Quantitative Biology

Authors and titles for February 2020

[151] arXiv:2002.11208 [pdf, other]

Title: Automatic Segmentation, Feature Extraction and Comparison of Healthy and Stroke Cerebral Vasculature

Aditi Deshpande, Nima Jamilpour, Bin Jiang, Chelsea Kidwell, Max Wintermark, Kaveh Laksari

Comments: 14 pages, 4 figures, 4 tables

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

[152] arXiv:2002.11267 [pdf, other]

Title: Ross-Macdonald Models: Which one should we use?

Mario Ignacio Simoy, Juan Pablo Aparicio

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

[153] arXiv:2002.11271 [pdf, other]

Title: Comparing copy-number profiles under multi-copy amplifications and deletions

Garance Cordonnier, Manuel Lafond

Subjects: Genomics (q-bio.GN); Data Structures and Algorithms (cs.DS)

[154] arXiv:2002.11532 [pdf, other]

Title: Bioconjugated oligonucleotides: recent developments and thera-eutic applications

Sébastien Benizri (ARNA), Arnaud Gissot (ARNA), Andrew Martin, Brune Vialet (ARNA), Mark Grinstaff (BU), Philippe Barthélémy (ARNA)

Journal-ref: Bioconjugate Chemistry, American Chemical Society, 2019, 30, pp.366-383

Subjects: Biomolecules (q-bio.BM)

[155] arXiv:2002.11592 [pdf, other]

Title: PolyFold: an interactive visual simulator for distance-based protein folding

Andrew McGehee, Sutanu Bhattacharya, Rahmatullah Roche, Debswapna Bhattacharya

Comments: 19 pages, 3 figures

Subjects: Biomolecules (q-bio.BM)

[156] arXiv:2002.11612 [pdf, other]

Title: Cell cycle and protein complex dynamics in discovering signaling pathways

Daniel Inostroza, Cecilia Hernández, Diego Seco, Gonzalo Navarro, Alvaro Olivera-Nappa

Journal-ref: Journal of Bioinformatics and Computational Biology 2019

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

[157] arXiv:2002.11870 [pdf, other]

Title: A Structure-based Memory Maintenance Model for Neural Tracking of Linguistic Structures

Nai Ding

Comments: 13 pages, 3 figures

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

[158] arXiv:2002.12100 [pdf, other]

Title: Millisecond insect tracking system

T. Thang Vo-Doan, Andrew D. Straw

Comments: 5 pages, 5 figures, supplemental data: this https URL , supplemental video: this https URL

Subjects: Quantitative Methods (q-bio.QM)

[159] arXiv:2002.12138 [pdf, other]

Title: The Chiral Puzzle of Life

Noemie Globus, Roger D. Blandford

Comments: 18 pages, 6 figures, accepted for publication in The Astrophysical Journal Letters. arXiv admin note: text overlap with arXiv:1911.02525

Subjects: Other Quantitative Biology (q-bio.OT); High Energy Astrophysical Phenomena (astro-ph.HE)

[160] arXiv:2002.12298 [pdf, other]

Title: Predicting the cumulative number of cases for the COVID-19 epidemic in China from early data

Zhihua Liu, Pierre Magal, Ousmane Seydi, Glenn Webb

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

[161] arXiv:2002.12316 [pdf, other]

Title: An epidemic model highlighting humane social awareness and vector-host lifespan ratio variation

Karunia Putra Wijaya, Joseph Páez Chávez, Dipo Aldila

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

[162] arXiv:2002.12429 [pdf, other]

Title: A modeling study of predator--prey interaction propounding honest signals and cues

Ahd Mahmoud Al-Salman, Joseph Páez Chávez, Karunia Putra Wijaya

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

[163] arXiv:2002.12443 [pdf, other]

Title: Optimal self-induced stochastic resonance in multiplex neural networks: electrical versus chemical synapses

