Quantitative Biology

Authors and titles for recent submissions

• Wed, 8 May 2024
• Tue, 7 May 2024
• Mon, 6 May 2024
• Fri, 3 May 2024
• Thu, 2 May 2024

Wed, 8 May 2024

[1]  arXiv:2405.04248 [pdf, ps, other]

Title: Neurocomputational Phenotypes in Female and Male Autistic Individuals

Authors: Michelle McCleod, Sean Borneman, Evie Malaia

Comments: 10 pages, 2 figures, 4 tables. Submitted to Journal of Science and Health, University of Alabama

Subjects: Neurons and Cognition (q-bio.NC); Chaotic Dynamics (nlin.CD)

[2]  arXiv:2405.04011 [pdf, other]

Title: Adjoint Sensitivity Analysis on Multi-Scale Bioprocess Stochastic Reaction Network

Authors: Keilung Choy, Wei Xie

Comments: 11 pages, 2 figures

Subjects: Molecular Networks (q-bio.MN); Machine Learning (stat.ML)

[3]  arXiv:2405.03913 [pdf, other]

Title: Digital Twin Calibration for Biological System-of-Systems: Cell Culture Manufacturing Process

Authors: Fuqiang Cheng, Wei Xie, Hua Zheng

Comments: 12 pages, 5 figures

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

[4]  arXiv:2405.03861 [pdf, other]

Title: Homeostasis in Input-Output Networks: Structure, Classification and Applications

Authors: Fernando Antoneli, Martin Golubitsky, Jiaxin Jin, Ian Stewart

Comments: 45 pages, 26 figures, submitted to the MBS special issue "Dynamical Systems in Life Sciences"

Subjects: Molecular Networks (q-bio.MN); Combinatorics (math.CO); Dynamical Systems (math.DS); Biological Physics (physics.bio-ph)

[5]  arXiv:2405.03829 [pdf, other]

Title: Unsupervised Machine Learning Identifies Latent Ultradian States in Multi-Modal Wearable Sensor Signals

Authors: Christopher Thornton, Billy C. Smith, Guillermo M. Besne, Bethany Little, Yujiang Wang

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

[6]  arXiv:2405.03726 [pdf, ps, other]

Title: sc-OTGM: Single-Cell Perturbation Modeling by Solving Optimal Mass Transport on the Manifold of Gaussian Mixtures

Authors: Andac Demir, Elizaveta Solovyeva, James Boylan, Mei Xiao, Fabrizio Serluca, Sebastian Hoersch, Jeremy Jenkins, Murthy Devarakonda, Bulent Kiziltan

Comments: ICLR 2024, Machine Learning for Genomics Explorations Workshop

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

[7]  arXiv:2405.03707 [pdf, ps, other]

Title: Quantifying indirect and direct vaccination effects arising in the SIR model

Authors: Lixin Lin, Homayoun Hamedmoghadam, Robert Shorten, Lewi Stone

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

[8]  arXiv:2405.04078 (cross-list from cs.LG) [pdf, other]

Title: WISER: Weak supervISion and supErvised Representation learning to improve drug response prediction in cancer

Authors: Kumar Shubham, Aishwarya Jayagopal, Syed Mohammed Danish, Prathosh AP, Vaibhav Rajan

Comments: ICML 2024

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

[9]  arXiv:2405.03931 (cross-list from math.DS) [pdf, ps, other]

Title: Incorporating changeable attitudes toward vaccination into an SIR infectious disease model

Authors: Yi Jiang, Kristin M. Kurianski, Jane H. Lee, Yanping Ma, Daniel Cicala, Glenn Ledder

Comments: 30 pages, 3 tables, 10 figures

Subjects: Dynamical Systems (math.DS); Populations and Evolution (q-bio.PE)

[10]  arXiv:2405.03879 (cross-list from stat.ML) [pdf, other]

Title: Scalable Amortized GPLVMs for Single Cell Transcriptomics Data

Authors: Sarah Zhao, Aditya Ravuri, Vidhi Lalchand, Neil D. Lawrence

Subjects: Machine Learning (stat.ML); Machine Learning (cs.LG); Genomics (q-bio.GN); Applications (stat.AP)

