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Quantitative Biology

Authors and titles for recent submissions

[ total of 100 entries: 1-82 | 83-100 ]
[ showing 82 entries per page: fewer | more | all ]

Fri, 31 May 2024

[1]  arXiv:2405.20264 [pdf, other]
Title: Transmission of multiple pathogens across species
Authors: Clotilde Djuikem, Julien Arino
Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS)
[2]  arXiv:2405.20203 [pdf, other]
Title: The development of drug resistance in metastatic tumours under chemotherapy: an evolutionary perspective
Authors: Federica Padovano, Luis Almeida, Chiara Villa
Comments: 33 pages, 10 Figures, 1 Supplementary material
Subjects: Cell Behavior (q-bio.CB)
[3]  arXiv:2405.20135 [pdf, ps, other]
Title: Bifurcation enhances temporal information encoding in the olfactory periphery
Authors: Kiri Choi, Will Rosenbluth, Isabella R. Graf, Nirag Kadakia, Thierry Emonet
Subjects: Neurons and Cognition (q-bio.NC)
[4]  arXiv:2405.19936 [pdf, ps, other]
Title: Free-ranging dogs quickly learn to recognize a rewarding person
Authors: Srijaya Nandi, Mousumi Chakraborty, Aesha Lahiri, Hindolii Gope, Sujata Khan Bhaduri, Anindita Bhadra
Subjects: Other Quantitative Biology (q-bio.OT)
[5]  arXiv:2405.19857 [pdf, ps, other]
Title: Biodiversity data standards for the organization and dissemination of complex research projects and digital twins: a guide
Authors: Carrie Andrew, Sharif Islam, Claus Weiland, Dag Endresen
Comments: 42 pages, 2 figures, 1 box, 1 table
Subjects: Other Quantitative Biology (q-bio.OT)
[6]  arXiv:2405.19824 [pdf, ps, other]
Title: Bayesian Uncertainty Quantification for Anaerobic Digestion models
Authors: Antoine Picard-Weibel (CIRSEE, LPP, MODAL), Gabriel Capson-Tojo (INRAE), Benjamin Guedj (MODAL, UCL-CS), Roman Moscoviz (CIRSEE)
Subjects: Biomolecules (q-bio.BM)
[7]  arXiv:2405.19587 [pdf, other]
Title: Bounding the softwired parsimony score of a phylogenetic network
Authors: Janosch Döcker, Simone Linz, Kristina Wicke
Subjects: Populations and Evolution (q-bio.PE); Combinatorics (math.CO)
[8]  arXiv:2405.20184 (cross-list from math.AG) [pdf, other]
Title: Phylogenetic degrees for Jukes-Cantor model
Authors: Rodica Andreea Dinu, Martin Vodička
Subjects: Algebraic Geometry (math.AG); Combinatorics (math.CO); Populations and Evolution (q-bio.PE)
[9]  arXiv:2405.19565 (cross-list from physics.soc-ph) [pdf, other]
Title: Unbending strategies shepherd cooperation and suppress extortion in spatial populations
Authors: Zijie Chen, Yuxin Geng, Xingru Chen, Feng Fu
Comments: 21 pages, 6 figures
Subjects: Physics and Society (physics.soc-ph); Computer Science and Game Theory (cs.GT); Populations and Evolution (q-bio.PE)
[10]  arXiv:2405.19478 (cross-list from nlin.PS) [pdf, other]
Title: New sector morphologies emerge from anisotropic colony growth
Authors: Daniel W. Swartz, Hyunseok Lee, Mehran Kardar, Kirill S. Korolev
Comments: 11 pages, 7 figures
Subjects: Pattern Formation and Solitons (nlin.PS); Biological Physics (physics.bio-ph); Populations and Evolution (q-bio.PE)
[11]  arXiv:2405.19420 (cross-list from cs.LG) [pdf, other]
Title: Using Contrastive Learning with Generative Similarity to Learn Spaces that Capture Human Inductive Biases
Authors: Raja Marjieh, Sreejan Kumar, Declan Campbell, Liyi Zhang, Gianluca Bencomo, Jake Snell, Thomas L. Griffiths
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Neurons and Cognition (q-bio.NC)