Marius E. Yamakou, Poul G. Hjorth, Erik A. Martens

Comments: 24 pages, 7 figures

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

[164] arXiv:2002.12541 [pdf, other]

Title: Machine Learning Models to Predict Inhibition of the Bile Salt Export Pump

Kevin S. McLoughlin, Claire G. Jeong, Thomas D. Sweitzer, Amanda J. Minnich, Margaret J. Tse, Brian J. Bennion, Jonathan E. Allen, Stacie Calad-Thomson, Thomas S. Rush, James M. Brase

Subjects: Quantitative Methods (q-bio.QM)

[165] arXiv:2002.12776 [pdf, other]

Title: ResNets, NeuralODEs and CT-RNNs are Particular Neural Regulatory Networks

Radu Grosu

Comments: 9 pages, 4 figures

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

[166] arXiv:2002.12784 [pdf, other]

Title: Dependence of chlorophyll content in leaves from light regime, electromagnetic fields and plant species

Alexander Kholmanskiy, Nataliya Zaytseva

Journal-ref: JOJ Hortic Arboric. 2020; 3(1): 555602

Subjects: Other Quantitative Biology (q-bio.OT)

[167] arXiv:2002.12831 [pdf, other]

Title: Sympatric speciation based on pure assortative mating

Rodrigo A. Caetano, Sergio Sanchez, Carolina L. N. Costa, Marcus A. M. de Aguiar

Comments: 30 pages, 10 figures

Subjects: Populations and Evolution (q-bio.PE); Adaptation and Self-Organizing Systems (nlin.AO)

[168] arXiv:2002.12868 [pdf, other]

Title: Neural Network Segmentation of Interstitial Fibrosis, Tubular Atrophy, and Glomerulosclerosis in Renal Biopsies

Brandon Ginley (1), Kuang-Yu Jen (2), Avi Rosenberg (3), Felicia Yen (2), Sanjay Jain (4), Agnes Fogo (5), Pinaki Sarder (1 and 6 and 7) ((1) Department of Pathology & Anatomical Sciences, University at Buffalo, the State University of New York, Buffalo, New York, (2) Department of Pathology and Laboratory Medicine, University of California, Davis Medical Center, Sacramento, California, (3) Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, (4) Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, (5) Departments of Pathology, Microbiology, Immunology and Medicine, Vanderbilt University, Nashville, Tennessee, (6) Department of Biostatistics, University at Buffalo, the State University of New York, Buffalo, New York, (7) Department of Biomedical Engineering, University at Buffalo, the State University of New York, Buffalo, New York)

Subjects: Tissues and Organs (q-bio.TO); Computer Vision and Pattern Recognition (cs.CV); Image and Video Processing (eess.IV)

[169] arXiv:2002.12883 [pdf, other]

Title: The ARF-AID system: Methods that preserve endogenous protein levels and facilitate rapidly inducible protein degradation

Kizhakke Mattada Sathyan, Thomas G. Scott, Michael J. Guertin

Comments: 43 pages, 8 figures

Subjects: Quantitative Methods (q-bio.QM)

[170] arXiv:2002.00044 (cross-list from cs.HC) [pdf, other]

Title: Design Principles and Clinician Preferences for Pharmacogenomic Clinical Decision Support Alerts

Timothy M. Herr, Therese A. Nelson, Justin B. Starren

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

[171] arXiv:2002.00047 (cross-list from cs.HC) [pdf, other]

Title: Design Principles Developed through User-Centered and Socio-Technical Methods Improve Clinician Satisfaction, Speed, and Confidence in Pharmacogenomic Clinical Decision Support

Timothy M. Herr, Therese A. Nelson, Luke V. Rasmussen, Yinan Zheng, Nicola Lancki, MPH, Justin B. Starren

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

[172] arXiv:2002.00111 (cross-list from physics.bio-ph) [pdf, other]

