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Quantitative Biology

Authors and titles for recent submissions

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Total of 104 entries : 1-50 51-100 101-104
Showing up to 50 entries per page: fewer | more | all

Mon, 22 Sep 2025 (showing 17 of 17 entries )

[1] arXiv:2509.16133 [cn-pdf, pdf, html, other]
Title: A Unified and Predictive Measure of Functional Diversity
Adji Bousso Dieng, Amey Pasarkar
Comments: A single index to accurately measure functional diversity at different biological levels
Subjects: Populations and Evolution (q-bio.PE)
[2] arXiv:2509.16070 [cn-pdf, pdf, html, other]
Title: A Hypothesis-First Framework for Mechanistic Model Evaluation and Selection in Neuroimaging
Dominic Boutet, Sylvain Baillet
Comments: 20 pages, 7 figures, 5 supplemental figures
Subjects: Neurons and Cognition (q-bio.NC) ; Quantitative Methods (q-bio.QM)
[3] arXiv:2509.15911 [cn-pdf, pdf, other]
Title: The evolution of asymmetrical regulation of physiology is central to aging
Mirre J P Simons, Marc Tatar
Comments: 22 pages, 5 figures
Subjects: Populations and Evolution (q-bio.PE)
[4] arXiv:2509.15854 [cn-pdf, pdf, other]
Title: Changes in Liver Fibrosis in Patients with Chronic Hepatitis B Treated with Pegylated Interferon Combined with Oral Antiviral Agents: A 48-Week Observation from a Prospective Cohort Study
Zhao Jinhua
Subjects: Tissues and Organs (q-bio.TO)
[5] arXiv:2509.15832 [cn-pdf, pdf, html, other]
Title: Overcoming Output Dimension Collapse: How Sparsity Enables Zero-shot Brain-to-Image Reconstruction at Small Data Scales
Kenya Otsuka, Yoshihiro Nagano, Yukiyasu Kamitani
Subjects: Neurons and Cognition (q-bio.NC)
[6] arXiv:2509.15787 [cn-pdf, pdf, html, other]
Title: A Visual Discrete Event-based Simulator for Protection of Plants against Herbivores Employed as Computational Optimization Game
Lucas Dietrich, Benjamin Förster, Peter Langendörfer, Thomas Hinze
Subjects: Populations and Evolution (q-bio.PE)
[7] arXiv:2509.15664 [cn-pdf, pdf, html, other]
Title: siDPT: siRNA Efficacy Prediction via Debiased Preference-Pair Transformer
Honggen Zhang, Xiangrui Gao, Lipeng Lai
Subjects: Genomics (q-bio.GN) ; Signal Processing (eess.SP) ; Quantitative Methods (q-bio.QM)
[8] arXiv:2509.15584 [cn-pdf, pdf, html, other]
Title: Polynomial Equivalence of Extended Chemical Reaction Models
Divya Bajaj, Jose Luis Castellanos, Ryan Knobel, Austin Luchsinger, Aiden Massie, Adrian Salinas, Pablo Santos, Ramiro Santos, Robert Schweller, Tim Wylie
Subjects: Molecular Networks (q-bio.MN) ; Computational Complexity (cs.CC)
[9] arXiv:2509.15460 [cn-pdf, pdf, html, other]
Title: Incorporating Visual Cortical Lateral Connection Properties into CNN: Recurrent Activation and Excitatory-Inhibitory Separation
Jin Hyun Park, Cheng Zhang, Yoonsuck Choe
Subjects: Neurons and Cognition (q-bio.NC) ; Artificial Intelligence (cs.AI) ; Computer Vision and Pattern Recognition (cs.CV)
[10] arXiv:2509.15338 [cn-pdf, pdf, html, other]
Title: Epidemic amplification by correlated superspreading
Noah Silva de Leonardi, Benjamin D. Dalziel
Subjects: Populations and Evolution (q-bio.PE)
[11] arXiv:2509.15278 [cn-pdf, pdf, other]
Title: Assessing metadata privacy in neuroimaging
Emilie Kibsgaard, Anita Sue Jwa, Christopher J Markiewicz, David Rodriguez Gonzalez, Judith Sainz Pardo, Russell A. Poldrack, Cyril R. Pernet
Comments: 19 pages, 7 tables, 2 figures, original analysis of 6 Open Datasets
Subjects: Other Quantitative Biology (q-bio.OT) ; Cryptography and Security (cs.CR) ; Computers and Society (cs.CY) ; Image and Video Processing (eess.IV)
[12] arXiv:2509.15796 (cross-list from cs.LG) [cn-pdf, pdf, html, other]
Title: Monte Carlo Tree Diffusion with Multiple Experts for Protein Design
Xuefeng Liu, Mingxuan Cao, Songhao Jiang, Xiao Luo, Xiaotian Duan, Mengdi Wang, Tobin R. Sosnick, Jinbo Xu, Rick Stevens
Subjects: Machine Learning (cs.LG) ; Artificial Intelligence (cs.AI) ; Biomolecules (q-bio.BM)
[13] arXiv:2509.15748 (cross-list from cs.CV) [cn-pdf, pdf, html, other]
Title: Hybrid Lie semi-group and cascade structures for the generalized Gaussian derivative model for visual receptive fields
Tony Lindeberg
Comments: 25 pages, 9 figures
Subjects: Computer Vision and Pattern Recognition (cs.CV) ; Neurons and Cognition (q-bio.NC)
[14] arXiv:2509.15429 (cross-list from cs.LG) [cn-pdf, pdf, html, other]
Title: Random Matrix Theory-guided sparse PCA for single-cell RNA-seq data
Victor Chardès
Comments: 16 figures
Subjects: Machine Learning (cs.LG) ; Biological Physics (physics.bio-ph) ; Quantitative Methods (q-bio.QM)
[15] arXiv:2509.15371 (cross-list from stat.ME) [cn-pdf, pdf, html, other]
Title: KoMbine: Propagating Statistical and Systematic Errors to Kaplan--Meier Curves
Jeffrey Roskes
Comments: submitted to JSS
Subjects: Methodology (stat.ME) ; Quantitative Methods (q-bio.QM)
[16] arXiv:2509.15344 (cross-list from eess.SY) [cn-pdf, pdf, html, other]
Title: Modeling Adaptive Tracking of Predictable Stimuli in Electric Fish
Yu Yang, Andreas Oliveira, Louis L. Whitcomb, Felipe Pait, Mario Sznaier, Noah J. Cowan
Comments: Submitted for joint consideration to the IEEE Control Systems Letters and American Control Conference 2026
Subjects: Systems and Control (eess.SY) ; Neurons and Cognition (q-bio.NC)
[17] arXiv:2509.15328 (cross-list from cs.LG) [cn-pdf, pdf, html, other]
Title: Kuramoto Orientation Diffusion Models
Yue Song, T. Anderson Keller, Sevan Brodjian, Takeru Miyato, Yisong Yue, Pietro Perona, Max Welling
Comments: NeurIPS 2025
Subjects: Machine Learning (cs.LG) ; Computer Vision and Pattern Recognition (cs.CV) ; Neurons and Cognition (q-bio.NC)