[11]  arXiv:2405.03799 (cross-list from cs.LG) [pdf, other]

Title: Synthetic Data from Diffusion Models Improve Drug Discovery Prediction

Authors: Bing Hu, Ashish Saragadam, Anita Layton, Helen Chen

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

Tue, 7 May 2024

[12]  arXiv:2405.03602 [pdf, other]

Title: One nose but two nostrils: Learn to align with sparse connections between two olfactory cortices

Authors: Bo Liu, Shanshan Qin, Venkatesh Murthy, Yuhai Tu

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

[13]  arXiv:2405.03601 [pdf, other]

Title: Firing rate model for brain rhythms controlled by astrocytes

Authors: Sergey V. Stasenko, Sergey M. Olenin, Eugene A. Grines, Tatiana A. Levanova

Comments: 12 pages, 4 figures

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

[14]  arXiv:2405.03370 [pdf, other]

Title: AntiFold: Improved antibody structure-based design using inverse folding

Authors: Magnus Haraldson Høie, Alissa Hummer, Tobias H. Olsen, Broncio Aguilar-Sanjuan, Morten Nielsen, Charlotte M. Deane

Subjects: Biomolecules (q-bio.BM); Quantitative Methods (q-bio.QM)

[15]  arXiv:2405.03346 [pdf, other]

Title: Population dynamics and games of variable size

Authors: Matheus Hansen, Fabio A. C. C. Chalub

Comments: 24 pages, 4 figures

Journal-ref: Matheus Hansen, Fabio A. C. C. Chalub. Population dynamics and games of variable size. Journal of Theoretical Biology 589, 111842, 2024

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

[16]  arXiv:2405.03148 [pdf, other]

Title: Counting Subnetworks Under Gene Duplication in Genetic Regulatory Networks

Authors: Ashley Scruse, Jonathan Arnold, Robert Robinson

Subjects: Molecular Networks (q-bio.MN); Combinatorics (math.CO)

[17]  arXiv:2405.02853 [pdf, ps, other]

Title: Development and validation of a short form of the medication literacy scale for Chinese College Students

Authors: Chen Zhenzhen (1,2), Ren Jiabao (1,2), Duan Tingyu (3), Chen Ke (4), Hou Ruyi (5), Li Yimiao (5), Zeng Leixiao (5), Meng Xiaoxuan (6), Wu Yibo (7), Liu Yu (2), ((1) College of Science, Minzu University of China, Beijing, China, (2) School of Nursing, China Medical University, Shenyang, Liaoning Province, China, (3) Hebei Institute of Communications, Hebei, China, (4) Department of Social Science and Humanities, Harbin Medical University, Harbin, Heilongjiang Province, China, (5) School of Journalism and Communication, Renmin University of China, Beijing, China, (6) Tianjin Medical University, Tianjin, China, (7) School of Public Health, Peking University, Beijing, China)

Comments: 25 pages, 3 figures,3 tables

Subjects: Other Quantitative Biology (q-bio.OT)

[18]  arXiv:2405.02820 [pdf, other]

Title: Coat stiffening explains the consensus pathway of clathrin-mediated endocytosis

Authors: Felix Frey (IST Austria), Ulrich S. Schwarz (Heidelberg University)

Comments: revtex, 12 pages, 5 figures in PDF-format

Subjects: Subcellular Processes (q-bio.SC); Soft Condensed Matter (cond-mat.soft)

[19]  arXiv:2405.02786 [pdf, other]

Title: A causal inference approach of monosynapses from spike trains

Authors: Zach Saccomano, Sam Mckenzie, Horacio Rotstein, Asohan Amarasingham

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

[20]  arXiv:2405.02767 [pdf, ps, other]

Title: A Decade in a Systematic Review: The Evolution and Impact of Cell Painting

Authors: Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras-Puigvert, Nigel Greene, Andreas Bender, Anne E. Carpenter

