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Quantitative Biology

Authors and titles for recent submissions, skipping first 65

[ total of 111 entries: 1-50 | 16-65 | 66-111 ]
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Mon, 27 May 2024 (continued, showing last 2 of 15 entries)

[66]  arXiv:2405.15036 (cross-list from cond-mat.stat-mech) [pdf, other]
Title: Input-driven circuit reconfiguration in critical recurrent neural networks
Authors: Marcelo O. Magnasco
Comments: Supplementary Movies Available Upon Request
Subjects: Statistical Mechanics (cond-mat.stat-mech); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)
[67]  arXiv:2405.14968 (cross-list from physics.bio-ph) [pdf, other]
Title: Compound Mutations in the Abl1 Kinase Cause Inhibitor Resistance by Shifting DFG Flip Mechanisms and Relative State Populations
Authors: Gabriel Monteiro da Silva, Kyle Lam, David C. Dalgarno, Brenda M. Rubenstein
Comments: 34 pages, 10 figures
Subjects: Biological Physics (physics.bio-ph); Biomolecules (q-bio.BM)

Fri, 24 May 2024

[68]  arXiv:2405.14810 [pdf, other]
Title: Prospective and retrospective coding in cortical neurons
Authors: Simon Brandt, Mihai Alexandru Petrovici, Walter Senn, Katharina Anna Wilmes, Federico Benitez
Subjects: Neurons and Cognition (q-bio.NC)
[69]  arXiv:2405.14690 [pdf, other]
Title: Multilevel functional data analysis modeling of human glucose response to meal intake
Authors: Marcos Matabuena, Joe Sartini, Francisco Gude
Subjects: Quantitative Methods (q-bio.QM); Applications (stat.AP)
[70]  arXiv:2405.14545 [pdf, other]
Title: A Cross-Field Fusion Strategy for Drug-Target Interaction Prediction
Authors: Hongzhi Zhang, Xiuwen Gong, Shirui Pan, Jia Wu, Bo Du, Wenbin Hu
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[71]  arXiv:2405.14536 [pdf, other]
Title: Regressor-free Molecule Generation to Support Drug Response Prediction
Authors: Kun Li, Xiuwen Gong, Shirui Pan, Jia Wu, Bo Du, Wenbin Hu
Comments: 22 pages, 7 figures, 9 tables,
Subjects: Molecular Networks (q-bio.MN); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[72]  arXiv:2405.14508 [pdf, other]
Title: Prediction of cancer dynamics under treatment using Bayesian neural networks: A simulated study
Authors: Even Moa Myklebust, Arnoldo Frigessi, Fredrik Schjesvold, Jasmine Foo, Kevin Leder, Alvaro Köhn-Luque
Comments: 22 pages, 10 figures
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)
[73]  arXiv:2405.14225 [pdf, other]
Title: ReactXT: Understanding Molecular "Reaction-ship" via Reaction-Contextualized Molecule-Text Pretraining
Authors: Zhiyuan Liu, Yaorui Shi, An Zhang, Sihang Li, Enzhi Zhang, Xiang Wang, Kenji Kawaguchi, Tat-Seng Chua
Comments: ACL 2024 Findings, 9 pages
Subjects: Quantitative Methods (q-bio.QM); Computation and Language (cs.CL); Multimedia (cs.MM)
[74]  arXiv:2405.14139 [pdf, other]
Title: Contribute to balance, wire in accordance: Emergence of backpropagation from a simple, bio-plausible neuroplasticity rule
Authors: Xinhao Fan, Shreesh P Mysore
Subjects: Neurons and Cognition (q-bio.NC); Machine Learning (cs.LG); Neural and Evolutionary Computing (cs.NE)
[75]  arXiv:2405.14120 [pdf, ps, other]
Title: DendroPy 5: a mature Python library for phylogenetic computing
Authors: Matthew Andres Moreno, Jeet Sukumaran, Mark T. Holder
Subjects: Populations and Evolution (q-bio.PE)
[76]  arXiv:2405.14028 [pdf, other]
Title: HoverFast: an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images
