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Quantitative Biology

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Total of 100 entries : 15-64 51-100
Showing up to 50 entries per page: fewer | more | all

Wed, 5 Mar 2025 (showing 19 of 19 entries )

[15] arXiv:2503.02794 [pdf, html, other]
Title: Social hierarchy shapes foraging decisions
Lisa Blum Moyse, Ahmed El Hady
Comments: arXiv admin note: text overlap with arXiv:2412.02381
Subjects: Populations and Evolution (q-bio.PE)
[16] arXiv:2503.02792 [pdf, html, other]
Title: Les Houches lectures on Theoretical Ecology: High-dimensional models and extreme events
Ada Altieri
Comments: Lectures given at Les Houches Summer School "Theory of Large Deviations and Applications" (July 2024)
Subjects: Populations and Evolution (q-bio.PE); Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech)
[17] arXiv:2503.02781 [pdf, html, other]
Title: Multimodal AI predicts clinical outcomes of drug combinations from preclinical data
Yepeng Huang, Xiaorui Su, Varun Ullanat, Ivy Liang, Lindsay Clegg, Damilola Olabode, Nicholas Ho, Bino John, Megan Gibbs, Marinka Zitnik
Subjects: Quantitative Methods (q-bio.QM)
[18] arXiv:2503.02726 [pdf, html, other]
Title: Measurement noise scaling laws for cellular representation learning
Gokul Gowri, Peng Yin, Allon M. Klein
Subjects: Quantitative Methods (q-bio.QM); Information Theory (cs.IT)
[19] arXiv:2503.02685 [pdf, html, other]
Title: TReND: Transformer derived features and Regularized NMF for neonatal functional network Delineation
Sovesh Mohapatra, Minhui Ouyang, Shufang Tan, Jianlin Guo, Lianglong Sun, Yong He, Hao Huang
Comments: 10 Pages, 5 figures
Subjects: Neurons and Cognition (q-bio.NC); Computer Vision and Pattern Recognition (cs.CV); Signal Processing (eess.SP); Quantitative Methods (q-bio.QM)
[20] arXiv:2503.02642 [pdf, other]
Title: Weight transport through spike timing for robust local gradients
Timo Gierlich, Andreas Baumbach, Akos F. Kungl, Kevin Max, Mihai A. Petrovici
Comments: 19 pages, 9 figures
Subjects: Neurons and Cognition (q-bio.NC); Emerging Technologies (cs.ET); Machine Learning (cs.LG); Neural and Evolutionary Computing (cs.NE)
[21] arXiv:2503.02636 [pdf, html, other]
Title: YARE-GAN: Yet Another Resting State EEG-GAN
Yeganeh Farahzadi, Morteza Ansarinia, Zoltan Kekecs
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI)
[22] arXiv:2503.02618 [pdf, other]
Title: ZAPBench: A Benchmark for Whole-Brain Activity Prediction in Zebrafish
Jan-Matthis Lueckmann, Alexander Immer, Alex Bo-Yuan Chen, Peter H. Li, Mariela D. Petkova, Nirmala A. Iyer, Luuk Willem Hesselink, Aparna Dev, Gudrun Ihrke, Woohyun Park, Alyson Petruncio, Aubrey Weigel, Wyatt Korff, Florian Engert, Jeff W. Lichtman, Misha B. Ahrens, Michał Januszewski, Viren Jain
Subjects: Neurons and Cognition (q-bio.NC); Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG)
[23] arXiv:2503.02569 [pdf, other]
Title: Prediction of amino acid content in live black soldier fly larvae using near infrared spectroscopy
R.M. Zaalberg, L.B. Andersen, S.J. Noel, A.J. Buitenhuis, K. Jensen, G. Gebreyesus
Comments: 28 pages, 2 figures, 3 supplementary files
Subjects: Quantitative Methods (q-bio.QM)
[24] arXiv:2503.02555 [pdf, html, other]
Title: Proliferating active disks with game dynamical interaction
Alejandro Almodóvar, Tobias Galla, Cristóbal López
