Quantitative Biology

Authors and titles for Apr 2019

[1]  arXiv:1904.00088 [pdf, other]

Title: Physical constraints on accuracy and persistence during breast cancer cell chemotaxis

Authors: Julien Varennes, Hye-ran Moon, Soutick Saha, Andrew Mugler, Bumsoo Han

Subjects: Cell Behavior (q-bio.CB)

[2]  arXiv:1904.00099 [pdf, other]

Title: Random matrix analysis of Ca$^{2+}$ signals in $β$-cell collectives

Authors: Dean Korošak, Marjan Slak Rupnik

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

[3]  arXiv:1904.00117 [pdf, other]

Title: Estimation of cell lineage trees by maximum-likelihood phylogenetics

Authors: Jean Feng, William S DeWitt III, Aaron McKenna, Noah Simon, Amy Willis, Frederick A Matsen IV

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

[4]  arXiv:1904.00214 [pdf, other]

Title: Serostatus Testing & Dengue Vaccine Cost-Benefit Thresholds

Authors: Carl A. B. Pearson, Kaja M. Abbas, Samuel Clifford, Stefan Flasche, Thomas J. Hladish

Subjects: Populations and Evolution (q-bio.PE)

[5]  arXiv:1904.00232 [pdf, ps, other]

Title: Unifying Modular and Core-Periphery Structure in Functional Brain Networks over Development

Authors: Shi Gu, Cedric Huchuan Xia, Rastko Ciric, Tyler M. Moore, Ruben C. Gur, Raquel E. Gur, Theodore D. Satterthwaite, Danielle S. Bassett

Subjects: Quantitative Methods (q-bio.QM)

[6]  arXiv:1904.00353 [pdf, ps, other]

Title: Long-range temporal correlation in Auditory Brainstem Responses to Spoken Syllable /da/

Authors: Marjan Mozaffarilegha, S. M. S. Movahed

Comments: 27 pages, 8 figures and one table

Journal-ref: Scientific Reports, volume 9, Article number: 1751 (2019)

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

[7]  arXiv:1904.00431 [pdf, other]

Title: Do Deep Neural Networks Model Nonlinear Compositionality in the Neural Representation of Human-Object Interactions?

Authors: Aditi Jha, Sumeet Agarwal

Comments: 4 pages, 2 figures; presented at CCN 2019

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

[8]  arXiv:1904.00445 [pdf, other]

Title: The KiTS19 Challenge Data: 300 Kidney Tumor Cases with Clinical Context, CT Semantic Segmentations, and Surgical Outcomes

Authors: Nicholas Heller, Niranjan Sathianathen, Arveen Kalapara, Edward Walczak, Keenan Moore, Heather Kaluzniak, Joel Rosenberg, Paul Blake, Zachary Rengel, Makinna Oestreich, Joshua Dean, Michael Tradewell, Aneri Shah, Resha Tejpaul, Zachary Edgerton, Matthew Peterson, Shaneabbas Raza, Subodh Regmi, Nikolaos Papanikolopoulos, Christopher Weight

Comments: 13 pages, 2 figures

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

[9]  arXiv:1904.00662 [pdf, ps, other]

Title: Unbiased on-lattice domain growth

Authors: Cameron A. Smith, Cécile Mailler, Christian A. Yates

Comments: 23 pages, 10 figures

Journal-ref: Phys. Rev. E 100, 063307 (2019)

Subjects: Quantitative Methods (q-bio.QM)

[10]  arXiv:1904.00825 [pdf, other]

Title: Simple unity among the fundamental equations of science

Authors: Steven A. Frank

Comments: arXiv admin note: text overlap with arXiv:1810.09262

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

[11]  arXiv:1904.00874 [pdf, other]

Title: Far-ranging generalist top predators enhance the stability of meta-foodwebs

Authors: Andreas Brechtel, Thilo Gross, Barbara Drossel

Journal-ref: Scientific Reportsvolume 9, Article number: 12268 (2019)

Subjects: Populations and Evolution (q-bio.PE)

[12]  arXiv:1904.00919 [pdf, ps, other]

Title: A Deterministic Method to Calculate the AIS Trauma Score from a Finite Element Organ Trauma Model (OTM)

Authors: C. Bastien, C. Neal-Sturgess, J. Christensen, L. Wen

Subjects: Tissues and Organs (q-bio.TO)

[13]  arXiv:1904.00986 [pdf, ps, other]

Title: A simple method for detecting chaos in nature

Authors: Daniel Toker, Friedrich T. Sommer, Mark D'Esposito

Subjects: Quantitative Methods (q-bio.QM); Chaotic Dynamics (nlin.CD)

[14]  arXiv:1904.00997 [pdf, ps, other]

Title: Quantitative phase microscopy spatial signatures of cancer cells

Authors: Darina Roitshtain, Lauren Wolbromsky, Evgeny Bal, Hayit Greenspan, Lisa L. Satterwhite, Natan T. Shaked

Journal-ref: Cytometry A. 2017 May;91(5):482-493

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

[15]  arXiv:1904.01096 [pdf, ps, other]

Title: Digging Deeper: Methodologies for High-Content Phenotyping and Knowledge-Abstraction in C. elegans

Authors: Nan Xu, Dhaval S. Patel, Hang Lu

Subjects: Quantitative Methods (q-bio.QM)

[16]  arXiv:1904.01166 [pdf, ps, other]

Title: The Configuration of the Perivascular System Transporting Macromolecules in the CNS (PREPRINT)

Authors: Beata Durcanova, Janine Appleton, Nyshidha Gurijala, Vasily Belov, Pilar Giffenig, Elisabeth Moeller, Matthew Hogan, Fredella Lee, Mikhail Papisov

Comments: 16 pages, 6 figures, 61 references

Subjects: Tissues and Organs (q-bio.TO)

[17]  arXiv:1904.01208 [pdf, other]

Title: Strategies that enforce linear payoff relationships under observation errors in Repeated Prisoner's Dilemma game

Authors: Azumi Mamiya, Genki Ichinose

Comments: 19 pages, 3 figures

Journal-ref: Journal of Theoretical Biology 477, 63-76 (2019)

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

[18]  arXiv:1904.01235 [pdf, other]

Title: BPPart and BPMax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model

Authors: Ali Ebrahimpour-Boroojeny, Sanjay Rajopadhye, Hamidreza Chitsaz

Subjects: Biomolecules (q-bio.BM); Genomics (q-bio.GN)

[19]  arXiv:1904.01485 [pdf, other]

Title: Alternative Scoring Method of Pleurisy in Slaughtered Pigs: Preliminary Investigations

Authors: Giuseppe Marruchella, Michael Odintzov Vaintrub, Andrea Di Provvido, Elena Farina, Giorgio Fragassi, Giorgio Vignola

Comments: Proceedings of SIPAS, 2018

Journal-ref: SIPAS, 2018, 375-380

Subjects: Tissues and Organs (q-bio.TO)

[20]  arXiv:1904.01637 [pdf, other]

Title: Learning Clinical Outcomes from Heterogeneous Genomic Data Sources

Authors: Safoora Yousefi, Amirreza Shaban, Mohamed Amgad, Ramraj Chandradevan, Lee A. D. Cooper

Subjects: Quantitative Methods (q-bio.QM); Genomics (q-bio.GN)

[21]  arXiv:1904.01655 [pdf, ps, other]

Title: A frame semantic overview of NLP-based information extraction for cancer-related EHR notes

Authors: Surabhi Datta, Elmer V Bernstam, Kirk Roberts

Comments: 2 figures, 4 tables

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

[22]  arXiv:1904.01847 [pdf, other]

Title: How the Avidity of Polymerase Binding to the -35/-10 Promoter Sites Affects Gene Expression

Authors: Tal Einav, Rob Phillips

Subjects: Subcellular Processes (q-bio.SC)

[23]  arXiv:1904.01862 [pdf, ps, other]

Title: Respiratory sympathetic modulation is augmented in chronic kidney disease

Authors: Manash Saha, Clément Menuet (INMED - INSERM U1249), Qi-Jian Sun, Peter Burke (NeuRA), Cara Hildreth, Andrew Allen, Jacqueline Phillips

Journal-ref: Respiratory Physiology and Neurobiology, Elsevier, In press

Subjects: Neurons and Cognition (q-bio.NC); Tissues and Organs (q-bio.TO)

[24]  arXiv:1904.01903 [pdf, ps, other]

Title: PyRod -- Tracing Water Molecules in Molecular Dynamics Simulations

Authors: David Schaller, Szymon Pach, Gerhard Wolber

Journal-ref: J.Chem.Inf.Model. (2019) 2818-2829

Subjects: Biomolecules (q-bio.BM)

[25]  arXiv:1904.01988 [pdf, other]

Title: Path mutual information for a class of biochemical reaction networks

Authors: Lorenzo Duso, Christoph Zechner

Comments: 6 pages, 2 figures

Subjects: Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)

[26]  arXiv:1904.02049 [pdf, other]

Title: No evidence of fish biodiversity effects on coral reef ecosystem functioning across scales

Authors: Tarik C. Gouhier, Pradeep Pillai

Journal-ref: Frontiers in Ecology and Evolution 7 (2019) 212

Subjects: Populations and Evolution (q-bio.PE)

[27]  arXiv:1904.02145 [pdf, other]

Title: Fitting stochastic predator-prey models using both population density and kill rate data

Authors: Frederic Barraquand, Olivier Gimenez

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

[28]  arXiv:1904.02523 [pdf, other]

Title: Explaining versus Describing Human Decisions. Hilbert Space Structures in Decision Theory

Authors: Sandro Sozzo

Comments: 16 pages, 1 figure, LateX

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

[29]  arXiv:1904.02576 [pdf, ps, other]

Title: The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA

Authors: Jack W Shepherd, Robert J Greenall, Matt I J Probert, Agnes Noy, Mark C Leake

Subjects: Biomolecules (q-bio.BM)

[30]  arXiv:1904.02600 [pdf, ps, other]

Title: Large-scale Species Tree Estimation

Authors: Erin Molloy, Tandy Warnow

Comments: 25 pages, no figures, submitted as a chapter for a book edited by Lacey Knowles and Laura Kubatko

Subjects: Populations and Evolution (q-bio.PE)

[31]  arXiv:1904.02610 [pdf, other]

Title: Diverse communities behave like typical random ecosystems

Authors: Wenping Cui, Robert Marsland III, Pankaj Mehta

Comments: 24 pages

Journal-ref: Phys. Rev. E 104, 034416 (2021)

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

[32]  arXiv:1904.02741 [pdf, other]

Title: Modeling Bottom-Up and Top-Down Attention with a Neurodynamic Model of V1

Authors: David Berga, Xavier Otazu

Comments: 27 pages, 19 figures

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

[33]  arXiv:1904.02866 [pdf, other]

