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Quantitative Biology

Authors and titles for recent submissions

[ total of 78 entries: 1-50 | 51-78 ]
[ showing 50 entries per page: fewer | more | all ]

Wed, 8 May 2024

[1]  arXiv:2405.04248 [pdf, ps, other]
Title: Neurocomputational Phenotypes in Female and Male Autistic Individuals
Authors: Michelle McCleod, Sean Borneman, Evie Malaia
Comments: 10 pages, 2 figures, 4 tables. Submitted to Journal of Science and Health, University of Alabama
Subjects: Neurons and Cognition (q-bio.NC); Chaotic Dynamics (nlin.CD)
[2]  arXiv:2405.04011 [pdf, other]
Title: Adjoint Sensitivity Analysis on Multi-Scale Bioprocess Stochastic Reaction Network
Authors: Keilung Choy, Wei Xie
Comments: 11 pages, 2 figures
Subjects: Molecular Networks (q-bio.MN); Machine Learning (stat.ML)
[3]  arXiv:2405.03913 [pdf, other]
Title: Digital Twin Calibration for Biological System-of-Systems: Cell Culture Manufacturing Process
Authors: Fuqiang Cheng, Wei Xie, Hua Zheng
Comments: 12 pages, 5 figures
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Machine Learning (stat.ML)
[4]  arXiv:2405.03861 [pdf, other]
Title: Homeostasis in Input-Output Networks: Structure, Classification and Applications
Authors: Fernando Antoneli, Martin Golubitsky, Jiaxin Jin, Ian Stewart
Comments: 45 pages, 26 figures, submitted to the MBS special issue "Dynamical Systems in Life Sciences"
Subjects: Molecular Networks (q-bio.MN); Combinatorics (math.CO); Dynamical Systems (math.DS); Biological Physics (physics.bio-ph)
[5]  arXiv:2405.03829 [pdf, other]
Title: Unsupervised Machine Learning Identifies Latent Ultradian States in Multi-Modal Wearable Sensor Signals
Authors: Christopher Thornton, Billy C. Smith, Guillermo M. Besne, Bethany Little, Yujiang Wang
Subjects: Neurons and Cognition (q-bio.NC)
[6]  arXiv:2405.03726 [pdf, ps, other]
Title: sc-OTGM: Single-Cell Perturbation Modeling by Solving Optimal Mass Transport on the Manifold of Gaussian Mixtures
Authors: Andac Demir, Elizaveta Solovyeva, James Boylan, Mei Xiao, Fabrizio Serluca, Sebastian Hoersch, Jeremy Jenkins, Murthy Devarakonda, Bulent Kiziltan
Comments: ICLR 2024, Machine Learning for Genomics Explorations Workshop
Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG)
[7]  arXiv:2405.03707 [pdf, ps, other]
Title: Quantifying indirect and direct vaccination effects arising in the SIR model
Authors: Lixin Lin, Homayoun Hamedmoghadam, Robert Shorten, Lewi Stone
Subjects: Populations and Evolution (q-bio.PE)
[8]  arXiv:2405.04078 (cross-list from cs.LG) [pdf, other]
Title: WISER: Weak supervISion and supErvised Representation learning to improve drug response prediction in cancer
Authors: Kumar Shubham, Aishwarya Jayagopal, Syed Mohammed Danish, Prathosh AP, Vaibhav Rajan
Comments: ICML 2024
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Quantitative Methods (q-bio.QM)
[9]  arXiv:2405.03931 (cross-list from math.DS) [pdf, ps, other]
Title: Incorporating changeable attitudes toward vaccination into an SIR infectious disease model
Authors: Yi Jiang, Kristin M. Kurianski, Jane H. Lee, Yanping Ma, Daniel Cicala, Glenn Ledder
Comments: 30 pages, 3 tables, 10 figures
Subjects: Dynamical Systems (math.DS); Populations and Evolution (q-bio.PE)
[10]  arXiv:2405.03879 (cross-list from stat.ML) [pdf, other]
Title: Scalable Amortized GPLVMs for Single Cell Transcriptomics Data
Authors: Sarah Zhao, Aditya Ravuri, Vidhi Lalchand, Neil D. Lawrence
Subjects: Machine Learning (stat.ML); Machine Learning (cs.LG); Genomics (q-bio.GN); Applications (stat.AP)
[11]  arXiv:2405.03799 (cross-list from cs.LG) [pdf, other]
Title: Synthetic Data from Diffusion Models Improve Drug Discovery Prediction
Authors: Bing Hu, Ashish Saragadam, Anita Layton, Helen Chen
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Quantitative Methods (q-bio.QM)