Fri, 19 Sep 2025 (showing 12 of 12 entries )

[18] arXiv:2509.14862 [cn-pdf, pdf, other]
Title: Modelling species distributions using remote sensing predictors: Comparing Dynamic Habitat Index and LULC
Maïri Souza Oliveira, Clémentine Préau, Samuel Alleaume, Maxime Lenormand, Sandra Luque
Comments: 27 pages, 7 figures + Appendix
Journal-ref: Ecological Indicators 179, 114198 (2025)
Subjects: Quantitative Methods (q-bio.QM) ; Populations and Evolution (q-bio.PE)
[19] arXiv:2509.14455 [cn-pdf, pdf, other]
Title: Charting trajectories of human thought using large language models
Matthew M Nour, Daniel C McNamee, Isaac Fradkin, Raymond J Dolan
Subjects: Neurons and Cognition (q-bio.NC)
[20] arXiv:2509.14446 [cn-pdf, pdf, html, other]
Title: Mouse vs. AI: A Neuroethological Benchmark for Visual Robustness and Neural Alignment
Marius Schneider, Joe Canzano, Jing Peng, Yuchen Hou, Spencer LaVere Smith, Michael Beyeler
Subjects: Neurons and Cognition (q-bio.NC)
[21] arXiv:2509.14418 [cn-pdf, pdf, other]
Title: Theoretical Note: The Relation Between Structure and Dynamics in Psychological Networks of Attitudes
Mark G. Orr, Emily S. Teti, Andrei Bura, Henning Mortveit
Subjects: Neurons and Cognition (q-bio.NC)
[22] arXiv:2509.14360 [cn-pdf, pdf, html, other]
Title: Embodied sensorimotor control: computational modeling of the neural control of movement
Muhammad Noman Almani, John Lazzari, Jeff Walker, Shreya Saxena
Comments: Review paper
Subjects: Neurons and Cognition (q-bio.NC) ; Artificial Intelligence (cs.AI)
[23] arXiv:2509.14287 [cn-pdf, pdf, html, other]
Title: Property-Isometric Variational Autoencoders for Sequence Modeling and Design
Elham Sadeghi, Xianqi Deng, I-Hsin Lin, Stacy M. Copp, Petko Bogdanov
Comments: 20 pages, 6 figures, preprint
Subjects: Quantitative Methods (q-bio.QM) ; Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG)
[24] arXiv:2509.14910 (cross-list from nlin.CD) [cn-pdf, pdf, html, other]
Title: Dynamic effects of electric field in hybrid coupling thermosensitive neuronal network
Ediline L. F. Nguessap (1), Antonio C. Roque (1), Fernando F. Ferreira (1) ((1) Department of Physics, FFCLRP, Sao Paulo, Brazil)
Subjects: Chaotic Dynamics (nlin.CD) ; Neurons and Cognition (q-bio.NC)
[25] arXiv:2509.14827 (cross-list from cs.CV) [cn-pdf, pdf, html, other]
Title: Template-Based Cortical Surface Reconstruction with Minimal Energy Deformation
Patrick Madlindl, Fabian Bongratz, Christian Wachinger
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)
[26] arXiv:2509.14788 (cross-list from cs.LG) [cn-pdf, pdf, html, other]
Title: Structure-Aware Contrastive Learning with Fine-Grained Binding Representations for Drug Discovery
Jing Lan, Hexiao Ding, Hongzhao Chen, Yufeng Jiang, Nga-Chun Ng, Gwing Kei Yip, Gerald W.Y. Cheng, Yunlin Mao, Jing Cai, Liang-ting Lin, Jung Sun Yoo
Subjects: Machine Learning (cs.LG) ; Artificial Intelligence (cs.AI) ; Biomolecules (q-bio.BM)
[27] arXiv:2509.14498 (cross-list from cond-mat.stat-mech) [cn-pdf, pdf, html, other]
Title: Data coarse graining can improve model performance
Alex Nguyen, David J. Schwab, Vudtiwat Ngampruetikorn
Comments: 7 pages, 4 figures
Subjects: Statistical Mechanics (cond-mat.stat-mech) ; Disordered Systems and Neural Networks (cond-mat.dis-nn) ; Machine Learning (cs.LG) ; Neurons and Cognition (q-bio.NC) ; Machine Learning (stat.ML)
[28] arXiv:2509.14468 (cross-list from physics.soc-ph) [cn-pdf, pdf, html, other]
Title: A generative model of function growth explains hidden self-similarities across biological and social systems
James Holehouse, S. Redner, Vicky Chuqiao Yang, P.L. Krapivsky, Jose Ignacio Arroyo, Geoffrey B West, Chris Kempes, Hyejin Youn
Comments: 11 pages main text, 7 main text figs, 9 pages of SI, 3 SI figs
Subjects: Physics and Society (physics.soc-ph) ; Statistical Mechanics (cond-mat.stat-mech) ; Adaptation and Self-Organizing Systems (nlin.AO) ; Biological Physics (physics.bio-ph) ; Populations and Evolution (q-bio.PE)
[29] arXiv:2509.14053 (cross-list from physics.soc-ph) [cn-pdf, pdf, html, other]
Title: Network representations reveal structured uncertainty in music
Lluc Bono Rosselló, Robert Jankowski, Hugues Bersini, Marián Boguñá, M. Ángeles Serrano
Subjects: Physics and Society (physics.soc-ph) ; Sound (cs.SD)

Thu, 18 Sep 2025 (showing 17 of 17 entries )

