Learning Gradient Fields for Molecular Conformation Generation

9 May 2021

Jian Tang

Papers citing "Learning Gradient Fields for Molecular Conformation Generation"

50 / 135 papers shown

Title
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
Generative Design of inorganic compounds using deep diffusion language models Rongzhi Dong Nihang Fu dirisuriya M. D. Siriwardane Jianjun Hu DiffM 25 1 0 30 Sep 2023
Beta Diffusion Mingyuan Zhou Tianqi Chen Zhendong Wang Huangjie Zheng DiffM 16 10 0 14 Sep 2023
Molecular Conformation Generation via Shifting Scores Zihan Zhou Ruiying Liu Chaolong Ying Ruimao Zhang Tianshu Yu DiffM 29 2 0 12 Sep 2023
Score-PA: Score-based 3D Part Assembly Junfeng Cheng Mingdong Wu Ruiyuan Zhang Guanqi Zhan Chao Wu Hao Dong 26 8 0 08 Sep 2023
May the Force be with You: Unified Force-Centric Pre-Training for 3D Molecular Conformations Rui Feng Qi Zhu Huan Tran Binghong Chen Aubrey Toland R. Ramprasad Chao Zhang AI4CE 14 9 0 24 Aug 2023
Diffusion probabilistic models enhance variational autoencoder for crystal structure generative modeling T. Pakornchote Natthaphon Choomphon-anomakhun Sorrjit Arrerut C. Atthapak S. Khamkaeo Thiparat Chotibut T. Bovornratanaraks DiffM 24 17 0 04 Aug 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
Crystal Structure Prediction by Joint Equivariant Diffusion Rui Jiao Wen-bing Huang Peijia Lin Jiaqi Han Pin Chen Yutong Lu Yang Liu DiffM 19 59 0 30 Jul 2023
Generalizing Graph ODE for Learning Complex System Dynamics across Environments Zijie Huang Yizhou Sun Wei Wang CML OOD AI4CE 27 24 0 10 Jul 2023
Towards Symmetry-Aware Generation of Periodic Materials Youzhi Luo Chengkai Liu Shuiwang Ji DiffM 21 21 0 06 Jul 2023
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation Danny Reidenbach Aditi S. Krishnapriyan 27 7 0 26 Jun 2023
3D molecule generation by denoising voxel grids Pedro H. O. Pinheiro Joshua Rackers J. Kleinhenz Michael R. Maser Omar Mahmood Andrew Watkins Stephen Ra Vishnu Sresht Saeed Saremi DiffM 34 20 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
Implicit Transfer Operator Learning: Multiple Time-Resolution Surrogates for Molecular Dynamics M. Schreiner Ole Winther Simon Olsson OOD AI4CE 38 13 0 29 May 2023
Learning to Jump: Thinning and Thickening Latent Counts for Generative Modeling Tianqi Chen Mingyuan Zhou DiffM 52 7 0 28 May 2023
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining Shengchao Liu Weitao Du Zhiming Ma Hongyu Guo Jian Tang 22 30 0 28 May 2023
The probability flow ODE is provably fast Sitan Chen Sinho Chewi Holden Lee Yuanzhi Li Jianfeng Lu Adil Salim DiffM 33 84 0 19 May 2023
PTQD: Accurate Post-Training Quantization for Diffusion Models Yefei He Luping Liu Jing Liu Weijia Wu Hong Zhou Bohan Zhuang DiffM MQ 22 100 0 18 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
Diffusion-based Generative AI for Exploring Transition States from 2D Molecular Graphs Seonghwan Kim Jeheon Woo Woo Youn Kim DiffM 30 25 0 20 Apr 2023
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design Zaixin Zhang Qi Liu Cheekong Lee Chang-Yu Hsieh Enhong Chen 15 18 0 12 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
GeoTMI:Predicting quantum chemical property with easy-to-obtain geometry via positional denoising Hyeonsu Kim Jeheon Woo Seonghwan Kim Seokhyun Moon Jun Hyeong Kim Woo Youn Kim AI4CE 24 6 0 28 Mar 2023
A Complete Survey on Generative AI (AIGC): Is ChatGPT from GPT-4 to GPT-5 All You Need? Chaoning Zhang Chenshuang Zhang Sheng Zheng Yu Qiao Chenghao Li ... Lik-Hang Lee Yang Yang Heng Tao Shen In So Kweon Choong Seon Hong 75 159 0 21 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
PFGM++: Unlocking the Potential of Physics-Inspired Generative Models Yilun Xu Ziming Liu Yonglong Tian Shangyuan Tong Max Tegmark Tommi Jaakkola AI4CE DiffM 14 65 0 08 Feb 2023
Generative Diffusion Models on Graphs: Methods and Applications C. Liu Wenqi Fan Yunqing Liu Jiatong Li Hang Li Hui Liu Jiliang Tang Qing Li MedIm DiffM 26 57 0 06 Feb 2023
Stable Target Field for Reduced Variance Score Estimation in Diffusion Models Yilun Xu Shangyuan Tong Tommi Jaakkola DiffM 15 26 0 01 Feb 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
GFPose: Learning 3D Human Pose Prior with Gradient Fields Hai Ci Min-Yu Wu Wenjie Zhu Xiaoxuan Ma Hao Dong Fangwei Zhong Yizhou Wang 3DH 13 61 0 16 Dec 2022
Latent Space Diffusion Models of Cryo-EM Structures Karsten Kreis Tim Dockhorn Zihao Li Ellen D. Zhong DiffM 27 15 0 25 Nov 2022
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
Improved Analysis of Score-based Generative Modeling: User-Friendly Bounds under Minimal Smoothness Assumptions Hongrui Chen Holden Lee Jianfeng Lu DiffM 13 124 0 03 Nov 2022
Protein Sequence and Structure Co-Design with Equivariant Translation Chence Shi Chuanrui Wang Jiarui Lu Bozitao Zhong Jian Tang DiffM 17 47 0 17 Oct 2022
GENIE: Higher-Order Denoising Diffusion Solvers Tim Dockhorn Arash Vahdat Karsten Kreis DiffM 41 104 0 11 Oct 2022
Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design Ilia Igashov Hannes Stärk Clément Vignac Victor Garcia Satorras P. Frossard Max Welling Michael M. Bronstein B. