Quantitative Biology

Authors and titles for recent submissions, skipping first 25

• Thu, 30 May 2024
• Wed, 29 May 2024
• Tue, 28 May 2024
• Mon, 27 May 2024
• Fri, 24 May 2024

Wed, 29 May 2024 (continued, showing last 17 of 20 entries)

[26]  arXiv:2405.18329 [pdf, other]

Title: Spatial-temporal analysis of neural desynchronization in sleep-like states reveals critical dynamics

Authors: Davor Curic, Surjeet Singh, Mojtaba Nazari, Majid H. Mohajerani, Joern Davidsen

Journal-ref: Vol. 132, Iss. 21, 24 Phys. Rev. Lett. 132, 218403, Published 22 May 2024

Subjects: Neurons and Cognition (q-bio.NC); Statistical Mechanics (cond-mat.stat-mech)

[27]  arXiv:2405.18327 [pdf, ps, other]

Title: Histopathology Based AI Model Predicts Anti-Angiogenic Therapy Response in Renal Cancer Clinical Trial

Authors: Jay Jasti, Hua Zhong, Vandana Panwar, Vipul Jarmale, Jeffrey Miyata, Deyssy Carrillo, Alana Christie, Dinesh Rakheja, Zora Modrusan, Edward Ernest Kadel III, Niha Beig, Mahrukh Huseni, James Brugarolas, Payal Kapur, Satwik Rajaram

Comments: 19 pages, 4 Figures

Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG)

[28]  arXiv:2405.17960 [pdf, other]

Title: Elementary Flux Modes as CRN Gears for Free Energy Transduction

Authors: Massimo Bilancioni, Massimiliano Esposito

Comments: 6 pages, 3 figures

Subjects: Molecular Networks (q-bio.MN); Statistical Mechanics (cond-mat.stat-mech)

[29]  arXiv:2405.17847 [pdf, other]

Title: Sparsification of Phylogenetic Covariance Matrices of $k$-Regular Trees

Authors: Sean S. Svihla, Manuel E. Lladser

Comments: 17 pages, 5 figures, final version to appear in the Proceedings of the 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA2024)

Subjects: Populations and Evolution (q-bio.PE); Discrete Mathematics (cs.DM); Combinatorics (math.CO); Probability (math.PR)

[30]  arXiv:2405.17833 [pdf, other]

Title: Neutral phylogenetic models and their role in tree-based biodiversity measures

Authors: Mike Steel

Comments: 19 pages, 5 figures

Subjects: Populations and Evolution (q-bio.PE)

[31]  arXiv:2405.17745 [pdf, other]

Title: Shaping the distribution of neural responses with interneurons in a recurrent circuit model

Authors: David Lipshutz, Eero P. Simoncelli

Subjects: Neurons and Cognition (q-bio.NC)

[32]  arXiv:2405.17530 [pdf, ps, other]

Title: Universal deterministic patterns in stochastic count data

Authors: Zhixing Cao, Yiling Wang, Ramon Grima

Comments: 13 pages, 5 figures

Subjects: Quantitative Methods (q-bio.QM); Data Analysis, Statistics and Probability (physics.data-an); Physics and Society (physics.soc-ph)

[33]  arXiv:2405.17515 [pdf, ps, other]

Title: EPI-VALID : Validation of an algorithm for identifying patients with epilepsy in the SNDS using data from the CONSTANCES cohort

Authors: Adeline Degremont (HAS), Catherine Bisquay (HAS), Pierre-Alain Jachiet

Comments: in French language

Subjects: Quantitative Methods (q-bio.QM)

[34]  arXiv:2405.17433 [pdf, ps, other]

Title: ScAtt: an Attention based architecture to analyze Alzheimer's disease at cell type level from single-cell RNA-sequencing data

Authors: Xiaoxia Liu, Robert R Butler III, Prashnna K Gyawali, Frank M Longo, Zihuai He

Subjects: Molecular Networks (q-bio.MN); Genomics (q-bio.GN)

[35]  arXiv:2405.18190 (cross-list from cs.LG) [pdf, other]