Tue, 7 May 2024

[12]  arXiv:2405.03602 [pdf, other]
Title: One nose but two nostrils: Learn to align with sparse connections between two olfactory cortices
Authors: Bo Liu, Shanshan Qin, Venkatesh Murthy, Yuhai Tu
Subjects: Neurons and Cognition (q-bio.NC); Biological Physics (physics.bio-ph)
[13]  arXiv:2405.03601 [pdf, other]
Title: Firing rate model for brain rhythms controlled by astrocytes
Authors: Sergey V. Stasenko, Sergey M. Olenin, Eugene A. Grines, Tatiana A. Levanova
Comments: 12 pages, 4 figures
Subjects: Neurons and Cognition (q-bio.NC)
[14]  arXiv:2405.03370 [pdf, other]
Title: AntiFold: Improved antibody structure-based design using inverse folding
Authors: Magnus Haraldson Høie, Alissa Hummer, Tobias H. Olsen, Broncio Aguilar-Sanjuan, Morten Nielsen, Charlotte M. Deane
Subjects: Biomolecules (q-bio.BM); Quantitative Methods (q-bio.QM)
[15]  arXiv:2405.03346 [pdf, other]
Title: Population dynamics and games of variable size
Authors: Matheus Hansen, Fabio A. C. C. Chalub
Comments: 24 pages, 4 figures
Journal-ref: Matheus Hansen, Fabio A. C. C. Chalub. Population dynamics and games of variable size. Journal of Theoretical Biology 589, 111842, 2024
Subjects: Populations and Evolution (q-bio.PE)
[16]  arXiv:2405.03148 [pdf, other]
Title: Counting Subnetworks Under Gene Duplication in Genetic Regulatory Networks
Authors: Ashley Scruse, Jonathan Arnold, Robert Robinson
Subjects: Molecular Networks (q-bio.MN); Combinatorics (math.CO)
[17]  arXiv:2405.02853 [pdf, ps, other]
Title: Development and validation of a short form of the medication literacy scale for Chinese College Students
Authors: Chen Zhenzhen (1,2), Ren Jiabao (1,2), Duan Tingyu (3), Chen Ke (4), Hou Ruyi (5), Li Yimiao (5), Zeng Leixiao (5), Meng Xiaoxuan (6), Wu Yibo (7), Liu Yu (2), ((1) College of Science, Minzu University of China, Beijing, China, (2) School of Nursing, China Medical University, Shenyang, Liaoning Province, China, (3) Hebei Institute of Communications, Hebei, China, (4) Department of Social Science and Humanities, Harbin Medical University, Harbin, Heilongjiang Province, China, (5) School of Journalism and Communication, Renmin University of China, Beijing, China, (6) Tianjin Medical University, Tianjin, China, (7) School of Public Health, Peking University, Beijing, China)
Comments: 25 pages, 3 figures,3 tables
Subjects: Other Quantitative Biology (q-bio.OT)
[18]  arXiv:2405.02820 [pdf, other]
Title: Coat stiffening explains the consensus pathway of clathrin-mediated endocytosis
Authors: Felix Frey (IST Austria), Ulrich S. Schwarz (Heidelberg University)
Comments: revtex, 12 pages, 5 figures in PDF-format
Subjects: Subcellular Processes (q-bio.SC); Soft Condensed Matter (cond-mat.soft)
[19]  arXiv:2405.02786 [pdf, other]
Title: A causal inference approach of monosynapses from spike trains
Authors: Zach Saccomano, Sam Mckenzie, Horacio Rotstein, Asohan Amarasingham
Subjects: Neurons and Cognition (q-bio.NC)
[20]  arXiv:2405.02767 [pdf, ps, other]
Title: A Decade in a Systematic Review: The Evolution and Impact of Cell Painting
Authors: Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras-Puigvert, Nigel Greene, Andreas Bender, Anne E. Carpenter
Comments: Supplementary Table/Code here: this https URL
Subjects: Subcellular Processes (q-bio.SC); Cell Behavior (q-bio.CB)
[21]  arXiv:2405.02674 [pdf, other]
Title: Ambush strategy enhances organisms' performance in rock-paper-scissors games
Authors: R. Barbalho, S. Rodrigues, M. Tenorio, J. Menezes
Comments: 8 pages, 5 figures
Subjects: Populations and Evolution (q-bio.PE); Adaptation and Self-Organizing Systems (nlin.AO); Pattern Formation and Solitons (nlin.PS); Biological Physics (physics.bio-ph); Quantitative Methods (q-bio.QM)