Title: The nature of the animacy organization in human ventral temporal cortex

Authors: Sushrut Thorat, Daria Proklova, Marius V. Peelen

Comments: 16 pages, 5 figures, code+data at - this https URL Update - added supplementary results and edited abstract

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

[34]  arXiv:1904.02979 [pdf, other]

Title: A stochastic individual-based model to explore the role of spatial interactions and antigen recognition in the immune response against solid tumours

Authors: Fiona R Macfarlane, Mark AJ Chaplain, Tommaso Lorenzi

Subjects: Cell Behavior (q-bio.CB); Dynamical Systems (math.DS)

[35]  arXiv:1904.02983 [pdf, ps, other]

Title: A proof of unlimited multistability for phosphorylation cycles

Authors: Elisenda Feliu, Alan D. Rendall, Carsten Wiuf

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

[36]  arXiv:1904.02995 [pdf, ps, other]

Title: When is an action caused from within? Quantifying the causal chain leading to actions in simulated agents

Authors: Bjørn Erik Juel, Renzo Comolatti, Giulio Tononi, Larissa Albantakis

Comments: Submitted and accepted to Alife 2019 conference. Revised version: edits include adding more references to relevant work and clarifying minor points in response to reviewers

Subjects: Quantitative Methods (q-bio.QM); Neurons and Cognition (q-bio.NC)

[37]  arXiv:1904.03093 [pdf, ps, other]

Title: Structure Learning in Coupled Dynamical Systems and Dynamic Causal Modelling

Authors: Amirhossein Jafarian, Peter Zeidman, Vladimir Litvak, Karl Friston

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

[38]  arXiv:1904.03102 [pdf, ps, other]

Title: Passive Cervical Spine Ligaments Provide Stability during Head Impacts in Vivo

Authors: Calvin Kuo, Jodie Sheffels, Michael Fanton, Ina Bianca Yu, Rosa Hamalainen, David Camarillo

Subjects: Tissues and Organs (q-bio.TO)

[39]  arXiv:1904.03133 [pdf, other]

Title: Global Small-Angle Scattering Data Analysis of Inverted Hexagonal Phases

Authors: Moritz P. K. Frewein, Michael Rumetshofer, Georg Pabst

Journal-ref: J. Appl. Cryst. 52, 403-414 (2019)

Subjects: Biomolecules (q-bio.BM); Soft Condensed Matter (cond-mat.soft)

[40]  arXiv:1904.03236 [pdf, other]

Title: Transmission of danger information past physical barriers by ants

Authors: A. Reyes, M. Curbelo, F. Tejera, A. Rivera, G. Simon, O. Ramos, M.S. Turner, E. Altshuler

Comments: 12 pages, 6 figures

Subjects: Populations and Evolution (q-bio.PE)

[41]  arXiv:1904.03290 [pdf, other]

Title: Dynamics of a birth-death process based on combinatorial innovation

Authors: Mike Steel, Wim Hordijk, Stuart A. Kauffman

Comments: 21 pages, 4 figures

Subjects: Populations and Evolution (q-bio.PE)

[42]  arXiv:1904.03328 [pdf, other]

Title: Mitigating Gyral Bias in Cortical Tractography via Asymmetric Fiber Orientation Distributions

Authors: Ye Wu, Yoonmi Hong, Yuanjing Feng, Dinggang Shen, Pew-Thian Yap

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

[43]  arXiv:1904.03399 [pdf, other]

Title: Functional Geometry of Human Connectome and Robustness of Gender Differences

Authors: Bosiljka Tadic, Miroslav Andjelkovic, Roderick Melnik

Comments: 13 pages, 7 figures

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

[44]  arXiv:1904.03410 [pdf, ps, other]

Title: The role of dose-density in combination cancer chemotherapy

Authors: Álvaro G. López, Kelly C. Iarosz, Antonio M. Batista, Jesús M. Seoane, Ricardo L. Viana, Miguel A. F. Sanjuán

Subjects: Populations and Evolution (q-bio.PE)

[45]  arXiv:1904.03531 [pdf, ps, other]

Title: Decoding hand kinematics from population responses in sensorimotor cortex during grasping

Authors: Elizaveta V. Okorokova, James M. Goodman, Nicholas G. Hatsopoulos, Sliman J. Bensmaia

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

[46]  arXiv:1904.03653 [pdf, ps, other]

Title: Conformational catalysis of cataract-associated aggregation by interacting intermediates in a human eye lens crystallin

Authors: Eugene Serebryany, Rostam Razban, Eugene I Shakhnovich

Comments: 26 pages, 6 figures+Supplementary

Subjects: Biomolecules (q-bio.BM); Tissues and Organs (q-bio.TO)

[47]  arXiv:1904.03675 [pdf, other]

Title: Trivial pursuits

Authors: Tarik C. Gouhier, Pradeep Pillai

Journal-ref: Frontiers in Ecology and Evolution 7 (2019) 236

Subjects: Populations and Evolution (q-bio.PE)

[48]  arXiv:1904.03801 [pdf, other]

Title: pdbmine: A Node.js API for the RCSB Protein Data Bank (PDB)

Authors: Newlyn N. Joseph, Raktim N. Roy, Thomas A. Steitz

Comments: 1 figure

Subjects: Genomics (q-bio.GN)

[49]  arXiv:1904.03826 [pdf, other]

Title: Species Tree Estimation Using ASTRAL: Practical Considerations

Authors: Siavash Mirarab

Subjects: Populations and Evolution (q-bio.PE)

[50]  arXiv:1904.03910 [pdf, ps, other]

Title: The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks

Authors: Bence Agg, Andrea Csaszar, Mate Szalay-Beko, Daniel V. Veres, Reka Mizsei, Peter Ferdinandy, Peter Csermely, Istvan A. Kovacs

Journal-ref: Bioinformatics 2019 35, 4490-4492

Subjects: Molecular Networks (q-bio.MN); Disordered Systems and Neural Networks (cond-mat.dis-nn); Computer Vision and Pattern Recognition (cs.CV); Biological Physics (physics.bio-ph)

[51]  arXiv:1904.04105 [pdf, ps, other]

Title: Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires

Authors: Alex J. Brown, Igor Snapkov, Rahmad Akbar, Milena Pavlović, Enkelejda Miho, Geir K. Sandve, Victor Greiff

Comments: 45 pages, 1 table, 1 figure

Journal-ref: Mol. Syst. Des. Eng. (2019)

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

[52]  arXiv:1904.04544 [pdf, other]

Title: Predicting synchronous firing of large neural populations from sequential recordings

Authors: Oleksandr Sorochynskyi, Stéphane Deny, Olivier Marre, Ulisse Ferrari

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

[53]  arXiv:1904.04677 [pdf, other]

Title: Twist-bend coupling, twist waves and the shape of DNA loops

Authors: S. K. Nomidis, M. Caraglio, M. Laleman, K. Phillips, E. Skoruppa, E. Carlon

Comments: 9 pages, 6 figures

Journal-ref: Phys. Rev. E 100, 022402 (2019)

Subjects: Biomolecules (q-bio.BM); Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech)

[54]  arXiv:1904.04707 [pdf, ps, other]

Title: Crowding-induced Elongated Conformation of Urea-unfolded Apoazurin: Investigating the Role of Crowder Shape In Silico

Authors: Fabio C. Zegarra, Dirar Homouz, Andrei G. Gasic, Lucas Babel, Michael Kovermann, Pernilla Wittung-Stafshede, Margaret S. Cheung

Comments: Accepted by the Journal of Physical Chemistry B

Journal-ref: Journal of Physical Chemistry B (2019)

Subjects: Biomolecules (q-bio.BM)

[55]  arXiv:1904.04931 [pdf, ps, other]

Title: Nowcasting Influenza Incidence with CDC Web Traffic Data: A Demonstration Using a Novel Data Set

Authors: Wendy K. Caldwell, Geoffrey Fairchild, Sara Y. Del Valle

Comments: 21 pages (including references and appendices; 12 pages prior to references), 5 figures (some include subfigures), ILI data available in csv form

Subjects: Populations and Evolution (q-bio.PE); Social and Information Networks (cs.SI)

[56]  arXiv:1904.05002 [pdf, ps, other]

Title: Predicting Earth's Carrying Capacity of Human Population as the Predator and the Natural Resources as the Prey in the Modified Lotka-Volterra Equations with Time-dependent Parameters

Authors: Cheng Sok Kin, Ian Man Ut, Lo Hang, U Ieng Hou, Ng Ka Weng, Un Soi Ha, Lei Ka Hin, Cheng Kun Heng, Tam Seak Tim, Chan Iong Kuai, Lee Wei Shan

Subjects: Populations and Evolution (q-bio.PE)

[57]  arXiv:1904.05021 [pdf, ps, other]

Title: Uterine muscle networks: Connectivity analysis of the EHG during pregnancy and Labor

Authors: Noujoud Nader, Mahmoud Hassan, Wassim Falou, Mohamad Khalil, Brynjar Karlsson, Catherine Marque

Subjects: Quantitative Methods (q-bio.QM)

[58]  arXiv:1904.05024 [pdf, ps, other]

Title: Geometric Meditation-Based Cognitive Behavioral Therapy in Obsessive-Compulsive Disorder: A Case Study

Authors: Fatemeh Torkamani, Farshad Nazaraghaie, Mohammad Nami

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

[59]  arXiv:1904.05031 [pdf, ps, other]

Title: Top-down predictions influence binocular rivalry through beta band rhythms: a qEEG-based investigation

Authors: Azadeh Mojdehfarahbakhsh, Saba Nouri, Abolfazl Alipour, Mohammad Nami

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

[60]  arXiv:1904.05036 [pdf, ps, other]

Title: Sleep and its relation to cognition and behaviour in preschool-aged children of the general population: a systematic review

Authors: Eve Reynaud (CRESS - U1153, EHESP), Marie-Françoise Vecchierini, Barbara Heude (CRESS - U1153), Marie-Aline Charles (CRESS - U1153), Sabine Plancoulaine (INSERM, CRESS - U1153)

Journal-ref: Journal of Sleep Research, Wiley, 2018, 27 (3), pp.e12636

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

[61]  arXiv:1904.05052 [pdf, ps, other]

Title: Classification of signaling proteins based on molecular star graph descriptors using Machine Learning models

Authors: Carlos Fernandez-Lozano, Ruben F. Cuinas, Jose A. Seoane, Enrique Fernandez-Blanco, Julian Dorado, Cristian R. Munteanu

Comments: 19 pages, 6 figures, 3 tables

Journal-ref: Journal of theoretical biology 384 (2015): 50-58

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

[62]  arXiv:1904.05198 [pdf, ps, other]

Title: Detection of Metallo-\b{eta}-Lactamases-Encoding Genes Among Clinical Isolates of Escherichia Coli in a Tertiary Care Hospital, Malaysia

