. Safarik University in Kosice)

Subjects: Neurons and Cognition (q-bio.NC)

[255] arXiv:2007.16138 [pdf, other]

Title: A Compositional Model of Consciousness based on Consciousness-Only

Camilo Miguel Signorelli, Quanlong Wang, Ilyas Khan

Comments: 19 pages

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

[256] arXiv:2007.16151 [pdf, other]

Title: Optimal periodic closure for minimizing risk in emerging disease outbreaks

Jason Hindes, Simone Bianco, Ira B. Schwartz

Comments: supplementary material included in ancillary files

Journal-ref: PLoS ONE 16(1): e0244706 (2021)

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

[257] arXiv:2007.16177 [pdf, other]

Title: Screening and evaluation of potential clinically significant HIV drug combinations against SARS-CoV-2 virus

Draško Tomić (1), Karolj Skala (1), Attila Marcel Szasz (2), Melinda Rezeli (3), Vesna Bačić Vrca (4), Boris Pirkić (5), Jozsef Petrik (6), Vladimir Janđel (7), Marija Milković Periša (8), Branka Medved Rogina (9), Josip Mesarić (10), Davor Davidović (1), Tomislav Lipić (10) ((1) Center for Informatics and Computing, Ruđer Bošković Institute, Zagreb, Croatia, (2) Department of Bioinformatics and Cancer Center, Semmelweis University Budapest, Hungary, (3) Department of Biomedical Engineering, Lund University, Lund, Sweden, (4) Central Hospital Pharmacy, Clinical Hospital Center Dubrava, Zagreb, Croatia, (5) Surgery, Orthopedics and Ophthalmology Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia, (6) Department of Medical Biochemistry and Hematology, Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia, (7) Deprtment of Obstetricy, Clinical Hospital Centre Zagreb, (8) Institute of Pathology, School of Medicine University of Zagreb, Zagreb, Croatia, (9) Laboratory for Information and Signal Processing, Division of Electronics, Ruđer Bosković Institute, Zagreb, Croatia, (10) Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia, (11) Machine Learning Lab and Knowledge Representations, Division of Electronics, Ruđer Bošković Institute, Zagreb, Croatia)

Comments: 8 pages, 4 figures

Subjects: Quantitative Methods (q-bio.QM)

[258] arXiv:2007.00317 (cross-list from physics.bio-ph) [pdf, other]

Title: Mathematical model for the thermal enhancement of radiation response: Thermodynamic approach

Adriana M. De Mendoza, Soňa Michlíková, Johann Berger, Jens Karschau, Leoni A. Kunz-Schughart, Damian D. McLeod

Comments: 12 pages, 3 figures, 2 table, 60 references

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

[259] arXiv:2007.00478 (cross-list from eess.IV) [pdf, other]

Title: PAD-UFES-20: a skin lesion dataset composed of patient data and clinical images collected from smartphones

Andre G. C. Pacheco, Gustavo R. Lima, Amanda S. Salomão, Breno A. Krohling, Igor P. Biral, Gabriel G. de Angelo, Fábio C. R. Alves Jr, José G. M. Esgario, Alana C. Simora, Pedro B. C. Castro, Felipe B. Rodrigues, Patricia H. L. Frasson, Renato A. Krohling, Helder Knidel, Maria C. S. Santos, Rachel B. do Espírito Santo, Telma L. S. G. Macedo, Tania R. P. Canuto, Luíz F. S. de Barros

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

[260] arXiv:2007.00756 (cross-list from stat.AP) [pdf, other]

Title: An Early Warning Approach to Monitor COVID-19 Activity with Multiple Digital Traces in Near Real-Time

Nicole E. Kogan, Leonardo Clemente, Parker Liautaud, Justin Kaashoek, Nicholas B. Link, Andre T. Nguyen, Fred S. Lu, Peter Huybers, Bernd Resch, Clemens Havas, Andreas Petutschnig, Jessica Davis, Matteo Chinazzi, Backtosch Mustafa, William P. Hanage, Alessandro Vespignani, Mauricio Santillana

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

[261] arXiv:2007.00776 (cross-list from cs.ET) [pdf, other]

Title: Emulation of Astrocyte Induced Neural Phase Synchrony in Spin-Orbit Torque Oscillator Neurons

Umang Garg, Kezhou Yang, Abhronil Sengupta

Subjects: Emerging Technologies (cs.ET); Neurons and Cognition (q-bio.NC)

[262] arXiv:2007.00858 (cross-list from cs.CV) [pdf, other]

Title: MSA-MIL: A deep residual multiple instance learning model based on multi-scale annotation for classification and visualization of glomerular spikes