[22]  arXiv:2405.02593 [pdf, ps, other]
Title: An Interdisciplinary Perspective of the Built-Environment Microbiome
Authors: John S. McAlister, Michael J. Blum, Yana Bromberg, Nina H. Fefferman, Qiang He, Eric Lofgren, Debra L. Miller, Courtney Schreiner, K. Selcuk Candan, Heather Szabo-Rogers, J. Michael Reed
Comments: 23 pages
Subjects: Populations and Evolution (q-bio.PE)
[23]  arXiv:2405.02524 [pdf, other]
Title: Simulation-based Inference of Developmental EEG Maturation with the Spectral Graph Model
Authors: Danilo Bernardo, Xihe Xie, Parul Verma, Jonathan Kim, Virginia Liu, Ye Wu, Pew-Thian Yap, Srikantan Nagarajan, Ashish Raj
Comments: 58 pages, 6 figures, 18 supplementary figures
Subjects: Neurons and Cognition (q-bio.NC)
[24]  arXiv:2405.02381 [pdf, ps, other]
Title: Interactions between eagles and semidomestic reindeer: lessons learned from field surveys and deterrents
Authors: Aemilius Johannes van der Meiden, Andres Lopez-Peinado, Peter Sunesson, Christian Emilsson, Navinder J Singh
Comments: 17 pages, 4 Figures, 1 Table
Subjects: Populations and Evolution (q-bio.PE)
[25]  arXiv:2405.02379 [pdf, other]
Title: Modelling the Stochastic Importation Dynamics and Establishment of Novel Pathogenic Strains using a General Branching Processes Framework
Authors: Jacob Curran-Sebastian, Frederik Mølkjær Andersen, Samir Bhatt
Subjects: Populations and Evolution (q-bio.PE); Probability (math.PR); Quantitative Methods (q-bio.QM)
[26]  arXiv:2405.02374 [pdf, other]
Title: Protein binding affinity prediction under multiple substitutions applying eGNNs on Residue and Atomic graphs combined with Language model information: eGRAL
Authors: Arturo Fiorellini-Bernardis, Sebastien Boyer, Christoph Brunken, Bakary Diallo, Karim Beguir, Nicolas Lopez-Carranza, Oliver Bent
Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[27]  arXiv:2405.02845 (cross-list from cs.LG) [pdf, other]
Title: Data-Efficient Molecular Generation with Hierarchical Textual Inversion
Authors: Seojin Kim, Jaehyun Nam, Sihyun Yu, Younghoon Shin, Jinwoo Shin
Subjects: Machine Learning (cs.LG); Molecular Networks (q-bio.MN)
[28]  arXiv:2405.02564 (cross-list from cs.CV) [pdf, ps, other]
Title: Leveraging the Human Ventral Visual Stream to Improve Neural Network Robustness
Authors: Zhenan Shao, Linjian Ma, Bo Li, Diane M. Beck
Subjects: Computer Vision and Pattern Recognition (cs.CV); Artificial Intelligence (cs.AI); Neurons and Cognition (q-bio.NC)
[29]  arXiv:2405.02534 (cross-list from cs.LG) [pdf, other]
Title: A Multi-Domain Multi-Task Approach for Feature Selection from Bulk RNA Datasets
Authors: Karim Salta, Tomojit Ghosh, Michael Kirby
Subjects: Machine Learning (cs.LG); Genomics (q-bio.GN)
[30]  arXiv:2405.02449 (cross-list from stat.ML) [pdf, other]
Title: Quality-Weighted Vendi Scores And Their Application To Diverse Experimental Design
Authors: Quan Nguyen, Adji Bousso Dieng
Comments: Published in International Conference on Machine Learning, ICML 2024. Code can be found in the Vertaix GitHub: this https URL Paper dedicated to Kwame Nkrumah
Subjects: Machine Learning (stat.ML); Materials Science (cond-mat.mtrl-sci); Machine Learning (cs.LG); Biomolecules (q-bio.BM)
[31]  arXiv:2405.02354 (cross-list from cs.LG) [pdf, ps, other]
Title: Heterogeneous network and graph attention auto-encoder for LncRNA-disease association prediction
Authors: Jin-Xing Liu, Wen-Yu Xi, Ling-Yun Dai, Chun-Hou Zheng, Ying-Lian Gao
Comments: 10 pages, 8 figures
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Quantitative Methods (q-bio.QM)

