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Quantitative Biology

Authors and titles for recent submissions, skipping first 50

[ total of 94 entries: 1-50 | 51-94 ]
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Tue, 14 May 2024 (continued, showing last 32 of 43 entries)

[51]  arXiv:2405.07245 [pdf, other]
Title: Ecology, Spatial Structure, and Selection Pressure Induce Strong Signatures in Phylogenetic Structure
Authors: Matthew Andres Moreno, Santiago Rodriguez-Papa, Emily Dolson
Subjects: Populations and Evolution (q-bio.PE); Neural and Evolutionary Computing (cs.NE)
[52]  arXiv:2405.07238 [pdf, ps, other]
Title: Handwriting Anomalies and Learning Disabilities through Recurrent Neural Networks and Geometric Pattern Analysis
Authors: Vasileios Alevizos, Clark Xu, Sabrina Edralin, Akebu Simasiku, Dimitra Malliarou, Zongliang Yue, Antonis Messinis
Subjects: Quantitative Methods (q-bio.QM)
[53]  arXiv:2405.07123 [pdf, other]
Title: CANA v1.0.0 and schematodes: efficient quantification of symmetry in Boolean automata
Authors: Austin M. Marcus, Jordan Rozum, Herbert Sizek, Luis M. Rocha
Comments: 5 pages 1 figure (two images in figure)
Subjects: Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)
[54]  arXiv:2405.07110 [pdf, other]
Title: A Vector Representation for Phylogenetic Trees
Authors: Cedric Chauve, Caroline Colijn, Louxin Zhang
Subjects: Populations and Evolution (q-bio.PE); Data Structures and Algorithms (cs.DS); Combinatorics (math.CO)
[55]  arXiv:2405.06851 [pdf, other]
Title: Nonlinear classification of neural manifolds with contextual information
Authors: Francesca Mignacco, Chi-Ning Chou, SueYeon Chung
Comments: 5 pages, 5 figures
Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Neural and Evolutionary Computing (cs.NE); Machine Learning (stat.ML)
[56]  arXiv:2405.06836 [pdf, other]
Title: Improving Targeted Molecule Generation through Language Model Fine-Tuning Via Reinforcement Learning
Authors: Salma J. Ahmed, Mustafa A. Elattar
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[57]  arXiv:2405.06732 [pdf, other]
Title: A Global Data-Driven Model for The Hippocampus and Nucleus Accumbens of Rat From The Local Field Potential Recordings (LFP)
Authors: Maedeh Sadeghi (1), Mahdi Aliyari Shoorehdeli (1), Shole jamali (2), Abbas Haghparast (2) ((1) Fault Detection and Identification (FDI) Laboratory, Faculty of Electrical Engineering, K. N. Toosi University of Technology, Tehran, Iran, (2) Neuroscience Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran)
Subjects: Neurons and Cognition (q-bio.NC); Machine Learning (cs.LG)
[58]  arXiv:2405.06729 [pdf, other]
Title: Fine-tuning Protein Language Models with Deep Mutational Scanning improves Variant Effect Prediction
Authors: Aleix Lafita, Ferran Gonzalez, Mahmoud Hossam, Paul Smyth, Jacob Deasy, Ari Allyn-Feuer, Daniel Seaton, Stephen Young
Comments: Machine Learning for Genomics Explorations workshop at ICLR 2024
Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG)
[59]  arXiv:2405.06725 [pdf, other]
Title: On the Shape of Brainscores for Large Language Models (LLMs)
Authors: Jingkai Li
Comments: Published as a workshop paper at ICLR AGI Workshop 2024
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Computation and Language (cs.CL); Machine Learning (cs.LG)
[60]  arXiv:2405.06724 [pdf, other]