Yilin Chen, Ming Li, Yongfei Wu, Xueyu Liu, Fang Hao, Daoxiang Zhou, Xiaoshuang Zhou, Chen Wang

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

[263] arXiv:2007.00897 (cross-list from cs.LG) [pdf, other]

Title: Deep brain state classification of MEG data

Ismail Alaoui Abdellaoui, Jesus Garcia Fernandez, Caner Sahinli, Siamak Mehrkanoon

Comments: 11 pages, 11 figures

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

[264] arXiv:2007.01099 (cross-list from cs.LG) [pdf, other]

Title: Reinforcement Learning and its Connections with Neuroscience and Psychology

Ajay Subramanian, Sharad Chitlangia, Veeky Baths

Comments: Accepted to Elsevier Neural Networks; 19 pages, 6 figures, 1 table

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

[265] arXiv:2007.01200 (cross-list from cs.LG) [pdf, other]

Title: A Semi-Supervised Generative Adversarial Network for Prediction of Genetic Disease Outcomes

Caio Davi, Ulisses Braga-Neto

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

[266] arXiv:2007.01251 (cross-list from eess.IV) [pdf, other]

Title: Image Processing and Quality Control for Abdominal Magnetic Resonance Imaging in the UK Biobank

Nicolas Basty, Yi Liu, Madeleine Cule, E. Louise Thomas, Jimmy D. Bell, Brandon Whitcher

Comments: Fixed 2 references

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

[267] arXiv:2007.01337 (cross-list from math.CO) [pdf, other]

Title: Metric Dimension of Hamming Graphs and Applications to Computational Biology

Lucas Laird

Subjects: Combinatorics (math.CO); Quantitative Methods (q-bio.QM)

[268] arXiv:2007.01383 (cross-list from eess.IV) [pdf, other]

Title: Deep Interactive Learning: An Efficient Labeling Approach for Deep Learning-Based Osteosarcoma Treatment Response Assessment

David Joon Ho, Narasimhan P. Agaram, Peter J. Schueffler, Chad M. Vanderbilt, Marc-Henri Jean, Meera R. Hameed, Thomas J. Fuchs

Comments: Accepted at MICCAI 2020

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

[269] arXiv:2007.01424 (cross-list from physics.soc-ph) [pdf, other]

Title: Active Control and Sustained Oscillations in actSIS Epidemic Dynamics

Yunxiu Zhou, Simon A. Levin, Naomi E. Leonard

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

[270] arXiv:2007.01516 (cross-list from cs.LG) [pdf, other]

Title: Deep interpretability for GWAS

Deepak Sharma, Audrey Durand, Marc-André Legault, Louis-Philippe Lemieux Perreault, Audrey Lemaçon, Marie-Pierre Dubé, Joelle Pineau

Comments: Accepted at ICML 2020 workshop on ML Interpretability for Scientific Discovery

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

[271] arXiv:2007.01583 (cross-list from physics.soc-ph) [pdf, other]

Title: COVID-19 lockdown induces disease-mitigating structural changes in mobility networks

Frank Schlosser, Benjamin F. Maier, Olivia Jack, David Hinrichs, Adrian Zachariae, Dirk Brockmann

Comments: 20 pages, 8 figures

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

[272] arXiv:2007.01927 (cross-list from cond-mat.soft) [pdf, other]

Title: Equilibrium mechanisms of self-limiting assembly

Michael F. Hagan, Gregory M. Grason

Comments: (2nd version: extensive revisions) 55 pages; 19 figures; 3 appendices

Journal-ref: Rev. Mod. Phys. 93, 025008 (2021)

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

[273] arXiv:2007.01935 (cross-list from stat.AP) [pdf, other]

Title: Statistical hypothesis testing versus machine-learning binary classification: distinctions and guidelines

Jingyi Jessica Li, Xin Tong

Journal-ref: Patterns 1(7) (2020) 100115

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

[274] arXiv:2007.01975 (cross-list from eess.IV) [pdf, other]

Title: Interpretation of Disease Evidence for Medical Images Using Adversarial Deformation Fields

Ricardo Bigolin Lanfredi, Joyce D. Schroeder, Clement Vachet, Tolga Tasdizen

Comments: Presented at MICCAI 2020

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

[275] arXiv:2007.02047 (cross-list from cs.LG) [pdf, other]

Title: Relationship between manifold smoothness and adversarial vulnerability in deep learning with local errors

Zijian Jiang, Jianwen Zhou, Haiping Huang

Comments: 10 pages, 8 figures, to appear in Chin. Phys. B (2021)

