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Quantitative Biology

Authors and titles for recent submissions, skipping first 69

[ total of 119 entries: 1-69 | 70-119 ]
[ showing 69 entries per page: fewer | more | all ]

Tue, 28 May 2024 (continued, showing last 5 of 32 entries)

[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

[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)
[76]  arXiv:2405.15489 [pdf, other]
Title: Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2
Authors: Yeqing Lin, Minji Lee, Zhao Zhang, Mohammed AlQuraishi
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[77]  arXiv:2405.15448 [pdf, other]
Title: Dynamical behavior of Predator-Prey with Allee Effect on Both Populations and Disease in Predator
Authors: Khushbu Singh, K. Kaladhar
Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS)
[78]  arXiv:2405.15206 [pdf, other]
Title: Maximum Caliber Infers Effective Coupling and Response from Spiking Networks
Authors: Kevin S. Chen, Ying-Jen Yang
Subjects: Neurons and Cognition (q-bio.NC); Biological Physics (physics.bio-ph)
[79]  arXiv:2405.15158 [pdf, other]
Title: ProtFAD: Introducing function-aware domains as implicit modality towards protein function perception
Authors: Mingqing Wang, Zhiwei Nie, Yonghong He, Zhixiang Ren
Comments: 16 pages, 6 figures, 5 tables
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[80]  arXiv:2405.15109 [pdf, other]
Title: An Update to the SBML Human-Readable Antimony Language
Authors: Lucian Smith, Herbert M Sauro
Subjects: Quantitative Methods (q-bio.QM); Molecular Networks (q-bio.MN)
[81]  arXiv:2405.14925 [pdf, other]
Title: PILOT: Equivariant diffusion for pocket conditioned de novo ligand generation with multi-objective guidance via importance sampling
Authors: Julian Cremer, Tuan Le, Frank Noé, Djork-Arné Clevert, Kristof T. Schütt
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Computational Engineering, Finance, and Science (cs.CE); Machine Learning (cs.LG)
[82]  arXiv:2405.14904 [pdf, other]
Title: Large deviation principles and evolutionary multiple structure alignment of non-coding RNA
Authors: Brandon Legried
Comments: 25 pages main document, 31 pages total with references and appendix, 1 figure
Subjects: Other Quantitative Biology (q-bio.OT)
[83]  arXiv:2405.14887 [pdf, ps, other]
Title: Modeling the dynamics of the Hepatitis B virus via a variable-order discrete system
Authors: Meriem Boukhobza, Amar Debbouche, Lingeshwaran Shangerganesh, Delfim F. M. Torres
Comments: This is a preprint whose final form is published in 'Chaos, Solitons and Fractals' (see this https URL)
Journal-ref: Chaos Solitons Fractals 184 (2024), Art. 114987, 8pp
Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS)
[84]  arXiv:2405.15701 (cross-list from eess.IV) [pdf, other]
Title: realSEUDO for real-time calcium imaging analysis
Authors: Iuliia Dmitrieva, Sergey Babkin, Adam S. Charles
Comments: 20 pages, 8 figures
Subjects: Image and Video Processing (eess.IV); Neurons and Cognition (q-bio.NC); Quantitative Methods (q-bio.QM); Computation (stat.CO)
[85]  arXiv:2405.15539 (cross-list from stat.ML) [pdf, other]
Title: A generalized neural tangent kernel for surrogate gradient learning
Authors: Luke Eilers, Raoul-Martin Memmesheimer, Sven Goedeke
Comments: 52 pages, 3 figures + 2 supplementary figures
Subjects: Machine Learning (stat.ML); Disordered Systems and Neural Networks (cond-mat.dis-nn); Machine Learning (cs.LG); Probability (math.PR); Neurons and Cognition (q-bio.NC)
[86]  arXiv:2405.15535 (cross-list from math.DS) [pdf, other]
Title: Formulating human risk response in epidemic models: exogenous vs endogenous approaches
Authors: Leah LeJeune, Navid Ghaffarzadegan, Lauren Childs, Omar Saucedo
Comments: 23 pages, 7 figures, submitted to European Journal of Operational Research
Subjects: Dynamical Systems (math.DS); Populations and Evolution (q-bio.PE)
[87]  arXiv:2405.15275 (cross-list from eess.IV) [pdf, other]
Title: NMGrad: Advancing Histopathological Bladder Cancer Grading with Weakly Supervised Deep Learning
Authors: Saul Fuster, Umay Kiraz, Trygve Eftestøl, Emiel A.M. Janssen, Kjersti Engan
Comments: this https URL
Subjects: Image and Video Processing (eess.IV); Computer Vision and Pattern Recognition (cs.CV); Quantitative Methods (q-bio.QM)
[88]  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)
[89]  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

[90]  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)
[91]  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)
[92]  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)
[93]  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)
[94]  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)
[95]  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)
[96]  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)
[97]  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)
[98]  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)
[99]  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)
[100]  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)
[101]  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)
[102]  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)
[103]  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)
[104]  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)
[105]  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)
[106]  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)
[107]  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)
[108]  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)
[109]  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)
[110]  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)
[111]  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)
[112]  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)
[113]  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)
[114]  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)
[115]  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)
[116]  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)
[117]  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)
[118]  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)
[119]  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)
[ total of 119 entries: 1-69 | 70-119 ]
[ showing 69 entries per page: fewer | more | all ]

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