Authors: Petros Liakopoulos, Julien Massonnet, Jonatan Bonjour, Medya Tekes Mizrakli, Simon Graham, Michel A. Cuendet, Amanda H. Seipel, Olivier Michielin, Doron Merkler, Andrew Janowczyk
Comments: 9 pages, 3 figures, 1 appendix
Subjects: Quantitative Methods (q-bio.QM)
[77]  arXiv:2405.13825 [pdf, other]
Title: Range-Limited Heaps' Law for Functional DNA Words in the Human Genome
Authors: Wentian Li, Yannis Almirantis, Astero Provata
Comments: 5 figures
Subjects: Genomics (q-bio.GN)
[78]  arXiv:2405.13394 [pdf, other]
Title: A theory of neural emulators
Authors: Catalin C. Mitelut
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI)
[79]  arXiv:2405.13305 [pdf, ps, other]
Title: Lessons to learn for better safeguarding of genetic resources during tree pandemics: the case of ash dieback in Europe
Authors: Jan-Peter George, Mari Rusanen, Egbert Beuker, Leena Yrjänä, Volkmar Timmermann, Nenad Potocic, Sakari Välimäki, Heino Konrad
Subjects: Populations and Evolution (q-bio.PE)
[80]  arXiv:2405.13239 [pdf, other]
Title: Jump-Switch-Flow: hybrid stochastic-deterministic solutions of compartmental models
Authors: Domenic P.J. Germano, Alexander E. Zarebski, Sophie Hautphenne, Robert Moss, Jennifer A. Flegg, Mark B. Flegg
Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS)
[81]  arXiv:2405.13182 [pdf, other]
Title: Robustly encoding certainty in a metastable neural circuit model
Authors: Heather L Cihak, Zachary P Kilpatrick
Comments: 14 pages, 10 figures
Subjects: Neurons and Cognition (q-bio.NC); Pattern Formation and Solitons (nlin.PS)
[82]  arXiv:2405.12998 [pdf, ps, other]
Title: The miscalibration of the honeybee odometer
Authors: Laura Luebbert, Lior Pachter
Comments: 16 pages
Subjects: Other Quantitative Biology (q-bio.OT); Biological Physics (physics.bio-ph)
[83]  arXiv:2405.14796 (cross-list from cs.CV) [pdf, other]
Title: Generative Plant Growth Simulation from Sequence-Informed Environmental Conditions
Authors: Mohamed Debbagh, Yixue Liu, Zhouzhou Zheng, Xintong Jiang, Shangpeng Sun, Mark Lefsrud
Subjects: Computer Vision and Pattern Recognition (cs.CV); Artificial Intelligence (cs.AI); Quantitative Methods (q-bio.QM)
[84]  arXiv:2405.14682 (cross-list from nlin.PS) [pdf, other]
Title: Turing instabilities for three interacting species
Authors: Vit Piskovsky
Comments: 6 pages, 1 figure
Subjects: Pattern Formation and Solitons (nlin.PS); Dynamical Systems (math.DS); Spectral Theory (math.SP); Quantitative Methods (q-bio.QM)
[85]  arXiv:2405.14607 (cross-list from nlin.CD) [pdf, other]
Title: Discontinuous transition to chaos in a canonical random neural network
Authors: Diego Pazó
Comments: Submitted to Physical Review E
Subjects: Chaotic Dynamics (nlin.CD); Neurons and Cognition (q-bio.NC)
[86]  arXiv:2405.14600 (cross-list from cs.AI) [pdf, other]
Title: Discretization of continuous input spaces in the hippocampal autoencoder
Authors: Adrian F. Amil, Ismael T. Freire, Paul F. M. J. Verschure
Subjects: Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)
[87]  arXiv:2405.14473 (cross-list from cs.LG) [pdf, other]
Title: Poisson Variational Autoencoder
Authors: Hadi Vafaii, Dekel Galor, Jacob L. Yates
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Neurons and Cognition (q-bio.NC)
[88]  arXiv:2405.14419 (cross-list from cs.CV) [pdf, other]
Title: Motion-based video compression for resource-constrained camera traps
