TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery
Mila - Quebec AI Institute（米拉-魁北克人工智能研究所）；University of Montreal（蒙特利尔大学）；Peking University（北京大学）；Shanghai Jiao Tong University（上海交通大学）；Tsinghua University（清华大学）
Machine learning has huge potential to revolutionize the field of drug discovery and is attracting increasing attention in recent years. However, lacking domain knowledge (e.g., which tasks to work on), standard benchmarks and data preprocessing pipelines are the main obstacles for machine learning researchers to work in this domain. To facilitate the progress of machine learning for drug discovery, we develop TorchDrug, a powerful and flexible machine learning platform for drug discovery built on top of PyTorch. TorchDrug benchmarks a variety of important tasks in drug discovery, including molecular property prediction, pretrained molecular representations, de novo molecular design and optimization, retrosynthsis prediction, and biomedical knowledge graph reasoning. State-of-the-art techniques based on geometric deep learning (or graph machine learning), deep generative models, reinforcement learning and knowledge graph reasoning are implemented for these tasks. TorchDrug features a hierarchical interface that facilitates customization from both novices and experts in this domain. Tutorials, benchmark results and documentation are available at https://torchdrug.ai. Code is released under Apache License 2.0.
DrugReason: Dynamic Multi-View Reasoning over Knowledge Graph and Language Evidence for Drug Repurposing
University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）；Stevens Institute of Technology（史蒂文斯理工学院）；Emory University（埃默里大学）；Massachusetts Institute of Technology（麻省理工学院）
Large Language Model Agent for Modular Task Execution in Drug Discovery
Department of Chemical Engineering, Carnegie Mellon University（化学工程系，卡内基梅隆大学）；Department of Material Science and Engineering, Carnegie Mellon University（材料科学与工程系，卡内基梅隆大学）；Department of Mechanical Engineering, Carnegie Mellon University（机械工程系，卡内基梅隆大学）
Hong Kong Baptist University（香港浸会大学）；Shanghai AI Laboratory（上海人工智能实验室）；Huazhong University of Science and Technology（华中科技大学）；Shanghai Jiao Tong University（上海交通大学）；Microsoft Research AI4Science（微软研究院AI科学部）
Pharmacophore-Conditioned Diffusion Model for Ligand-Based De Novo Drug Design
Department of Chemistry Carnegie Mellon University（化学系卡内基梅隆大学）；Department of Machine Learning Carnegie Mellon University（机器学习系卡内基梅隆大学）；Departments of Chemistry and Biomedical Engineering Carnegie Mellon University（化学与生物医学工程系卡内基梅隆大学）
URSA: Chemistry-Aware Benchmark for Utilitarian Retrosynthesis Assessment
Insilico Medicine AI Limited（Insilico Medicine AI有限公司）；Independent researcher（独立研究者）；Insilico Medicine Canada Inc.（Insilico Medicine加拿大公司）；Insilico Medicine Hong Kong Ltd.（Insilico Medicine香港有限公司）
FlexiFlow: decomposable flow matching for generation of flexible molecular ensemble
Molecular AI, Discovery Sciences, R&D AstraZeneca（分子人工智能、发现科学、研发阿斯图瑞卡制药）；Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg（计算机科学与工程、查尔姆斯理工大学和哥德堡大学）；KTH Royal Institute of Technology（皇家理工学院）；Science for Life Laboratory（生命科学实验室）；Stockholm University（斯德哥尔摩大学）
FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning
University of Southern California（南加利福尼亚大学）；National University of Singapore（新加坡国立大学）；University of Science and Technology of China（中国科学技术大学）；Westlake University（西湖大学）；Hunan University（湖南大学）
Unified Molecule Pre-training with Flexible 2D and 3D Modalities: Single and Paired Modality Integration
Computational Bioscience Research Center, King Abdullah University of Science and Technology（国王阿卜杜勒·阿齐兹科技大学计算生物科学研究中心）；Institute for Infocomm Research, A*STAR（信息与通信研究机构，A*STAR）；School of Computing and Information Systems, Singapore Management University（新加坡管理大学计算机与信息系统学院）
Human-level molecular optimization driven by mol-gene evolution
Hainan Institute of Zhejiang University（浙江大学海南研究院）；Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University（浙江大学海洋学院海洋生物与药理研究所）；College of Pharmaceutical Sciences and Cancer Center, Zhejiang University（浙江大学药学院与癌症中心）
Sculpting Molecules in Text-3D Space: A Flexible Substructure Aware Framework for Text-Oriented Molecular Optimization
Institute of Information Engineering, Chinese Academy of Sciences（中国科学院信息工程研究所）；Huawei Technologies（华为技术有限公司）；The University of Hong Kong（香港大学）；Harbin Institute of Technology（哈尔滨工业大学）；Academy of Mathematics and Systems Science, Chinese Academy of Sciences（中国科学院数学与系统科学研究院）