Authors: Fazlul MKK, Deepthi S, Farzana Y, Najnin A, Rashid Ma, Munira B, Srikumar C, Nazmul

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

[63]  arXiv:1904.05217 [pdf, other]

Title: Combining Mathematical Morphology and the Hilbert Transform for Fully Automatic Nuclei Detection in Fluorescence Microscopy

Authors: Carl J. Nelson, Philip T. G. Jackson, Boguslaw Obara

Comments: 11 pages, 5 figures, 1 table. Pre-review submission

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

[64]  arXiv:1904.05238 [pdf, other]

Title: A Physical Model for Self-Similar Seashells

Authors: Paul A. Reiser

Comments: 34 pages, 5 figures

Subjects: Quantitative Methods (q-bio.QM)

[65]  arXiv:1904.05311 [pdf, ps, other]

Title: Limit cycle bifurcations of a reduced Topp system

Authors: Valery A. Gaiko

Comments: 14 pages, 5 figures. arXiv admin note: substantial text overlap with arXiv:1504.03353, arXiv:1104.3019, arXiv:0902.2433

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

[66]  arXiv:1904.05375 [pdf, other]

Title: Scanner Invariant Representations for Diffusion MRI Harmonization

Authors: Daniel Moyer, Greg Ver Steeg, Chantal M. W. Tax, Paul M. Thompson

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

[67]  arXiv:1904.05412 [pdf, ps, other]

Title: A generalized kinetic framework applied to whole-cell catalysis in biofilm flow reactors clarifies performance enhancements

Authors: Mir Pouyan Zarabadi, Manon Couture, Steve J. Charette, Jesse Greener

Comments: Main paper 4 pages 3 figures. Plus supporting information

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

[68]  arXiv:1904.05434 [pdf, ps, other]

Title: Doppler Fluctuation Spectroscopy of Intracellular Dynamics in Living Tissue

Authors: Zhe Li, Hao Sun, John Turek, Shadia Jalal, Michael Childress, David D. Nolte

Comments: 24 pages, 9 figures, published in Journal of the Optical Society of America A

Journal-ref: J. Opt. Soc. Am. A 36, 665-677 (2019)

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

[69]  arXiv:1904.05467 [pdf, ps, other]

Title: Improved visual function in a case of ultra-low vision following ischemic encephalopathy following transcranial electrical stimulation; A case study

Authors: Ali-Mohammad Kamali, Mohammad Javad Gholamzadeh, Seyedeh Zahra Mousavi, Maryam Vasaghi Gharamaleki, Mohammad Nami

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

[70]  arXiv:1904.05581 [pdf, other]

Title: Understanding how T helper cells learn to coordinate effective immune responses through the lens of reinforcement learning

Authors: Takuya Kato, Tetsuya J. Kobayashi

Comments: 9 pages, 5 figures

Journal-ref: Phys. Rev. Research 3, 013222 (2021)

Subjects: Populations and Evolution (q-bio.PE)

[71]  arXiv:1904.05675 [pdf, other]

Title: Intelligent Measurement Analysis on Single Cell Raman Images for the Diagnosis of Follicular Thyroid Carcinoma

Authors: Aurelien Pelissier

Comments: The manuscript's content is currently being discussed with the co-authors before submission

Subjects: Quantitative Methods (q-bio.QM); Cell Behavior (q-bio.CB)

[72]  arXiv:1904.05834 [pdf, ps, other]

Title: Identification of similarity amongst eucalyptus planted areas based on leaf-cutting ant nest sizes

Authors: D M L Barbato, J M A De Andrade, J J De Groote

Comments: 17 pages 4 figures; Added a reference

Subjects: Populations and Evolution (q-bio.PE)

[73]  arXiv:1904.06156 [pdf, ps, other]

Title: Interpretable Classification from Skin Cancer Histology Slides Using Deep Learning: A Retrospective Multicenter Study

Authors: Peizhen Xie, Ke Zuo, Yu Zhang, Fangfang Li, Mingzhu Yin, Kai Lu

Comments: 6 pages,3 figures

Subjects: Tissues and Organs (q-bio.TO); Artificial Intelligence (cs.AI)

[74]  arXiv:1904.06161 [pdf, other]

Title: A mean first passage time genome rearrangement distance

Authors: Andrew Francis, Henry Wynn

Comments: 19 pages, 4 figures

Subjects: Populations and Evolution (q-bio.PE); Genomics (q-bio.GN)

[75]  arXiv:1904.06183 [pdf, other]

Title: Angular Velocity Estimation of Image Motion Mimicking the Honeybee Tunnel Centring Behaviour

Authors: Huatian Wang, Qinbing Fu, Hongxin Wang, Jigen Peng, Paul Baxter, Cheng Hu, Shigang Yue

Comments: 7 pages, 8 figures, conference, IEEE format. arXiv admin note: text overlap with arXiv:1904.02356

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

[76]  arXiv:1904.06326 [pdf, ps, other]

Title: Modeling tumorspheres reveals cancer stem cell niche building and plasticity

Authors: L. Benítez, L. Barberis, C. A. Condat

Comments: 18 pg

Subjects: Cell Behavior (q-bio.CB); Other Condensed Matter (cond-mat.other)

[77]  arXiv:1904.06377 [pdf, ps, other]

Title: Chronic stress may disrupt covariant fluctuations of vitamin D and cortisol plasma levels in pregnant sheep during the last trimester: a preliminary report

Authors: Colin Wakefield, Ben Janoschek, Yael Frank, Floyd Karp, Nicholas Reyes, Jay Schulkin, Martin G. Frasch

Comments: See also this https URL for data and results

Subjects: Tissues and Organs (q-bio.TO)

[78]  arXiv:1904.06507 [pdf, other]

Title: On the effect of forcing of fold bifurcations and early-warning signals in population dynamics

Authors: Flavia Remo, Gabriel Fuhrmann, Tobias Jäger

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

[79]  arXiv:1904.06514 [pdf, other]

Title: Shedding light on the dark matter of the biomolecular structural universe: Progress in RNA 3D structure prediction

Authors: Fabrizio Pucci, Alexander Schug

Comments: 14 pages, 4 figures

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

[80]  arXiv:1904.06517 [pdf, other]

Title: Improving detection of protein-ligand binding sites with 3D segmentation

Authors: Marta M. Stepniewska-Dziubinska, Piotr Zielenkiewicz, Pawel Siedlecki

Journal-ref: Sci Rep 10, 5035 (2020)

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

[81]  arXiv:1904.06639 [pdf, other]

Title: Robustness against additional noise in cellular information transmission

Authors: Takehiro Tottori, Masashi Fujii, Shinya Kuroda

Journal-ref: Phys. Rev. E 100, 042403 (2019)

Subjects: Molecular Networks (q-bio.MN)

[82]  arXiv:1904.06645 [pdf, ps, other]

Title: Brain on the 3D Visual Art through Virtual Reality; Introducing Neuro-Art in a Case Investigation

Authors: Ali-Mohammad Kamali, Mohammad Taghi Najafi, Mohammad Nami

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

[83]  arXiv:1904.06667 [pdf, ps, other]

Title: Are the better cooperators dormant or quiescent?

Authors: Thibaut Sellinger (1), Johannes Müller (2 and 3), Volker Hösel (2), Aurélien Tellier (1) ((1) Section of Population Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Germany, (2) Center for Mathematics, Technische Universität München, Germany, (3) Institute for Computational Biology, Helmholtz Center Munich, Germany)

Subjects: Populations and Evolution (q-bio.PE)

[84]  arXiv:1904.06712 [pdf, ps, other]

Title: Bilateral symmetry strengthens the perceptual salience of figure against ground

Authors: Birgitta Dresp-Langley

Journal-ref: 2019, Symmetry, 11(2), 225

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

[85]  arXiv:1904.06800 [pdf, other]

Title: Uneven rock-paper-scissors models: patterns and coexistence

Authors: J. Menezes, B. Moura, T. A. Pereira

Comments: 6 pages, 7 figures

Journal-ref: EPL, 126 (2019) 18003

Subjects: Populations and Evolution (q-bio.PE); Pattern Formation and Solitons (nlin.PS); Biological Physics (physics.bio-ph)

[86]  arXiv:1904.06973 [pdf, other]

Title: Disease gene prioritization using network topological analysis from a sequence based human functional linkage network

Authors: Ali Jalilvand, Behzad Akbari, Fatemeh Zare Mirakabad, Foad Ghaderi

Subjects: Molecular Networks (q-bio.MN); Genomics (q-bio.GN)

[87]  arXiv:1904.07032 [pdf, ps, other]

Title: Deep neural networks can predict mortality from 12-lead electrocardiogram voltage data

Authors: Sushravya Raghunath, Alvaro E. Ulloa Cerna, Linyuan Jing, David P. vanMaanen, Joshua Stough, Dustin N. Hartzel, Joseph B. Leader, H. Lester Kirchner, Christopher W. Good, Aalpen A. Patel, Brian P. Delisle, Amro Alsaid, Dominik Beer, Christopher M. Haggerty, Brandon K. Fornwalt

Comments: An updated version of this paper is now published with Nature Medicine (2020)

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

[88]  arXiv:1904.07113 [pdf, ps, other]

Title: A tale of two species: How humans shape dog behaviour in urban habitats

Authors: Debottam Bhattacharjee, Rohan Sarkar, Shubhra Sau, Anindita Bhadra

Comments: 3 figures, 14 pages of supplementary material

Subjects: Populations and Evolution (q-bio.PE)

[89]  arXiv:1904.07197 [pdf, ps, other]

Title: Identification of Parameters for Large-scale Kinetic Models

Authors: Ugur G. Abdulla, Roby Poteau

Comments: 20 pages, 21 Figures, 5 Tables

Journal-ref: Journal of Computational Physics, 26 November 2020, 110026

Subjects: Quantitative Methods (q-bio.QM); Numerical Analysis (math.NA)

[90]  arXiv:1904.07208 [pdf, ps, other]

Title: More testing or more disease? A counterfactual approach to explaining observed increases in positive tests over time

Authors: Jessica G. Young, Sarah J. Willis, Katherine Hsu, Michael Klompas, Julia L. Marcus

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

[91]  arXiv:1904.07231 [pdf, ps, other]

Title: Critical elements for connectivity analysis of brain networks

Authors: Jean Faber, Priscila C. Antoneli, Guillem Via, Noemi S. Araújo, Daniel J. L. L. Pinheiro, Esper Cavalheiro

Comments: 39 pages, 14 figures and 4 tables

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

[92]  arXiv:1904.07589 [pdf, ps, other]

Title: The Impact of UCMAS Training Program on Potentiating Cognitive Capacity among 9-12 Year-Old Primary Schoolers in Shiraz

Authors: Ali-Mohammad Kamali, Fatemeh Shamsi, Zahra Zeraatpisheh, Mohammad-Mojtaba Kamelmanesh, Mohammad Nami