Authors: Malika Nisal Ratnayake, Lex Gallon, Adel N. Toosi, Alan Dorin
Comments: 6 pages, 2 figures, 2 tables
Subjects: Computer Vision and Pattern Recognition (cs.CV); Artificial Intelligence (cs.AI); Quantitative Methods (q-bio.QM)
[89]  arXiv:2405.14370 (cross-list from math.AT) [pdf, other]
Title: New Aspects of Analyzing Amyloid Fibrils
Authors: Xiaoxi Lin, Yunpeng Zi, Jie Wu
Comments: Comments are welcomed!
Subjects: Algebraic Topology (math.AT); Biomolecules (q-bio.BM)
[90]  arXiv:2405.14289 (cross-list from cond-mat.dis-nn) [pdf, other]
Title: Generating-functional analysis of random Lotka-Volterra systems: A step-by-step guide
Authors: Tobias Galla
Comments: 81 pages, 8 figures
Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Populations and Evolution (q-bio.PE)
[91]  arXiv:2405.14108 (cross-list from cs.LG) [pdf, other]
Title: Deep Learning for Protein-Ligand Docking: Are We There Yet?
Authors: Alex Morehead, Nabin Giri, Jian Liu, Jianlin Cheng
Comments: 22 pages, 1 table, 22 figures. Under review. Code, data, tutorials, and benchmark results are available at this https URL
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Biomolecules (q-bio.BM); Quantitative Methods (q-bio.QM)
[92]  arXiv:2405.13854 (cross-list from cond-mat.stat-mech) [pdf, other]
Title: On the dynamics of convolutional recurrent neural networks near their critical point
Authors: Aditi Chandra, Marcelo O. Magnasco
Subjects: Statistical Mechanics (cond-mat.stat-mech); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)
[93]  arXiv:2405.13655 (cross-list from eess.IV) [pdf, other]
Title: A Deep Learning Approach to Multi-Fiber Parameter Estimation and Uncertainty Quantification in Diffusion MRI
Authors: William Consagra, Lipeng Ning, Yogesh Rathi
Subjects: Image and Video Processing (eess.IV); Quantitative Methods (q-bio.QM); Applications (stat.AP); Computation (stat.CO)
[94]  arXiv:2405.13643 (cross-list from cs.CE) [pdf, other]
Title: Fully automated construction of three-dimensional finite element simulations from Optical Coherence Tomography
Authors: Ross Straughan, Karim Kadry, Sahil A. Parikh, Elazer R. Edelman, Farhad R. Nezami
Journal-ref: Comp. Bio. Med. Volume 165, October 2023, 107341
Subjects: Computational Engineering, Finance, and Science (cs.CE); Tissues and Organs (q-bio.TO)
[95]  arXiv:2405.13521 (cross-list from cond-mat.stat-mech) [pdf, ps, other]
Title: Run-and-tumble particle with saturating rates
Authors: Kavita Jain, Sakuntala Chatterjee
Subjects: Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)
[96]  arXiv:2405.13424 (cross-list from cond-mat.stat-mech) [pdf, other]
Title: Emergent behaviour and phase transitions in spatially distributed multi-cellular metabolic networks
Authors: K. Narayanankutty, J. A. Pereiro-Morejon, A. Ferrero, V. Onesto, S. Forciniti, L. L. del Mercato, R. Mulet, A. De Martino, D. S. Tourigny, D. De Martino
Comments: Main(14 pages)+ supporting information(14 pages). Comments are welcome
Subjects: Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)
[97]  arXiv:2405.13171 (cross-list from cs.HC) [pdf, ps, other]
Title: Launching Your VR Neuroscience Laboratory
Authors: Ying Choon Wu, Christopher Maymon, Jonathon Paden, Weichen Liu
Journal-ref: In Virtual Reality in Behavioral Neuroscience: New Insights and Methods (pp. 25-46). Cham: Springer International Publishing (2023)
Subjects: Human-Computer Interaction (cs.HC); Neurons and Cognition (q-bio.NC)