Subjects: Populations and Evolution (q-bio.PE); Statistical Mechanics (cond-mat.stat-mech)
[25] arXiv:2503.02523 [pdf, other]
Title: Unlocking tropical forest complexity: How tree assemblages in secondary forests boost biodiversity conservation
Maïri Souza Oliveira, Maxime Lenormand, Sandra Luque, Nelson A. Zamora, Samuel Alleaume, Adriana C. Aguilar Porras, Marvin U. Castillo, Eduardo Chacón-Madrigal, Diego Delgado, Luis Gustavo Hernández Sánchez, Marie-Ange Ngo Bieng, Ruperto M. Quesada, Gilberth S. Solano, Pedro M. Zúñiga
Comments: 28 pages, 7 figures + Appendix
Subjects: Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)
[26] arXiv:2503.02500 [pdf, other]
Title: The Neural Basis of Groove Sensations: Implications for Music-Based Interventions and Dance Therapy in Parkinson's Disease
Chen-Gia Tsai, Chia-Wei Li
Comments: The 4th International Symposium on Music and Health Promotion, April 11-12, Hsinchu, Taiwan
Subjects: Neurons and Cognition (q-bio.NC)
[27] arXiv:2503.02486 [pdf, html, other]
Title: Spatial competition and repulsion: pattern formation and the role of movement
Cristóbal López, Eduardo H. Colombo, Emilio Hernández-García, Ricardo Martinez-Garcia
Comments: 13 pages, 6 figures
Subjects: Populations and Evolution (q-bio.PE); Statistical Mechanics (cond-mat.stat-mech); Pattern Formation and Solitons (nlin.PS); Biological Physics (physics.bio-ph)
[28] arXiv:2503.02351 [pdf, html, other]
Title: MindSimulator: Exploring Brain Concept Localization via Synthetic FMRI
Guangyin Bao, Qi Zhang, Zixuan Gong, Zhuojia Wu, Duoqian Miao
Comments: 23 pages, ICLR 2025
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI)
[29] arXiv:2503.02058 [pdf, html, other]
Title: RiboGen: RNA Sequence and Structure Co-Generation with Equivariant MultiFlow
Dana Rubin, Allan dos Santos Costa, Manvitha Ponnapati, Joseph Jacobson
Comments: 5 pages
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[30] arXiv:2503.01994 [pdf, other]
Title: Fungal Genetic Variants in Oceanic Environments
Sade A. Davenport (1), Scott H. Harrison (2) ((1) Intelligence Community Postdoctoral Research Fellowship Program and North Carolina Agricultural and Technical State University, (2) Department of Biology, North Carolina Agricultural and Technical State University)
Comments: 13 pages, 4 figures
Subjects: Populations and Evolution (q-bio.PE); Genomics (q-bio.GN)
[31] arXiv:2503.01910 [pdf, html, other]
Title: dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen
Cheng Tan, Yijie Zhang, Zhangyang Gao, Yufei Huang, Haitao Lin, Lirong Wu, Fandi Wu, Mathieu Blanchette, Stan. Z. Li
Comments: AAAI 2025 Oral
Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI)
[32] arXiv:2503.02057 (cross-list from cs.CL) [pdf, html, other]
Title: Hebbian learning the local structure of language
P. Myles Eugenio
Comments: 10 figures, 14 pages
Subjects: Computation and Language (cs.CL); Artificial Intelligence (cs.AI); Neurons and Cognition (q-bio.NC)
[33] arXiv:2503.01906 (cross-list from cs.LG) [pdf, html, other]
Title: Learning to Chain Operations by Routing Information Through a Global Workspace
Hugo Chateau-Laurent, Rufin VanRullen
Comments: 12 pages, 14 figures, submitted to CCN
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Computer Vision and Pattern Recognition (cs.CV); Neurons and Cognition (q-bio.NC)

Tue, 4 Mar 2025 (showing 30 of 30 entries )

[34] arXiv:2503.01834 [pdf, other]
