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Quantitative Biology

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Total of 99 entries : 1-50 51-99
Showing up to 50 entries per page: fewer | more | all

Thu, 14 Nov 2024 (showing 18 of 18 entries )

[1] arXiv:2411.08512 [pdf, html, other]
Title: From noisy cell size control to population growth: when variability can be beneficial
Arthur Genthon
Subjects: Populations and Evolution (q-bio.PE); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph)
[2] arXiv:2411.08387 [pdf, html, other]
Title: Steady-State and Dynamical Behavior of a PDE Model of Multilevel Selection with Pairwise Group-Level Competition
Konstantinos Alexiou, Daniel B. Cooney
Comments: 60 pages. 12 figures
Subjects: Populations and Evolution (q-bio.PE); Analysis of PDEs (math.AP); Physics and Society (physics.soc-ph)
[3] arXiv:2411.08343 [pdf, html, other]
Title: Brain Treebank: Large-scale intracranial recordings from naturalistic language stimuli
Christopher Wang, Adam Uri Yaari, Aaditya K Singh, Vighnesh Subramaniam, Dana Rosenfarb, Jan DeWitt, Pranav Misra, Joseph R. Madsen, Scellig Stone, Gabriel Kreiman, Boris Katz, Ignacio Cases, Andrei Barbu
Comments: 36 pages, 17 figures; Accepted at NeurIPS Dataset and Benchmarks 2024
Subjects: Neurons and Cognition (q-bio.NC)
[4] arXiv:2411.08327 [pdf, html, other]
Title: A universal formula explains cell size distributions in lineages
Kaan Öcal, Michael P.H. Stumpf
Comments: 5 pages, 2 figures
Subjects: Quantitative Methods (q-bio.QM); Cell Behavior (q-bio.CB)
[5] arXiv:2411.08251 [pdf, other]
Title: Rethinking category-selectivity in human visual cortex
J. Brendan Ritchie, Susan G. Wardle, Maryam Vaziri-Pashkam, Dwight J. Kravitz, Chris I. Baker
Subjects: Neurons and Cognition (q-bio.NC)
[6] arXiv:2411.08221 [pdf, html, other]
Title: SynapsNet: Enhancing Neuronal Population Dynamics Modeling via Learning Functional Connectivity
Parsa Delavari, Ipek Oruc, Timothy H Murphy
Subjects: Neurons and Cognition (q-bio.NC); Machine Learning (cs.LG)
[7] arXiv:2411.08140 [pdf, other]
Title: ConFER: A Neurally Constrained Computational Model of Context-Dependent Fear Extinction Recall and Relapse
Shreya K. Rajagopal, Thad A. Polk
Subjects: Neurons and Cognition (q-bio.NC)
[8] arXiv:2411.08083 [pdf, html, other]
Title: An age-structured diffusive model for epidemic modelling: Lie symmetries and exact solutions
Roman Cherniha, Vasyl' Davydovych
Subjects: Populations and Evolution (q-bio.PE); Mathematical Physics (math-ph)
[9] arXiv:2411.08082 [pdf, html, other]
Title: Explainable Deep Learning Framework for SERS Bio-quantification
Jihan K. Zaki, Jakub Tomasik, Jade A. McCune, Sabine Bahn, Pietro Liò, Oren A. Scherman
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Other Quantitative Biology (q-bio.OT)
[10] arXiv:2411.08077 [pdf, html, other]
