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Biomolecules

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Total of 18 entries
Showing up to 50 entries per page: fewer | more | all

Mon, 25 Nov 2024 (showing 3 of 3 entries )

[1] arXiv:2411.14778 (cross-list from cond-mat.soft) [pdf, html, other]
Title: Entropic tug of war: Topological constraints spontaneously rectify the dynamics of a polymer with heterogeneous fluctuations
Adam H. T. P. Höfler, Iurii Chubak, Christos N. Likos, Jan Smrek
Subjects: Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Biomolecules (q-bio.BM)
[2] arXiv:2411.14726 (cross-list from cs.LG) [pdf, html, other]
Title: Enhancing Molecular Design through Graph-based Topological Reinforcement Learning
Xiangyu Zhang
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM)
[3] arXiv:2411.14464 (cross-list from q-bio.QM) [pdf, html, other]
Title: JESTR: Joint Embedding Space Technique for Ranking Candidate Molecules for the Annotation of Untargeted Metabolomics Data
Apurva Kalia, Dilip Krishnan, Soha Hassoun
Comments: 7 pages, 5 figures, 2 tables
Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Biomolecules (q-bio.BM)

Fri, 22 Nov 2024 (showing 3 of 3 entries )

[4] arXiv:2411.14293 [pdf, other]
Title: Machine learning framework to predict the performance of lipid nanoparticles for nucleic acid delivery
Gaurav Kumar, Arezoo M. Ardekani
Comments: This is a preprint of a manuscript under review
Subjects: Biomolecules (q-bio.BM)
[5] arXiv:2411.14079 [pdf, other]
Title: Interpretable QSPR Modeling using Recursive Feature Machines and Multi-scale Fingerprints
Jiaxuan Shen, Haitao Zhang, Yunjie Wang, Yilong Wang, Song Tao, Bo Qiu, Ng Shyh-Chang
Subjects: Biomolecules (q-bio.BM)
[6] arXiv:2411.13688 (cross-list from cs.LG) [pdf, other]
Title: Investigating Graph Neural Networks and Classical Feature-Extraction Techniques in Activity-Cliff and Molecular Property Prediction
Markus Dablander
Comments: Doctoral Thesis (Mathematical Institute, University of Oxford)
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM); Machine Learning (stat.ML)

Thu, 21 Nov 2024 (showing 5 of 5 entries )

[7] arXiv:2411.13390 [pdf, html, other]
Title: Energy-based generative models for monoclonal antibodies
Paul Pereira, Hervé Minoux, Aleksandra M. Walczak, Thierry Mora
Subjects: Biomolecules (q-bio.BM)
[8] arXiv:2411.13280 [pdf, html, other]
Title: Structure-Based Molecule Optimization via Gradient-Guided Bayesian Update
Keyue Qiu, Yuxuan Song, Jie Yu, Hongbo Ma, Ziyao Cao, Zhilong Zhang, Yushuai Wu, Mingyue Zheng, Hao Zhou, Wei-Ying Ma
Comments: 27 pages, 17 figures
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI)
[9] arXiv:2411.13189 [pdf, other]
Title: OpenMS WebApps: Building User-Friendly Solutions for MS Analysis
Tom David Müller (1 and 2), Arslan Siraj (1 and 2), Axel Walter (1 and 2), Jihyung Kim (1 and 2), Samuel Wein (1 and 2), Johannes von Kleist (1), Ayesha Feroz (1 and 2), Matteo Pilz (1 and 2), Kyowon Jeong (1 and 2), Justin Cyril Sing (3 and 4), Joshua Charkow (3 and 4), Hannes Luc Röst (3 and 4), Timo Sachsenberg (1 and 2) ((1) University of Tübingen, (2) Institute for Bioinformatics and Medical Informatics, (3) Donnelly Centre for Cellular and Biomolecular Research, (4) University of Toronto)
Comments: 19 pages, 5 figures
Subjects: Biomolecules (q-bio.BM); Human-Computer Interaction (cs.HC)
[10] arXiv:2411.12886 [pdf, html, other]
Title: NPGPT: Natural Product-Like Compound Generation with GPT-based Chemical Language Models
Koh Sakano, Kairi Furui, Masahito Ohue
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG); Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)
[11] arXiv:2411.12853 (cross-list from cs.LG) [pdf, html, other]
Title: Integrating Secondary Structures Information into Triangular Spatial Relationships (TSR) for Advanced Protein Classification
Poorya Khajouie, Titli Sarkar, Krishna Rauniyar, Li Chen, Wu Xu, Vijay Raghavan
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM)

