D3MES: Diffusion Transformer with multihead equivariant self-attention for 3D molecule generation
School of Physics and Electronic Engineering, Jiangsu University（江苏大学物理与电子工程学院）；Jiangsu Engineering Research Center on Quantum Perception and Intelligent Detection of Agricultural Information（江苏省农业信息量子感知与智能检测工程研究中心）
Understanding and predicting the diverse conformational states of molecules is crucial for advancing fields such as chemistry, material science, and drug development. Despite significant progress in generative models, accurately generating complex and biologically or material-relevant molecular structures remains a major challenge. In this work, we introduce a diffusion model for three-dimensional (3D) molecule generation that combines a classifiable diffusion model, Diffusion Transformer, with multihead equivariant self-attention. This method addresses two key challenges: correctly attaching hydrogen atoms in generated molecules through learning representations of molecules after hydrogen atoms are removed; and overcoming the limitations of existing models that cannot generate molecules across multiple classes simultaneously. The experimental results demonstrate that our model not only achieves state-of-the-art performance across several key metrics but also exhibits robustness and versatility, making it highly suitable for early-stage large-scale generation processes in molecular design, followed by validation and further screening to obtain molecules with specific properties.
Equivariant Energy-Guided SDE for Inverse Molecular Design
Tsinghua University（清华大学）；Renmin University of China（中国人民大学）；Huawei（华为）；Tsinghua-Huawei Joint Center for AI（清华-华为联合人工智能中心）；BNRist Center（北京国家信息科学与技术研究中心）；Gaoling School of Artificial Intelligence, Renmin University of China（中国人民大学高瓴人工智能学院）；Beijing Key Laboratory of Big Data Management and Analysis Methods（大数据管理与分析方法北京市重点实验室）
Manipulating 3D Molecules in a Fixed-Dimensional E(3)-Equivariant Latent Space
Institute for AI Industry Research (AIR), Tsinghua University（人工智能产业研究院（AIR），清华大学）；Department of Computer Science and Technology, Tsinghua University（计算机科学与技术系，清华大学）；Qiuzhen College, Tsinghua University（启真学院，清华大学）
Equivariant Flow Matching with Hybrid Probability Transport
Institute of AI Industry Research(AIR), Tsinghua University（清华大学人工智能产业研究院（AIR））；Stanford University（斯坦福大学）；Beijing Academy of Artificial Intelligence（北京智源人工智能研究院）
Equivariant Asynchronous Diffusion: An Adaptive Denoising Schedule for Accelerated Molecular Conformation Generation
Shanghai Academy of Artificial Intelligence for Science, SAIS（上海人工智能科学研究院，SAIS）；College of Chemistry and Chemical Engineering, Xiamen University（厦门大学化学与化工学院）；Artificial Intelligence Innovation and Incubation (AI 3 ) Institute, Fudan University（复旦大学人工智能创新与孵化（AI 3）研究院）
Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks
Institute of AI Industry Research (AIR), Tsinghua University（清华大学人工智能产业研究院）；University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；Shanghai Institute of Materia Medica, Chinese Academy of Sciences（中国科学院上海药物研究所）
UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design
Tsinghua University（清华大学）；Institute for AI Industry Research (AIR), Tsinghua University（清华大学人工智能产业研究院）；Renmin University of China（中国人民大学）；Bytedance（字节跳动）
Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein Binding
Lingang Laboratory（梁岗实验室）；Department of Electronic Engineering, Tsinghua University（清华大学电子工程系）；Institute for AI Industry Research (AIR), Tsinghua University（清华大学人工智能产业研究所）；Institute for Artificial Intelligence, Peking University（北京大学人工智能研究所）；Department of Computer Science and Technology, Tsinghua University（清华大学计算机科学与技术系）；Department of Pharmaceutical and Artificial-Intelligence Sciences, Shanghai Jiao Tong University School of Medicine（上海交通大学医学院药学与人工智能科学系）；Institute of Medical Artificial Intelligence, Shanghai Jiao Tong University（上海交通大学医学人工智能研究所）
An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning
Tsinghua University（清华大学）；Institute for AI Industry Research, Tsinghua University（清华大学人工智能产业研究院）；Renmin University of China（中国人民大学）；University of Pisa（比萨大学）
Molecule Graph Networks with Many-body Equivariant Interactions
Graduate School of Frontier Sciences, The University of Tokyo（东京大学前沿科学研究生院）；School of Physical and Mathematical Sciences, Nanyang Technological University（南洋理工大学物理与数学科学学院）；Center for Basic Research on Materials, National Institute for Materials Science（材料基础研究机构，日本国家材料科学研究所）；RIKEN Center for Advanced Intelligence Project（RIKEN高级智能项目中心）
State Key Laboratory of General Artificial Intelligence, Peking University, Beijing, China（一般人工智能国家重点实验室，北京大学，北京，中国）；Huazhong University of Science and Technology, Wuhan, China（华中科技大学，武汉，中国）；Microsoft Research Asia, Beijing, China（微软亚洲研究院，北京，中国）；Zhongguancun Academy, Beijing, China（中关村学院，北京，中国）
Structure-based Drug Design with Equivariant Diffusion Models
École Polytechnique Fédérale de Lausanne（洛桑联邦理工学院）；University of Cambridge（剑桥大学）；Cornell University（康奈尔大学）；Prescient Design, Genentech（普雷赛特设计公司，基因泰克公司）；Chinese Academy of Mathematics and System Science（中国科学院数学与系统科学研究院）；Heart and Lung Research Institute, University of Cambridge（剑桥大学心肺研究所）；University of Rome “La Sapienza”（罗马大学）；Microsoft Research AI4Science（微软研究院AI4Science）；University of Amsterdam（阿姆斯特丹大学）；University of Oxford（牛津大学）；AITHYRA Institute（艾西拉研究所）