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

[93]  arXiv:1904.07780 [pdf, ps, other]

Title: Quantifying cancer epithelial-mesenchymal plasticity and its association with stemness and immune response

Authors: Dongya Jia, Xuefei Li, Federico Bocci, Shubham Tripathi, Youyuan Deng, Mohit Kumar Jolly, Jose N. Onuchic, Herbert Levine

Comments: 50 pages, 6 figures

Subjects: Cell Behavior (q-bio.CB); Molecular Networks (q-bio.MN)

[94]  arXiv:1904.07860 [pdf, ps, other]

Title: Base spacing distribution analysis for human genome

Authors: Andrzej Z. Górski, Monika Piwowar

Comments: LaTeX, 9 figures

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

[95]  arXiv:1904.07952 [pdf, other]

Title: Response of Selective Attention in Middle Temporal Area

Authors: Linda Wang

Comments: 9 pages, preprint

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

[96]  arXiv:1904.08094 [pdf, ps, other]

Title: Molecular Diversity and Network Complexity in Growing Protocells

Authors: Atsushi Kamimura, Kunihiko Kaneko

Comments: 16 pages, 7 figures, submitted for publication

Subjects: Cell Behavior (q-bio.CB); Molecular Networks (q-bio.MN)

[97]  arXiv:1904.08182 [pdf, other]

Title: Mathematical modeling of variability in intracellular signaling

Authors: Carolin Loos, Jan Hasenauer

Subjects: Quantitative Methods (q-bio.QM)

[98]  arXiv:1904.08190 [pdf, ps, other]

Title: Regulation of Heart Beats by the Autonomous Nervous System in Health and Disease: Point-Process-Theory based Models and Simulation [V-I]

Authors: Bosco Emmanuel

Comments: 42 pages 20 figures

Subjects: Quantitative Methods (q-bio.QM)

[99]  arXiv:1904.08648 [pdf, ps, other]

Title: The lubricity of mucin solutions is robust toward changes in physiological conditions

Authors: Jian Song, Benjamin Winkeljann, Oliver Lieleg

Journal-ref: ACS Appl. Bio Mater. 2019, 2, 8, 3448-3457

Subjects: Biomolecules (q-bio.BM); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)

[100]  arXiv:1904.08767 [pdf, other]

Title: Stochastic mechanism for improving selectivity of olfactory projection neurons

Authors: Alexander Vidybida

Comments: 13 pages, 4 figures, 2 tables, 8 equations, 38 refs

Journal-ref: Neurophysiology (2019) 51: 152-159

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

[101]  arXiv:1904.08873 [pdf, ps, other]

Title: Codes, Functions, and Causes: A Critique of Brette's Conceptual Analysis of Coding

Authors: David Barack, Andrew Jaegle

Comments: Invited commentary on Romain Brette: "Is coding a relevant metaphor for the brain?" (forthcoming in Behavioral and Brain Sciences). 4 pages, including bibliography

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

[102]  arXiv:1904.08886 [pdf, other]

Title: Quantification of Nematic Cell Polarity in Three-dimensional Tissues

Authors: André Scholich, Simon Syga, Hernán Morales-Navarrete, Fabián Segovia-Miranda, Hidenori Nonaka, Kirstin Meyer, Walter de Back, Lutz Brusch, Yannis Kalaidzidis, Marino Zerial, Frank Jülicher, Benjamin M. Friedrich

Comments: 27 pages, 9 color figures

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

[103]  arXiv:1904.08937 [pdf, other]

Title: Testing for differential abundance in compositional counts data, with application to microbiome studies

Authors: Barak Brill, Amnon Amir, Ruth Heller

Subjects: Genomics (q-bio.GN); Applications (stat.AP)

[104]  arXiv:1904.09061 [pdf, ps, other]

Title: Random Fragments Classification of Microbial Marker Clades with Multi-class SVM and N-Best Algorithm

Authors: Jingwei Liu

Comments: 17 pages, 59 figurea

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

[105]  arXiv:1904.09233 [pdf, other]

Title: Deep Cytometry: Deep learning with Real-time Inference in Cell Sorting and Flow Cytometry

Authors: Yueqin Li, Ata Mahjoubfar, Claire Lifan Chen, Kayvan Reza Niazi, Li Pei, Bahram Jalali

Journal-ref: Scientific Reports 9 (2019) 11088

Subjects: Quantitative Methods (q-bio.QM); Neural and Evolutionary Computing (cs.NE); Optics (physics.optics)

[106]  arXiv:1904.09243 [pdf, ps, other]

Title: Repurposing of Ring Framework through TR screening

Authors: Surendra Kumar, Cheongyun Jang, Lalita Subedi, Sun Yeou Kim, Mi-hyun Kim

Comments: 22 pages, 10 figures, peer-reviewing of the manuscript was refused even though submitted to a journal

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

[107]  arXiv:1904.09367 [pdf, other]

Title: The Community Simulator: A Python package for microbial ecology

Authors: Robert Marsland III, Wenping Cui, Joshua Goldford, Pankaj Mehta

Comments: 14 pages, 6 figures

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

[108]  arXiv:1904.09504 [pdf, ps, other]

Title: Functional brain network architecture supporting the learning of social networks in humans

Authors: Steven H. Tompson, Ari E. Kahn, Emily B. Falk, Jean M. Vettel, Danielle S. Bassett

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

[109]  arXiv:1904.09847 [pdf, other]

Title: Spatial Population Genetics: It's About Time

Authors: Gideon S. Bradburd, Peter L. Ralph

Journal-ref: Annual Review of Ecology, Evolution, and Systematics Vol. 50:427-449 (2019)

Subjects: Populations and Evolution (q-bio.PE)

[110]  arXiv:1904.10124 [pdf, ps, other]

Title: Relation of the Weibull Shape Parameter with the Healthy Life Years Lost Estimates: Analytic Derivation and Estimation from an Extended Life Table

Authors: Christos H Skiadas, Charilaos Skiadas

Subjects: Populations and Evolution (q-bio.PE)

[111]  arXiv:1904.10337 [pdf, other]

Title: MinCall - MinION end2end convolutional deep learning basecaller

Authors: Neven Miculinić, Marko Ratković, Mile Šikić

Comments: 2nd international workshop on deep learning for precision medicine, ECML-PKDD 2017

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

[112]  arXiv:1904.10375 [pdf, ps, other]

Title: Morphogenesis Software based on Epigenetic Code Concept

Authors: N. Bessonov, O.Butuzova, A.Minarsky, R. Penner, C. Soule, A. Tosenberger, N. Morozova

Journal-ref: Computational and Structural Biotechnology Journal 17 (2019) p.1203

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

[113]  arXiv:1904.10393 [pdf, other]

Title: Estimations of Integrated Information Based on Algorithmic Complexity and Dynamic Querying

Authors: Alberto Hernández-Espinosa, Héctor Zenil, Narsis A. Kiani, Jesper Tegnér

Comments: 33 pages + Appendix = 44 pages

Journal-ref: Entropy, 2019

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

[114]  arXiv:1904.10394 [pdf, other]

Title: Cell damage and mitigation in Swiss albino mice: experiment and modelling

Authors: Urmimala Dey, Archisman Ghosh, Syed Abbas, A Taraphder, Madhumita Roy

Journal-ref: Alexandria Engineering Journal 59, 1345-1357 (2020)

Subjects: Tissues and Organs (q-bio.TO); Populations and Evolution (q-bio.PE)

[115]  arXiv:1904.10396 [pdf, other]

Title: Is coding a relevant metaphor for building AI? A commentary on "Is coding a relevant metaphor for the brain?", by Romain Brette

Authors: Adam Santoro, Felix Hill, David Barrett, David Raposo, Matthew Botvinick, Timothy Lillicrap

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

[116]  arXiv:1904.10398 [pdf, other]

Title: Fallopian tube anatomy predicts pregnancy and pregnancy outcomes after tubal reversal surgery

Authors: Rafael S. de Souza, Gary S. Berger

Comments: Accepted for publication at Statistical Methods in Medical Research

Subjects: Tissues and Organs (q-bio.TO); Applications (stat.AP)

[117]  arXiv:1904.10399 [pdf, other]

Title: Spike-Based Winner-Take-All Computation: Fundamental Limits and Order-Optimal Circuits

Authors: Lili Su, Chia-Jung Chang, Nancy Lynch

Subjects: Neurons and Cognition (q-bio.NC); Distributed, Parallel, and Cluster Computing (cs.DC)

[118]  arXiv:1904.10441 [pdf, other]

Title: Characterizing the nonlinear structure of shared variability in cortical neuron populations using latent variable models

Authors: Matthew R Whiteway, Karolina Socha, Vincent Bonin, Daniel A Butts

Subjects: Neurons and Cognition (q-bio.NC); Quantitative Methods (q-bio.QM)

[119]  arXiv:1904.10498 [pdf, ps, other]

Title: Information Based Centralization of Locomotion in Animals and Robots

Authors: Izaak D. Neveln, Amoolya Tirumalai, Simon Sponberg

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

[120]  arXiv:1904.10508 [pdf, ps, other]

Title: Quantum-Inspired Computing: Can it be a Microscopic Computing Model of the Brain?

Authors: Yasunao Katayama

Comments: 31 pages, 10 figures

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

[121]  arXiv:1904.10528 [pdf, ps, other]

Title: Putting Mind Back into Nature: A Tribute to Henry P. Stapp

Authors: David E. Presti

Comments: 9 pages; 4 figures; A contribution to a collection of essays honoring Henry P. Stapp on the occasion of his 90th birthday in Spring 2018

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

[122]  arXiv:1904.10664 [pdf, other]

Title: Coalescence in the diffusion limit of a Bienayme-Galton-Watson branching process

Authors: Conrad J. Burden, Albert C. Soewongsono

Comments: 28 pages, 6 figures; rewrite to make the paper more self-contained

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

[123]  arXiv:1904.10718 [pdf, ps, other]

Title: Backbone chemical shift assignments of human 14-3-3$σ$

Authors: João Neves (UGSF), Isabelle Landrieu (UGSF), Hamida Merzougui (UGSF), Emmanuelle Boll (UGSF), Xavier Hanoulle (UGSF), François-Xavier Cantrelle (UGSF)

Journal-ref: Biomolecular NMR Assignments, Springer, 2019, 13 (1), pp.103-107

Subjects: Biomolecules (q-bio.BM)

[124]  arXiv:1904.10845 [pdf, other]

Title: How self-regulation, the storage effect and their interaction contribute to coexistence in stochastic and seasonal environments

Authors: Coralie Picoche, Frederic Barraquand

Comments: 27 pages, 9 figures, Theor Ecol (2019)

Subjects: Populations and Evolution (q-bio.PE)

[125]  arXiv:1904.10899 [pdf, other]

