Learning Neural Generative Dynamics for Molecular Conformation Generation

20 February 2021

Jian Tang

Papers citing "Learning Neural Generative Dynamics for Molecular Conformation Generation"

50 / 73 papers shown

Title
PolyConf: Unlocking Polymer Conformation Generation through Hierarchical Generative Models Fanmeng Wang Wentao Guo Qi Ou Hongshuai Wang Haitao Lin Hongteng Xu Zhifeng Gao AI4CE 30 1 0 11 Apr 2025
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 46 1 0 13 Mar 2025
Conformation Generation using Transformer Flows Sohil Shah V. Koltun MedIm AI4CE 26 0 0 16 Nov 2024
ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation Majdi Hassan Nikhil Shenoy Jungyoon Lee Hannes Stärk Stephan Thaler Dominique Beaini 27 6 0 29 Oct 2024
Equivariant Blurring Diffusion for Hierarchical Molecular Conformer Generation Jiwoong Park Yang Shen DiffM 23 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 30 1 0 14 Oct 2024
REBIND: Enhancing ground-state molecular conformation via force-based graph rewiring Taewon Kim Hyunjin Seo Sungsoo Ahn Eunho Yang AI4CE 32 1 0 04 Oct 2024
Mitigating Exposure Bias in Score-Based Generation of Molecular Conformations Sijia Wang Chen Wang Zhenhao Zhao Jiqiang Zhang Weiran Cai 21 0 0 21 Sep 2024
Geometry Informed Tokenization of Molecules for Language Model Generation Xiner Li Limei Wang Youzhi Luo Carl N. Edwards Shurui Gui Yuchao Lin Heng Ji Shuiwang Ji 29 6 0 19 Aug 2024
SubGDiff: A Subgraph Diffusion Model to Improve Molecular Representation Learning Jiying Zhang Zijing Liu Yu Wang Yu Li DiffM 39 1 0 09 May 2024
On Diffusion Process in SE(3)-invariant Space Zihan Zhou Ruiying Liu Jiachen Zheng Xiaoxue Wang Tianshu Yu DiffM 32 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 32 20 0 01 Mar 2024
Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling Yuwei Yang Siqi Ouyang Xueyu Hu Mingyue Zheng Hao Zhou Lei Li 32 1 0 22 Feb 2024
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation Xiangru Tang Howard Dai Elizabeth Knight Fang Wu Yunyang Li Tianxiao Li Mark B. Gerstein 19 25 0 13 Feb 2024
Weisfeiler Leman for Euclidean Equivariant Machine Learning Snir Hordan Tal Amir Nadav Dym 44 5 0 04 Feb 2024
Diffusion-Driven Generative Framework for Molecular Conformation Prediction Bobin Yang Jie Deng Zhenghan Chen Ruoxue Wu DiffM 29 0 0 22 Dec 2023
SE(3)-Invariant Multiparameter Persistent Homology for Chiral-Sensitive Molecular Property Prediction Andac Demir Francis Prael B. Kiziltan 19 2 0 12 Dec 2023
Swallowing the Bitter Pill: Simplified Scalable Conformer Generation Yuyang Wang Ahmed A. A. Elhag Navdeep Jaitly J. Susskind Miguel Angel Bautista DiffM 27 19 0 27 Nov 2023
Multiparameter Persistent Homology for Molecular Property Prediction Andac Demir B. Kiziltan 22 1 0 17 Nov 2023
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 24 1 0 05 Nov 2023
Towards equilibrium molecular conformation generation with GFlowNets Alexandra Volokhova Michal Koziarski Alex Hernández-García Cheng-Hao Liu Santiago Miret Pablo Lemos Luca Thiede Zichao Yan Alán Aspuru-Guzik Yoshua Bengio 24 9 0 20 Oct 2023
On Accelerating Diffusion-based Molecular Conformation Generation in SE(3)-invariant Space Zihan Zhou Ruiying Liu Tianshu Yu DiffM 30 0 0 07 Oct 2023
Molecular Conformation Generation via Shifting Scores Zihan Zhou Ruiying Liu Chaolong Ying Ruimao Zhang Tianshu Yu DiffM 29 2 0 12 Sep 2023
Leveraging Side Information for Ligand Conformation Generation using Diffusion-Based Approaches Nhat-Khang Ngô Truong Son-Hy Yuan Yao DiffM 30 0 0 02 Aug 2023
