Quantitative Biology

Authors and titles for recent submissions

• Fri, 21 Jun 2024
• Wed, 19 Jun 2024
• Tue, 18 Jun 2024
• Mon, 17 Jun 2024
• Fri, 14 Jun 2024

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Fri, 21 Jun 2024 (showing first 25 of 41 entries )

[1] arXiv:2406.14516 [pdf, html, other]

Title: Extended error threshold mechanism in {\it quasispecies} theory via population dynamics

Hermano Velten, Carlos Felipe Pinheiro, Alcides Castro e Silva

Comments: 5 pages, 1 figure

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

[2] arXiv:2406.14432 [pdf, html, other]

Title: Inverse population genetic problems with noise: inferring extent and structure of haplotype blocks from point allele frequencies

Oliver Keatinge Clay

Comments: 7 pages, 2 figures

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

[3] arXiv:2406.14358 [pdf, other]

Title: The neural correlates of logical-mathematical symbol systems processing resemble that of spatial cognition more than natural language processing

Yuannan Li, Shan Xu, Jia Liu

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

[4] arXiv:2406.14307 [pdf, html, other]

Title: QuST-LLM: Integrating Large Language Models for Comprehensive Spatial Transcriptomics Analysis

Chao Hui Huang

Comments: 12 pages, 7 figures

Subjects: Genomics (q-bio.GN); Computation and Language (cs.CL); Computer Vision and Pattern Recognition (cs.CV)

[5] arXiv:2406.14246 [pdf, html, other]

Title: Non-Negative Universal Differential Equations With Applications in Systems Biology

Maren Philipps, Antonia Körner, Jakob Vanhoefer, Dilan Pathirana, Jan Hasenauer

Comments: 6 pages, This work has been submitted to IFAC for possible publication. Initial submission was March 18, 2024

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Dynamical Systems (math.DS); Machine Learning (stat.ML)

[6] arXiv:2406.14187 [pdf, other]

Title: A mapping-free NLP-based technique for sequence search in Nanopore long-reads

Tomasz Strzoda, Lourdes Cruz-Garcia, Mustafa Najim, Christophe Badie, Joanna Polanska

Comments: 25 pages, 9 figures

Subjects: Genomics (q-bio.GN)

[7] arXiv:2406.14142 [pdf, other]

Title: Geometric Self-Supervised Pretraining on 3D Protein Structures using Subgraphs

Michail Chatzianastasis, George Dasoulas, Michalis Vazirgiannis

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

[8] arXiv:2406.14100 [pdf, html, other]

Title: Self-Attention in Transformer Networks Explains Monkeys' Gaze Pattern in Pac-Man Game

Zhongqiao Lin, Yunwei Li, Tianming Yang

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

[9] arXiv:2406.14062 [pdf, html, other]

Title: An agent-based model of behaviour change calibrated to reversal learning data

Roben Delos Reyes, Hugo Lyons Keenan, Cameron Zachreson

Comments: 23 pages, 5 figures

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

[10] arXiv:2406.14034 [pdf, other]

Title: Methylglyoxal induces cardiac dysfunction through mechanisms involving altered intracellular calcium handling in the rat heart

Hélène Peyret (PPF), Céline Konecki (PPF, CHU Reims), Christine Terryn (PICT), Florine Dubuisson (PPF), Hervé Millart (PPF), Catherine Feliu (PPF, CHU Reims), Zoubir Djerada (PPF, CHU Reims)

Journal-ref: Chemico-Biological Interactions, 2024, 394, pp.110949

Subjects: Subcellular Processes (q-bio.SC)

[11] arXiv:2406.13889 [pdf, html, other]

Title: Network-community analysis of cellular senescence

Alda Sabalic, Victoria Moiseeva, Andres Cisneros, Oleg Deryagin, Eusebio Perdiguero, Pura Muñoz-Canoves, Jordi Garcia-Ojalvo

Comments: 20 pages, 11 figures

Subjects: Quantitative Methods (q-bio.QM)

[12] arXiv:2406.13839 [pdf, html, other]

Title: RNA-FrameFlow: Flow Matching for de novo 3D RNA Backbone Design

Rishabh Anand, Chaitanya K. Joshi, Alex Morehead, Arian R. Jamasb, Charles Harris, Simon V. Mathis, Kieran Didi, Bryan Hooi, Pietro Liò

Comments: To be presented as an Oral at ICML 2024 Structured Probabilistic Inference & Generative Modeling Workshop, and a Spotlight at ICML 2024 AI4Science Workshop

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

[13] arXiv:2406.13822 [pdf, other]

Title: Association of neighborhood disadvantage with cognitive function and cortical disorganization in an unimpaired cohort

Apoorva Safai, Erin Jonaitis, Rebecca E Langhough, William R Buckingham, Sterling C. Johnson, W. Ryan Powell, Amy J. H. Kind, Barbara B. Bendlin, Pallavi Tiwari

Subjects: Neurons and Cognition (q-bio.NC); Applications (stat.AP)