Title: Intercellular contact is sufficient to drive Fibroblast to Myofibroblast transitions
Vasuretha Chandar, Benjamin M. Goykadosh, Harikrishnan Parameswaran
Subjects: Cell Behavior (q-bio.CB)
[35] arXiv:2503.01761 [pdf, other]
Title: A comprehensive and reliable protocol for manual segmentation of the human claustrum using high-resolution MRI
Steven Seung-Suk Kang, Joseph Bodenheimer, Kayley Morris, Tracey Butler
Subjects: Neurons and Cognition (q-bio.NC)
[36] arXiv:2503.01459 [pdf, html, other]
Title: Primer C-VAE: An interpretable deep learning primer design method to detect emerging virus variants
Hanyu Wang, Emmanuel K. Tsinda, Anthony J. Dunn, Francis Chikweto, Alain B. Zemkoho
Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG)
[37] arXiv:2503.01376 [pdf, html, other]
Title: Pushing the boundaries of Structure-Based Drug Design through Collaboration with Large Language Models
Bowen Gao, Yanwen Huang, Yiqiao Liu, Wenxuan Xie, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan
Subjects: Biomolecules (q-bio.BM)
[38] arXiv:2503.01250 [pdf, html, other]
Title: A Study on the Specialist Predator with the Allee Effect on the Prey
Tanmay Das, Mahatsab Mandal
Comments: 15 pages, 5 figures
Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS)
[39] arXiv:2503.01226 [pdf, html, other]
Title: Dementia Insights: A Context-Based MultiModal Approach
Sahar Sinene Mehdoui, Abdelhamid Bouzid, Daniel Sierra-Sosa, Adel Elmaghraby
Subjects: Neurons and Cognition (q-bio.NC); Machine Learning (cs.LG)
[40] arXiv:2503.01179 [pdf, html, other]
Title: Algebraic approaches for the decomposition of reaction networks and the determination of existence and number of steady states
Joseph M. Sauder, Bruce P. Ayati, Ryan Kinser
Subjects: Quantitative Methods (q-bio.QM)
[41] arXiv:2503.00913 [pdf, other]
Title: Applying computational protein design to therapeutic antibody discovery -- current state and perspectives
Weronika Bielska, Igor Jaszczyszyn, Pawel Dudzic, Bartosz Janusz, Dawid Chomicz, Sonia Wrobel, Victor Greiff, Ryan Feehan, Jared Adolf-Bryfogle, Konrad Krawczyk
Subjects: Biomolecules (q-bio.BM)
[42] arXiv:2503.00776 [pdf, html, other]
Title: Validity of the total quasi-steady-state approximation in stochastic biochemical reaction networks
Yun Min Song, Kangmin Lee, Jae Kyoung Kim
Comments: 11 pages, 2 figures
Subjects: Molecular Networks (q-bio.MN); Probability (math.PR)
[43] arXiv:2503.00655 [pdf, html, other]
Title: Implicit Generative Modeling by Kernel Similarity Matching
Shubham Choudhary, Paul Masset, Demba Ba
Comments: 37 Pages, 9 figures
Subjects: Neurons and Cognition (q-bio.NC); Signal Processing (eess.SP)
[44] arXiv:2503.00648 [pdf, html, other]
Title: T-cell receptor specificity landscape revealed through de novo peptide design
Gian Marco Visani, Michael N. Pun, Anastasia A. Minervina, Philip Bradley, Paul Thomas, Armita Nourmohammad
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG)
[45] arXiv:2503.00197 [pdf, html, other]
Title: Unveiling sex dimorphism in the healthy cardiac anatomy: fundamental differences between male and female heart shapes
Beatrice Moscoloni, Cameron Beeche, Julio A. Chirinos, Patrick Segers, Mathias Peirlinck
Subjects: Tissues and Organs (q-bio.TO)
[46] arXiv:2503.00165 [pdf, other]
Title: Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold2
Enming Xing, Junjie Zhang, Shen Wang, Xiaolin Cheng
Subjects: Biomolecules (q-bio.BM)