Title: DBgDel: Database-Enhanced Gene Deletion Framework for Growth-Coupled Production in Genome-Scale Metabolic Models
Ziwei Yang, Takeyuki Tamura
Subjects: Quantitative Methods (q-bio.QM); Databases (cs.DB)
[11] arXiv:2411.08073 [pdf, html, other]
Title: LoRA-BERT: a Natural Language Processing Model for Robust and Accurate Prediction of long non-coding RNAs
Nicholas Jeon, Xiaoning Qian, Lamin SaidyKhan, Paul de Figueiredo, Byung-Jun Yoon
Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG)
[12] arXiv:2411.08072 [pdf, html, other]
Title: Modeling variable guide efficiency in pooled CRISPR screens with ContrastiveVI+
Ethan Weinberger, Ryan Conrad, Tal Ashuach
Comments: 15 pages, 4 figures, will be included in the AIDrugX workshop in Neurips 2024
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Genomics (q-bio.GN); Machine Learning (stat.ML)
[13] arXiv:2411.08059 [pdf, other]
Title: Segmentized quarantine policy for managing a tradeoff between containment of infectious disease and social cost of quarantine
Jungwoo Kim, Taesik Lee
Journal-ref: IISE Annual Conference and Expo 2022
Subjects: Populations and Evolution (q-bio.PE); Systems and Control (eess.SY)
[14] arXiv:2411.08739 (cross-list from cs.LG) [pdf, html, other]
Title: Bayesian Comparisons Between Representations
Heiko H. Schütt
Subjects: Machine Learning (cs.LG); Quantitative Methods (q-bio.QM)
[15] arXiv:2411.08308 (cross-list from eess.SP) [pdf, other]
Title: A Novel Approach to Characterize Dynamics of ECG-Derived Skin Nerve Activity via Time-Varying Spectral Analysis
Youngsun Kong, Farnoush Baghestani, William D'Angelo, I-Ping Chen, Ki H. Chon
Comments: Submitted to IEEE Transactions on Affective Computing for publication consideration
Subjects: Signal Processing (eess.SP); Neurons and Cognition (q-bio.NC)
[16] arXiv:2411.08306 (cross-list from cs.LG) [pdf, html, other]
Title: SDDBench: A Benchmark for Synthesizable Drug Design
Songtao Liu, Zhengkai Tu, Hanjun Dai, Peng Liu
Subjects: Machine Learning (cs.LG); Quantitative Methods (q-bio.QM)
[17] arXiv:2411.08286 (cross-list from cs.LG) [pdf, html, other]
Title: Hashing for Protein Structure Similarity Search
Jin Han, Wu-Jun Li
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Quantitative Methods (q-bio.QM)
[18] arXiv:2411.08058 (cross-list from physics.chem-ph) [pdf, html, other]
Title: Enzymatic Mpemba Effect: Slowing of biochemical reactions by increasing enzyme concentration
Tetsuhiro S. Hatakeyama
Comments: 5 pages, 4 figure
Subjects: Chemical Physics (physics.chem-ph); Statistical Mechanics (cond-mat.stat-mech); Biomolecules (q-bio.BM)

Wed, 13 Nov 2024 (showing 7 of 7 entries )

[19] arXiv:2411.07986 [pdf, html, other]
Title: Maximum likelihood estimation of log-affine models using detailed-balanced reaction networks
Oskar Henriksson, Carlos Améndola, Jose Israel Rodriguez, Polly Y. Yu
Comments: 22 pages, 2 figures. Comments welcome!