Towards Symmetry-Aware Generation of Periodic Materials Youzhi Luo Chengkai Liu Shuiwang Ji DiffM 21 21 0 06 Jul 2023
ChiENN: Embracing Molecular Chirality with Graph Neural Networks Piotr Gaiñski Michał Koziarski Jacek Tabor Marek Śmieja GNN 32 3 0 05 Jul 2023
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation Danny Reidenbach Aditi S. Krishnapriyan 27 7 0 26 Jun 2023
Automated 3D Pre-Training for Molecular Property Prediction Xu Wang Huan Zhao Weiwei Tu Quanming Yao AI4CE 26 35 0 13 Jun 2023
Von Mises Mixture Distributions for Molecular Conformation Generation K. Swanson Jake Williams Eric Jonas 22 6 0 13 Jun 2023
Efficient and Equivariant Graph Networks for Predicting Quantum Hamiltonian Haiyang Yu Zhao Xu X. Qian Xiaoning Qian Shuiwang Ji 28 24 0 08 Jun 2023
Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration Haitao Lin Yufei Huang Haotian Zhang Lirong Wu Siyuan Li Zhiyuan Chen Stan Z. Li DiffM 14 23 0 30 May 2023
Manifold Diffusion Fields Ahmed A. A. Elhag Yuyang Wang J. Susskind Miguel Angel Bautista DiffM AI4CE 36 4 0 24 May 2023
CREMP: Conformer-Rotamer Ensembles of Macrocyclic Peptides for Machine Learning Colin A. Grambow Hayley Weir Christian N Cunningham Tommaso Biancalani Kangway V Chuang 18 4 0 14 May 2023
3D Molecular Geometry Analysis with 2D Graphs Zhao Xu Yaochen Xie Youzhi Luo Xuan Zhang Xinyi Xu Meng Liu Kaleb Dickerson Cheng Deng Maho Nakata Shuiwang Ji 19 1 0 01 May 2023
Neural Diffeomorphic Non-uniform B-spline Flows S. Hong S. Chun 24 1 0 07 Apr 2023
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 24 0 0 05 Apr 2023
A Survey on Graph Diffusion Models: Generative AI in Science for Molecule, Protein and Material Mengchun Zhang Maryam Qamar Taegoo Kang Yuna Jung Chenshuang Zhang Sung-Ho Bae Chaoning Zhang DiffM MedIm 31 44 0 04 Apr 2023
Infinite Physical Monkey: Do Deep Learning Methods Really Perform Better in Conformation Generation? Haotian Zhang Jintu Zhang Huifeng Zhao Dejun Jiang Yafeng Deng 22 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 58 10 0 01 Mar 2023
PrefixMol: Target- and Chemistry-aware Molecule Design via Prefix Embedding Zhangyang Gao Yuqi Hu Cheng Tan Stan Z. Li 26 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 25 15 0 14 Feb 2023
Rigid Body Flows for Sampling Molecular Crystal Structures Jonas Köhler Michele Invernizzi P. D. Haan Frank Noé AI4CE 25 27 0 26 Jan 2023
DiffSDS: A language diffusion model for protein backbone inpainting under geometric conditions and constraints Zhangyang Gao Cheng Tan Stan Z. Li DiffM 21 19 0 22 Jan 2023
DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding Haitao Lin Yufei Huang Odin Zhang Siqi Ma Meng Liu X. Li Lirong Wu Shuiwang Ji Tingjun Hou Stan Z. Li DiffM 16 60 0 21 Nov 2022
NVDiff: Graph Generation through the Diffusion of Node Vectors Xiaohui Chen Yukun Li Aonan Zhang Liping Liu DiffM 15 21 0 19 Nov 2022
Improving Molecular Pretraining with Complementary Featurizations Yanqiao Zhu Dingshuo Chen Yuanqi Du Yingze Wang Qiang Liu Shu Wu AI4CE 31 6 0 29 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 41 20 0 12 Sep 2022
Diffusion-based Molecule Generation with Informative Prior Bridges Lemeng Wu Chengyue Gong Xingchao Liu Mao Ye Qiang Liu DiffM 20 108 0 02 Sep 2022
Thermal half-lives of azobenzene derivatives: virtual screening based on intersystem crossing using a machine learning potential Simon Axelrod E. Shakhnovich Rafael Gómez-Bombarelli 16 20 0 23 Jul 2022
Your Autoregressive Generative Model Can be Better If You Treat It as an Energy-Based One Yezhen Wang Tong Che Bo-wen Li Kaitao Song Hengzhi Pei Yoshua Bengio Dongsheng Li 12 3 0 26 Jun 2022