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Biomolecules

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Total of 18 entries
Showing up to 25 entries per page: fewer | more | all

Fri, 21 Jun 2024 (showing 7 of 7 entries )

[1] arXiv:2406.13839 [pdf, html, other]
Title: RNA-FrameFlow: Flow Matching for de novo 3D RNA Backbone Design
Rishabh Anand, Chaitanya K. Joshi, Alex Morehead, Arian R. Jamasb, Charles Harris, Simon V. Mathis, Kieran Didi, Bryan Hooi, Pietro Liò
Comments: To be presented as an Oral at ICML 2024 Structured Probabilistic Inference & Generative Modeling Workshop, and a Spotlight at ICML 2024 AI4Science Workshop
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG); Genomics (q-bio.GN)
[2] arXiv:2406.14442 (cross-list from cs.LG) [pdf, html, other]
Title: Graph Representation Learning Strategies for Omics Data: A Case Study on Parkinson's Disease
Elisa Gómez de Lope (1), Saurabh Deshpande (1), Ramón Viñas Torné (2), Pietro Liò (3), Enrico Glaab (1 and 4), Stéphane P. A. Bordas (1) ((1) University of Luxembourg, (2) École polytechnique fédérale de Lausanne (EPFL), (3) University of Cambridge, (4) On behalf of the NCER-PD Consortium)
Comments: Submitted to Machine Learning in Computational Biology 2024 as an extended abstract, 2 pages + 1 appendix
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Computational Engineering, Finance, and Science (cs.CE); Biomolecules (q-bio.BM); Molecular Networks (q-bio.MN)
[3] arXiv:2406.14142 (cross-list from q-bio.QM) [pdf, other]
Title: Geometric Self-Supervised Pretraining on 3D Protein Structures using Subgraphs
Michail Chatzianastasis, George Dasoulas, Michalis Vazirgiannis
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Biomolecules (q-bio.BM)
[4] arXiv:2406.13869 (cross-list from cs.LG) [pdf, html, other]
Title: Global Human-guided Counterfactual Explanations for Molecular Properties via Reinforcement Learning
Danqing Wang, Antonis Antoniades, Kha-Dinh Luong, Edwin Zhang, Mert Kosan, Jiachen Li, Ambuj Singh, William Yang Wang, Lei Li
Comments: Accepted by KDD 2024
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM)
[5] arXiv:2406.13864 (cross-list from cs.LG) [pdf, html, other]
Title: Evaluating representation learning on the protein structure universe
Arian R. Jamasb, Alex Morehead, Chaitanya K. Joshi, Zuobai Zhang, Kieran Didi, Simon V. Mathis, Charles Harris, Jian Tang, Jianlin Cheng, Pietro Lio, Tom L. Blundell
Comments: ICLR 2024
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM)
[6] arXiv:2406.12919 (cross-list from cs.LG) [pdf, html, other]
Title: Understanding active learning of molecular docking and its applications
Jeonghyeon Kim, Juno Nam, Seongok Ryu
Subjects: Machine Learning (cs.LG); Chemical Physics (physics.chem-ph); Biomolecules (q-bio.BM)
[7] arXiv:2406.12910 (cross-list from cs.LG) [pdf, other]
Title: Human-level molecular optimization driven by mol-gene evolution
Jiebin Fang (1 and 2), Churu Mao (2), Yuchen Zhu (3), Xiaoming Chen (2), Chang-Yu Hsieh (3), Zhongjun Ma (1 and 2) ((1) Hainan Institute of Zhejiang University, (2) Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, (3) College of Pharmaceutical Sciences and Cancer Center, Zhejiang University)
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Neural and Evolutionary Computing (cs.NE); Chemical Physics (physics.chem-ph); Biomolecules (q-bio.BM)

Wed, 19 Jun 2024

No updates for this time period.