Journal-ref: Chin. Phys. B Vol. 30, No. 4 (2021) 048702

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

[276] arXiv:2007.02198 (cross-list from cs.CE) [pdf, other]

Title: Scalable Bayesian Functional Connectivity Inference for Multi-Electrode Array Recordings

Yun Zhao, Richard Jiang, Zhenni Xu, Elmer Guzman, Paul K. Hansma, Linda Petzold

Comments: in BIOKDD 2020

Subjects: Computational Engineering, Finance, and Science (cs.CE); Neurons and Cognition (q-bio.NC)

[277] arXiv:2007.02283 (cross-list from physics.soc-ph) [pdf, other]

Title: Superposition of waves for modeling COVID-19 epidemic in the world and in the countries with the maximum number of infected people in the first half of 2020

E.M. Koltsova, E.S. Kurkina1, A.M. Vasetsky

Comments: 21 pages, 8 figures, 9 tables

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

[278] arXiv:2007.02511 (cross-list from physics.bio-ph) [pdf, other]

Title: Less is More: Wiring-Economical Modular Networks Support Self-Sustained Firing-Economical Neural Avalanches for Efficient Processing

Junhao Liang, Sheng-Jun Wang, Changsong Zhou

Comments: 19 pages, 6 figures

Journal-ref: National Science Review, nwab102, Published: 10 June 2021

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

[279] arXiv:2007.02695 (cross-list from cs.IT) [pdf, other]

Title: Two-Stage Adaptive Pooling with RT-qPCR for COVID-19 Screening

Anoosheh Heidarzadeh, Krishna R. Narayanan

Comments: 23 pages, 3 figures, 4 tables

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

[280] arXiv:2007.02774 (cross-list from physics.soc-ph) [pdf, other]

Title: The role of time scale in the spreading of asymmetrically interacting diseases

Paulo Cesar Ventura, Yamir Moreno, Francisco A. Rodrigues

Comments: 11 pages and 8 figures

Journal-ref: Phys. Rev. Research 3, 013146 (2021)

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

[281] arXiv:2007.02830 (cross-list from cond-mat.soft) [pdf, other]

Title: Designing metachronal waves of cilia

Fanlong Meng, Rachel R. Bennett, Nariya Uchida, Ramin Golestanian

Comments: F. M. and R. R. B. contributed equally to this work

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

[282] arXiv:2007.03040 (cross-list from cs.DS) [pdf, other]

Title: Near-Linear Time Edit Distance for Indel Channels

Arun Ganesh, Aaron Sy

Comments: Appears in WABI 2020

Subjects: Data Structures and Algorithms (cs.DS); Quantitative Methods (q-bio.QM)

[283] arXiv:2007.03173 (cross-list from math.DS) [pdf, other]

Title: Distributed Delay Differential Equation Representations of Cyclic Differential Equations

Tyler Cassidy

Journal-ref: SIAM Journal on Applied Mathematics, 2021, Vol. 81, No. 4 : pp. 1742-1766

Subjects: Dynamical Systems (math.DS); Quantitative Methods (q-bio.QM)

[284] arXiv:2007.03208 (cross-list from math.AT) [pdf, other]

Title: A Topological Approach to Inferring the Intrinsic Dimension of Convex Sensing Data

Min-Chun Wu, Vladimir Itskov

Subjects: Algebraic Topology (math.AT); Combinatorics (math.CO); Neurons and Cognition (q-bio.NC); Machine Learning (stat.ML)

[285] arXiv:2007.03287 (cross-list from physics.soc-ph) [pdf, other]

Title: Two-pathogen model with competition on clustered networks

Peter Mann, V. Anne Smith, John B. O. Mitchell, Simon Dobson

Comments: 9 pages, 5 figures

Journal-ref: Phys. Rev. E 103, 062308 (2021)

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

[286] arXiv:2007.03366 (cross-list from math.PR) [pdf, other]

Title: Spread of premalignant mutant clones and cancer initiation in multilayered tissue

Jasmine Foo, Einar Bjarki Gunnarsson, Kevin Leder, Kathleen Storey

Comments: 49 pages, 11 figures, accepted for publication in Annals of Applied Probability

Journal-ref: Annals of Applied Probability 33(1) (2023) 299-343

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

[287] arXiv:2007.03599 (cross-list from eess.AS) [pdf, other]

Title: X-vectors: New Quantitative Biomarkers for Early Parkinson's Disease Detection from Speech

Laetitia Jeancolas, Dijana Petrovska-Delacrétaz, Graziella Mangone, Badr-Eddine Benkelfat, Jean-Christophe Corvol, Marie Vidailhet, Stéphane Lehéricy, Habib Benali

Comments: Submitted

Journal-ref: Frontiers in Neuroinformatics, 15 (2021)

Subjects: Audio and Speech Processing (eess.AS); Sound (cs.SD); Quantitative Methods (q-bio.QM)

[288] arXiv:2007.03750 (cross-list from cs.AI) [pdf, other]

Title: Deep Reinforcement Learning and its Neuroscientific Implications

Matthew Botvinick, Jane X. Wang, Will Dabney, Kevin J. Miller, Zeb Kurth-Nelson

Comments: 22 pages, 5 figures

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

[289] arXiv:2007.03774 (cross-list from cs.CL) [pdf, other]

Title: The curious case of developmental BERTology: On sparsity, transfer learning, generalization and the brain

Xin Wang

Comments: 9 pages, 5 figures, 1 table

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

[290] arXiv:2007.04019 (cross-list from physics.soc-ph) [pdf, other]

Title: Hyperbolic models for the spread of epidemics on networks: kinetic description and numerical methods

Giulia Bertaglia, Lorenzo Pareschi

Journal-ref: Esaim Math. Model. Numer. Anal. 55 (2021) 381-407

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

[291] arXiv:2007.04130 (cross-list from physics.soc-ph) [pdf, other]

Title: Disproportionate incidence of COVID-19 in African Americans correlates with dynamic segregation

Aleix Bassolas, Sandro Sousa, Vincenzo Nicosia

Comments: 35 pages, 4 figures + 31 suppl. figures, 2 tables

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

[292] arXiv:2007.04192 (cross-list from cs.MA) [pdf, other]

Title: Agent-Based Modelling: An Overview with Application to Disease Dynamics

Affan Shoukat, Seyed M. Moghadas

Comments: review of agent-based systems

Subjects: Multiagent Systems (cs.MA); Quantitative Methods (q-bio.QM)

[293] arXiv:2007.04210 (cross-list from physics.soc-ph) [pdf, other]

Title: Epidemic Spreading and Equilibrium Social Distancing in Heterogeneous Networks

Hamed Amini, Andreea Minca

Comments: 31 pages, 2 figures

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

[294] arXiv:2007.04245 (cross-list from cs.CL) [pdf, other]

Title: Mental representations of objects reflect the ways in which we interact with them

Ka Chun Lam, Francisco Pereira, Maryam Vaziri-Pashkam, Kristin Woodard, Emalie McMahon

Comments: 17 pages, 13 figures, 6 tables

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

[295] arXiv:2007.04299 (cross-list from cs.HC) [pdf, other]

Title: Visual analytics of COVID-19 dissemination in S\~ao Paulo state, Brazil

Wilson E. Marcílio-Jr, Danilo M. Eler, Rogério E. Garcia, Ronaldo C. M. Correia, Rafael M. B. Rodrigues

Subjects: Human-Computer Interaction (cs.HC); Populations and Evolution (q-bio.PE)

[296] arXiv:2007.04578 (cross-list from cs.AI) [pdf, other]

Title: On the Reliability and Generalizability of Brain-inspired Reinforcement Learning Algorithms

Dongjae Kim, Jee Hang Lee, Jae Hoon Shin, Minsu Abel Yang, Sang Wan Lee

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

[297] arXiv:2007.04777 (cross-list from eess.IV) [pdf, other]

Title: Self-supervised edge features for improved Graph Neural Network training

Arijit Sehanobish, Neal G. Ravindra, David van Dijk

Comments: Comments welcome. arXiv admin note: substantial text overlap with arXiv:2006.12971

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

[298] arXiv:2007.04827 (cross-list from physics.soc-ph) [pdf, other]

Title: Optimizing testing policies for detecting COVID-19 outbreaks

Janni Yuval, Mor Nitzan, Neta Ravid Tannenbaum, Boaz Barak

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

[299] arXiv:2007.04982 (cross-list from cs.LG) [pdf, other]

Title: Recursion and evolution: Part II

Alexandros Arvanitakis

Subjects: Machine Learning (cs.LG); Logic in Computer Science (cs.LO); Neurons and Cognition (q-bio.NC); Populations and Evolution (q-bio.PE)

[300] arXiv:2007.05035 (cross-list from physics.soc-ph) [pdf, other]

Title: Fixed-time descriptive statistics underestimate extremes of epidemic curve ensembles

Jonas L. Juul, Kaare Græsbøll, Lasse Engbo Christiansen, Sune Lehmann

Comments: 4 pages, 2 figures

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