Title
Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling Shuqi Lu Xiaohong Ji Bohang Zhang Lin Yao Siyuan Liu Zhifeng Gao Linfeng Zhang Guolin Ke AI4CE 38 1 0 13 Mar 2025
UniGenX: Unified Generation of Sequence and Structure with Autoregressive Diffusion Gongbo Zhang Y. Li Renqian Luo Pipi Hu Zeru Zhao ... Maik Riechert Li-ming Yuan Lei Chen Haiguang Liu Tao Qin DiffM 36 0 0 09 Mar 2025
Equivariant Blurring Diffusion for Hierarchical Molecular Conformer Generation Jiwoong Park Yang Shen DiffM 20 0 0 26 Oct 2024
Physical Consistency Bridges Heterogeneous Data in Molecular Multi-Task Learning Yuxuan Ren Dihan Zheng Chang-Shu Liu Peiran Jin Yu Shi Lin Huang Jiyan He Shengjie Luo Tao Qin Tie-Yan Liu AI4CE 22 1 0 14 Oct 2024
FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation Kaiyuan Gao Qizhi Pei Jinhua Zhu Kun He Lijun Wu Lijun Wu 14 6 0 29 Mar 2024
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation Odin Zhang Yufei Huang Shichen Cheng Mengyao Yu Xujun Zhang ... Yu Kang Sunliang Cui P. Pan Chang-Yu Hsieh Tingjun Hou 21 4 0 15 Mar 2024
On Diffusion Process in SE(3)-invariant Space Zihan Zhou Ruiying Liu Jiachen Zheng Xiaoxue Wang Tianshu Yu DiffM 20 1 0 03 Mar 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 29 20 0 01 Mar 2024
Weisfeiler Leman for Euclidean Equivariant Machine Learning Snir Hordan Tal Amir Nadav Dym 44 5 0 04 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 15 0 0 28 Jan 2024
Gradual Optimization Learning for Conformational Energy Minimization Artem Tsypin L. Ugadiarov Kuzma Khrabrov Alexander Telepov Egor Rumiantsev Alexey Skrynnik Aleksandr I. Panov Dmitry Vetrov E. Tutubalina Artur Kadurin 11 1 0 05 Nov 2023
On Accelerating Diffusion-based Molecular Conformation Generation in SE(3)-invariant Space Zihan Zhou Ruiying Liu Tianshu Yu DiffM 25 0 0 07 Oct 2023
Molecular Conformation Generation via Shifting Scores Zihan Zhou Ruiying Liu Chaolong Ying Ruimao Zhang Tianshu Yu DiffM 24 2 0 12 Sep 2023
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation Danny Reidenbach Aditi S. Krishnapriyan 12 7 0 26 Jun 2023
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining Shengchao Liu Weitao Du Zhiming Ma Hongyu Guo Jian Tang 22 29 0 28 May 2023
Infinite Physical Monkey: Do Deep Learning Methods Really Perform Better in Conformation Generation? Haotian Zhang Jintu Zhang Huifeng Zhao Dejun Jiang Yafeng Deng 9 1 0 08 Mar 2023
Deep Learning Methods for Small Molecule Drug Discovery: A Survey Wenhao Hu Yingying Liu Xuanyu Chen Wenhao Chai Hangyue Chen Hongwei Wang Gaoang Wang 44 10 0 01 Mar 2023
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow Fangce Sun Zhihao Zhan Hongyu Guo Ming Zhang Jian Tang 11 6 0 23 Feb 2023
PrefixMol: Target- and Chemistry-aware Molecule Design via Prefix Embedding Zhangyang Gao Yuqi Hu Cheng Tan Stan Z. Li 13 13 0 14 Feb 2023
Do Deep Learning Methods Really Perform Better in Molecular Conformation Generation? G. Zhou Zhifeng Gao Zhewei Wei Hang Zheng Guolin Ke OOD AI4CE BDL 15 15 0 14 Feb 2023
DiffSDS: A language diffusion model for protein backbone inpainting under geometric conditions and constraints Zhangyang Gao Cheng Tan Stan Z. Li DiffM 11 19 0 22 Jan 2023
Protein Sequence and Structure Co-Design with Equivariant Translation Chence Shi Chuanrui Wang Jiarui Lu Bozitao Zhong Jian Tang DiffM 4 47 0 17 Oct 2022
Unified 2D and 3D Pre-Training of Molecular Representations Jinhua Zhu Yingce Xia Lijun Wu Shufang Xie Tao Qin Wen-gang Zhou Houqiang Li Tie-Yan Liu AI4CE 49 67 0 14 Jul 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 19 75 0 28 Mar 2022
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 63 176 0 20 Mar 2022
GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation Minkai Xu Lantao Yu Yang Song Chence Shi Stefano Ermon Jian Tang BDL DiffM 6 491 0 06 Mar 2022
Auto-Encoding Molecular Conformations R. Winter Frank Noé Djork-Arné Clevert AI4CE 28 12 0 05 Jan 2021