[30] arXiv:2509.14166 [cn-pdf, pdf, html, other]
Title: Reaction-diffusion models of invasive tree pest spread: quantifying the spread of oak processionary moth in the UK
Jamie P. McKeown, Laura E. Wadkin, Nick G. Parker, Andrew Golightly, Andrew W. Baggaley
Comments: 19 pages, 8 figures, 2 tables
Subjects: Populations and Evolution (q-bio.PE) ; Quantitative Methods (q-bio.QM)
[31] arXiv:2509.14037 [cn-pdf, pdf, html, other]
Title: PhenoGnet: A Graph-Based Contrastive Learning Framework for Disease Similarity Prediction
Ranga Baminiwatte, Kazi Jewel Rana, Aaron J. Masino
Subjects: Genomics (q-bio.GN) ; Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG)
[32] arXiv:2509.13875 [cn-pdf, pdf, other]
Title: Personalized Detection of Stress via hdrEEG: Linking Neuro-markers to Cortisol, HRV, and Self-Report
N. B. Maimon, Ganit Baruchin, Itamar Grotto, Nathan Intrator, Talya Zeimer, Ofir Chibotero, Efrat Danino
Subjects: Neurons and Cognition (q-bio.NC)
[33] arXiv:2509.13612 [cn-pdf, pdf, html, other]
Title: Rest2Visual: Predicting Visually Evoked fMRI from Resting-State Scans
Chuyang Zhou, Ziao Ji, Daochang Liu, Dongang Wang, Chenyu Wang, Chang Xu
Subjects: Neurons and Cognition (q-bio.NC) ; Computer Vision and Pattern Recognition (cs.CV)
[34] arXiv:2509.13481 [cn-pdf, pdf, other]
Title: Complex-valued Phase Synchrony Reveals Directional Coupling in FMRI and Tracks Medication Effects
Sir-Lord Wiafe, Najme Soleimani, Masoud Seraji, Bradley Baker, Robyn Miller, Ashkan Faghiri, Vince D. Calhoun
Comments: 5 pages, 3 Figures, conference
Subjects: Neurons and Cognition (q-bio.NC)
[35] arXiv:2509.13476 [cn-pdf, pdf, html, other]
Title: A Geometric Graph-Based Deep Learning Model for Drug-Target Affinity Prediction
Md Masud Rana, Farjana Tasnim Mukta, Duc D. Nguyen
Subjects: Biomolecules (q-bio.BM) ; Machine Learning (cs.LG)
[36] arXiv:2509.13459 [cn-pdf, pdf, html, other]
Title: Why all roads don't lead to Rome: Representation geometry varies across the human visual cortical hierarchy
Arna Ghosh, Zahraa Chorghay, Shahab Bakhtiari, Blake A. Richards
Comments: 9 pages, 4 figures
Subjects: Neurons and Cognition (q-bio.NC) ; Machine Learning (cs.LG) ; Neural and Evolutionary Computing (cs.NE)
[37] arXiv:2509.13428 [cn-pdf, pdf, other]
Title: Autonomous Reporting of Normal Chest X-rays by Artificial Intelligence in the United Kingdom. Can We Take the Human Out of the Loop?
Katrina Nash, James Vaz, Ahmed Maiter, Christopher Johns, Nicholas Woznitza, Aditya Kale, Abdala Espinosa Morgado, Rhidian Bramley, Mark Hall, David Lowe, Alex Novak, Sarim Ather
Subjects: Populations and Evolution (q-bio.PE) ; Computer Vision and Pattern Recognition (cs.CV)
[38] arXiv:2509.13376 [cn-pdf, pdf, other]
Title: Unleashing the power of computational insights in revealing the complexity of biological systems in the new era of spatial multi-omics
Zhiwei Fan, Tiangang Wang, Kexin Huang, Binwu Ying, Xiaobo Zhou
Comments: 43 pages, 9 figures, 1 table
Subjects: Quantitative Methods (q-bio.QM) ; Machine Learning (cs.LG)
[39] arXiv:2509.13344 [cn-pdf, pdf, html, other]
