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Quantitative Biology

Authors and titles for recent submissions, skipping first 65

[ total of 94 entries: 1-25 | 16-40 | 41-65 | 66-90 | 91-94 ]
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Tue, 14 May 2024 (continued, showing last 17 of 43 entries)

[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 (showing first 8 of 12 entries)

[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)
[ total of 94 entries: 1-25 | 16-40 | 41-65 | 66-90 | 91-94 ]
[ showing 25 entries per page: fewer | more | all ]

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