Title: Modeling supercoiled DNA interacting with an anchored cluster of proteins: towards a quantitative estimation of chromosomal DNA supercoiling

Jean-Charles Walter, Thibaut Lepage, Jérôme Dorignac, Frédéric Geniet, Andrea Parmeggiani, John Palmeri, Jean-Yves Bouet, Ivan Junier

Comments: 5 pages + Supplementary Info (including 3 figures)

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

[173] arXiv:2002.00254 (cross-list from eess.SP) [pdf, other]

Title: Electrocardiogram Generation and Feature Extraction Using a Variational Autoencoder

V. V. Kuznetsov, V. A. Moskalenko, N. Yu. Zolotykh

Comments: 6 pages, 6 figures Submitted to IJCNN 2020

Subjects: Signal Processing (eess.SP); Machine Learning (cs.LG); Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)

[174] arXiv:2002.00485 (cross-list from cond-mat.soft) [pdf, other]

Title: Concentration dependence of diffusion-limited reaction rates and its consequences

Sumantra Sarkar

Comments: Accepted in Phys. Rev. X. Look for SI to the right. -->

Subjects: Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Chemical Physics (physics.chem-ph); Subcellular Processes (q-bio.SC)

[175] arXiv:2002.00527 (cross-list from cs.CL) [pdf, other]

Title: Phylogenetic signal in phonotactics

Jayden L. Macklin-Cordes, Claire Bowern, Erich R. Round

Comments: Main text: 32 pages, 17 figures, 1 table. Supplementary Information: 17 pages, 1 figure. Code and data available at this http URL. This article is in review but not yet accepted for publication in a journal

Subjects: Computation and Language (cs.CL); Populations and Evolution (q-bio.PE)

[176] arXiv:2002.00534 (cross-list from physics.soc-ph) [pdf, other]

Title: Measuring Nestedness: A comparative study of the performance of different metrics

Claudia Payrato-Borras, Laura Hernandez, Yamir Moreno

Comments: 23 pages and 7 figures. The abstract has been shortened to comply with space limit

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

[177] arXiv:2002.00539 (cross-list from cs.NE) [pdf, other]

Title: Evolving Neural Networks through a Reverse Encoding Tree

Haoling Zhang, Chao-Han Huck Yang, Hector Zenil, Narsis A. Kiani, Yue Shen, Jesper N. Tegner

Comments: Accepted to IEEE Congress on Evolutionary Computation (IEEE CEC) 2020. Lecture Presentation

Journal-ref: 2020 IEEE Congress on Evolutionary Computation (CEC)

Subjects: Neural and Evolutionary Computing (cs.NE); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Systems and Control (eess.SY); Populations and Evolution (q-bio.PE)

[178] arXiv:2002.00920 (cross-list from stat.AP) [pdf, other]

Title: Non-linear regression models for behavioral and neural data analysis

Vincent Adam, Alexandre Hyafil

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

[179] arXiv:2002.01049 (cross-list from physics.soc-ph) [pdf, other]

Title: Enhanced Ability of Information Gathering May Intensify Disagreement Among Groups

Hiroki Sayama

Comments: 11 pages, 6 figures; accepted for publication in Physical Review E

Journal-ref: Phys. Rev. E 102, 012303 (2020)

Subjects: Physics and Society (physics.soc-ph); Analysis of PDEs (math.AP); Pattern Formation and Solitons (nlin.PS); Populations and Evolution (q-bio.PE)

[180] arXiv:2002.01117 (cross-list from cs.HC) [pdf, other]

Title: Spatio-Temporal Dynamics of Visual Imagery for Intuitive Brain-Computer Interface

Seo-Hyun Lee, Minji Lee, Seong-Whan Lee

Comments: 5 pages, 4 figures, 3 tables

Subjects: Human-Computer Interaction (cs.HC); Neurons and Cognition (q-bio.NC)

[181] arXiv:2002.01120 (cross-list from cs.HC) [pdf, other]