[14] arXiv:2406.13765 [pdf, html, other]

Title: A game of life with dormancy

Daniel Henrik Nevermann, Claudius Gros, Jay T. Lennon

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

[15] arXiv:2406.13489 [pdf, html, other]

Title: Efficient gPC-based quantification of probabilistic robustness for systems in neuroscience

Uros Sutulovic, Daniele Proverbio, Rami Katz, Giulia Giordano

Subjects: Quantitative Methods (q-bio.QM)

[16] arXiv:2406.13292 [pdf, html, other]

Title: An interpretable generative multimodal neuroimaging-genomics framework for decoding Alzheimer's disease

Giorgio Dolci (1,2), Federica Cruciani (1), Md Abdur Rahaman (2), Anees Abrol (2), Jiayu Chen (2), Zening Fu (2), Ilaria Boscolo Galazzo (1), Gloria Menegaz (1), Vince D. Calhoun (2) ((1) Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy, (2) Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, USA)

Comments: 27 pages, 7 figures, submitted to a journal

Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Image and Video Processing (eess.IV)

[17] arXiv:2406.13141 [pdf, html, other]

Title: Implant-to-Wearable Communication through the Human Body: Exploring the Effects of Encapsulated Capacitive and Galvanic Transmitters

Anyu Jiang, Cassandra Acebal, Brook Heyd, Trustin White, Gurleen Kainth, Arunashish Datta, Shreyas Sen, Adam Khalifa, Baibhab Chatterjee

Subjects: Tissues and Organs (q-bio.TO)

[18] arXiv:2406.12950 [pdf, html, other]

Title: MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction

Yuyan Liu, Sirui Ding, Sheng Zhou, Wenqi Fan, Qiaoyu Tan

Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Computational Engineering, Finance, and Science (cs.CE); Computation and Language (cs.CL); Machine Learning (cs.LG)

[19] arXiv:2406.12949 [pdf, html, other]

Title: Integrating time-resolved $nrf2$ gene-expression data into a full GUTS model as a proxy for toxicodynamic damage in zebrafish embryo

Florian Schunck, Bernhard Kodritsch, Wibke Busch, Martin Krauss, Andreas Focks

Subjects: Quantitative Methods (q-bio.QM); Dynamical Systems (math.DS); Applications (stat.AP)

[20] arXiv:2406.12906 [pdf, other]

Title: Entropy-statistical approach to phase-locking detection of pulse oscillations: application for the analysis of biosignal synchronization

Petr Boriskov, Vadim Putrolaynen, Andrei Velichko, Kristina Peltonen

Comments: 23 pages, 12 figures, 3 tables

Subjects: Neurons and Cognition (q-bio.NC); Machine Learning (cs.LG); Adaptation and Self-Organizing Systems (nlin.AO)

[21] arXiv:2406.12895 [pdf, html, other]

Title: Temporal Complexity of a Hopfield-Type Neural Model in Random and Scale-Free Graphs

Marco Cafiso, Paolo Paradisi

Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Mathematical Physics (math-ph); Numerical Analysis (math.NA); Adaptation and Self-Organizing Systems (nlin.AO)

[22] arXiv:2406.14549 (cross-list from cs.CV) [pdf, html, other]

Title: Uncovering Latent Memories: Assessing Data Leakage and Memorization Patterns in Large Language Models

Sunny Duan, Mikail Khona, Abhiram Iyer, Rylan Schaeffer, Ila R Fiete

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

[23] arXiv:2406.14481 (cross-list from cs.LG) [pdf, html, other]

Title: Revealing Vision-Language Integration in the Brain with Multimodal Networks

Vighnesh Subramaniam, Colin Conwell, Christopher Wang, Gabriel Kreiman, Boris Katz, Ignacio Cases, Andrei Barbu

Comments: ICML 2024; 23 pages, 11 figures

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

[24] arXiv:2406.14442 (cross-list from cs.LG) [pdf, html, other]

Title: Graph Representation Learning Strategies for Omics Data: A Case Study on Parkinson's Disease

Elisa Gómez de Lope (1), Saurabh Deshpande (1), Ramón Viñas Torné (2), Pietro Liò (3), Enrico Glaab (1 and 4), Stéphane P. A. Bordas (1) ((1) University of Luxembourg, (2) École polytechnique fédérale de Lausanne (EPFL), (3) University of Cambridge, (4) On behalf of the NCER-PD Consortium)

Comments: Submitted to Machine Learning in Computational Biology 2024 as an extended abstract, 2 pages + 1 appendix

Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Computational Engineering, Finance, and Science (cs.CE); Biomolecules (q-bio.BM); Molecular Networks (q-bio.MN)

[25] arXiv:2406.14427 (cross-list from cs.AI) [pdf, html, other]

Title: Control when confidence is costly

Itzel Olivos-Castillo, Paul Schrater, Xaq Pitkow

Comments: 9 pages, 4 figures, submitted to NeurIPS 2024

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