Comments: Supplementary Table/Code here: this https URL

Subjects: Subcellular Processes (q-bio.SC); Cell Behavior (q-bio.CB)

[21]  arXiv:2405.02674 [pdf, other]

Title: Ambush strategy enhances organisms' performance in rock-paper-scissors games

Authors: R. Barbalho, S. Rodrigues, M. Tenorio, J. Menezes

Comments: 8 pages, 5 figures

Subjects: Populations and Evolution (q-bio.PE); Adaptation and Self-Organizing Systems (nlin.AO); Pattern Formation and Solitons (nlin.PS); Biological Physics (physics.bio-ph); Quantitative Methods (q-bio.QM)

[22]  arXiv:2405.02593 [pdf, ps, other]

Title: An Interdisciplinary Perspective of the Built-Environment Microbiome

Authors: John S. McAlister, Michael J. Blum, Yana Bromberg, Nina H. Fefferman, Qiang He, Eric Lofgren, Debra L. Miller, Courtney Schreiner, K. Selcuk Candan, Heather Szabo-Rogers, J. Michael Reed

Comments: 23 pages

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

[23]  arXiv:2405.02524 [pdf, other]

Title: Simulation-based Inference of Developmental EEG Maturation with the Spectral Graph Model

Authors: Danilo Bernardo, Xihe Xie, Parul Verma, Jonathan Kim, Virginia Liu, Ye Wu, Pew-Thian Yap, Srikantan Nagarajan, Ashish Raj

Comments: 58 pages, 6 figures, 18 supplementary figures

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

[24]  arXiv:2405.02381 [pdf, ps, other]

Title: Interactions between eagles and semidomestic reindeer: lessons learned from field surveys and deterrents

Authors: Aemilius Johannes van der Meiden, Andres Lopez-Peinado, Peter Sunesson, Christian Emilsson, Navinder J Singh

Comments: 17 pages, 4 Figures, 1 Table

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

[25]  arXiv:2405.02379 [pdf, other]

Title: Modelling the Stochastic Importation Dynamics and Establishment of Novel Pathogenic Strains using a General Branching Processes Framework

Authors: Jacob Curran-Sebastian, Frederik Mølkjær Andersen, Samir Bhatt

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

[26]  arXiv:2405.02374 [pdf, other]

Title: Protein binding affinity prediction under multiple substitutions applying eGNNs on Residue and Atomic graphs combined with Language model information: eGRAL

Authors: Arturo Fiorellini-Bernardis, Sebastien Boyer, Christoph Brunken, Bakary Diallo, Karim Beguir, Nicolas Lopez-Carranza, Oliver Bent

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

[27]  arXiv:2405.02845 (cross-list from cs.LG) [pdf, other]

Title: Data-Efficient Molecular Generation with Hierarchical Textual Inversion

Authors: Seojin Kim, Jaehyun Nam, Sihyun Yu, Younghoon Shin, Jinwoo Shin

Subjects: Machine Learning (cs.LG); Molecular Networks (q-bio.MN)

[28]  arXiv:2405.02564 (cross-list from cs.CV) [pdf, ps, other]

Title: Leveraging the Human Ventral Visual Stream to Improve Neural Network Robustness

Authors: Zhenan Shao, Linjian Ma, Bo Li, Diane M. Beck

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

[29]  arXiv:2405.02534 (cross-list from cs.LG) [pdf, other]

Title: A Multi-Domain Multi-Task Approach for Feature Selection from Bulk RNA Datasets

Authors: Karim Salta, Tomojit Ghosh, Michael Kirby

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

[30]  arXiv:2405.02449 (cross-list from stat.ML) [pdf, other]

Title: Quality-Weighted Vendi Scores And Their Application To Diverse Experimental Design

Authors: Quan Nguyen, Adji Bousso Dieng

Comments: Published in International Conference on Machine Learning, ICML 2024. Code can be found in the Vertaix GitHub: this https URL Paper dedicated to Kwame Nkrumah