Title: A Novel Framework for Visual Motion Imagery Classification Using 3D Virtual BCI Platform

Byoung-Hee Kwon, Ji-Hoon Jeong, Dong-Joo Kim

Comments: 5 pages, 4 figures, 2 tables

Subjects: Human-Computer Interaction (cs.HC); Neurons and Cognition (q-bio.NC)

[182] arXiv:2002.01126 (cross-list from cs.NE) [pdf, other]

Title: Neural Oscillations for Encoding and Decoding Declarative Memory using EEG Signals

Jenifer Kalafatovich, Minji Lee

Subjects: Neural and Evolutionary Computing (cs.NE); Signal Processing (eess.SP); Neurons and Cognition (q-bio.NC)

[183] arXiv:2002.01289 (cross-list from cs.DS) [pdf, other]

Title: Extracting Dense and Connected Subgraphs in Dual Networks by Network Alignment

Pietro Hiram Guzzi, Emanuel Salerno, Giuseppe Tradigo, Pierangelo Veltri

Subjects: Data Structures and Algorithms (cs.DS); Social and Information Networks (cs.SI); Molecular Networks (q-bio.MN)

[184] arXiv:2002.01571 (cross-list from nlin.AO) [pdf, other]

Title: Antifragility Predicts the Robustness and Evolvability of Biological Networks through Multi-class Classification with a Convolutional Neural Network

Hyobin Kim, Stalin Muñoz, Pamela Osuna, Carlos Gershenson

Comments: 22 pages, 10 figures

Subjects: Adaptation and Self-Organizing Systems (nlin.AO); Machine Learning (cs.LG); Cellular Automata and Lattice Gases (nlin.CG); Molecular Networks (q-bio.MN)

[185] arXiv:2002.01608 (cross-list from nlin.PS) [pdf, other]

Title: Stable Asymmetric Spike Equilibria for the Gierer-Meinhardt Model with a Precursor Field

Theodore Kolokolnikov, Frédéric Paquin-Lefebvre, Michael J. Ward

Comments: 22 pages, 14 figures

Journal-ref: IMA Journal of Applied Mathematics, 2020, Vol. 85, No. 4 : pp. 605-634

Subjects: Pattern Formation and Solitons (nlin.PS); Quantitative Methods (q-bio.QM)

[186] arXiv:2002.01925 (cross-list from cs.LG) [pdf, other]

Title: Machine Learning for Predicting Epileptic Seizures Using EEG Signals: A Review

Khansa Rasheed, Adnan Qayyum, Junaid Qadir, Shobi Sivathamboo, Patrick Kwan, Levin Kuhlmann, Terence O'Brien, Adeel Razi

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

[187] arXiv:2002.01958 (cross-list from physics.med-ph) [pdf, other]

Title: Magnetically controlled vector based on E coli Nissle 1917

S.V. Gorobets, O.Yu. Gorobets, I.V. Sharau, Yu.V. Milenko

Comments: 25 pages

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

[188] arXiv:2002.01982 (cross-list from eess.IV) [pdf, other]

Title: Multimodal fusion of imaging and genomics for lung cancer recurrence prediction

Vaishnavi Subramanian, Minh N. Do, Tanveer Syeda-Mahmood

Comments: Accepted for presentation at International Symposium on Biomedical Imaging (ISBI) 2020 (Iowa City). 5 pages, last page references

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

[189] arXiv:2002.02001 (cross-list from stat.ME) [pdf, other]

Title: A guide to state-space modeling of ecological time series

Marie Auger-Méthé, Ken Newman, Diana Cole, Fanny Empacher, Rowenna Gryba, Aaron A. King, Vianney Leos-Barajas, Joanna Mills Flemming, Anders Nielsen, Giovanni Petris, Len Thomas

Comments: 71 pages, 4 figures

Subjects: Methodology (stat.ME); Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)

[190] arXiv:2002.02497 (cross-list from eess.IV) [pdf, other]

