Biomolecules

Authors and titles for recent submissions

• Tue, 26 Nov 2024
• Mon, 25 Nov 2024
• Fri, 22 Nov 2024
• Thu, 21 Nov 2024
• Wed, 20 Nov 2024

See today's new changes

Tue, 26 Nov 2024 (continued, showing last 2 of 8 entries )

[7] arXiv:2411.15208 (cross-list from cs.LG) [pdf, html, other]

Title: M2oE: Multimodal Collaborative Expert Peptide Model

Zengzhu Guo, Zhiqi Ma

Comments: accepted by bibm 2024

Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Biomolecules (q-bio.BM)

[8] arXiv:2411.15183 (cross-list from physics.chem-ph) [pdf, html, other]

Title: Balancing property optimization and constraint satisfaction for constrained multi-property molecular optimization

Xin Xia, Yajie Zhang, Xiangxiang Zeng, Xingyi Zhang, Chunhou Zheng, Yansen Su

Subjects: Chemical Physics (physics.chem-ph); Artificial Intelligence (cs.AI); Biomolecules (q-bio.BM)

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

[9] 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)

[10] 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)

[11] 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 )

[12] 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)

[13] 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)

[14] 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 )

[15] 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)

[16] 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)

[17] 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)

[18] 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)

[19] 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 )

[20] 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)

[21] 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)

[22] 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)