Subjects: Machine Learning (stat.ML); Materials Science (cond-mat.mtrl-sci); Machine Learning (cs.LG); Biomolecules (q-bio.BM)

[31]  arXiv:2405.02354 (cross-list from cs.LG) [pdf, ps, other]

Title: Heterogeneous network and graph attention auto-encoder for LncRNA-disease association prediction

Authors: Jin-Xing Liu, Wen-Yu Xi, Ling-Yun Dai, Chun-Hou Zheng, Ying-Lian Gao

Comments: 10 pages, 8 figures

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

Mon, 6 May 2024

[32]  arXiv:2405.02136 [pdf, other]

Title: bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties

Authors: Jose Gavalda-Garcia, Adrian Diaz, Wim Vranken

Subjects: Quantitative Methods (q-bio.QM)

[33]  arXiv:2405.02117 [pdf, ps, other]

Title: Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling

Authors: Radek Erban, Stefanie Winkelmann

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

[34]  arXiv:2405.02076 [pdf, other]

Title: SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data

Authors: Ajit J. Nirmal, Peter K. Sorger

Comments: 6 pages, 1 figure

Subjects: Quantitative Methods (q-bio.QM); Tissues and Organs (q-bio.TO)

[35]  arXiv:2405.02038 [pdf, other]

Title: Dimensionality reduction of neuronal degeneracy reveals two interfering physiological mechanisms

Authors: Arthur Fyon, Alessio Franci, Pierre Sacré, Guillaume Drion

Subjects: Neurons and Cognition (q-bio.NC); Mathematical Physics (math-ph); Cell Behavior (q-bio.CB)

[36]  arXiv:2405.01896 [pdf, ps, other]

Title: A Step Test to Evaluate the Susceptibility to Severe High-Altitude Illness in Field Conditions

Authors: Eric Hermand (URePSSS, H&P), Léo Lesaint, Laura Denis (H&P), Jean-Paul Richalet (INSEP), François Lhuissier (H&P)

Comments: High Altitude Medicine and Biology, 2024

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

[37]  arXiv:2405.01715 [pdf, other]

Title: Identification of SNPs in genomes using GRAMEP, an alignment-free method based on the Principle of Maximum Entropy

Authors: Matheus Henrique Pimenta-Zanon, André Yoshiaki Kashiwabara, André Luís Laforga Vanzela, Fabricio Martins Lopes

Subjects: Genomics (q-bio.GN); Information Theory (cs.IT); Applications (stat.AP)

[38]  arXiv:2405.01703 [pdf, other]

Title: Fluid-structure interaction simulations for the prediction of fractional flow reserve in pediatric patients with anomalous aortic origin of a coronary artery

Authors: Charles Puelz, Craig G. Rusin, Dan Lior, Shagun Sachdeva, Tam T. Doan, Lindsay F. Eilers, Dana Reaves-O'Neal, Silvana Molossi

Subjects: Tissues and Organs (q-bio.TO); Medical Physics (physics.med-ph)

[39]  arXiv:2405.01664 [pdf, ps, other]

Title: Stress-induced Eukaryotic Translational Regulatory Mechanisms

Authors: Dilawar Ahmad Mir, Zhengxin Ma, Jordan Horrocks, Aric N Rogers

Comments: 37 Pages, Figures 7, Review Article

Subjects: Molecular Networks (q-bio.MN)

[40]  arXiv:2405.01616 [pdf, other]

Title: Generative Active Learning for the Search of Small-molecule Protein Binders

Authors: Maksym Korablyov, Cheng-Hao Liu, Moksh Jain, Almer M. van der Sloot, Eric Jolicoeur, Edward Ruediger, Andrei Cristian Nica, Emmanuel Bengio, Kostiantyn Lapchevskyi, Daniel St-Cyr, Doris Alexandra Schuetz, Victor Ion Butoi, Jarrid Rector-Brooks, Simon Blackburn, Leo Feng, Hadi Nekoei, SaiKrishna Gottipati, Priyesh Vijayan, Prateek Gupta, Ladislav Rampášek, Sasikanth Avancha, Pierre-Luc Bacon, William L. Hamilton, Brooks Paige, Sanchit Misra, Stanislaw Kamil Jastrzebski, Bharat Kaul, Doina Precup, José Miguel Hernández-Lobato, Marwin Segler, Michael Bronstein, Anne Marinier, Mike Tyers, Yoshua Bengio