Title: Mutation-Bias Learning in Games

Authors: Johann Bauer, Sheldon West, Eduardo Alonso, Mark Broom

Subjects: Machine Learning (cs.LG); Multiagent Systems (cs.MA); Dynamical Systems (math.DS); Optimization and Control (math.OC); Populations and Evolution (q-bio.PE)

[36]  arXiv:2405.18051 (cross-list from stat.AP) [pdf, other]

Title: Predicting Progression Events in Multiple Myeloma from Routine Blood Work

Authors: Maximilian Ferle, Nora Grieb, Markus Kreuz, Uwe Platzbecker, Thomas Neumuth, Kristin Reiche, Alexander Oeser, Maximilian Merz

Comments: 18 pages, 8 figures, 4, tables

Subjects: Applications (stat.AP); Quantitative Methods (q-bio.QM)

[37]  arXiv:2405.18006 (cross-list from physics.bio-ph) [pdf, other]

Title: Mathematical models of the Arabidopsis circadian oscillator

Authors: Lucas Henao, Saúl Ares, Pablo Catalán

Journal-ref: Biophysica 4 (2024) 267-282

Subjects: Biological Physics (physics.bio-ph); Pattern Formation and Solitons (nlin.PS); Molecular Networks (q-bio.MN)

[38]  arXiv:2405.17992 (cross-list from cs.CL) [pdf, other]

Title: fMRI predictors based on language models of increasing complexity recover brain left lateralization

Authors: Laurent Bonnasse-Gahot, Christophe Pallier

Subjects: Computation and Language (cs.CL); Artificial Intelligence (cs.AI); Neurons and Cognition (q-bio.NC)

[39]  arXiv:2405.17903 (cross-list from cs.CV) [pdf, other]

Title: Reliable Object Tracking by Multimodal Hybrid Feature Extraction and Transformer-Based Fusion

Authors: Hongze Sun, Rui Liu, Wuque Cai, Jun Wang, Yue Wang, Huajin Tang, Yan Cui, Dezhong Yao, Daqing Guo

Comments: 16 pages, 7 figures, 9 tabes; This work has been submitted for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible

Subjects: Computer Vision and Pattern Recognition (cs.CV); Neurons and Cognition (q-bio.NC)

[40]  arXiv:2405.17802 (cross-list from cs.LG) [pdf, other]

Title: Multi-level Interaction Modeling for Protein Mutational Effect Prediction

Authors: Yuanle Mo, Xin Hong, Bowen Gao, Yinjun Jia, Yanyan Lan

Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Biomolecules (q-bio.BM)

[41]  arXiv:2405.17656 (cross-list from cs.LG) [pdf, other]

Title: Alignment is Key for Applying Diffusion Models to Retrosynthesis

Authors: Najwa Laabid, Severi Rissanen, Markus Heinonen, Arno Solin, Vikas Garg

Comments: 28 pages, 9 figures

Subjects: Machine Learning (cs.LG); Quantitative Methods (q-bio.QM)

[42]  arXiv:2405.17578 (cross-list from cond-mat.stat-mech) [pdf, ps, other]

Title: Cell migration: Beyond Brownian motion

Authors: Rainer Klages

Comments: 4 pages, 1 figure

Journal-ref: Biophys. J. 123, 1167-1169 (2024)

Subjects: Statistical Mechanics (cond-mat.stat-mech); Cell Behavior (q-bio.CB)

Tue, 28 May 2024

[43]  arXiv:2405.17395 [pdf, other]

Title: CrEIMBO: Cross Ensemble Interactions in Multi-view Brain Observations

Authors: Noga Mudrik, Ryan Ly, Oliver Ruebel, Adam S. Charles

Subjects: Neurons and Cognition (q-bio.NC); Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)

[44]  arXiv:2405.17349 [pdf, other]

Title: Metric structural human connectomes: localization and multifractality of eigenmodes

Authors: Anna Bobyleva, Alexander Gorsky, Sergei Nechaev, Olga Valba, Nikita Pospelov

Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech)

[45]  arXiv:2405.17066 [pdf, other]