Title: Seeding hESCs to achieve optimal colony clonality

Authors: Laura E Wadkin, Sirio Orozco-Fuentes, Irina Neganova, Sanja Bojic, Alex Laude, Majlina Lako, Nicholas G Parker, Anvar Shukurov

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

[126]  arXiv:1904.10924 [pdf, ps, other]

Title: Alterations in Structural Correlation Networks with Prior Concussion in Collision-Sport Athletes

Authors: Muhammad Usman Sadiq, Diana Svaldi, Trey Shenk, Evan Breedlove, Victoria Poole, Greg Tamer, Kausar Abbas, Thomas Talavage

Journal-ref: Originally published at: Annual meeting of the Organization for Human Brain Mapping, OHBM 2018

Subjects: Quantitative Methods (q-bio.QM); Neural and Evolutionary Computing (cs.NE); Neurons and Cognition (q-bio.NC)

[127]  arXiv:1904.11136 [pdf, other]

Title: Corticospinal Tract (CST) reconstruction based on fiber orientation distributions(FODs) tractography

Authors: Youshan Zhang

Journal-ref: 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE), Taichung, 2018, pp. 305-310

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

[128]  arXiv:1904.11219 [pdf, ps, other]

Title: "Favoring my playmate seems fair": Inhibitory control and theory of mind in preschoolers' self-disadvantaging behaviors

Authors: Dongjie Xie, Meng Pei, Yanjie Su

Comments: 24 pages, 3 figures

Journal-ref: Journal of Experimental Child Psychology, 2019

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

[129]  arXiv:1904.11280 [pdf, other]

Title: Predicting Stroke from Electronic Health Records

Authors: Chidozie Shamrock Nwosu, Soumyabrata Dev, Peru Bhardwaj, Bharadwaj Veeravalli, Deepu John

Comments: Published in Proc. 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2019

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

[130]  arXiv:1904.11372 [pdf, other]

Title: A Multi-agent approach for $\textit{in silico}$ simulations of micro-biological systems

Authors: Daniele Proverbio, Luca Gallo, Barbara Passalacqua, Jacopo Pellegrino, Marco Maggiora

Journal-ref: Swarm Intell 14, 313-331 (2020)

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

[131]  arXiv:1904.11633 [pdf, other]

Title: Parameter regions that give rise to 2[n/2]+1 positive steady states in the n-site phosphorylation system

Authors: Magalí Giaroli, Rick Rischter, Mercedes Pérez Millán, Alicia Dickenstein

Comments: 20 pages. The maple and SAGE files with our computations are available at: this http URL

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

[132]  arXiv:1904.11702 [pdf, ps, other]

Title: Voluntary phantom hand and finger movements in transhumeral amputees could be used to naturally control polydigital prostheses

Authors: Nathanael Jarrasse (AGATHE, ISIR, CNRS), Caroline Nicol (ISM), Florian Richer (ISIR), Amelie Touillet (IRR), Noël Martinet (IRR), Jean Paysant (IRR), Jozina de Graaf (ISM)

Journal-ref: 2017 International Conference on Rehabilitation Robotics (ICORR), Jul 2017, London, France. pp.1239-1245

Subjects: Neurons and Cognition (q-bio.NC); Signal Processing (eess.SP); Medical Physics (physics.med-ph); Tissues and Organs (q-bio.TO)

[133]  arXiv:1904.11713 [pdf, ps, other]

Title: Passive nonlinear dendritic interactions as a general computational resource in functional spiking neural networks

Authors: Andreas Stöckel, Chris Eliasmith

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

[134]  arXiv:1904.12021 [pdf, other]

Title: Best Match Graphs and Reconciliation of Gene Trees with Species Trees

Authors: Manuela Geiß, Marcos E. González, Alitzel López Sánchez, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernández Rosales, Peter F. Stadler

Subjects: Populations and Evolution (q-bio.PE); Discrete Mathematics (cs.DM)

[135]  arXiv:1904.12023 [pdf, other]

Title: Discovering Common Change-Point Patterns in Functional Connectivity Across Subjects

Authors: Mengyu Dai, Zhengwu Zhang, Anuj Srivastava

Journal-ref: Published in Medical Image Analysis, 2019

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

[136]  arXiv:1904.12133 [pdf, other]

Title: Neuronal mechanisms for sequential activation of memory items: dynamics and reliability

Authors: Elif Köksal-Ersöz, Carlos Aguilar, Pascal Chossat, Martin Krupa, Frédéric Lavigne

Comments: 24 pages, 11 figures

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

[137]  arXiv:1904.12341 [pdf, ps, other]

Title: Statistical methods for the quantitative genetic analysis of high-throughput phenotyping data

Authors: Gota Morota, Diego Jarquin, Malachy T. Campbell, Hiroyoshi Iwata

Subjects: Genomics (q-bio.GN)

[138]  arXiv:1904.12353 [pdf, other]

Title: TiCoNE 2: A Composite Clustering Model for Robust Cluster Analyses on Noisy Data

Authors: Christian Wiwie, Richard Röttger, Jan Baumbach

Subjects: Quantitative Methods (q-bio.QM)

[139]  arXiv:1904.12420 [pdf, other]

Title: A mechanism for sarcomere breathing: volume change and advective flow within the myofilament lattice

Authors: Julie A Cass, C. Dave Williams, Tom C Irving, Eric Lauga, Sage Malingen, Tom L. Daniel, Simon N. Sponberg

Comments: 4 figs, 3 supplemental movies, 1 supplemental figure

Subjects: Subcellular Processes (q-bio.SC); Tissues and Organs (q-bio.TO)

[140]  arXiv:1904.12652 [pdf, ps, other]

Title: Genome analysis and pleiotropy assessment using causal networks with loss of function mutation and metabolomics

Authors: Azam Yazdani, Akram Yazdani, Sarah H. Elsea, Daniel J. Schaid, Michael R. Kosorok, Gita Dangol, Ahmad Samiei

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

[141]  arXiv:1904.12684 [pdf, ps, other]

Title: Human Spermbots for Cancer-Relevant Drug Delivery

Authors: Haifeng Xu, Mariana Medina-Sanchez, Daniel R. Brison, Richard J. Edmondson, Stephen S. Taylor, Louisa Nelson, Kang Zeng, Steven Bagley, Carla Ribeiro, Lina P. Restrepo, Elkin Lucena, Christine K. Schmidt, Oliver G. Schmidt

Subjects: Cell Behavior (q-bio.CB)

[142]  arXiv:1904.12798 [pdf, other]

Title: Mathematical studies of the dynamics of finite-size binary neural networks: A review of recent progress

Authors: Diego Fasoli, Stefano Panzeri

Comments: 27 pages, 7 figures

Subjects: Neurons and Cognition (q-bio.NC); Dynamical Systems (math.DS)

[143]  arXiv:1904.12895 [pdf, ps, other]

Title: Energy Balance in Cell Phone Radiofrequency Radiation Exposed Mice and Rats

Authors: Bernard J. Feldman

Comments: 4 pages, no figures

Subjects: Tissues and Organs (q-bio.TO)

[144]  arXiv:1904.12914 [pdf, other]

Title: A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns

Authors: Robert Marsland III, Wenping Cui, Pankaj Mehta

Comments: 35 pages, 10 figures

Journal-ref: Scientific Reports 10:3308 (2020)

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

[145]  arXiv:1904.12937 [pdf, ps, other]

Title: Generative models as parsimonious descriptions of sensorimotor loops

Authors: Manuel Baltieri, Christopher L. Buckley

Comments: Commentary on Brette (2019) this https URL

Journal-ref: Behav Brain Sci 42 (2019) e218

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

[146]  arXiv:1904.12960 [pdf, ps, other]

Title: Modelling Diffuse Subcellular Protein Structures as Dynamic Social Networks

Authors: Andrew Durden

Comments: Master's Thesis Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree. Under Direction of: Shannon Quinn

Subjects: Subcellular Processes (q-bio.SC)

[147]  arXiv:1904.12964 [pdf, ps, other]

Title: Vaccination with Leishmania mexicana LPG induces PD-1 in CD8+ and PD-L2 in macrophages thereby suppressing the immune response: A model to assess vaccine efficacy

Authors: M.B.Martínez Salazar, J.Delgado Domínguez, J.Silva Estrada, C.González Bonilla, I.Becker

Comments: 7 pages, 5 figures

Journal-ref: Vaccine Volume 32, Issue 11, 5 March 2014, Pages 1259-1265

Subjects: Cell Behavior (q-bio.CB)

[148]  arXiv:1904.13007 [pdf, other]

Title: Reconstruction of Natural Visual Scenes from Neural Spikes with Deep Neural Networks

Authors: Yichen Zhang, Shanshan Jia, Yajing Zheng, Zhaofei Yu, Yonghong Tian, Siwei Ma, Tiejun Huang, Jian K. Liu

Comments: 35 pages, 10 figures

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

[149]  arXiv:1904.13026 [pdf, other]

Title: Antiepileptic drugs induce subcritical dynamics in human cortical networks

Authors: Christian Meisel

Comments: 17 pages, 4 figures

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

[150]  arXiv:1904.13240 [pdf, ps, other]

Title: Generating protein sequences from antibiotic resistance genes data using Generative Adversarial Networks

Authors: Prabal Chhibbar, Arpit Joshi

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

[151]  arXiv:1904.00448 (cross-list from cond-mat.soft) [pdf, other]

Title: Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces

Authors: Bortolo Mognetti, Pietro Cicuta, Lorenzo Di Michele

Comments: 63 pages, review

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

[152]  arXiv:1904.00710 (cross-list from cond-mat.soft) [pdf, other]

Title: Solvated Membrane Nanodiscoids: A Probe For The Effects Of Gaussian Curvature

Authors: R. G. Morris, T. R. Dafforn, M. S. Turner

Comments: Main manuscript: 6 pages (incl. references) and 4 figures. Supplementary: 11 pages and 1 figure

Subjects: Soft Condensed Matter (cond-mat.soft); Subcellular Processes (q-bio.SC)

[153]  arXiv:1904.00892 (cross-list from math.DS) [pdf, other]

Title: A Center Manifold Reduction Technique for a System of Randomly Coupled Oscillators

Authors: Dimitrios Moirogiannis, Keith Hayton, Marcelo Magnasco

Subjects: Dynamical Systems (math.DS); Biological Physics (physics.bio-ph); Neurons and Cognition (q-bio.NC); Quantitative Methods (q-bio.QM)

[154]  arXiv:1904.01070 (cross-list from cs.LG) [pdf, ps, other]

Title: Multimodal Sparse Classifier for Adolescent Brain Age Prediction

Authors: Peyman Hosseinzadeh Kassani, Alexej Gossmann, Yu-Ping Wang

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

[155]  arXiv:1904.01991 (cross-list from physics.bio-ph) [pdf, ps, other]