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

[41]  arXiv:2405.02003 (cross-list from cond-mat.stat-mech) [pdf, ps, other]

Title: Smoothly vanishing density in the contact process by an interplay of disorder and long-distance dispersal

Authors: R. Juhász, I. A. Kovács

Comments: 8 pages, 6 figures

Subjects: Statistical Mechanics (cond-mat.stat-mech); Disordered Systems and Neural Networks (cond-mat.dis-nn); Populations and Evolution (q-bio.PE)

[42]  arXiv:2405.01989 (cross-list from math.OC) [pdf, other]

Title: Parameter estimation in ODEs: assessing the potential of local and global solvers

Authors: M. Fernández de Dios, Ángel M. González-Rueda, Julio R. Banga, Julio González-Díaz, David R. Penas

Subjects: Optimization and Control (math.OC); Quantitative Methods (q-bio.QM)

[43]  arXiv:2405.01983 (cross-list from cs.AI) [pdf, other]

Title: Model-based reinforcement learning for protein backbone design

Authors: Frederic Renard, Cyprien Courtot, Alfredo Reichlin, Oliver Bent

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

[44]  arXiv:2405.01974 (cross-list from cs.LG) [pdf, other]

Title: Multitask Extension of Geometrically Aligned Transfer Encoder

Authors: Sung Moon Ko, Sumin Lee, Dae-Woong Jeong, Hyunseung Kim, Chanhui Lee, Soorin Yim, Sehui Han

Comments: 7 pages, 3 figures, 2 tables

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

[45]  arXiv:2405.01960 (cross-list from cond-mat.soft) [pdf, other]

Title: Proliferation-driven mechanical feedback regulates cell dynamics in growing tissues

Authors: Sumit Sinha, Xin Li, Abdul N Malmi-Kakkada, D. Thirumalai

Comments: 5 figures. arXiv admin note: text overlap with arXiv:2202.04806

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

[46]  arXiv:2405.01554 (cross-list from cs.LG) [pdf, other]

Title: Early-stage detection of cognitive impairment by hybrid quantum-classical algorithm using resting-state functional MRI time-series

Authors: Junggu Choi, Tak Hur, Daniel K. Park, Na-Young Shin, Seung-Koo Lee, Hakbae Lee, Sanghoon Han

Comments: 28 pages, 10 figures

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

Fri, 3 May 2024

[47]  arXiv:2405.01385 [pdf, other]

Title: Anti-seizure medication tapering is associated with delta band power reduction in a dose, region and time-dependent manner

Authors: Guillermo M. Besne, Nathan Evans, Mariella Panagiotopoulou, Billy Smith, Fahmida A Chowdhury, Beate Diehl, John S Duncan, Andrew W McEvoy, Anna Miserocchi, Jane de Tisi, Mathew Walker, Peter N. Taylor, Chris Thornton, Yujiang Wang

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

[48]  arXiv:2405.01148 [pdf, other]

Title: Qualia and the Formal Structure of Meaning

Authors: Xerxes D. Arsiwalla

Comments: 28 pages

Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Category Theory (math.CT); History and Philosophy of Physics (physics.hist-ph)

[49]  arXiv:2405.01012 [pdf, other]

Title: Correcting Biased Centered Kernel Alignment Measures in Biological and Artificial Neural Networks

Authors: Alex Murphy, Joel Zylberberg, Alona Fyshe

Comments: ICLR 2024 Re-Align Workshop

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

[50]  arXiv:2405.00838 [pdf, other]

Title: Cross-modality Matching and Prediction of Perturbation Responses with Labeled Gromov-Wasserstein Optimal Transport