[47] arXiv:2503.00143 [pdf, html, other]
Title: RecCrysFormer: Refined Protein Structural Prediction from 3D Patterson Maps via Recycling Training Runs
Tom Pan, Evan Dramko, Mitchell D. Miller, George N. Phillips Jr., Anastasios Kyrillidis
Comments: 16 pages, 9 figures. To be published in Proceedings of CPAL 2025
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Optimization and Control (math.OC)
[48] arXiv:2503.00096 [pdf, html, other]
Title: BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology
Ludovico Mitchener, Jon M Laurent, Benjamin Tenmann, Siddharth Narayanan, Geemi P Wellawatte, Andrew White, Lorenzo Sani, Samuel G Rodriques
Comments: 8 main text pages, 5 main figures
Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI)
[49] arXiv:2503.00089 [pdf, html, other]
Title: Protein Structure Tokenization: Benchmarking and New Recipe
Xinyu Yuan, Zichen Wang, Marcus Collins, Huzefa Rangwala
Comments: Preprint
Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[50] arXiv:2503.00048 [pdf, html, other]
Title: Dynamical analysis of an HIV infection model including quiescent cells and immune response
Ibrahim Nali, Attila Dénes, Abdessamad Tridane, Xueyong Zhou
Subjects: Populations and Evolution (q-bio.PE)
[51] arXiv:2503.00016 [pdf, html, other]
Title: Time-Irreversible Quantum-Classical Dynamics of Molecular Models in the Brain
Alessandro Sergi, Antonino Messina, Rosalba Saija, Gabriella Martino, Maria Teresa Caccamo, Min-Fang Kuo, Michael A. Nitsche
Journal-ref: Symmetry 2025, 17, 285
Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Other Condensed Matter (cond-mat.other); Biological Physics (physics.bio-ph); Quantum Physics (quant-ph)
[52] arXiv:2503.00008 [pdf, html, other]
Title: An Efficient Algorithm for Determining the Equivalence of Zero-one Reaction Networks
Yue Jiao, Xiaoxian Tang
Subjects: Molecular Networks (q-bio.MN)
[53] arXiv:2503.01718 (cross-list from cs.LG) [pdf, html, other]
Title: Learning Surrogate Equations for the Analysis of an Agent-Based Cancer Model
Kevin Burrage, Pamela Burrage, Justin N. Kreikemeyer, Adelinde M. Uhrmacher, Hasitha N. Weerasinghe
Comments: 15 pages, 6 figures
Subjects: Machine Learning (cs.LG); Quantitative Methods (q-bio.QM)
[54] arXiv:2503.01304 (cross-list from cond-mat.stat-mech) [pdf, html, other]
Title: Encounter-based model of a run-and-tumble particle with stochastic resetting
Paul C Bressloff
Comments: 28 pages, 8 figures
Subjects: Statistical Mechanics (cond-mat.stat-mech); Quantitative Methods (q-bio.QM)
[55] arXiv:2503.01248 (cross-list from eess.IV) [pdf, html, other]
Title: Automated Retinal Layer and Fluid Segmentation and Cross-sectional Analysis using Spectral Domain Optical Coherence Tomography Images for Diabetic Retinopathy
S. Chen, D. Ma, M. Raviselvan, S. Sundaramoorthy, K. Popuri, M. J. Ju, M. V. Sarunic, D. Ratra, M. F. Beg
Comments: 16 pages, 9 figures
Subjects: Image and Video Processing (eess.IV); Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Tissues and Organs (q-bio.TO)
[56] arXiv:2503.00965 (cross-list from physics.bio-ph) [pdf, other]
Title: Insights into new mechanosensitive behaviors of G protein-coupled receptors
Aakanskha J Shetty, Alexei Sirbu, Paolo Annibale
Comments: 16 pages, 7 figures
Subjects: Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB); Subcellular Processes (q-bio.SC)
[57] arXiv:2503.00638 (cross-list from cs.CR) [pdf, other]