Title: Molecular Self-Organization of Three-Component Lipid Membranes

Authors: Austin Osby, Theja N. De Silva

Comments: 5 pages and 4 figures

Journal-ref: The Arsenal: Volume 3, Issue 1 (Spring 2020)

Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Subcellular Processes (q-bio.SC)

[156]  arXiv:1904.02021 (cross-list from cs.LG) [pdf, other]

Title: Unsupervised Progressive Learning and the STAM Architecture

Authors: James Smith, Cameron Taylor, Seth Baer, Constantine Dovrolis

Comments: Accepted by the 2021 International Joint Conference on Artificial Intelligence (IJCAI 2021)

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

[157]  arXiv:1904.02048 (cross-list from cs.CV) [pdf, other]

Title: Towards Computational Models and Applications of Insect Visual Systems for Motion Perception: A Review

Authors: Qinbing Fu, Hongxin Wang, Cheng Hu, Shigang Yue

Comments: 90 pages, 34 figures, a comprehensive review paper

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

[158]  arXiv:1904.02052 (cross-list from cs.CV) [pdf, other]

Title: Estimating Chlorophyll a Concentrations of Several Inland Waters with Hyperspectral Data and Machine Learning Models

Authors: Philipp M. Maier, Sina Keller

Comments: Accepted at ISPRS Geospatial Week 2019 in Enschede

Subjects: Computer Vision and Pattern Recognition (cs.CV); Quantitative Methods (q-bio.QM); Applications (stat.AP)

[159]  arXiv:1904.02243 (cross-list from eess.SP) [pdf, other]

Title: Optimized Preprocessing and Machine Learning for Quantitative Raman Spectroscopy in Biology

Authors: Emily E Storey, Amr S. Helmy

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

[160]  arXiv:1904.02309 (cross-list from cs.LG) [pdf, other]

Title: On functions computed on trees

Authors: Roozbeh Farhoodi, Khashayar Filom, Ilenna Simone Jones, Konrad Paul Kording

Comments: 52 pages, 10 figures. The final version. To appear in Neural Computation. May vary slightly from published version

Journal-ref: Neural Computation 31 (2019), no. 11, 2075--2137

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

[161]  arXiv:1904.02946 (cross-list from cond-mat.soft) [pdf, other]

Title: Cell motility, synchronization, and cell traction orientational order

Authors: M. Leoni

Comments: 11 pages. 3 figures

Subjects: Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)

[162]  arXiv:1904.03024 (cross-list from eess.IV) [pdf, ps, other]

Title: A biologically constrained encoding solution for long-term storage of images onto synthetic DNA

Authors: Melpomeni Dimopoulou, Marc Antonini, Pascal Barbry, Raja Appuswamy

Comments: Submitted to EUSIPCO 2019 conference

Subjects: Image and Video Processing (eess.IV); Multimedia (cs.MM); Genomics (q-bio.GN)

[163]  arXiv:1904.03235 (cross-list from math.CO) [pdf, ps, other]

Title: Neural Codes and the Factor Complex

Authors: Alexander Ruys de Perez, Laura Felicia Matusevich, Anne Shiu

Comments: Added a new section that takes computational considerations into account. That is, it compares an algorithm to determine max intersection completeness derived from our results with brute force methods

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

[164]  arXiv:1904.03442 (cross-list from physics.pop-ph) [pdf, other]

Title: Does it Swing? Microtiming Deviations and Swing Feeling in Jazz

Authors: George Datseris, Annika Ziereis, Thorsten Albrecht, York Hagmayer, Viola Priesemann, Theo Geisel

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

[165]  arXiv:1904.03474 (cross-list from math.AP) [pdf, other]

Title: A PDE model for bleb formation and interaction with linker proteins

Authors: Philipp Werner, Martin Burger, Jan-Frederik Pietschmann

Subjects: Analysis of PDEs (math.AP); Cell Behavior (q-bio.CB)

[166]  arXiv:1904.03524 (cross-list from stat.AP) [pdf, ps, other]

Title: A Big Data Analytics Framework to Predict the Risk of Opioid Use Disorder

Authors: Md Mahmudul Hasan, Md. Noor-E-Alam, Mehul Rakeshkumar Patel, Alicia Sasser Modestino, Leon D. Sanchez, Gary Young

Subjects: Applications (stat.AP); Computers and Society (cs.CY); Quantitative Methods (q-bio.QM)

[167]  arXiv:1904.03603 (cross-list from cs.NE) [pdf, other]

Title: Human Intracranial EEG Quantitative Analysis and Automatic Feature Learning for Epileptic Seizure Prediction

Authors: Ramy Hussein, Mohamed Osama Ahmed, Rabab Ward, Z. Jane Wang, Levin Kuhlmann, Yi Guo

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

[168]  arXiv:1904.03625 (cross-list from physics.bio-ph) [pdf, ps, other]

Title: Electric-induced reversal of morphogenesis in Hydra

Authors: Erez Braun, Hillel Ori

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

[169]  arXiv:1904.04198 (cross-list from nlin.AO) [pdf, other]

Title: Single-species fragmentation: the role of density-dependent feedbacks

Authors: V. Dornelas, E. H. Colombo, C. Anteneodo

Journal-ref: Phys. Rev. E 99, 062225 (2019)

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

[170]  arXiv:1904.04328 (cross-list from physics.bio-ph) [pdf, other]

Title: A buckling instability and its influence on microtubule orientation in plant cells

Authors: Sven Bachmann, Richard Froese, Eric N Cytrynbaum

Comments: To appear in SIAM Journal on Applied Mathematics (SIAP); v1->v2: change of title and reorganization of the presentation of the results

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

[171]  arXiv:1904.04409 (cross-list from physics.bio-ph) [pdf, ps, other]

Title: Globular bundles and entangled network of proteins (CorA) by a coarse-grained Monte Carlo simulation

Authors: Warin Jetsadawisut (1), Sunan Kitjaruwankul (2), Panisak Boonamnaj (1), Pornthep Sompornpisut (1), R.B. Pandey (3) ((1) Chulalongkorn University, Bangkok, Thailand, (2) Kasetsart University Sriracha Campus, Chonburi, Thailand, (3) University of Southern Mississippi, Hattiesburg, MS USA)

Comments: 18 pages, 14 figures, 34 references

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

[172]  arXiv:1904.04579 (cross-list from cs.NE) [pdf, ps, other]

Title: A Concept-Value Network as a Brain Model

Authors: Kieran Greer

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

[173]  arXiv:1904.05026 (cross-list from stat.AP) [pdf, ps, other]

Title: Early features associated with the neurocognitive development at 36 months of age: the AuBE study

Authors: Sabine Plancoulaine, Camille Stagnara, Sophie Flori, Flora Bat-Pitault, Jian-Sheng Lin, Hugues Patural (SNA-EPIS), Patricia Franco (CRNL)

Journal-ref: Sleep Medicine, Elsevier, 2017, 30, pp.222-228

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

[174]  arXiv:1904.05042 (cross-list from stat.AP) [pdf, ps, other]

Title: Night sleep duration trajectories and associated factors among preschool children from the EDEN cohort

Authors: Sabine Plancoulaine (INSERM, CRESS - U1153), Eve Reynaud (CRESS - U1153, INSERM), Anne Forhan (CRESS - U1153, INSERM), Sandrine Lioret (CRESS - U1153, INSERM), Barbara Heude (CRESS - U1153, INSERM), Marie-Aline Charles (CRESS - U1153, INSERM)

Journal-ref: Sleep Medicine, Elsevier, 2018, 48, pp.194-201

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

[175]  arXiv:1904.05043 (cross-list from stat.AP) [pdf, ps, other]

Title: Association of night-waking and inattention/hyperactivity symptoms trajectories in preschool-aged children

Authors: Eve Reynaud (INSERM, CRESS - U1153), Anne Forhan (INSERM, CRESS - U1153), Barbara Heude (INSERM, CRESS - U1153), Marie-Aline Charles (INSERM, CRESS - U1153), Sabine Plancoulaine (INSERM, CRESS - U1153)

Journal-ref: Scientific Reports, Nature Publishing Group, 2018, 8 (1)

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

[176]  arXiv:1904.05070 (cross-list from stat.AP) [pdf, ps, other]

Title: Cord-blood vitamin D level and night sleep duration in preschoolers in the EDEN mother-child birth cohort

Authors: Chu Yan Yong (INSERM, CRESS - U1153), Eve Reynaud (INSERM, CRESS - U1153), Anne Forhan (INSERM, CRESS - U1153), Partricia Dargent-Molina (INSERM, CRESS - U1153), Barbara Heude (INSERM, CRESS - U1153), Marie-Aline Charles (INSERM, CRESS - U1153), Sabine Plancoulaine (INSERM, CRESS - U1153)

Journal-ref: Sleep Medicine, Elsevier, 2019, 53, pp.70-74

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

[177]  arXiv:1904.05183 (cross-list from physics.bio-ph) [pdf, ps, other]

Title: Helical and oscillatory microswimmer motility statistics from differential dynamic microscopy

Authors: Ottavio A. Croze, Vincent A. Martinez, Theresa Jakuszeit, Dario Dell'Arciprete, Wilson C. K. Poon, Martin A. Bees

Comments: 26 pages, 9 figures

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

[178]  arXiv:1904.05493 (cross-list from cs.AI) [pdf, other]

Title: Non-locally Encoder-Decoder Convolutional Network for Whole Brain QSM Inversion

Authors: Juan Liu, Kevin M. Koch

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

[179]  arXiv:1904.05528 (cross-list from cs.CR) [pdf, ps, other]

Title: Review on DNA Cryptography

Authors: Mandrita Mondal, Kumar S. Ray

Comments: 21 pages, 12 figures, 6 tables

Journal-ref: International Journal of Bioinformatics and Intelligent Computing. 2023;2(1):44-72

Subjects: Cryptography and Security (cs.CR); Biomolecules (q-bio.BM)

[180]  arXiv:1904.05846 (cross-list from physics.bio-ph) [pdf, other]

Title: Load-dependent adaptation near zero load in the bacterial flagellar motor

Authors: Jasmine A Nirody, Ashley L. Nord, Richard M. Berry

Comments: 13 pages, 5 figures

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

[181]  arXiv:1904.05946 (cross-list from physics.chem-ph) [pdf, ps, other]

Title: Partial covariance two-dimensional mass spectrometry for determination of biomolecular primary structure

Authors: Taran Driver, Ruth Ayers, Rüdiger Pipkorn, Bridgette Cooper, Nikhil Bachhawat, Serguei Patchkovskii, Vitali Averbukh, David R. Klug, Jon P. Marangos, Leszek J. Frasinski, Marina Edelson-Averbukh

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

[182]  arXiv:1904.06083 (cross-list from cs.SD) [pdf, other]

Title: DNN-based Acoustic-to-Articulatory Inversion using Ultrasound Tongue Imaging