Title: Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation

Authors: Jeff Guo, Philippe Schwaller

Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)

[46]  arXiv:2405.17032 [pdf, other]

Title: Exact phylodynamic likelihood via structured Markov genealogy processes

Authors: Aaron A. King, Qianying Lin, Edward L. Ionides

Subjects: Quantitative Methods (q-bio.QM); Probability (math.PR); Populations and Evolution (q-bio.PE); Applications (stat.AP)

[47]  arXiv:2405.16946 [pdf, other]

Title: Biological Neurons Compete with Deep Reinforcement Learning in Sample Efficiency in a Simulated Gameworld

Authors: Moein Khajehnejad, Forough Habibollahi, Aswin Paul, Adeel Razi, Brett J. Kagan

Comments: 13 Pages, 6 Figures - 38 Supplementary Pages, 6 Supplementary Figures, 4 Supplementary Tables

Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI)

[48]  arXiv:2405.16922 [pdf, other]

Title: Theories of synaptic memory consolidation and intelligent plasticity for continual learning

Authors: Friedemann Zenke, Axel Laborieux

Comments: An introductory-level book chapter. 34 pages, 14 figures

Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Neural and Evolutionary Computing (cs.NE)

[49]  arXiv:2405.16870 [pdf, other]

Title: Active gel model for one-dimensional cell migration coupling actin flow and adhesion dynamics

Authors: Valentin Wössner, Oliver M. Drozdowski, Falko Ziebert, Ulrich S. Schwarz (Heidelberg University)

Comments: Revtex, 31 pages, 7 figures

Subjects: Cell Behavior (q-bio.CB); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)

[50]  arXiv:2405.16865 [pdf, other]

Title: An Investigation of Conformal Isometry Hypothesis for Grid Cells

Authors: Dehong Xu, Ruiqi Gao, Wen-Hao Zhang, Xue-Xin Wei, Ying Nian Wu

Comments: arXiv admin note: text overlap with arXiv:2310.19192

Subjects: Neurons and Cognition (q-bio.NC); Machine Learning (cs.LG); Machine Learning (stat.ML)

[51]  arXiv:2405.16861 [pdf, other]

Title: NCIDiff: Non-covalent Interaction-generative Diffusion Model for Improving Reliability of 3D Molecule Generation Inside Protein Pocket

Authors: Joongwon Lee, Wonho Zhung, Woo Youn Kim

Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG); Biological Physics (physics.bio-ph)

[52]  arXiv:2405.16695 [pdf, other]

Title: Oscillations in neuronal activity: a neuron-centered spatiotemporal model of the Unfolded Protein Response in prion diseases

Authors: Elliot M. Miller, Tat Chung D. Chan, Carlos Montes-Matamoros, Omar Sharif, Laurent Pujo-Menjouet, Michael R. Lindstrom

Comments: 35 pages, 11 tables, 13 figures

Subjects: Neurons and Cognition (q-bio.NC); Dynamical Systems (math.DS)

[53]  arXiv:2405.16524 [pdf, other]

Title: Exploration of methods for computing sensitivities in ODE models at dynamic and steady states

Authors: Polina Lakrisenko, Dilan Pathirana, Daniel Weindl, Jan Hasenauer

Subjects: Quantitative Methods (q-bio.QM)

[54]  arXiv:2405.16357 [pdf, other]

Title: Exploring the Enigma of Neural Dynamics Through A Scattering-Transform Mixer Landscape for Riemannian Manifold

Authors: Tingting Dan, Ziquan Wei, Won Hwa Kim, Guorong Wu

Comments: 15 pages, 6 figures

Subjects: Neurons and Cognition (q-bio.NC)

[55]  arXiv:2405.16346 [pdf, other]

Title: A modular and scalable web platform for computational phylogenetics

Authors: Nyckollas Brandão, André Jesus, André Páscoa, Alexandre P. Francisco, Mário Ramirez, Cátia Vaz

Comments: 12 pages, 5 figures

Subjects: Populations and Evolution (q-bio.PE); Social and Information Networks (cs.SI)

[56]  arXiv:2405.15968 [pdf, other]