Subjects: Molecular Networks (q-bio.MN); Algebraic Geometry (math.AG); Dynamical Systems (math.DS)
[20] arXiv:2411.07388 [pdf, html, other]
Title: Firing Rate Models as Associative Memory: Excitatory-Inhibitory Balance for Robust Retrieval
Simone Betteti, Giacomo Baggio, Francesco Bullo, Sandro Zampieri
Comments: 20 pages, 7 figures
Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Artificial Intelligence (cs.AI); Dynamical Systems (math.DS)
[21] arXiv:2411.07258 [pdf, other]
Title: A lipidated peptide derived from the C-terminal tail of the vasopressin 2 receptor shows promise as a new \b{eta}-arrestin inhibitor
Rebecca L. Brouillette, Christine E. Mona, Michael Desgagné, Malihe Hassanzedeh, Émile Breault, Frédérique Lussier, Karine Belleville, Jean-Michel Longpré, Michel Grandbois, Pierre-Luc Boudreault, Élie Besserer-Offroy, Philippe Sarret
Subjects: Molecular Networks (q-bio.MN)
[22] arXiv:2411.07243 [pdf, html, other]
Title: Neuropsychology and Explainability of AI: A Distributional Approach to the Relationship Between Activation Similarity of Neural Categories in Synthetic Cognition
Michael Pichat, Enola Campoli, William Pogrund, Jourdan Wilson, Michael Veillet-Guillem, Anton Melkozerov, Paloma Pichat, Armanush Gasparian, Samuel Demarchi, Judicael Poumay
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Neural and Evolutionary Computing (cs.NE)
[23] arXiv:2411.07821 (cross-list from math.DS) [pdf, html, other]
Title: Population growth on a time varying network
Michel Benaïm, Claude Lobry, Tewfik Sari, Edouard Strickler
Comments: 43 pages
Subjects: Dynamical Systems (math.DS); Probability (math.PR); Populations and Evolution (q-bio.PE)
[24] arXiv:2411.07798 (cross-list from physics.chem-ph) [pdf, html, other]
Title: MDRefine: a Python package for refining Molecular Dynamics trajectories with experimental data
Ivan Gilardoni, Valerio Piomponi, Thorben Fröhlking, Giovanni Bussi
Comments: 39 pages, 20 figures
Subjects: Chemical Physics (physics.chem-ph); Biological Physics (physics.bio-ph); Computational Physics (physics.comp-ph); Biomolecules (q-bio.BM)
[25] arXiv:2411.07503 (cross-list from eess.IV) [pdf, other]
Title: A Novel Automatic Real-time Motion Tracking Method for Magnetic Resonance Imaging-guided Radiotherapy: Leveraging the Enhanced Tracking-Learning-Detection Framework with Automatic Segmentation
Shengqi Chen, Zilin Wang, Jianrong Dai, Shirui Qin, Ying Cao, Ruiao Zhao, Jiayun Chen, Guohua Wu, Yuan Tang
Subjects: Image and Video Processing (eess.IV); Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Medical Physics (physics.med-ph); Tissues and Organs (q-bio.TO)

Tue, 12 Nov 2024 (showing first 25 of 38 entries )

[26] arXiv:2411.07110 [pdf, html, other]
Title: Hierarchical genotype networks and incipient ecological speciation in Q$\beta$ phage quasispecies
Luis F Seoane, Henry Secaira-Morocho, Ester Lázaro, Susanna Manrubia
Comments: 15 pages (main), 8 pages (appendixes), 4 figures (main), 6 figures (appendixes)
Subjects: Populations and Evolution (q-bio.PE); Adaptation and Self-Organizing Systems (nlin.AO); Biological Physics (physics.bio-ph); Molecular Networks (q-bio.MN)
[27] arXiv:2411.07081 [pdf, other]
Title: On the Non-Oxygenic Origins of Thylakoids
Luc Cornet
Comments: 2 Figures, 1 Table
Subjects: Populations and Evolution (q-bio.PE)
[28] arXiv:2411.06802 [pdf, html, other]
Title: Identifying the impact of local connectivity patterns on dynamics in excitatory-inhibitory networks
Yuxiu Shao (1 and 2), David Dahmen (3), Stefano Recanatesi (4), Eric Shea-Brown (5 and 6), Srdjan Ostojic (2) ((1) School of Systems Science, Beijing Normal University, Beijing, China, (2) Laboratoire de Neurosciences Cognitives et Computationnelles, INSERM U960, Ecole Normale Superieure - PSL Research University, Paris, France, (3) Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience, Jülich Research Center, Jülich, Germany, (4) Technion, Israel Institute of Technology, Haifa, Israel, (5) Department of Applied Mathematics and Computational Neuroscience Center, University of Washington, Seattle, WA, USA, (6) Allen Institute for Brain Science, Seattle, WA, USA)
