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Quantitative Biology

Authors and titles for recent submissions, skipping first 38

[ total of 78 entries: 1-25 | 14-38 | 39-63 | 64-78 ]
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Mon, 6 May 2024 (continued, showing last 8 of 15 entries)

[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 (showing first 17 of 19 entries)

[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)
[ total of 78 entries: 1-25 | 14-38 | 39-63 | 64-78 ]
[ showing 25 entries per page: fewer | more | all ]

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