Mon, 6 May 2024

[32]  arXiv:2405.02136 [pdf, other]
Title: bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties
Authors: Jose Gavalda-Garcia, Adrian Diaz, Wim Vranken
Subjects: Quantitative Methods (q-bio.QM)
[33]  arXiv:2405.02117 [pdf, ps, other]
Title: Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling
Authors: Radek Erban, Stefanie Winkelmann
Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph)
[34]  arXiv:2405.02076 [pdf, other]
Title: SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data
Authors: Ajit J. Nirmal, Peter K. Sorger
Comments: 6 pages, 1 figure
Subjects: Quantitative Methods (q-bio.QM); Tissues and Organs (q-bio.TO)
[35]  arXiv:2405.02038 [pdf, other]
Title: Dimensionality reduction of neuronal degeneracy reveals two interfering physiological mechanisms
Authors: Arthur Fyon, Alessio Franci, Pierre Sacré, Guillaume Drion
Subjects: Neurons and Cognition (q-bio.NC); Mathematical Physics (math-ph); Cell Behavior (q-bio.CB)
[36]  arXiv:2405.01896 [pdf, ps, other]
Title: A Step Test to Evaluate the Susceptibility to Severe High-Altitude Illness in Field Conditions
Authors: Eric Hermand (URePSSS, H&P), Léo Lesaint, Laura Denis (H&P), Jean-Paul Richalet (INSEP), François Lhuissier (H&P)
Comments: High Altitude Medicine and Biology, 2024
Subjects: Tissues and Organs (q-bio.TO)
[37]  arXiv:2405.01715 [pdf, other]
Title: Identification of SNPs in genomes using GRAMEP, an alignment-free method based on the Principle of Maximum Entropy
Authors: Matheus Henrique Pimenta-Zanon, André Yoshiaki Kashiwabara, André Luís Laforga Vanzela, Fabricio Martins Lopes
Subjects: Genomics (q-bio.GN); Information Theory (cs.IT); Applications (stat.AP)
[38]  arXiv:2405.01703 [pdf, other]
Title: Fluid-structure interaction simulations for the prediction of fractional flow reserve in pediatric patients with anomalous aortic origin of a coronary artery
Authors: Charles Puelz, Craig G. Rusin, Dan Lior, Shagun Sachdeva, Tam T. Doan, Lindsay F. Eilers, Dana Reaves-O'Neal, Silvana Molossi
Subjects: Tissues and Organs (q-bio.TO); Medical Physics (physics.med-ph)
[39]  arXiv:2405.01664 [pdf, ps, other]
Title: Stress-induced Eukaryotic Translational Regulatory Mechanisms
Authors: Dilawar Ahmad Mir, Zhengxin Ma, Jordan Horrocks, Aric N Rogers
Comments: 37 Pages, Figures 7, Review Article
Subjects: Molecular Networks (q-bio.MN)
[40]  arXiv:2405.01616 [pdf, other]
Title: Generative Active Learning for the Search of Small-molecule Protein Binders
Authors: Maksym Korablyov, Cheng-Hao Liu, Moksh Jain, Almer M. van der Sloot, Eric Jolicoeur, Edward Ruediger, Andrei Cristian Nica, Emmanuel Bengio, Kostiantyn Lapchevskyi, Daniel St-Cyr, Doris Alexandra Schuetz, Victor Ion Butoi, Jarrid Rector-Brooks, Simon Blackburn, Leo Feng, Hadi Nekoei, SaiKrishna Gottipati, Priyesh Vijayan, Prateek Gupta, Ladislav Rampášek, Sasikanth Avancha, Pierre-Luc Bacon, William L. Hamilton, Brooks Paige, Sanchit Misra, Stanislaw Kamil Jastrzebski, Bharat Kaul, Doina Precup, José Miguel Hernández-Lobato, Marwin Segler, Michael Bronstein, Anne Marinier, Mike Tyers, Yoshua Bengio
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[41]  arXiv:2405.02003 (cross-list from cond-mat.stat-mech) [pdf, ps, other]
Title: Smoothly vanishing density in the contact process by an interplay of disorder and long-distance dispersal
Authors: R. Juhász, I. A. Kovács
Comments: 8 pages, 6 figures
Subjects: Statistical Mechanics (cond-mat.stat-mech); Disordered Systems and Neural Networks (cond-mat.dis-nn); Populations and Evolution (q-bio.PE)
[42]  arXiv:2405.01989 (cross-list from math.OC) [pdf, other]
Title: Parameter estimation in ODEs: assessing the potential of local and global solvers
Authors: M. Fernández de Dios, Ángel M. González-Rueda, Julio R. Banga, Julio González-Díaz, David R. Penas
Subjects: Optimization and Control (math.OC); Quantitative Methods (q-bio.QM)
[43]  arXiv:2405.01983 (cross-list from cs.AI) [pdf, other]
Title: Model-based reinforcement learning for protein backbone design
Authors: Frederic Renard, Cyprien Courtot, Alfredo Reichlin, Oliver Bent
Subjects: Artificial Intelligence (cs.AI); Biomolecules (q-bio.BM)
[44]  arXiv:2405.01974 (cross-list from cs.LG) [pdf, other]
Title: Multitask Extension of Geometrically Aligned Transfer Encoder
Authors: Sung Moon Ko, Sumin Lee, Dae-Woong Jeong, Hyunseung Kim, Chanhui Lee, Soorin Yim, Sehui Han
Comments: 7 pages, 3 figures, 2 tables
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Quantitative Methods (q-bio.QM)
[45]  arXiv:2405.01960 (cross-list from cond-mat.soft) [pdf, other]
Title: Proliferation-driven mechanical feedback regulates cell dynamics in growing tissues
Authors: Sumit Sinha, Xin Li, Abdul N Malmi-Kakkada, D. Thirumalai
Comments: 5 figures. arXiv admin note: text overlap with arXiv:2202.04806
Subjects: Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)
[46]  arXiv:2405.01554 (cross-list from cs.LG) [pdf, other]
Title: Early-stage detection of cognitive impairment by hybrid quantum-classical algorithm using resting-state functional MRI time-series
Authors: Junggu Choi, Tak Hur, Daniel K. Park, Na-Young Shin, Seung-Koo Lee, Hakbae Lee, Sanghoon Han
Comments: 28 pages, 10 figures
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Neurons and Cognition (q-bio.NC)