Authors: Jayoung Ryu, Romain Lopez, Charlotte Bunne, Aviv Regev

Comments: 16 pages, 4 figures, correspondence to Aviv Regev and Romain Lopez

Subjects: Genomics (q-bio.GN); Optimization and Control (math.OC)

[51]  arXiv:2405.00810 [pdf, other]

Title: A Simple Comparison of Biochemical Systems Theory and Metabolic Control Analysis

Authors: Herbert M Sauro

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

[52]  arXiv:2405.00753 [pdf, other]

Title: HMAMP: Hypervolume-Driven Multi-Objective Antimicrobial Peptides Design

Authors: Li Wang, Yiping Li, Xiangzheng Fu, Xiucai Ye, Junfeng Shi, Gary G. Yen, Xiangxiang Zeng

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

[53]  arXiv:2405.00751 [pdf, other]

Title: F$^3$low: Frame-to-Frame Coarse-grained Molecular Dynamics with SE(3) Guided Flow Matching

Authors: Shaoning Li, Yusong Wang, Mingyu Li, Jian Zhang, Bin Shao, Nanning Zheng, Jian Tang

Comments: Accepted by ICLR 2024 GEM workshop

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

[54]  arXiv:2405.00702 [pdf, ps, other]

Title: Cold plasma treatment boosts barley germination and seedling vigor: Insights into soluble sugar, starch, and protein modifications

Authors: Mohamed Ali Benabderrahim, Imen Bettaieb, Hédia Hannachi, Mokhtar Rejili, Thierry Dufour

Journal-ref: Journal of Cereal Science, Vol. 116, 103852 (2024)

Subjects: Other Quantitative Biology (q-bio.OT)

[55]  arXiv:2405.01437 (cross-list from cs.GT) [pdf, other]

Title: Two competing populations with a common environmental resource

Authors: Keith Paarporn, James Nelson

Comments: Submission to CDC 24

Subjects: Computer Science and Game Theory (cs.GT); Systems and Control (eess.SY); Populations and Evolution (q-bio.PE)

[56]  arXiv:2405.01155 (cross-list from cs.LG) [pdf, other]

Title: SynFlowNet: Towards Molecule Design with Guaranteed Synthesis Pathways

Authors: Miruna Cretu, Charles Harris, Julien Roy, Emmanuel Bengio, Pietro Liò

Comments: Presented at ICLR 2024 GEM Workshop

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

[57]  arXiv:2405.01105 (cross-list from cs.CV) [pdf, other]

Title: Image segmentation of treated and untreated tumor spheroids by Fully Convolutional Networks

Authors: Matthias Streller, Soňa Michlíková, Willy Ciecior, Katharina Lönnecke, Leoni A. Kunz-Schughart, Steffen Lange, Anja Voss-Böhme

Comments: 28 pages, 21 figures

Subjects: Computer Vision and Pattern Recognition (cs.CV); Quantitative Methods (q-bio.QM); Tissues and Organs (q-bio.TO)

[58]  arXiv:2405.01015 (cross-list from stat.ML) [pdf, other]

Title: Network reconstruction via the minimum description length principle

Authors: Tiago P. Peixoto

Comments: 17 pages, 10 figures. Code and documentation are available at this https URL

Subjects: Machine Learning (stat.ML); Machine Learning (cs.LG); Social and Information Networks (cs.SI); Data Analysis, Statistics and Probability (physics.data-an); Populations and Evolution (q-bio.PE)

[59]  arXiv:2405.00972 (cross-list from cs.CL) [pdf, other]

Title: CACTUS: Chemistry Agent Connecting Tool-Usage to Science

Authors: Andrew D. McNaughton, Gautham Ramalaxmi, Agustin Kruel, Carter R. Knutson, Rohith A. Varikoti, Neeraj Kumar

Subjects: Computation and Language (cs.CL); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Chemical Physics (physics.chem-ph); Quantitative Methods (q-bio.QM)

[60]  arXiv:2405.00949 (cross-list from cs.LG) [pdf, other]

Title: The Role of Model Architecture and Scale in Predicting Molecular Properties: Insights from Fine-Tuning RoBERTa, BART, and LLaMA

