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Quantitative Biology

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Total of 100 entries : 34-83 51-100
Showing up to 50 entries per page: fewer | more | all

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 20 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)
[65] arXiv:2502.21217 [pdf, other]
Title: Dynamic Markov Blanket Detection for Macroscopic Physics Discovery
Jeff Beck, Maxwell J. D. Ramstead
Comments: 22 pages, 11 figures
Subjects: Neurons and Cognition (q-bio.NC)
[66] arXiv:2502.21129 [pdf, html, other]
Title: Microscopic Propagator Imaging (MPI) with Diffusion MRI
Tommaso Zajac, Gloria Menegaz, Marco Pizzolato
Subjects: Neurons and Cognition (q-bio.NC); Machine Learning (cs.LG); Biological Physics (physics.bio-ph); Medical Physics (physics.med-ph)
[67] arXiv:2502.21125 [pdf, html, other]
Title: Eukaryotes evade information storage-replication rate trade-off with endosymbiont assistance leading to larger genomes
Parthasarathi Sahu, Sashikanta Barik, Koushik Ghosh, Hemachander Subramanian
Subjects: Genomics (q-bio.GN)
[68] arXiv:2502.21072 [pdf, html, other]
Title: Innovation-exnovation dynamics on trees and trusses
Edward D. Lee, Ernesto Ortega-Díaz
Subjects: Populations and Evolution (q-bio.PE); Adaptation and Self-Organizing Systems (nlin.AO)
[69] arXiv:2502.20939 [pdf, html, other]
Title: Modeling cell differentiation in neuroblastoma: insights into development, malignancy, and treatment relapse
Simon F. Martina-Perez, Luke A. Heirene, Jennifer C. Kasemeier, Paul M. Kulesa, Ruth E. Baker
Subjects: Quantitative Methods (q-bio.QM); Tissues and Organs (q-bio.TO)
[70] arXiv:2502.20862 [pdf, html, other]
Title: Analysis of Evolving Cortical Neuronal Networks Using Visual Informatics
Ho Fai Po, Akke Mats Houben, Anna-Christina Haeb, Yordan P. Raykov, Daniel Tornero, Jordi Soriano, David Saad
Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Data Analysis, Statistics and Probability (physics.data-an); Physics and Society (physics.soc-ph)
[71] arXiv:2502.20753 [pdf, other]
Title: Deviance Detection and Regularity Sensitivity in Dissociated Neuronal Cultures
Zhuo Zhang, Amit Yaron, Dai Akita, Tomoyo Isoguchi Shiramatsu, Zenas C. Chao, Hirokazu Takahashi
Subjects: Neurons and Cognition (q-bio.NC)
[72] arXiv:2502.20602 [pdf, other]
Title: Evidence for strong modality-dependence of chronotype assessment from real world calendar app data
Sourabh Gapate, Royan Kamyar, Benjamin Smarr
Comments: 13 pages, 3 figures
Subjects: Other Quantitative Biology (q-bio.OT)
[73] arXiv:2502.20417 [pdf, html, other]
Title: Accurate 3D Grapevine Structure Extraction from High-Resolution Point Clouds
Harry Dobbs, Casey Peat, Oliver Batchelor, James Atlas, Richard Green
Subjects: Other Quantitative Biology (q-bio.OT); Image and Video Processing (eess.IV)
[74] arXiv:2502.20408 [pdf, html, other]
Title: Brain-Inspired Exploration of Functional Networks and Key Neurons in Large Language Models
Yiheng Liu, Xiaohui Gao, Haiyang Sun, Bao Ge, Tianming Liu, Junwei Han, Xintao Hu
Comments: 13 pages, 5 figures
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Computation and Language (cs.CL); Machine Learning (cs.LG)
[75] arXiv:2502.21290 (cross-list from cs.AI) [pdf, html, other]
Title: Contextualizing biological perturbation experiments through language
Menghua Wu, Russell Littman, Jacob Levine, Lin Qiu, Tommaso Biancalani, David Richmond, Jan-Christian Huetter
Comments: The Thirteenth International Conference on Learning Representations (2025)
Subjects: Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Quantitative Methods (q-bio.QM)
[76] arXiv:2502.21274 (cross-list from cs.LG) [pdf, html, other]
Title: BAnG: Bidirectional Anchored Generation for Conditional RNA Design
Roman Klypa, Alberto Bietti, Sergei Grudinin
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Biomolecules (q-bio.BM)
[77] arXiv:2502.21256 (cross-list from cs.LG) [pdf, html, other]
Title: ALVI Interface: Towards Full Hand Motion Decoding for Amputees Using sEMG
Aleksandr Kovalev, Anna Makarova, Petr Chizhov, Matvey Antonov, Gleb Duplin, Vladislav Lomtev, Viacheslav Gostevskii, Vladimir Bessonov, Andrey Tsurkan, Mikhail Korobok, Aleksejs Timčenko
Comments: 6 pages, video demo: this https URL
Subjects: Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)
[78] arXiv:2502.21167 (cross-list from math.DS) [pdf, html, other]
Title: Decomposable and essentially univariate mass-action systems: Extensions of the deficiency one theorem
Abhishek Deshpande, Stefan Müller
Comments: 29 pages, 3 figures
Subjects: Dynamical Systems (math.DS); Molecular Networks (q-bio.MN)
[79] arXiv:2502.21142 (cross-list from cs.AI) [pdf, html, other]
Title: Multimodal Dreaming: A Global Workspace Approach to World Model-Based Reinforcement Learning
Léopold Maytié, Roland Bertin Johannet, Rufin VanRullen
Comments: Under review in a conference
Subjects: Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)
[80] arXiv:2502.21077 (cross-list from cs.CV) [pdf, html, other]
Title: Enhancing deep neural networks through complex-valued representations and Kuramoto synchronization dynamics
Sabine Muzellec, Andrea Alamia, Thomas Serre, Rufin VanRullen
Subjects: Computer Vision and Pattern Recognition (cs.CV); Artificial Intelligence (cs.AI); Adaptation and Self-Organizing Systems (nlin.AO); Neurons and Cognition (q-bio.NC)
[81] arXiv:2502.21033 (cross-list from math.NA) [pdf, html, other]
Title: A data augmentation strategy for deep neural networks with application to epidemic modelling
Muhammad Awais, Abu Sayfan Ali, Giacomo Dimarco, Federica Ferrarese, Lorenzo Pareschi
Subjects: Numerical Analysis (math.NA); Machine Learning (cs.LG); Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE); Machine Learning (stat.ML)
[82] arXiv:2502.20779 (cross-list from cs.CL) [pdf, html, other]
Title: Triple Phase Transitions: Understanding the Learning Dynamics of Large Language Models from a Neuroscience Perspective
Yuko Nakagi, Keigo Tada, Sota Yoshino, Shinji Nishimoto, Yu Takagi
Comments: 46 pages
Subjects: Computation and Language (cs.CL); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)
[83] arXiv:2502.20773 (cross-list from physics.soc-ph) [pdf, html, other]
Title: Response of social norms to individual differences in error-proneness
Quang Anh Le, Seung Ki Baek
Subjects: Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)
Total of 100 entries : 34-83 51-100
Showing up to 50 entries per page: fewer | more | all