Fri, 3 May 2024 (showing first 4 of 19 entries)

[47]  arXiv:2405.01385 [pdf, other]
Title: Anti-seizure medication tapering is associated with delta band power reduction in a dose, region and time-dependent manner
Authors: Guillermo M. Besne, Nathan Evans, Mariella Panagiotopoulou, Billy Smith, Fahmida A Chowdhury, Beate Diehl, John S Duncan, Andrew W McEvoy, Anna Miserocchi, Jane de Tisi, Mathew Walker, Peter N. Taylor, Chris Thornton, Yujiang Wang
Subjects: Neurons and Cognition (q-bio.NC)
[48]  arXiv:2405.01148 [pdf, other]
Title: Qualia and the Formal Structure of Meaning
Authors: Xerxes D. Arsiwalla
Comments: 28 pages
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Category Theory (math.CT); History and Philosophy of Physics (physics.hist-ph)
[49]  arXiv:2405.01012 [pdf, other]
Title: Correcting Biased Centered Kernel Alignment Measures in Biological and Artificial Neural Networks
Authors: Alex Murphy, Joel Zylberberg, Alona Fyshe
Comments: ICLR 2024 Re-Align Workshop
Subjects: Neurons and Cognition (q-bio.NC); Computer Vision and Pattern Recognition (cs.CV)
[50]  arXiv:2405.00838 [pdf, other]
Title: Cross-modality Matching and Prediction of Perturbation Responses with Labeled Gromov-Wasserstein Optimal Transport
Authors: Jayoung Ryu, Romain Lopez, Charlotte Bunne, Aviv Regev
Comments: 16 pages, 4 figures, correspondence to Aviv Regev and Romain Lopez
Subjects: Genomics (q-bio.GN); Optimization and Control (math.OC)
[ total of 78 entries: 1-50 | 51-78 ]
[ showing 50 entries per page: fewer | more | all ]

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