Thu, 30 May 2024

[12]  arXiv:2405.19228 [pdf, ps, other]
Title: Motor Imagery Task Alters Dynamics of Human Body Posture
Authors: Fatemeh Delavari, Seyyed Mohammad Reza Hashemi Golpayegani, Mohammad Ali Ahmadi-Pajouh
Subjects: Neurons and Cognition (q-bio.NC); Signal Processing (eess.SP)
[13]  arXiv:2405.19221 [pdf, ps, other]
Title: Domain adaptation in small-scale and heterogeneous biological datasets
Authors: Seyedmehdi Orouji, Martin C. Liu, Tal Korem, Megan A. K. Peters
Comments: main manuscript + supplement
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG)
[14]  arXiv:2405.19159 [pdf, ps, other]
Title: Precision microfluidic control of neuronal ensembles in cultured cortical networks
Authors: Hakuba Murota, Hideaki Yamamoto, Nobuaki Monma, Shigeo Sato, Ayumi Hirano-Iwata
Comments: 30 pages, 6 figures, 6 supplementary figures
Subjects: Neurons and Cognition (q-bio.NC)
[15]  arXiv:2405.19057 [pdf, other]
Title: Metadata-guided Feature Disentanglement for Functional Genomics
Authors: Alexander Rakowski, Remo Monti, Viktoriia Huryn, Marta Lemanczyk, Uwe Ohler, Christoph Lippert
Subjects: Genomics (q-bio.GN)
[16]  arXiv:2405.18788 [pdf, other]
Title: TVB C++: A Fast and Flexible Back-End for The Virtual Brain
Authors: Ignacio Martín, Gorka Zamora, Jan Fousek, Michael Schirner, Petra Ritter, Viktor Jirsa, Gustavo Deco, Gustavo Patow
Subjects: Neurons and Cognition (q-bio.NC)
[17]  arXiv:2405.18779 [pdf, other]
Title: Categorization of 31 computational methods to detect spatially variable genes from spatially resolved transcriptomics data
Authors: Guanao Yan, Shuo Harper Hua, Jingyi Jessica Li
Subjects: Quantitative Methods (q-bio.QM); Applications (stat.AP)
[18]  arXiv:2405.18768 [pdf, other]
Title: RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching
Authors: Divya Nori, Wengong Jin
Comments: Accepted to ICML 2024
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[19]  arXiv:2405.18760 [pdf, ps, other]
Title: Local nature of 0.1 Hz oscillations in microcirculation is confirmed by imaging photoplethysmography
Authors: Irina A. Mizeva, Natalia P. Podolyan, Oleg V. Mamontov, Anastasiia V. Sakovskaia, Alexei A. Kamshilin
Comments: 25 pages, 5 figures
Subjects: Tissues and Organs (q-bio.TO)
[20]  arXiv:2405.18724 [pdf, other]
Title: Adapting Differential Molecular Representation with Hierarchical Prompts for Multi-label Property Prediction
Authors: Linjia Kang, Songhua Zhou, Shuyan Fang, Shichao Liu, Wen Zhang
Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[21]  arXiv:2405.18658 [pdf, other]
Title: D-CoRP: Differentiable Connectivity Refinement for Functional Brain Networks
Authors: Haoyu Hu, Hongrun Zhang, Chao Li
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI)
[22]  arXiv:2405.18639 [pdf, other]
Title: Improving Speech Decoding from ECoG with Self-Supervised Pretraining
Authors: Brian A. Yuan, Joseph G. Makin
Subjects: Neurons and Cognition (q-bio.NC); Computation and Language (cs.CL); Machine Learning (cs.LG); Sound (cs.SD); Audio and Speech Processing (eess.AS)
[23]  arXiv:2405.18587 [pdf, other]
Title: Emergence and long-term maintenance of modularity in spiking neural networks with plasticity
Authors: Raphäel Bergoin, Alessandro Torcini, Gustavo Deco, Mathias Quoy, Gorka Zamora-López
Comments: 35 pages, 6 figures
Subjects: Neurons and Cognition (q-bio.NC); Adaptation and Self-Organizing Systems (nlin.AO)
[24]  arXiv:2405.18456 [pdf, ps, other]
Title: The association between neighborhood obesogenic factors and prostate cancer risk and mortality: the Southern Community Cohort Study
Authors: Fekede Asefa Kumsa, Jay H. Fowke, Soheil Hashtarkhani, Brianna M. White, Martha J. Shrubsole, Arash Shaban-Nejad
Comments: 18 Pages, 1 Figure, 8 Tables
Journal-ref: Front Oncol Frontiers in Oncology, 2024 Apr 9:14:1343070
Subjects: Quantitative Methods (q-bio.QM)
[25]  arXiv:2405.18452 [pdf, other]
Title: Immune cells interactions in the tumor microenvironment
Authors: Mobina Tousian, Christian Solis Calero, Julio Cesar Perez Sansalvador
Comments: 12 pages, 8 figures, 0 tables
Subjects: Cell Behavior (q-bio.CB); Biological Physics (physics.bio-ph)
[26]  arXiv:2405.19180 (cross-list from astro-ph.EP) [pdf, ps, other]
Title: Observation of Significant Photosynthesis in Garden Cress and Cyanobacteria under Simulated Illumination from a K Dwarf Star
Authors: Iva Vilović, Dirk Schulze-Makuch, René Heller
Subjects: Earth and Planetary Astrophysics (astro-ph.EP); Other Quantitative Biology (q-bio.OT)
[27]  arXiv:2405.18986 (cross-list from cs.LG) [pdf, other]
Title: Robust Optimization in Protein Fitness Landscapes Using Reinforcement Learning in Latent Space
Authors: Minji Lee, Luiz Felipe Vecchietti, Hyunkyu Jung, Hyun Joo Ro, Meeyoung Cha, Ho Min Kim
Comments: ICML 2024
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM); Quantitative Methods (q-bio.QM)
[28]  arXiv:2405.18968 (cross-list from cs.AI) [pdf, other]
Title: UniIF: Unified Molecule Inverse Folding
Authors: Zhangyang Gao, Jue Wang, Cheng Tan, Lirong Wu, Yufei Huang, Siyuan Li, Zhirui Ye, Stan Z. Li
Subjects: Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Quantitative Methods (q-bio.QM)
[29]  arXiv:2405.18763 (cross-list from math.PR) [pdf, ps, other]
Title: Stationary distribution approximations of Two-island Wright-Fisher and seed-bank models using Stein's method
Authors: Han L. Gan, Maite Wilke-Berenguer
Comments: 37 pages
Subjects: Probability (math.PR); Populations and Evolution (q-bio.PE)
[30]  arXiv:2405.18749 (cross-list from cs.LG) [pdf, other]
Title: A SARS-CoV-2 Interaction Dataset and VHH Sequence Corpus for Antibody Language Models
Authors: Hirofumi Tsuruta, Hiroyuki Yamazaki, Ryota Maeda, Ryotaro Tamura, Akihiro Imura
Subjects: Machine Learning (cs.LG); Genomics (q-bio.GN)
[31]  arXiv:2405.18655 (cross-list from cs.LG) [pdf, other]
Title: CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data
Authors: Ping-Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien-Yu Chen, Geir Kjetil Sandve, Tatiana Belova, Marieke Lydia Kuijjer
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Genomics (q-bio.GN)
[32]  arXiv:2405.18605 (cross-list from cs.CL) [pdf, ps, other]
Title: BioBERT-based Deep Learning and Merged ChemProt-DrugProt for Enhanced Biomedical Relation Extraction
Authors: Bridget T. McInnes, Jiawei Tang, Darshini Mahendran, Mai H. Nguyen
Subjects: Computation and Language (cs.CL); Information Retrieval (cs.IR); Molecular Networks (q-bio.MN)
[33]  arXiv:2405.18507 (cross-list from cs.LG) [pdf, other]
Title: Injecting Hierarchical Biological Priors into Graph Neural Networks for Flow Cytometry Prediction
Authors: Fatemeh Nassajian Mojarrad, Lorenzo Bini, Thomas Matthes, Stéphane Marchand-Maillet
Comments: 14 pages, ICML Conference Workshop 2024. arXiv admin note: text overlap with arXiv:2402.18610
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Quantitative Methods (q-bio.QM)