Authors: Dagoberto Porras, Alexander Sepúlveda-Sepúlveda, Tamás Gábor Csapó

Comments: 8 pages, 5 figures, Accepted to IJCNN 2019

Subjects: Sound (cs.SD); Audio and Speech Processing (eess.AS); Tissues and Organs (q-bio.TO)

[183]  arXiv:1904.06375 (cross-list from physics.bio-ph) [pdf, ps, other]

Title: Molecular simulations have boosted knowledge of CRISPR/Cas9: A Review

Authors: Angana Ray, Rosa Di Felice

Comments: 24 pages, 10 figures, few figures are from previously published work for which appropriate permissions have been taken

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

[184]  arXiv:1904.06890 (cross-list from cs.CV) [pdf, ps, other]

Title: Algorithms used for the Cell Segmentation Benchmark Competition at ISBI 2019 by RWTH-GE

Authors: Dennis Eschweiler, Johannes Stegmaier

Comments: 4 pages, algorithms used for the Cell Segmentation Benchmark competition at IEEE International Symposium on Biomedical Imaging (ISBI) 2019 in Venice, Italy

Subjects: Computer Vision and Pattern Recognition (cs.CV); Cell Behavior (q-bio.CB)

[185]  arXiv:1904.06977 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: On non-negative solutions to large systems of random linear equations

Authors: Stefan Landmann, Andreas Engel

Comments: 10 pages, 5 figures

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Populations and Evolution (q-bio.PE)

[186]  arXiv:1904.07149 (cross-list from physics.app-ph) [pdf, ps, other]

Title: Ionic Electro active Polymer-Based Soft Actuators and Their Applications in Microfluidic Micropumps, Microvalves, and Micromixers: A Review

Authors: Mohsen Annabestani, Mahdi Fardmanesh

Subjects: Applied Physics (physics.app-ph); Quantitative Methods (q-bio.QM)

[187]  arXiv:1904.07360 (cross-list from physics.ins-det) [pdf, ps, other]

Title: Interferometric scattering enables fluorescence-free electrokinetic trapping of single nanoparticles in free solution

Authors: Allison H. Squires, Abhijit A. Lavania, Peter D. Dahlberg, W. E. Moerner

Comments: Manuscript and SI; videos available upon request

Subjects: Instrumentation and Detectors (physics.ins-det); Applied Physics (physics.app-ph); Biological Physics (physics.bio-ph); Optics (physics.optics); Quantitative Methods (q-bio.QM)

[188]  arXiv:1904.07414 (cross-list from stat.AP) [pdf, other]

Title: Metrics for Graph Comparison: A Practitioner's Guide

Authors: Peter Wills, Francois G. Meyer

Subjects: Applications (stat.AP); Social and Information Networks (cs.SI); Data Analysis, Statistics and Probability (physics.data-an); Neurons and Cognition (q-bio.NC)

[189]  arXiv:1904.07441 (cross-list from eess.SP) [pdf, other]

Title: fMRI Based Cerebral Instantaneous Parameters for Automatic Alzheimer's, Mild Cognitive Impairment and Healthy Subject Classification

Authors: Esmaeil Seraj, Mehran Yazdi, Nastaran Shahparian

Subjects: Signal Processing (eess.SP); Computational Engineering, Finance, and Science (cs.CE); Image and Video Processing (eess.IV); Neurons and Cognition (q-bio.NC); Quantitative Methods (q-bio.QM)

[190]  arXiv:1904.07620 (cross-list from physics.med-ph) [pdf, other]

Title: Impaired coronary blood flow at higher heart rates during atrial fibrillation: investigation via multiscale modelling

Authors: Stefania Scarsoglio, Caterina Gallo, Andrea Saglietto, Luca Ridolfi, Matteo Anselmino

Comments: 8 pages, 5 figures, 3 tables

Journal-ref: Computer Methods and Programs in Biomedicine, 175: 95-102, 2019

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

[191]  arXiv:1904.07772 (cross-list from cs.CV) [pdf, other]

Title: Cryo-Electron Microscopy Image Analysis Using Multi-Frequency Vector Diffusion Maps

Authors: Yifeng Fan, Zhizhen Zhao

Subjects: Computer Vision and Pattern Recognition (cs.CV); Biomolecules (q-bio.BM)

[192]  arXiv:1904.08007 (cross-list from cs.SE) [pdf, other]

Title: Metamorphic Testing for Quality Assurance of Protein Function Prediction Tools

Authors: Morteza Pourreza Shahri, Madhusudan Srinivasan, Gillian Reynolds, Diane Bimczok, Indika Kahanda, Upulee Kanewala

Comments: 8 pages, First IEEE International Conference On Artificial Intelligence Testing

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

[193]  arXiv:1904.08034 (cross-list from cs.LG) [pdf, other]

Title: People infer recursive visual concepts from just a few examples

Authors: Brenden M. Lake, Steven T. Piantadosi

Comments: In press at "Computational Brain & Behavior"

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

[194]  arXiv:1904.08102 (cross-list from cs.LG) [pdf, other]

Title: Batched Stochastic Bayesian Optimization via Combinatorial Constraints Design

Authors: Kevin K. Yang, Yuxin Chen, Alycia Lee, Yisong Yue

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

[195]  arXiv:1904.08127 (cross-list from physics.bio-ph) [pdf, other]

Title: A precise relationship among Buller's drop, ballistospore and gill morphology enables maximal packing of spores within gilled mushrooms

Authors: Martina Iapichino, Yen Wen Wang, Savannah Gentry, Anne Pringle, Agnese Seminara

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

[196]  arXiv:1904.08216 (cross-list from physics.bio-ph) [pdf, ps, other]

Title: Exactly solvable model of gene expression in proliferating bacterial cell population with stochastic protein bursts and protein partitioning

Authors: Jakub Jędrak, Maciej Kwiatkowski, Anna Ochab-Marcinek

Comments: 14 pages, 4 figures, accepted in Physical Review E

Subjects: Biological Physics (physics.bio-ph); Molecular Networks (q-bio.MN)

[197]  arXiv:1904.08319 (cross-list from physics.bio-ph) [pdf, other]

Title: Confinement enhances the diversity of microbial flow fields

Authors: Raphaël Jeanneret, Dmitri O. Pushkin, Marco Polin

Comments: Accepted for publication in Physical Review Letters. 5 pages and 4 figures, plus Supplementary Material

Journal-ref: Phys. Rev. Lett. 123, 248102 (2019)

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

[198]  arXiv:1904.08467 (cross-list from nlin.AO) [pdf, ps, other]

Title: Spike-burst chimera states in an adaptive exponential integrate-and-fire neuronal network

Authors: Moises S. Santos, Paulo R. Protachevicz, Kelly C. Iarosz, Iberê L. Caldas, Ricardo L. Viana, Fernando S. Borges, Hai-Peng Ren, José D. Szezech Jr, Antonio M. Batista, Celso Grebogi

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

[199]  arXiv:1904.08514 (cross-list from cs.LG) [pdf, other]

Title: DeepNovoV2: Better de novo peptide sequencing with deep learning

Authors: Rui Qiao, Ngoc Hieu Tran, Lei Xin, Baozhen Shan, Ming Li, Ali Ghodsi

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

[200]  arXiv:1904.08675 (cross-list from nlin.PS) [pdf, other]

Title: A trio of heteroclinic bifurcations arising from a model of spatially-extended Rock-Paper-Scissors

Authors: Claire M Postlethwaite, Alastair M Rucklidge

Comments: 36 pages, 8 figures

Journal-ref: Nonlinearity 32 (2019) 1375-1407

Subjects: Pattern Formation and Solitons (nlin.PS); Populations and Evolution (q-bio.PE)

[201]  arXiv:1904.08967 (cross-list from math.PR) [pdf, ps, other]

Title: Stochastically modeled weakly reversible reaction networks with a single linkage class

Authors: David F. Anderson, Daniele Cappelletti, Jinsu Kim

Subjects: Probability (math.PR); Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)

[202]  arXiv:1904.09200 (cross-list from cond-mat.soft) [pdf, other]

Title: Re-enterant efficiency of phototaxis in Chlamydomonas reinhardtii cells

Authors: Sujeet Kumar Choudhary, Aparna Baskaran, Prerna Sharma

Subjects: Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)

[203]  arXiv:1904.09340 (cross-list from physics.flu-dyn) [pdf, other]

Title: Don't be jelly: Exploring effective jellyfish locomotion

Authors: Jason G. Miles, Nicholas A. Battista

Comments: 42 pages, 25 figures

Subjects: Fluid Dynamics (physics.flu-dyn); Quantitative Methods (q-bio.QM)

[204]  arXiv:1904.09406 (cross-list from physics.comp-ph) [pdf, other]

Title: DeepMoD: Deep learning for Model Discovery in noisy data

Authors: Gert-Jan Both, Subham Choudhury, Pierre Sens, Remy Kusters

Subjects: Computational Physics (physics.comp-ph); Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)

[205]  arXiv:1904.09485 (cross-list from cond-mat.soft) [pdf, other]

Title: Conformational Heterogeneity in Human Interphase Chromosome Organization Reconciles the FISH and Hi-C Paradox

Authors: Guang Shi, D. Thirumalai

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

[206]  arXiv:1904.09584 (cross-list from physics.soc-ph) [pdf, ps, other]

Title: Modelling Hierarchical Flocking

Authors: Yongnan Jia, Tamas Vicsek

Comments: 13 pages, 7 figures

Subjects: Physics and Society (physics.soc-ph); Adaptation and Self-Organizing Systems (nlin.AO); Quantitative Methods (q-bio.QM)

[207]  arXiv:1904.09651 (cross-list from cs.LG) [pdf, ps, other]

Title: An improved sex specific and age dependent classification model for Parkinson's diagnosis using handwriting measurement

Authors: Ujjwal Gupta, Hritik Bansal, Deepak Joshi

Comments: Journal of Computer Methods and Programs in Biomedicine(Accepted on 27 December 2019)

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

[208]  arXiv:1904.09662 (cross-list from stat.AP) [pdf, ps, other]

Title: Genomics models in radiotherapy: from mechanistic to machine learning

Authors: John Kang, James T. Coates, Robert L. Strawderman, Barry S. Rosenstein, Sarah L. Kerns

Comments: 32 pages, 3 figures, 3 tables

Journal-ref: Medical Physics 2020

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

[209]  arXiv:1904.09771 (cross-list from math.CO) [pdf, ps, other]

Title: Extremal properties of the Colless balance index for rooted binary trees

Authors: Mareike Fischer, Lina Herbst, Kristina Wicke

Comments: ATTENTION: THIS MANUSCRIPT HAS BEEN SUBSUMED BY ANOTHER MANUSCRIPT: ARXIV IDENTIFIER arXiv:1907.05064 Keywords: Tree balance; Colless index; Sackin index; greedy tree structure; Blancmange curve; Takagi curve