Authors: Lee Youngmin, Lang S.I.D. Andrew, Cai Duoduo, Wheat R. Stephen

Subjects: Machine Learning (cs.LG); Computation and Language (cs.CL); Chemical Physics (physics.chem-ph); Biomolecules (q-bio.BM)

[61]  arXiv:2405.00899 (cross-list from cs.HC) [pdf, other]

Title: Characterising the Creative Process in Humans and Large Language Models

Authors: Surabhi S. Nath, Peter Dayan, Claire Stevenson

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

[62]  arXiv:2405.00833 (cross-list from eess.SP) [pdf, other]

Title: Modelling the nanopore sequencing process with Helicase HMMs

Authors: Xuechun Xu, Joakim Jaldén

Comments: 8 pages, 7 figures and 1 table. Journal manuscript

Subjects: Signal Processing (eess.SP); Genomics (q-bio.GN)

[63]  arXiv:2405.00817 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Chaotic behavior in Lotka-Volterra and May-Leonard models of biodiversity

Authors: D. Bazeia, M. Bongestab, B. F. de Oliveira

Comments: 8 pages, 7 figures, to appear in Chaos: An Interdisciplinary Journal of Nonlinear Science

Subjects: Statistical Mechanics (cond-mat.stat-mech); Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

[64]  arXiv:2405.00719 (cross-list from eess.SP) [pdf, other]

Title: EEG-Deformer: A Dense Convolutional Transformer for Brain-computer Interfaces

Authors: Yi Ding, Yong Li, Hao Sun, Rui Liu, Chengxuan Tong, Cuntai Guan

Comments: 10 pages, 9 figures. This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible

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

[65]  arXiv:2405.00679 (cross-list from cs.NE) [pdf, other]

Title: Exploring mechanisms of Neural Robustness: probing the bridge between geometry and spectrum

Authors: Konstantin Holzhausen, Mia Merlid, Håkon Olav Torvik, Anders Malthe-Sørenssen, Mikkel Elle Lepperød

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

Thu, 2 May 2024 (showing first 4 of 13 entries)

[66]  arXiv:2405.00541 [pdf, other]

Title: New Trends on the Systems Approach to Modeling SARS-CoV-2 Pandemics in a Globally Connected Planet

Authors: Giulia Bertaglia, Andrea Bondesan, Diletta Burini, Raluca Eftimie, Lorenzo Pareschi, Giuseppe Toscani

Subjects: Populations and Evolution (q-bio.PE); Adaptation and Self-Organizing Systems (nlin.AO); Physics and Society (physics.soc-ph)

[67]  arXiv:2405.00530 [pdf, ps, other]

Title: The Highly Durable Antibacterial Gel-like Coatings for Textiles

Authors: Seyedali Mirmohammadsadeghi, Davis Juhas, Mikhail Parker, Kristina Peranidze, Dwight Austin Van Horn, Aayushi Sharma, Dhruvi Patel, Tatyana A. Sysoeva, Vladislav Klepov, Vladimir Reukov

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

[68]  arXiv:2405.00513 [pdf, ps, other]

Title: 3D MR Fingerprinting for Dynamic Contrast-Enhanced Imaging of Whole Mouse Brain

Authors: Yuran Zhu, Guanhua Wang, Yuning Gu, Walter Zhao, Jiahao Lu, Junqing Zhu, Christina J. MacAskill, Andrew Dupuis, Mark A. Griswold, Dan Ma, Chris A. Flask, Xin Yu

Subjects: Quantitative Methods (q-bio.QM)

[69]  arXiv:2405.00333 [pdf, other]

Title: Reevaluating coexistence and stability in ecosystem networks to address ecological transients: methods and implications

Authors: Sarah A. Vollert, Christopher Drovandi, Matthew P. Adams

Subjects: Populations and Evolution (q-bio.PE); Applications (stat.AP)

• Wed, 8 May 2024
• Tue, 7 May 2024
• Mon, 6 May 2024
• Fri, 3 May 2024
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