Title: Spatial modeling algorithms for reactions and transport (SMART) in biological cells

Authors: Emmet A. Francis, Justin G. Laughlin, Jørgen S. Dokken, Henrik N.T. Finsberg, Christopher T. Lee, Marie E. Rognes, Padmini Rangamani

Subjects: Quantitative Methods (q-bio.QM); Molecular Networks (q-bio.MN)

[57]  arXiv:2405.15928 [pdf, other]

Title: PatchProt: Hydrophobic patch prediction using protein foundation models

Authors: Dea Gogishvili, Emmanuel Minois-Genin, Jan van Eck, Sanne Abeln

Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)

[58]  arXiv:2405.15905 [pdf, ps, other]

Title: Tangent space functional reconfigurations in individuals at risk for alcohol use disorder

Authors: Mahdi Moghaddam, Mario Dzemidzic, Daniel Guerrero, Mintao Liu, Jonathan Alessi, Martin H. Plawecki, Jaroslaw Harezlak, David Kareken, Joaquín Goñi

Comments: 29 pages, 9 Figures, 2 Tables, 3 Supplementary Figures, 1 Supplementary Table

Subjects: Neurons and Cognition (q-bio.NC)

[59]  arXiv:2405.15841 [pdf, other]

Title: Dual network structure of the AV node

Authors: Anna V. Maltsev, Yasir Z. Barlas, Adina Hazan, Rui Zhang, Michela Ottolia, Joshua I. Goldhaber

Comments: 14 pages, 8 figures at the end of the manuscript, two videos and three datasets in the Source folder

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph)

[60]  arXiv:2405.15840 [pdf, other]

Title: Learning the Language of Protein Structure

Authors: Benoit Gaujac, Jérémie Donà, Liviu Copoiu, Timothy Atkinson, Thomas Pierrot, Thomas D. Barrett

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG)

[61]  arXiv:2405.15812 [pdf, other]

Title: Pseudo Channel: Time Embedding for Motor Imagery Decoding

Authors: Zhengqing Miao, Meirong Zhao

Comments: 13 pages, 5 figures

Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI)

[62]  arXiv:2405.15810 [pdf, ps, other]

Title: Peripheral Nervous System Responses to Food Stimuli: Analysis Using Data Science Approaches

Authors: Maelle Moranges (CRNL, LIRIS), Marc Plantevit (LIRIS, LRE), Moustafa Bensafi (CRNL)

Journal-ref: Basic Protocols on Emotions, Senses, and Foods, Springer US; Springer US, pp.233-246, 2023, Methods and Protocols in Food Science, 978-1-0716-2933-8

Subjects: Neurons and Cognition (q-bio.NC)

[63]  arXiv:2405.15805 [pdf, other]

Title: DSAM: A Deep Learning Framework for Analyzing Temporal and Spatial Dynamics in Brain Networks

Authors: Bishal Thapaliya, Robyn Miller, Jiayu Chen, Yu-Ping Wang, Esra Akbas, Ram Sapkota, Bhaskar Ray, Pranav Suresh, Santosh Ghimire, Vince Calhoun, Jingyu Liu

Comments: 18 Pages, 4 figures

Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)

[64]  arXiv:2405.17189 (cross-list from physics.soc-ph) [pdf, other]

Title: Rebound in epidemic control: How misaligned vaccination timing amplifies infection peaks

Authors: Piergiorgio Castioni, Sergio Gòmez, Clara Granell, Alex Arenas

Comments: 18 pages, 7 figures

Subjects: Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

[65]  arXiv:2405.17143 (cross-list from physics.bio-ph) [pdf, other]

Title: Uncovering multiscale structure in the variability of larval zebrafish navigation

Authors: Gautam Sridhar, Massimo Vergassola, Joao C. Marques, Michael B. Orger, Antonio Carlos Costa, Claire Wyart

Comments: 31 pages, 7 main figures, 1 supplementary table and 8 supplementary figures

Subjects: Biological Physics (physics.bio-ph); Neurons and Cognition (q-bio.NC); Quantitative Methods (q-bio.QM)