Title: Boolean matrix logic programming for active learning of gene functions in genome-scale metabolic network models
Authors: Lun Ai, Stephen H. Muggleton, Shi-Shun Liang, Geoff S. Baldwin
Subjects: Molecular Networks (q-bio.MN); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[61]  arXiv:2405.06718 [pdf, ps, other]
Title: Vector-borne threats: Sustainable approaches to their diagnosis and treatment
Authors: Areesha Naveed, Ayesha Haidar, Rameen Atique, Arshi Saeed, Bushra Anwar, Ambreen Talib, Uzma Bilal, Javeria Sharif, Ayesha Nadeem, Sania Tariq, Ayesha Muazzam, Abdul Samad
Comments: 4 Figure, 1 table
Subjects: Other Quantitative Biology (q-bio.OT)
[62]  arXiv:2405.06708 [pdf, other]
Title: LangCell: Language-Cell Pre-training for Cell Identity Understanding
Authors: Suyuan Zhao, Jiahuan Zhang, Yizhen Luo, Yushuai Wu, Zaiqing Nie
Comments: 27 pages, 21 figures, conference
Subjects: Genomics (q-bio.GN); Artificial Intelligence (cs.AI); Computation and Language (cs.CL)
[63]  arXiv:2405.06693 [pdf, other]
Title: SurfPro: Functional Protein Design Based on Continuous Surface
Authors: Zhenqiao Song, Tinglin Huang, Lei Li, Wengong Jin
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[64]  arXiv:2405.06690 [pdf, other]
Title: DrugLLM: Open Large Language Model for Few-shot Molecule Generation
Authors: Xianggen Liu, Yan Guo, Haoran Li, Jin Liu, Shudong Huang, Bowen Ke, Jiancheng Lv
Comments: 17 pages, 3 figures
Subjects: Biomolecules (q-bio.BM); Computation and Language (cs.CL); Machine Learning (cs.LG)
[65]  arXiv:2405.06663 [pdf, other]
Title: Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship
Authors: Eunji Ko, Seul Lee, Minseon Kim, Dongki Kim
Comments: ICLR 2024 MLGenX Workshop (Spotlight)
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[66]  arXiv:2405.06662 [pdf, ps, other]
Title: Language Interaction Network for Clinical Trial Approval Estimation
Authors: Chufan Gao, Tianfan Fu, Jimeng Sun
Subjects: Biomolecules (q-bio.BM); Computation and Language (cs.CL); Machine Learning (cs.LG)
[67]  arXiv:2405.06659 [pdf, other]
Title: ControlMol: Adding Substruture Control To Molecule Diffusion Models
Authors: Qi Zhengyang, Liu Zijing, Zhang Jiying, Cao He, Li Yu
Comments: 9 pages,7 figures
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Chemical Physics (physics.chem-ph)
[68]  arXiv:2405.06658 [pdf, other]
Title: ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering
Authors: Yiqing Shen, Outongyi Lv, Houying Zhu, Yu Guang Wang
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[69]  arXiv:2405.06657 [pdf, other]
Title: Molecular Docking via Weighted Subgraph Isomorphism on Quantum Annealers
Authors: Emanuele Triuzzi, Riccardo Mengoni, Domenico Bonanni, Daniele Ottaviani, Andrea Beccari, Gianluca Palermo
Subjects: Biomolecules (q-bio.BM); Computational Engineering, Finance, and Science (cs.CE); Emerging Technologies (cs.ET)
[70]  arXiv:2405.06655 [pdf, ps, other]
Title: RNA Secondary Structure Prediction Using Transformer-Based Deep Learning Models
Authors: Yanlin Zhou, Tong Zhan, Yichao Wu, Bo Song, Chenxi Shi
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[71]  arXiv:2405.06654 [pdf, other]
Title: PROflow: An iterative refinement model for PROTAC-induced structure prediction
Authors: Bo Qiang, Wenxian Shi, Yuxuan Song, Menghua Wu
Comments: Published at the GEM workshop, ICLR 2024
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[72]  arXiv:2405.06653 [pdf, other]