Tue, 18 Jun 2024 (showing 3 of 3 entries )

[8] arXiv:2406.10867 (cross-list from cs.LG) [pdf, html, other]
Title: Geometric-informed GFlowNets for Structure-Based Drug Design
Grayson Lee, Tony Shen, Martin Ester
Comments: Accepted at MoML 2024 as Spotlight
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM)
[9] arXiv:2406.10840 (cross-list from cs.LG) [pdf, html, other]
Title: CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph
Haitao Lin, Guojiang Zhao, Odin Zhang, Yufei Huang, Lirong Wu, Zicheng Liu, Siyuan Li, Cheng Tan, Zhifeng Gao, Stan Z. Li
Comments: 9 pages main context
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Biomolecules (q-bio.BM)
[10] arXiv:2406.10513 (cross-list from cs.LG) [pdf, html, other]
Title: Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Space
Mohamed Amine Ketata, Nicholas Gao, Johanna Sommer, Tom Wollschläger, Stephan Günnemann
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM)

Mon, 17 Jun 2024 (showing 3 of 3 entries )

[11] arXiv:2406.09586 [pdf, html, other]
Title: Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer
Tinglin Huang, Zhenqiao Song, Rex Ying, Wengong Jin
Subjects: Biomolecules (q-bio.BM)
[12] arXiv:2406.09841 (cross-list from cs.LG) [pdf, html, other]
Title: Learning Multi-view Molecular Representations with Structured and Unstructured Knowledge
Yizhen Luo, Kai Yang, Massimo Hong, Xing Yi Liu, Zikun Nie, Hao Zhou, Zaiqing Nie
Comments: 12 pages, 4 figures
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM)
[13] arXiv:2406.09817 (cross-list from physics.chem-ph) [pdf, html, other]
Title: Efficient and Precise Force Field Optimization for Biomolecules Using DPA-2
Junhan Chang, Duo Zhang, Yuqing Deng, Hongrui Lin, Zhirong Liu, Linfeng Zhang, Hang Zheng, Xinyan Wang
Subjects: Chemical Physics (physics.chem-ph); Biomolecules (q-bio.BM)

Fri, 14 Jun 2024 (showing 5 of 5 entries )

[14] arXiv:2406.08980 [pdf, html, other]
Title: From Theory to Therapy: Reframing SBDD Model Evaluation via Practical Metrics
Bowen Gao, Haichuan Tan, Yanwen Huang, Minsi Ren, Xiao Huang, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[15] arXiv:2406.08961 [pdf, html, other]
Title: SIU: A Million-Scale Structural Small Molecule-Protein Interaction Dataset for Unbiased Bioactivity Prediction
Yanwen Huang, Bowen Gao, Yinjun Jia, Hongbo Ma, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[16] arXiv:2406.08886 [pdf, html, other]
Title: Bistability in filamentous actin through monomer-sequestration of an effector species
Panayiotis Foteinopoulos, Bela M. Mulder
Subjects: Biomolecules (q-bio.BM); Biological Physics (physics.bio-ph)
[17] arXiv:2406.09346 (cross-list from cs.LG) [pdf, html, other]
Title: Scoreformer: A Surrogate Model For Large-Scale Prediction of Docking Scores
Álvaro Ciudad, Adrián Morales-Pastor, Laura Malo, Isaac Filella-Mercè, Victor Guallar, Alexis Molina
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Biomolecules (q-bio.BM)
[18] arXiv:2406.08506 (cross-list from physics.chem-ph) [pdf, html, other]
Title: RGFN: Synthesizable Molecular Generation Using GFlowNets
Michał Koziarski, Andrei Rekesh, Dmytro Shevchuk, Almer van der Sloot, Piotr Gaiński, Yoshua Bengio, Cheng-Hao Liu, Mike Tyers, Robert A. Batey
Subjects: Chemical Physics (physics.chem-ph); Machine Learning (cs.LG); Biomolecules (q-bio.BM)
Total of 18 entries
Showing up to 25 entries per page: fewer | more | all