Wed, 20 Nov 2024 (showing 3 of 3 entries )

[12] arXiv:2411.12597 [pdf, html, other]
Title: GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking
Yiliang Yuan, Mustafa Misir
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[13] arXiv:2411.12370 [pdf, html, other]
Title: Rapid response to fast viral evolution using AlphaFold 3-assisted topological deep learning
JunJie Wee, Guo-Wei Wei
Comments: 21 pages, 4 figures
Subjects: Biomolecules (q-bio.BM); Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)
[14] arXiv:2411.11875 (cross-list from cs.IR) [pdf, html, other]
Title: Exploring Optimal Transport-Based Multi-Grained Alignments for Text-Molecule Retrieval
Zijun Min, Bingshuai Liu, Liang Zhang, Jia Song, Jinsong Su, Song He, Xiaochen Bo
Comments: BIBM 2024 Regular Paper
Subjects: Information Retrieval (cs.IR); Artificial Intelligence (cs.AI); Computation and Language (cs.CL); Biomolecules (q-bio.BM)

Tue, 19 Nov 2024 (showing 4 of 4 entries )

[15] arXiv:2411.11366 [pdf, html, other]
Title: SCOP: A Sequence-Structure Contrast-Aware Framework for Protein Function Prediction
Runze Ma, Chengxin He, Huiru Zheng, Xinye Wang, Haiying Wang, Yidan Zhang, Lei Duan
Comments: Accepted as BIBM 2024 conference paper
Subjects: Biomolecules (q-bio.BM)
[16] arXiv:2411.11808 (cross-list from q-bio.QM) [pdf, html, other]
Title: Character-level Tokenizations as Powerful Inductive Biases for RNA Foundational Models
Adrián Morales-Pastor, Raquel Vázquez-Reza, Miłosz Wieczór, Clàudia Valverde, Manel Gil-Sorribes, Bertran Miquel-Oliver, Álvaro Ciudad, Alexis Molina
Comments: First version. Work in progress
Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Biomolecules (q-bio.BM)
[17] arXiv:2411.10821 (cross-list from cs.LG) [pdf, html, other]
Title: GeomCLIP: Contrastive Geometry-Text Pre-training for Molecules
Teng Xiao, Chao Cui, Huaisheng Zhu, Vasant G. Honavar
Comments: BIBM 2024
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM)
[18] arXiv:2411.10548 (cross-list from cs.LG) [pdf, html, other]
Title: BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery
Peter St. John, Dejun Lin, Polina Binder, Malcolm Greaves, Vega Shah, John St. John, Adrian Lange, Patrick Hsu, Rajesh Illango, Arvind Ramanathan, Anima Anandkumar, David H Brookes, Akosua Busia, Abhishaike Mahajan, Stephen Malina, Neha Prasad, Sam Sinai, Lindsay Edwards, Thomas Gaudelet, Cristian Regep, Martin Steinegger, Burkhard Rost, Alexander Brace, Kyle Hippe, Luca Naef, Keisuke Kamata, George Armstrong, Kevin Boyd, Zhonglin Cao, Han-Yi Chou, Simon Chu, Allan dos Santos Costa, Sajad Darabi, Eric Dawson, Kieran Didi, Cong Fu, Mario Geiger, Michelle Gill, Darren Hsu, Gagan Kaushik, Maria Korshunova, Steven Kothen-Hill, Youhan Lee, Meng Liu, Micha Livne, Zachary McClure, Jonathan Mitchell, Alireza Moradzadeh, Ohad Mosafi, Youssef Nashed, Saee Paliwal, Yuxing Peng, Sara Rabhi, Farhad Ramezanghorbani, Danny Reidenbach, Camir Ricketts, Brian Roland, Kushal Shah, Tyler Shimko, Hassan Sirelkhatim, Savitha Srinivasan, Abraham C Stern, Dorota Toczydlowska, Srimukh Prasad Veccham, Niccolò Alberto Elia Venanzi, Anton Vorontsov, Jared Wilber, Isabel Wilkinson, Wei Jing Wong, Eva Xue, Cory Ye, Xin Yu, Yang Zhang, Guoqing Zhou, Becca Zandstein, Christian Dallago, Bruno Trentini, Emine Kucukbenli, Saee Paliwal, Timur Rvachov, Eddie Calleja, Johnny Israeli, Harry Clifford, Risto Haukioja, Nicholas Haemel, Kyle Tretina, Neha Tadimeti, Anthony B Costa
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM)
Total of 18 entries
Showing up to 50 entries per page: fewer | more | all