Title: POSERS: Steganography-Driven Molecular Tagging Using Randomized DNA Sequences
Lena Hochrein, Peter Nejjar, Ali Tafazoli Yazdi
Subjects: Cryptography and Security (cs.CR); Probability (math.PR); Biomolecules (q-bio.BM)
[58] arXiv:2503.00612 (cross-list from cond-mat.dis-nn) [pdf, html, other]
Title: Statistical Mechanics of Semantic Compression
Tankut Can
Comments: 20 pages (including appendix), 3 figures
Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Computation and Language (cs.CL); Neurons and Cognition (q-bio.NC)
[59] arXiv:2503.00586 (cross-list from eess.IV) [pdf, html, other]
Title: Cross-Attention Fusion of MRI and Jacobian Maps for Alzheimer's Disease Diagnosis
Shijia Zhang, Xiyu Ding, Brian Caffo, Junyu Chen, Cindy Zhang, Hadi Kharrazi, Zheyu Wang
Comments: Submitted to MICCAI 2025
Subjects: Image and Video Processing (eess.IV); Computer Vision and Pattern Recognition (cs.CV); Quantitative Methods (q-bio.QM)
[60] arXiv:2503.00289 (cross-list from physics.bio-ph) [pdf, html, other]
Title: Phylogenetic Corrections and Higher-Order Sequence Statistics in Protein Families: The Potts Model vs MSA Transformer
Kisan Khatri, Ronald M. Levy, Allan Haldane
Comments: 7 pages, 5 figures, Also presented in BPS2025 Annual Meeting, Los Angeles, California
Subjects: Biological Physics (physics.bio-ph); Populations and Evolution (q-bio.PE)
[61] arXiv:2503.00198 (cross-list from physics.med-ph) [pdf, html, other]
Title: Redefining spectral unmixing for in-vivo brain tissue analysis from hyperspectral imaging
Martin Hartenberger, Huzeyfe Ayaz, Fatih Ozlugedik, Charly Caredda, Luca Giannoni, Fred Langle, Laurin Lux, Jonas Weidner, Alex Berger, Florian Kofler, Martin Menten, Bruno Montcel, Ilias Tachtsidis, Daniel Rueckert, Ivan Ezhov
Subjects: Medical Physics (physics.med-ph); Quantitative Methods (q-bio.QM)
[62] arXiv:2503.00080 (cross-list from quant-ph) [pdf, html, other]
Title: Exploring the Potential of QEEGNet for Cross-Task and Cross-Dataset Electroencephalography Encoding with Quantum Machine Learning
Chi-Sheng Chen, Samuel Yen-Chi Chen, Huan-Hsin Tseng
Subjects: Quantum Physics (quant-ph); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)
[63] arXiv:2503.00073 (cross-list from cs.CV) [pdf, html, other]
Title: Forecasting Whole-Brain Neuronal Activity from Volumetric Video
Alexander Immer, Jan-Matthis Lueckmann, Alex Bo-Yuan Chen, Peter H. Li, Mariela D. Petkova, Nirmala A. Iyer, Aparna Dev, Gudrun Ihrke, Woohyun Park, Alyson Petruncio, Aubrey Weigel, Wyatt Korff, Florian Engert, Jeff W. Lichtman, Misha B. Ahrens, Viren Jain, Michał Januszewski
Subjects: Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)

Mon, 3 Mar 2025 (showing first 1 of 25 entries )

[64] arXiv:2502.21268 [pdf, html, other]
Title: Stochastic dynamics at the back of a gene drive propagation wave
Léna Kläy (1), Léo Girardin (2), Florence Débarre (1), Vincent Calvez (3) ((1) Institute of Ecology and Environmental Sciences Paris (IEES Paris), Sorbonne Université, CNRS, IRD, INRAE, Université Paris Est Creteil, Université de Paris, Paris Cedex 5, France, (2) Institut Camille Jordan, UMR 5208 CNRS and Universite Claude Bernard Lyon 1, France, (3) CNRS, Univ Brest, UMR 6205, Laboratoire de Mathématiques de Bretagne Atlantique, France)
Subjects: Populations and Evolution (q-bio.PE)
Total of 100 entries : 15-64 51-100
Showing up to 50 entries per page: fewer | more | all