[66]  arXiv:2405.16931 (cross-list from physics.optics) [pdf, other]

Title: ChiSCAT: unsupervised learning of recurrent cellular micro-motion patterns from a chaotic speckle pattern

Authors: Andrii Trelin, Sophie Kussauer, Paul Weinbrenner, Anja Clasen, Robert David, Christian Rimmbach, Friedemann Reinhard

Subjects: Optics (physics.optics); Quantitative Methods (q-bio.QM)

[67]  arXiv:2405.16885 (cross-list from stat.ME) [pdf, other]

Title: Hidden Markov modelling of spatio-temporal dynamics of measles in 1750-1850 Finland

Authors: Tiia-Maria Pasanen, Jouni Helske, Tarmo Ketola

Subjects: Methodology (stat.ME); Populations and Evolution (q-bio.PE)

[68]  arXiv:2405.16714 (cross-list from cs.CL) [pdf, other]

Title: Crafting Interpretable Embeddings by Asking LLMs Questions

Authors: Vinamra Benara, Chandan Singh, John X. Morris, Richard Antonello, Ion Stoica, Alexander G. Huth, Jianfeng Gao

Subjects: Computation and Language (cs.CL); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)

[69]  arXiv:2405.16391 (cross-list from cs.LG) [pdf, other]

Title: When does compositional structure yield compositional generalization? A kernel theory

Authors: Samuel Lippl, Kim Stachenfeld

Subjects: Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)

[70]  arXiv:2405.16248 (cross-list from eess.IV) [pdf, ps, other]

Title: Combining Radiomics and Machine Learning Approaches for Objective ASD Diagnosis: Verifying White Matter Associations with ASD

Authors: Junlin Song, Yuzhuo Chen, Yuan Yao, Zetong Chen, Renhao Guo, Lida Yang, Xinyi Sui, Qihang Wang, Xijiao Li, Aihua Cao, Wei Li

Subjects: Image and Video Processing (eess.IV); Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Quantitative Methods (q-bio.QM)

[71]  arXiv:2405.16179 (cross-list from math.DS) [pdf, ps, other]

Title: Network reduction and absence of Hopf Bifurcations in dual phosphorylation networks with three Intermediates

Authors: Elisenda Feliu, Nidhi Kaihnsa

Subjects: Dynamical Systems (math.DS); Symbolic Computation (cs.SC); Molecular Networks (q-bio.MN)

[72]  arXiv:2405.16123 (cross-list from cs.AI) [pdf, other]

Title: Retro-prob: Retrosynthetic Planning Based on a Probabilistic Model

Authors: Chengyang Tian, Yangpeng Zhang, Yang Liu

Subjects: Artificial Intelligence (cs.AI); Biomolecules (q-bio.BM)

[73]  arXiv:2405.16035 (cross-list from math.CO) [pdf, other]

Title: A dissimilarity measure for semidirected networks

Authors: Michael Maxfield, Jingcheng Xu, Cécile Ané

Subjects: Combinatorics (math.CO); Populations and Evolution (q-bio.PE)

[74]  arXiv:2405.15976 (cross-list from cs.CV) [pdf, other]

Title: Understanding the Impact of Training Set Size on Animal Re-identification

Authors: Aleksandr Algasov, Ekaterina Nepovinnykh, Tuomas Eerola, Heikki Kälviäinen, Charles V. Stewart, Lasha Otarashvili, Jason A. Holmberg

Subjects: Computer Vision and Pattern Recognition (cs.CV); Populations and Evolution (q-bio.PE)

Mon, 27 May 2024 (showing first 1 of 15 entries)

[75]  arXiv:2405.15544 [pdf, other]

Title: Knowledge-enhanced Relation Graph and Task Sampling for Few-shot Molecular Property Prediction

Authors: Zeyu Wang, Tianyi Jiang, Yao Lu, Xiaoze Bao, Shanqing Yu, Bin Wei, Qi Xuan

Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)

• Thu, 30 May 2024
• Wed, 29 May 2024
• Tue, 28 May 2024
• Mon, 27 May 2024
• Fri, 24 May 2024