Title: Benchmarking Dimensionality Reduction Techniques for Spatial Transcriptomics
Md Ishtyaq Mahmud, Veena Kochat, Suresh Satpati, Jagan Mohan Reddy Dwarampudi, Kunal Rai, Tania Banerjee
Comments: This paper is accepted to the 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB 2025), 10 page and have 4 figures
Subjects: Genomics (q-bio.GN) ; Machine Learning (cs.LG)
[40] arXiv:2509.14167 (cross-list from cs.LG) [cn-pdf, pdf, html, other]
Title: Deconstructing Intraocular Pressure: A Non-invasive Multi-Stage Probabilistic Inverse Framework
Md Rezwan Jaher, Abul Mukid Mohammad Mukaddes, A. B. M. Abdul Malek
Comments: 43 pages, 10 figures (including supplementary material)
Subjects: Machine Learning (cs.LG) ; Quantitative Methods (q-bio.QM) ; Applications (stat.AP) ; Methodology (stat.ME)
[41] arXiv:2509.14118 (cross-list from math.OC) [cn-pdf, pdf, html, other]
Title: Multi-Source Neural Activity Indices and Spatial Filters for EEG/MEG Inverse Problem: An Extension to MNE-Python
Julia Jurkowska, Joanna Dreszer, Monika Lewandowska, Krzysztof Tołpa, Tomasz Piotrowski
Subjects: Optimization and Control (math.OC) ; Neurons and Cognition (q-bio.NC)
[42] arXiv:2509.14029 (cross-list from cs.LG) [cn-pdf, pdf, html, other]
Title: Deep Learning-Driven Peptide Classification in Biological Nanopores
Samuel Tovey, Julian Hoßbach, Sandro Kuppel, Tobias Ensslen, Jan C. Behrends, Christian Holm
Comments: 29 pages (incl. references) 7 figures
Subjects: Machine Learning (cs.LG) ; Signal Processing (eess.SP) ; Computational Physics (physics.comp-ph) ; Biomolecules (q-bio.BM)
[43] arXiv:2509.13867 (cross-list from cond-mat.stat-mech) [cn-pdf, pdf, html, other]
Title: Plasticity-induced multistability on fast and slow timescales enables optimal information encoding and spontaneous sequence discrimination
Giacomo Barzon, Daniel M. Busiello, Giorgio Nicoletti
Subjects: Statistical Mechanics (cond-mat.stat-mech) ; Neurons and Cognition (q-bio.NC)
[44] arXiv:2509.13556 (cross-list from physics.bio-ph) [cn-pdf, pdf, html, other]
Title: Collective multicellular patterns arising from cadherin-linked cytoskeletal domains
XinXin Du, Ido Lavi, Michael J. Shelley
Comments: 4 Figures
Subjects: Biological Physics (physics.bio-ph) ; Cell Behavior (q-bio.CB)
[45] arXiv:2509.13372 (cross-list from eess.IV) [cn-pdf, pdf, html, other]
Title: Generative AI Pipeline for Interactive Prompt-driven 2D-to-3D Vascular Reconstruction for Fontan Geometries from Contrast-Enhanced X-Ray Fluoroscopy Imaging
Prahlad G Menon
Subjects: Image and Video Processing (eess.IV) ; Artificial Intelligence (cs.AI) ; Computer Vision and Pattern Recognition (cs.CV) ; Emerging Technologies (cs.ET) ; Quantitative Methods (q-bio.QM)
[46] arXiv:2509.13360 (cross-list from eess.IV) [cn-pdf, pdf, html, other]
Title: PREDICT-GBM: Platform for Robust Evaluation and Development of Individualized Computational Tumor Models in Glioblastoma
L. Zimmer, J. Weidner, M. Balcerak, F. Kofler, I. Ezhov, B. Menze, B. Wiestler
Subjects: Image and Video Processing (eess.IV) ; Computer Vision and Pattern Recognition (cs.CV) ; Machine Learning (cs.LG) ; Quantitative Methods (q-bio.QM)