Wed, 29 May 2024

[34]  arXiv:2405.18419 [pdf, other]
Title: Exploring the Evolution of Altruistic Punishment with a PDE Model of Cultural Multilevel Selection
Authors: Daniel B. Cooney
Comments: 78 pages, 16 figures
Subjects: Populations and Evolution (q-bio.PE); Physics and Society (physics.soc-ph)
[35]  arXiv:2405.18402 [pdf, other]
Title: Antigenic Cooperation in Viral Populations: Redistribution of Loads Among Altruistic Viruses and Maximal Load per Altruist
Authors: Leonid Bunimovich, Athulya Ram
Comments: 37 pages, 9 figures
Subjects: Populations and Evolution (q-bio.PE)
[36]  arXiv:2405.18343 [pdf, other]
Title: On in-silico estimation of left ventricular end-diastolic pressure from cardiac strains
Authors: Emilio A. Mendiola, Raza Rana Mehdi, Dipan J. Shah, Reza Avazmohammadi
Subjects: Tissues and Organs (q-bio.TO)
[37]  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)
[38]  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)
[39]  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)
[40]  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)
[41]  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)
[42]  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)
[43]  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)
[44]  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)
[45]  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)
[46]  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)
[47]  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)
[48]  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)
[49]  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)
[50]  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)
[51]  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)
[52]  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)
[53]  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 (showing first 29 of 32 entries)

[54]  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)
[55]  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)
[56]  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)
[57]  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)
[58]  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)
[59]  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)
[60]  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)
[61]  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)
[62]  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)
[63]  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)
[64]  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)
[65]  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)
[66]  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)
[67]  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)
[68]  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)
[69]  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)
[70]  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)
[71]  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)
[72]  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)
[73]  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)
[74]  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)
[75]  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)
[76]  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)
[77]  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)
[78]  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)
[79]  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)
[80]  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)
[81]  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)
[82]  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)
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