Wed, 22 May 2024

[98]  arXiv:2405.12941 [pdf, other]
Title: Metacognitive particles, mental action and the sense of agency
Authors: Lars Sandved-Smith, Lancelot Da Costa
Comments: 13 pages, 4 figures
Subjects: Neurons and Cognition (q-bio.NC); Adaptation and Self-Organizing Systems (nlin.AO); Biological Physics (physics.bio-ph)
[99]  arXiv:2405.12897 [pdf, other]
Title: Principles of bursty mRNA expression and irreversibility in single cells and extrinsically varying populations
Authors: James Holehouse
Comments: 15 pages, 6 figures
Subjects: Subcellular Processes (q-bio.SC); Statistical Mechanics (cond-mat.stat-mech); Populations and Evolution (q-bio.PE)
[100]  arXiv:2405.12815 [pdf, ps, other]
Title: Could a Computer Architect Understand our Brain?
Authors: Valentin Puente-Varona
Subjects: Neurons and Cognition (q-bio.NC)
[101]  arXiv:2405.12645 [pdf, other]
Title: Implementing feature binding through dendritic networks of a single neuron
Authors: Yuanhong Tang, Shanshan Jia, Tiejun Huang, Zhaofei Yu, Jian K. Liu
Subjects: Neurons and Cognition (q-bio.NC)
[102]  arXiv:2405.12564 [pdf, other]
Title: ProtT3: Protein-to-Text Generation for Text-based Protein Understanding
Authors: Zhiyuan Liu, An Zhang, Hao Fei, Enzhi Zhang, Xiang Wang, Kenji Kawaguchi, Tat-Seng Chua
Comments: ACL 2024, 9 pages
Subjects: Quantitative Methods (q-bio.QM); Computation and Language (cs.CL); Multimedia (cs.MM)
[103]  arXiv:2405.12422 [pdf, ps, other]
Title: Extraction of Human DNA from Soil: Protocol Adaptations
Authors: Wera M Schmerer
Comments: 11 pages, 3 figures
Subjects: Quantitative Methods (q-bio.QM)
[104]  arXiv:2405.12344 [pdf, other]
Title: A Test of the Thermodynamics of Evolution
Authors: Daniel Sadasivan, Cole Cantu, Cecilia Marsh, Andrew Graham
Comments: 10 pages, 3 figures
Subjects: Populations and Evolution (q-bio.PE)
[105]  arXiv:2405.12258 [pdf, ps, other]
Title: Scientific Hypothesis Generation by a Large Language Model: Laboratory Validation in Breast Cancer Treatment
Authors: Abbi Abdel-Rehim, Hector Zenil, Oghenejokpeme Orhobor, Marie Fisher, Ross J. Collins, Elizabeth Bourne, Gareth W. Fearnley, Emma Tate, Holly X. Smith, Larisa N. Soldatova, Ross D. King
Comments: 20 pages, 7 tables. Supplementary information available
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Cell Behavior (q-bio.CB)
[106]  arXiv:2405.12225 [pdf, other]
Title: Unraveling the Autism spectrum heterogeneity: Insights from ABIDE I Database using data/model-driven permutation testing approaches
Authors: F.J. Alcaide, I.A. Illan, J. Ramirez, J.M. Gorriz
Comments: 54 pages, 14 figures
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Image and Video Processing (eess.IV); Signal Processing (eess.SP)
[107]  arXiv:2405.12961 (cross-list from cs.LG) [pdf, other]
Title: Energy Rank Alignment: Using Preference Optimization to Search Chemical Space at Scale
Authors: Shriram Chennakesavalu, Frank Hu, Sebastian Ibarraran, Grant M. Rotskoff
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Chemical Physics (physics.chem-ph); Quantitative Methods (q-bio.QM)
[108]  arXiv:2405.12906 (cross-list from cs.DM) [pdf, ps, other]
Title: Exponential Steepest Ascent from Valued Constraint Graphs of Pathwidth Four
Authors: Artem Kaznatcheev, Melle van Marle
Comments: 16 pgs., 2 figures
Subjects: Discrete Mathematics (cs.DM); Data Structures and Algorithms (cs.DS); Populations and Evolution (q-bio.PE)
[109]  arXiv:2405.12519 (cross-list from cs.LG) [pdf, other]
Title: MAGE: Model-Level Graph Neural Networks Explanations via Motif-based Graph Generation
Authors: Zhaoning Yu, Hongyang Gao
Comments: arXiv admin note: text overlap with arXiv:2405.08419
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Quantitative Methods (q-bio.QM)
[110]  arXiv:2405.12410 (cross-list from cs.DM) [pdf, other]
Title: Local search for valued constraint satisfaction parameterized by treedepth
Authors: Artem Kaznatcheev
Comments: 7 pgs
Subjects: Discrete Mathematics (cs.DM); Data Structures and Algorithms (cs.DS); Neural and Evolutionary Computing (cs.NE); Populations and Evolution (q-bio.PE)
[111]  arXiv:2405.12235 (cross-list from cs.LG) [pdf, ps, other]
Title: Hypergraph: A Unified and Uniform Definition with Application to Chemical Hypergraph
Authors: Daniel T. Chang
Comments: arXiv admin note: text overlap with arXiv:2310.03623 by other authors
Subjects: Machine Learning (cs.LG); Quantitative Methods (q-bio.QM)
[ total of 111 entries: 1-50 | 16-65 | 66-111 ]
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