Wed, 17 Sep 2025 (showing first 4 of 22 entries )

[47] arXiv:2509.13300 [cn-pdf, pdf, html, other]
Title: AmpliconHunter: A Scalable Tool for PCR Amplicon Prediction from Microbiome Samples
Rye Howard-Stone, Ion Mandiou
Comments: 2025 ICCABS conference
Subjects: Genomics (q-bio.GN)
[48] arXiv:2509.13294 [cn-pdf, pdf, html, other]
Title: Accelerating Protein Molecular Dynamics Simulation with DeepJump
Allan dos Santos Costa, Manvitha Ponnapati, Dana Rubin, Tess Smidt, Joseph Jacobson
Subjects: Biomolecules (q-bio.BM) ; Machine Learning (cs.LG)
[49] arXiv:2509.13290 [cn-pdf, pdf, other]
Title: Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks
David Kouřil, Trevor Manz, Tereza Clarence, Nils Gehlenborg
Subjects: Genomics (q-bio.GN)
[50] arXiv:2509.13216 [cn-pdf, pdf, html, other]
Title: Flow-Based Fragment Identification via Binding Site-Specific Latent Representations
Rebecca Manuela Neeser, Ilia Igashov, Arne Schneuing, Michael Bronstein, Philippe Schwaller, Bruno Correia
Subjects: Biomolecules (q-bio.BM) ; Machine Learning (cs.LG)
Total of 104 entries : 1-50 51-100 101-104
Showing up to 50 entries per page: fewer | more | all