Subjects: Combinatorics (math.CO); Populations and Evolution (q-bio.PE)

[210]  arXiv:1904.09800 (cross-list from math.DS) [pdf, ps, other]

Title: Stabilized Partitioning of Metapopulations Networks

Authors: Dinesh Kumar, Soumyendu Raha

Comments: 11 Pages, 2 Figures

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

[211]  arXiv:1904.09805 (cross-list from math.DS) [pdf, other]

Title: On equilibrium properties of the replicator-mutator equation in deterministic and random games

Authors: Manh Hong Duong, The Anh Han

Comments: 23 pages

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

[212]  arXiv:1904.09844 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Resilience for stochastic systems interacting via a quasi-degenerate network

Authors: Sara Nicoletti, Duccio Fanelli, Niccolò Zagli, Malbor Asllani, Giorgio Battistelli, Timoteo Carletti, Luigi Chisci, Giacomo Innocenti, Roberto Livi

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Pattern Formation and Solitons (nlin.PS); Biological Physics (physics.bio-ph); Populations and Evolution (q-bio.PE)

[213]  arXiv:1904.09922 (cross-list from math.PR) [pdf, other]

Title: The Effect of Recombination on the Speed of Evolution

Authors: Nantawat Udomchatpitak

Comments: 65 pages

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

[214]  arXiv:1904.10353 (cross-list from cs.LG) [pdf, ps, other]

Title: Read classification using semi-supervised deep learning

Authors: Tomislav Šebrek, Jan Tomljanović, Josip Krapac, Mile Šikić

Comments: 2nd International Workshop on Deep Learning for Precision Medicine, ECML-PKDD, 2017, Skopje, Nothern Macedonia

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

[215]  arXiv:1904.10443 (cross-list from physics.app-ph) [pdf, ps, other]

Title: A toxicology-informed, safer by design approach for the fabrication of transparent electrodes based on silver nanowires

Authors: Djadidi Toybou (ISTerre), Caroline Celle (LITEN), Catherine Aude-Garcia (LCBM - UMR 5249), Thierry Rabilloud (LCBM - UMR 5249), Jean-Pierre Simonato (LITEN)

Journal-ref: Environmental science: Nano, Royal Society of Chemistry, 2019, 6 (2), pp.684-694

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

[216]  arXiv:1904.10489 (cross-list from cs.DC) [pdf, other]

Title: Chunkflow: Distributed Hybrid Cloud Processing of Large 3D Images by Convolutional Nets

Authors: Jingpeng Wu, William M. Silversmith, Kisuk Lee, H. Sebastian Seung

Subjects: Distributed, Parallel, and Cluster Computing (cs.DC); Computer Vision and Pattern Recognition (cs.CV); Neurons and Cognition (q-bio.NC)

[217]  arXiv:1904.11020 (cross-list from physics.bio-ph) [pdf, other]

Title: Chemokinetic scattering, trapping, and avoidance of active Brownian particles

Authors: Justus A. Kromer, Noelia de la Cruz, Benjamin M. Friedrich

Comments: 17 pages, 10 figures; accepted for publication in Physical Review Letters

Journal-ref: Phys. Rev. Lett. 124, 118101 (2020)

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

[218]  arXiv:1904.11081 (cross-list from physics.soc-ph) [pdf, other]

Title: Evolutionary dynamics of group cooperation with asymmetrical environmental feedback

Authors: Yanxuan Shao, Xin Wang, Feng Fu

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

[219]  arXiv:1904.11154 (cross-list from physics.bio-ph) [pdf, other]

Title: Topology, Landscapes, and Biomolecular Energy Transport

Authors: Justin E. Elenewski, Kirill A. Velizhanin, Michael Zwolak

Comments: Final published version + supplementary info

Journal-ref: Nature Communications 10, 4662 (2019)

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

[220]  arXiv:1904.11161 (cross-list from physics.bio-ph) [pdf, other]

Title: The role of topology and mechanics in uniaxially growing cell networks

Authors: Alexander Erlich, Gareth W. Jones, Françoise Tisseur, Derek E. Moulton, Alain Goriely

Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Cell Behavior (q-bio.CB)

[221]  arXiv:1904.11223 (cross-list from cs.LG) [pdf, other]

Title: Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders

Authors: Matteo Manica, Ali Oskooei, Jannis Born, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez

Comments: 11 pages, 5 figures, 1 table, Workshop on Computational Biology at the International Conference on Machine Learning (ICML), Long Beach, CA, 2019

Journal-ref: Mol. Pharmaceutics 2019

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

[222]  arXiv:1904.11453 (cross-list from physics.bio-ph) [pdf, other]

Title: A polymer model of bacterial supercoiled DNA including structural transitions of the double helix

Authors: Thibaut Lepage, Ivan Junier

Comments: To appear in Physica A

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

[223]  arXiv:1904.11553 (cross-list from nlin.AO) [pdf, other]

Title: Directed Flow of Information in Chimera States

Authors: Nicolás Deschle, Andreas Daffertshofer, Demian Battaglia, Erik A. Martens

Journal-ref: Frontiers in Applied Mathematics and Statistics, 5(28), 2019

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

[224]  arXiv:1904.11583 (cross-list from math.PR) [pdf, ps, other]

Title: Time-dependent product-form Poisson distributions for reaction networks with higher order complexes

Authors: David F. Anderson, David Schnoerr, Chaojie Yuan

Comments: Corrected an error in the proof of Lemma 2.1. Added examples and images from simulation results

Subjects: Probability (math.PR); Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)

[225]  arXiv:1904.11675 (cross-list from cond-mat.soft) [pdf, ps, other]

Title: Collective dynamics of microtubule-based 3D active fluids from single microtubules

Authors: Teagan E. Bate, Edward J. Jarvis, Megan E. Varney, Kun-Ta Wu

Subjects: Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Subcellular Processes (q-bio.SC)

[226]  arXiv:1904.11793 (cross-list from physics.soc-ph) [pdf, other]

Title: Geometric renormalization unravels self-similarity of the multiscale human connectome

Authors: Muhua Zheng, Antoine Allard, Patric Hagmann, Yasser Alemán-Gómez, M. Ángeles Serrano

Journal-ref: Proceedings of the National Academy of Sciences, 117(33), 20244-20253 (2020)

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

[227]  arXiv:1904.12161 (cross-list from math.DS) [pdf, other]

Title: The geometry of rest-spike bistability

Authors: Giuseppe Ilario Cirillo, Rodolphe Sepulchre

Comments: 19 pages, 8 figures

Subjects: Dynamical Systems (math.DS); Neurons and Cognition (q-bio.NC)

[228]  arXiv:1904.12206 (cross-list from cs.LG) [pdf, other]

Title: Temporal-Clustering Invariance in Irregular Healthcare Time Series

Authors: Mohammad Taha Bahadori, Zachary Chase Lipton

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

[229]  arXiv:1904.12340 (cross-list from math.DS) [pdf, ps, other]

Title: Memory and mutualism in species sustainability: a time-fractional Lotka-Volterra model with harvesting

Authors: Mohammad M. Amirian, I.N.Towers, Z.Jovanoski, Andrew J. Irwin

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

[230]  arXiv:1904.12432 (cross-list from math.CO) [pdf, other]

Title: Ranking top-k trees in tree-based phylogenetic networks

Authors: Momoko Hayamizu, Kazuhisa Makino

Comments: 6 pages, 1 figure

Subjects: Combinatorics (math.CO); Discrete Mathematics (cs.DM); Populations and Evolution (q-bio.PE)

[231]  arXiv:1904.12456 (cross-list from physics.bio-ph) [pdf, ps, other]

Title: A new method of brain stimulation at ultra-high frequency

Authors: Yousef Jamali, Mohammad Jamali, Mehdi Golshani

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

[232]  arXiv:1904.12460 (cross-list from physics.bio-ph) [pdf, ps, other]

Title: Theory of cyborg: a new approach to fish locomotion control

Authors: Mohammad Jamali, Yousef Jamali, Mehdi Golshani

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

[233]  arXiv:1904.12591 (cross-list from cs.DC) [pdf, other]

Title: Winner-Take-All Computation in Spiking Neural Networks

Authors: Nancy Lynch, Cameron Musco, Merav Parter

Subjects: Distributed, Parallel, and Cluster Computing (cs.DC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Neural and Evolutionary Computing (cs.NE); Neurons and Cognition (q-bio.NC)

[234]  arXiv:1904.12690 (cross-list from cs.CV) [pdf, other]

Title: Capturing human categorization of natural images at scale by combining deep networks and cognitive models

Authors: Ruairidh M. Battleday, Joshua C. Peterson, Thomas L. Griffiths

Comments: 29 pages; 4 figures. arXiv admin note: text overlap with arXiv:1711.04855

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

[235]  arXiv:1904.12958 (cross-list from cs.AI) [pdf, ps, other]

Title: Predictive Situation Awareness for Ebola Virus Disease using a Collective Intelligence Multi-Model Integration Platform: Bayes Cloud

Authors: Cheol Young Park, Shou Matsumoto, Jubyung Ha, YoungWon Park

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

[236]  arXiv:1904.12972 (cross-list from physics.soc-ph) [pdf, other]

Title: Epistasis between cultural traits drives paradigm shifts in cultural evolution

Authors: Ignacio Pascual, Jacobo Aguirre, Susanna Manrubia, José A. Cuesta

Comments: 12 pages, 6 figures, uses SelfArxone.cls

Journal-ref: Royal Society Open Science 7, 191813 (2020)

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

[237]  arXiv:1904.13009 (cross-list from physics.bio-ph) [pdf, ps, other]

Title: Collective dynamics and self-organization of active particles on random networks

Authors: Hanqing Nan, Yu Zheng, Shaohua Chen, Christopher Eddy, Jianxiang Tian, Wenxiang Xu, Bo Sun, Yang Jiao

Comments: 5 pages, 4 figures

Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Cell Behavior (q-bio.CB)

[238]  arXiv:1904.13052 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Minimal model of permutation symmetry in unsupervised learning

Authors: Tianqi Hou, K.Y. Michael Wong, Haiping Huang

Comments: 36 pages, 110 equations, 5 figures; a complete picture about physical laws of unsupervised learning in neural networks presented

Journal-ref: 2019 J. Phys. A: Math. Theor. 52 414001

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

[239]  arXiv:1904.05773 (cross-list from eess.IV) [pdf, other]

Title: Diagnosis of Celiac Disease and Environmental Enteropathy on Biopsy Images Using Color Balancing on Convolutional Neural Networks

Authors: Kamran Kowsari, Rasoul Sali, Marium N. Khan, William Adorno, S. Asad Ali, Sean R. Moore, Beatrice C. Amadi, Paul Kelly, Sana Syed, Donald E. Brown

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