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Quantitative Biology

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

Thu, 6 Mar 2025 (showing 14 of 14 entries )

[1] arXiv:2503.03503 [pdf, html, other]
Title: Collaborative Expert LLMs Guided Multi-Objective Molecular Optimization
Jiajun Yu, Yizhen Zheng, Huan Yee Koh, Shirui Pan, Tianyue Wang, Haishuai Wang
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[2] arXiv:2503.03310 [pdf, html, other]
Title: Optimal virulence strategies in epidemiological models with asymptomatic transmission
C. Brandon Ogbunugafor, Sudam Surasinghe
Subjects: Populations and Evolution (q-bio.PE)
[3] arXiv:2503.03131 [pdf, html, other]
Title: Spatially-Structured Models of Viral Dynamics: A Scoping Review
Thomas Williams, James M. McCaw, James M. Osborne
Subjects: Quantitative Methods (q-bio.QM)
[4] arXiv:2503.03001 [pdf, html, other]
Title: Multicellular self-organization in Escherichia coli
Devina Puri, Kyle R. Allison
Comments: 19 pages, 5 figures
Subjects: Cell Behavior (q-bio.CB)
[5] arXiv:2503.02997 [pdf, html, other]
Title: Enabling Fast, Accurate, and Efficient Real-Time Genome Analysis via New Algorithms and Techniques
Can Firtina
Comments: PhD Thesis submitted to ETH Zurich
Subjects: Genomics (q-bio.GN); Hardware Architecture (cs.AR); Data Structures and Algorithms (cs.DS); Emerging Technologies (cs.ET)
[6] arXiv:2503.02981 [pdf, other]
Title: Modeling Iodine Deficiency
Paul Fong, Albert Li, Zoe Meadows, Rati Pillai, Chelsea Proutt, Alex Schneider
Comments: 46 pages, 8 figures,
Subjects: Tissues and Organs (q-bio.TO); Biomolecules (q-bio.BM)
[7] arXiv:2503.03688 (cross-list from physics.bio-ph) [pdf, html, other]
Title: A model for boundary-driven tissue morphogenesis
Daniel S. Alber, Shiheng Zhao, Alexandre O. Jacinto, Eric F. Wieschaus, Stanislav Y. Shvartsman, Pierre A. Haas
Comments: 18 pages, 9 figures, supplemental movie available on request
Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Tissues and Organs (q-bio.TO)
[8] arXiv:2503.03540 (cross-list from math.DS) [pdf, html, other]
Title: An SIRS model with hospitalizations: economic impact by disease severity
Jacopo Borsotti
Subjects: Dynamical Systems (math.DS); Populations and Evolution (q-bio.PE)
[9] arXiv:2503.03485 (cross-list from cs.LG) [pdf, html, other]
Title: TEDDY: A Family Of Foundation Models For Understanding Single Cell Biology
Alexis Chevalier, Soumya Ghosh, Urvi Awasthi, James Watkins, Julia Bieniewska, Nichita Mitrea, Olga Kotova, Kirill Shkura, Andrew Noble, Michael Steinbaugh, Julien Delile, Christoph Meier, Leonid Zhukov, Iya Khalil, Srayanta Mukherjee, Judith Mueller
Subjects: Machine Learning (cs.LG); Quantitative Methods (q-bio.QM)
[10] arXiv:2503.03246 (cross-list from physics.chem-ph) [pdf, html, other]
Title: Time-dependent DFT-based study of bacteriochlorophyll a optical properties within the B800 part of Rhodoblastus acidophilus light-harvesting complex
Evgenia A. Kovaleva, Lyudmila V. Begunovich, Maxim M. Korshunov
Subjects: Chemical Physics (physics.chem-ph); Optics (physics.optics); Biomolecules (q-bio.BM)
[11] arXiv:2503.03199 (cross-list from eess.IV) [pdf, html, other]
Title: PathRWKV: Enabling Whole Slide Prediction with Recurrent-Transformer
Sicheng Chen, Tianyi Zhang, Dankai Liao, Dandan Li, Low Chang Han, Yanqin Jiang, Yueming Jin, Shangqing Lyu
Comments: 11 pages, 2 figures
Subjects: Image and Video Processing (eess.IV); Quantitative Methods (q-bio.QM)
[12] arXiv:2503.03152 (cross-list from eess.IV) [pdf, html, other]
Title: UnPuzzle: A Unified Framework for Pathology Image Analysis
Dankai Liao, Sicheng Chen, Nuwa Xi, Qiaochu Xue, Jieyu Li, Lingxuan Hou, Zeyu Liu, Chang Han Low, Yufeng Wu, Yiling Liu, Yanqin Jiang, Dandan Li, Yueming Jin, Shangqing Lyu
Comments: 11 pages,2 figures
Subjects: Image and Video Processing (eess.IV); Quantitative Methods (q-bio.QM)
[13] arXiv:2503.03126 (cross-list from physics.bio-ph) [pdf, html, other]
Title: Controlling tissue size by active fracture
Wei Wang, Brian A. Camley
Comments: 6+10 pages, 3+4 figures, +1 table
Subjects: Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB); Quantitative Methods (q-bio.QM); Tissues and Organs (q-bio.TO)
[14] arXiv:2503.02923 (cross-list from physics.bio-ph) [pdf, other]
Title: Electron spin dynamics guide cell motility
Kai Wang, Gabrielle Gilmer, Matheus Candia Arana, Hirotaka Iijima, Juliana Bergmann, Antonio Woollard, Boris Mesits, Meghan McGraw, Brian Zoltowski, Paola Cappellaro, Alex Ungar, David Pekker, David H. Waldeck, Sunil Saxena, Seth Lloyd, Fabrisia Ambrosio
Comments: Article with supplementary material
Subjects: Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB); Quantum Physics (quant-ph)

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 first 17 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)
Total of 100 entries : 1-50 51-100
Showing up to 50 entries per page: fewer | more | all