Title: A unified cross-attention model for predicting antigen binding specificity to both HLA and TCR molecules
Authors: Chenpeng Yu, Xing Fang, Hui Liu
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[73]  arXiv:2405.06651 [pdf, ps, other]
Title: Using GANs for De Novo Protein Design Targeting Microglial IL-3R$α$ to Inhibit Alzheimer's Progression
Authors: Arnav Swaroop
Comments: 9 pages total
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)
[74]  arXiv:2405.06649 [pdf, other]
Title: ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction
Authors: Mingyu Jin, Haochen Xue, Zhenting Wang, Boming Kang, Ruosong Ye, Kaixiong Zhou, Mengnan Du, Yongfeng Zhang
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG); Molecular Networks (q-bio.MN)
[75]  arXiv:2405.06648 [pdf, other]
Title: Protein atom traps as seeing by neutron scattering
Authors: Georgii Koniukov
Subjects: Biomolecules (q-bio.BM); Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)
[76]  arXiv:2405.06645 [pdf, other]
Title: On Recovering Higher-order Interactions from Protein Language Models
Authors: Darin Tsui, Amirali Aghazadeh
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[77]  arXiv:2405.06644 [pdf, ps, other]
Title: The Mathematics of Chlorophyll Photoexcitation
Authors: Archit Chaturvedi
Subjects: Biomolecules (q-bio.BM)
[78]  arXiv:2405.06642 [pdf, other]
Title: PPFlow: Target-aware Peptide Design with Torsional Flow Matching
Authors: Haitao Lin, Odin Zhang, Huifeng Zhao, Dejun Jiang, Lirong Wu, Zicheng Liu, Yufei Huang, Stan Z. Li
Comments: 18 pages
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[79]  arXiv:2405.07983 (cross-list from physics.bio-ph) [pdf, other]
Title: Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling
Authors: Zhuoyi Liu, Alex T. Grigas, Jacob Sumner, Edward Knab, Caitlin M. Davis, Corey S. O'Hern
Subjects: Biological Physics (physics.bio-ph); Biomolecules (q-bio.BM)
[80]  arXiv:2405.07899 (cross-list from physics.bio-ph) [pdf, other]
Title: Mechanically-driven growth and competition in a Voronoi model of tissues
Authors: Louis Brezin, Kirill S. Korolev
Comments: 20 pages, 5 figures
Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Populations and Evolution (q-bio.PE)
[81]  arXiv:2405.07752 (cross-list from math.DS) [pdf, other]
Title: Feedback-delay dependence of the stability of cluster periodic orbits in populations of degrade-and-fire oscillators with common activator
Authors: Bastien Fernandez, Matteo Tanzi
Comments: 26 pages, 2 figures
Subjects: Dynamical Systems (math.DS); Classical Analysis and ODEs (math.CA); Populations and Evolution (q-bio.PE)
[82]  arXiv:2405.07442 (cross-list from cs.SD) [pdf, ps, other]
Title: Rene: A Pre-trained Multi-modal Architecture for Auscultation of Respiratory Diseases
Authors: Pengfei Zhang, Zhihang Zheng, Shichen Zhang, Minghao Yang, Shaojun Tang
Subjects: Sound (cs.SD); Artificial Intelligence (cs.AI); Audio and Speech Processing (eess.AS); Quantitative Methods (q-bio.QM)

Mon, 13 May 2024

[83]  arXiv:2405.06628 [pdf, ps, other]
Title: Optimal epidemic control by social distancing and vaccination of an infection structured by time since infection: the covid-19 case study
Authors: Alberto d'Onofrio, Mimmo Iannelli, Piero Manfredi, Gabriela Marinoschi
Comments: 24 pages, 2 figures
Journal-ref: SIAM J. Appl. Math, S199-S224, 2023
Subjects: Populations and Evolution (q-bio.PE); Analysis of PDEs (math.AP); Optimization and Control (math.OC)
[84]  arXiv:2405.06511 [pdf, other]
Title: Towards Less Biased Data-driven Scoring with Deep Learning-Based End-to-end Database Search in Tandem Mass Spectrometry
Authors: Yonghan Yu, Ming Li
Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI)
[85]  arXiv:2405.06500 [pdf, ps, other]
Title: Advantageous and disadvantageous inequality aversion can be taught through vicarious learning of others' preferences
Authors: Shen Zhang, Oriel FeldmanHall, Sébastien Hétu, A. Ross Otto
Comments: 40 pages for main text 15 pages for Supplemental 6 figures
Subjects: Neurons and Cognition (q-bio.NC)
[86]  arXiv:2405.06457 [pdf, ps, other]
Title: Characterization of mood and emotion regulation in females with PMS/PMDD using near-infrared spectroscopy to assess prefrontal cerebral blood flow and the mood questionnaire
Authors: Makiko Aoki, Masato Suzuki, Satoshi Suzuki, Kosuke Oiwa, Yoshitaka Maeda, Hisayo Okayama
Comments: 5 pages, 4 figures, 1 table, 2024 IEEE International Conference on Robotics and Automation (ICRA 2024)
Subjects: Other Quantitative Biology (q-bio.OT)
[87]  arXiv:2405.06377 [pdf, ps, other]
Title: The Evolution of Language and Human Rationality
Authors: Robert Worden
Comments: 12 pages; presented at the 14th EvoLang conference, 2024
Subjects: Neurons and Cognition (q-bio.NC); Populations and Evolution (q-bio.PE)
[88]  arXiv:2405.06303 [pdf, other]
Title: Automated Cell Structure Extraction for 3D Electron Microscopy by Deep Learning
Authors: Jin Kousaka, Atsuko H. Iwane, Yuichi Togashi
Subjects: Quantitative Methods (q-bio.QM)
[89]  arXiv:2405.06110 [pdf, other]
Title: Combined topological and spatial constraints are required to capture the structure of neural connectomes
Authors: Anastasiya Salova, István A. Kovács
Comments: 24 pages, 20 figures
Subjects: Neurons and Cognition (q-bio.NC); Biological Physics (physics.bio-ph)
[90]  arXiv:2405.06072 [pdf, ps, other]
Title: Contribution of Coincidence Detection to Speech Segregation in Noisy Environments
Authors: Asaf Zorea, Miriam Furst
Subjects: Neurons and Cognition (q-bio.NC)
[91]  arXiv:2405.06032 [pdf, other]
Title: Champuru 2: Improved scoring of alignments and a user-friendly graphical interface
Authors: Yann Spöri, Jean-François Flot
Comments: 13 pages, 3 figures
Subjects: Quantitative Methods (q-bio.QM)
[92]  arXiv:2405.05998 [pdf, other]
Title: Whole Genome Transformer for Gene Interaction Effects in Microbiome Habitat Specificity
Authors: Zhufeng Li, Sandeep S Cranganore, Nicholas Youngblut, Niki Kilbertus
Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG)
[93]  arXiv:2405.06178 (cross-list from eess.IV) [pdf, other]
Title: ACTION: Augmentation and Computation Toolbox for Brain Network Analysis with Functional MRI
Authors: Yuqi Fang, Junhao Zhang, Linmin Wang, Qianqian Wang, Mingxia Liu
Comments: 14 pages, 5 figures, 5 tables
Subjects: Image and Video Processing (eess.IV); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)
[94]  arXiv:2405.06075 (cross-list from physics.soc-ph) [pdf, other]
Title: The Building Blocks of Consciousness
Authors: Robin W. Spencer
Comments: 13 pages, 1 figure
Subjects: Physics and Society (physics.soc-ph); Neurons and Cognition (q-bio.NC)
[ total of 94 entries: 1-50 | 51-94 ]
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