Title: On the limits of cross-domain generalization in automated X-ray prediction

Joseph Paul Cohen, Mohammad Hashir, Rupert Brooks, Hadrien Bertrand

Comments: Full paper at MIDL2020

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

[191] arXiv:2002.02590 (cross-list from physics.soc-ph) [pdf, other]

Title: A Time Delay Dynamic System with External Source for the Local Outbreak of 2019-nCoV

Yu Chen, Jin Cheng, Yu Jiang, Keji Liu

Comments: 13 pages, 13figures

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

[192] arXiv:2002.02601 (cross-list from stat.ML) [pdf, other]

Title: Bidimensional linked matrix factorization for pan-omics pan-cancer analysis

Eric F. Lock, Jun Young Park, Katherine A. Hoadley

Comments: 26 pages, 5 figures

Journal-ref: Annals of Applied Statistics 2022, Vol. 16, No. 1, 193-215

Subjects: Machine Learning (stat.ML); Machine Learning (cs.LG); Quantitative Methods (q-bio.QM); Applications (stat.AP); Methodology (stat.ME)

[193] arXiv:2002.02607 (cross-list from physics.soc-ph) [pdf, other]

Title: Self-awareness based resource allocation strategy for containment of epidemic spreading

Xiaolong Chen, Quanhui Liu, Ruijie Wang, Qing Li, Wei Wang

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

[194] arXiv:2002.02779 (cross-list from stat.ML) [pdf, other]

Title: Generating Digital Twins with Multiple Sclerosis Using Probabilistic Neural Networks

Jonathan R. Walsh, Aaron M. Smith, Yannick Pouliot, David Li-Bland, Anton Loukianov, Charles K. Fisher

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

[195] arXiv:2002.03248 (cross-list from astro-ph.EP) [pdf, other]

Title: Implications of Abiotic Oxygen Buildup for Earth-like Complex Life

Manasvi Lingam

Comments: Published in The Astronomical Journal; 9 pages; 2 figures

Journal-ref: The Astronomical Journal, Vol. 159, No. 4, 144 (2020)

Subjects: Earth and Planetary Astrophysics (astro-ph.EP); Solar and Stellar Astrophysics (astro-ph.SR); Populations and Evolution (q-bio.PE)

[196] arXiv:2002.03472 (cross-list from eess.IV) [pdf, other]

Title: Biologically Inspired Visual System Architecture for Object Recognition in Autonomous Systems

Dan Malowany, Hugo Guterman

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

[197] arXiv:2002.03542 (cross-list from math.CO) [pdf, other]

Title: Oriented Matroids and Combinatorial Neural Codes

Alexander Kunin, Caitlin Lienkaemper, Zvi Rosen

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

[198] arXiv:2002.03553 (cross-list from cs.LG) [pdf, other]

Title: A Spike in Performance: Training Hybrid-Spiking Neural Networks with Quantized Activation Functions

Aaron R. Voelker, Daniel Rasmussen, Chris Eliasmith

Comments: 8 pages, 7 page supplementary

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

[199] arXiv:2002.03586 (cross-list from cs.SC) [pdf, other]

Title: First-Order Tests for Toricity

Hamid Rahkooy, Thomas Sturm

Journal-ref: Proc. CASC 2020, LNCS 12291, pp.510-527, Springer 2020

Subjects: Symbolic Computation (cs.SC); Molecular Networks (q-bio.MN)

[200] arXiv:2002.03679 (cross-list from physics.bio-ph) [pdf, other]

Title: Flagellar length control in biflagellate eukaryotes: time-of-flight, shared pool, train traffic and cooperative phenomena

Swayamshree Patra, Frank Jülicher, Debashish Chowdhury

Comments: Revised presentation, 36 pages, including 17 figures

Journal-ref: NEW JOURNAL OF PHYSICS, vol. 22, 083009 (2020)

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