Comments: 25 pages, 15 figures
Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Neural and Evolutionary Computing (cs.NE)
[29] arXiv:2411.06798 [pdf, other]
Title: LA4SR: illuminating the dark proteome with generative AI
David R. Nelson, Ashish Kumar Jaiswal, Noha Ismail, Alexandra Mystikou, Kourosh Salehi-Ashtiani
Subjects: Genomics (q-bio.GN); Artificial Intelligence (cs.AI); Computation and Language (cs.CL); Quantitative Methods (q-bio.QM)
[30] arXiv:2411.06676 [pdf, other]
Title: Expansion microscopy reveals neural circuit organization in genetic animal models
Shakila Behzadi (New Jersey Institute of Technology), Jacquelin Ho (Albert Einstein College of Medicine), Zainab Tanvir (Rutgers University), Gal Haspel (New Jersey Institute of Technology), Limor Freifeld (Technion), Kristen E. Severi (New Jersey Institute of Technology)
Subjects: Neurons and Cognition (q-bio.NC)
[31] arXiv:2411.06551 [pdf, html, other]
Title: A vector Allee effect in mosquito dynamics
J. Banasiak, Bime M. Ghakanyuy, Gideon A. Ngwa
Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS)
[32] arXiv:2411.06539 [pdf, other]
Title: Multiphysics continuum mechanics models to advance glaucoma research: State-of-the-art and future perspectives
Daniel Sebastia-Saez, Jinyuan Luo, Mengqi Qin, Tao Chen, Cynthia Yu-Wai-Man
Subjects: Tissues and Organs (q-bio.TO)
[33] arXiv:2411.06519 [pdf, html, other]
Title: A Unified View of Allostery
Eric Rouviere, Olivier Rivoire, Rama Ranganathan
Subjects: Biomolecules (q-bio.BM)
[34] arXiv:2411.06431 [pdf, html, other]
Title: A comprehensive representation of selection at loci with multiple alleles that allows complex forms of genotypic fitness
Nikolas Vellnow, Toni I. Gossmann, David Waxman
Comments: 27 Pages, 4 figures
Subjects: Populations and Evolution (q-bio.PE); Biological Physics (physics.bio-ph); Computational Physics (physics.comp-ph)
[35] arXiv:2411.06359 [pdf, html, other]
Title: Evaluating tDCS Intervention Effectiveness via Functional Connectivity Network on Resting-State EEG Data in Major Depressive Disorder
Vishwani Singh, Rohit Verma, Shaurya Shriyam, Tapan K. Gandhi
Comments: 10 pages
Subjects: Quantitative Methods (q-bio.QM); Neurons and Cognition (q-bio.NC)
[36] arXiv:2411.06331 [pdf, html, other]
Title: GenoHoption: Bridging Gene Network Graphs and Single-Cell Foundation Models
Jiabei Cheng, Jiachen Li, Kaiyuan Yang, Hongbin Shen, Ye Yuan
Subjects: Quantitative Methods (q-bio.QM)
[37] arXiv:2411.06118 [pdf, other]
Title: Wind Tunnel Study of the Forces Due to Drafting in Dolphin Mother-Calf pairs
D Weihs, M Ringel
Comments: 8 figures
Subjects: Quantitative Methods (q-bio.QM)
[38] arXiv:2411.06036 [pdf, html, other]
Title: cgNA+min: computation of sequence-dependent dsDNA energy-minimising minicircle configurations
Raushan Singh, Jaroslaw Glowacki, Marius Beaud, Federica Padovano, Robert S. Manning, John H. Maddocks
Subjects: Biomolecules (q-bio.BM); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)
[39] arXiv:2411.06035 [pdf, html, other]
Title: Identifying Virulence Determinants In Pathogenic Mycobacteria Via Changes In Host Cell Mitochondrial Morphology
Shannon Quinn, Amr Abbadi, Seyed Alireza Vaezi, Russell K. Karls, Frederick D. Quinn
Subjects: Subcellular Processes (q-bio.SC)
[40] arXiv:2411.06029 [pdf, html, other]
Title: Validation of an LLM-based Multi-Agent Framework for Protein Engineering in Dry Lab and Wet Lab
Zan Chen, Yungeng Liu, Yu Guang Wang, Yiqing Shen
Subjects: Quantitative Methods (q-bio.QM)
[41] arXiv:2411.06024 [pdf, html, other]
Title: TourSynbio-Search: A Large Language Model Driven Agent Framework for Unified Search Method for Protein Engineering
Yungeng Liu, Zan Chen, Yu Guang Wang, Yiqing Shen
Subjects: Quantitative Methods (q-bio.QM)
[42] arXiv:2411.05966 [pdf, html, other]
Title: Energy Efficient Protein Language Models: Leveraging Small Language Models with LoRA for Controllable Protein Generation
Aayush Shah, Shankar Jayaratnam
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[43] arXiv:2411.05862 [pdf, html, other]
Title: From Electrode to Global Brain: Integrating Multi- and Cross-Scale Brain Connections and Interactions Under Cross-Subject and Within-Subject Scenarios
Chen Zhige, Qin Chengxuan
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI)
[44] arXiv:2411.05849 [pdf, html, other]
Title: Input-Driven Dynamics for Robust Memory Retrieval in Hopfield Networks
Simone Betteti, Giacomo Baggio, Francesco Bullo, Sandro Zampieri
Comments: 24 pages, 15 figures
Subjects: Neurons and Cognition (q-bio.NC); Statistical Mechanics (cond-mat.stat-mech); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Dynamical Systems (math.DS)
[45] arXiv:2411.05825 [pdf, html, other]
Title: SurfGNN: A robust surface-based prediction model with interpretability for coactivation maps of spatial and cortical features
Zhuoshuo Li (1), Jiong Zhang (2), Youbing Zeng (1), Jiaying Lin (1), Dan Zhang (3), Jianjia Zhang (1), Duan Xu (4), Hosung Kim (5), Bingguang Liu (6), Mengting Liu (1) ((1) Department of Biomedical Engineering, Sun Yat-sen University, Shenzhen, China, (2) Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, China, (3) School of Cyber Science and Engineering, Ningbo University of Technology, Ningbo, China, (4) Department of Radiology, School of Medicine, University of California San Francisco, San Francisco, CA, USA, (5) USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA, (6) Department of Radiology, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China)
Comments: 15 pages, 6 figures
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Computer Vision and Pattern Recognition (cs.CV)
[46] arXiv:2411.05812 [pdf, html, other]
Title: Low-Rank + Sparse Decomposition (LR+SD) for EEG Artifact Removal
Jerome Gilles, Travis Meyer, Pamela K. Douglas
Journal-ref: Proceedings of the Second International Workshop on Sparsity Techniques in Medical Imaging (STMI 2014), Boston, USA, September 2014
Subjects: Neurons and Cognition (q-bio.NC); Signal Processing (eess.SP)
[47] arXiv:2411.05811 [pdf, html, other]
Title: Neurophysiological Analysis in Motor and Sensory Cortices for Improving Motor Imagination
Si-Hyun Kim, Sung-Jin Kim, Dae-Hyeok Lee
Comments: 4 pages, 3 figures, 1 table, Name of Conference: International Winter Conference on Brain-Computer Interface
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI)
[48] arXiv:2411.05809 [pdf, html, other]
Title: Is it me, or is A larger than B: Uncovering the determinants of relational cognitive dissonance resolution
Tomer Barak, Yonatan Loewenstein
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI)
[49] arXiv:2411.05800 [pdf, other]
Title: Review of a Heaviside step sequence function and the recursive Heaviside step sequence function for modeling human mental state
Changsoo Shin
Comments: p15 seven figures
Subjects: Neurons and Cognition (q-bio.NC)
[50] arXiv:2411.05795 [pdf, html, other]
Title: Polymerization and replication of primordial RNA explained by clay-water interface dynamics
Carla Alejandre, Adrián Aguirre-Tamaral, Carlos Briones, Jacobo Aguirre
Comments: This file contains the main manuscript (6 figures) and the Supplementary Information (4 sections and 7 Supplementary figures)
Subjects: Biomolecules (q-bio.BM); Populations and Evolution (q-bio.PE)
Total of 99 entries : 1-50 51-99
Showing up to 50 entries per page: fewer | more | all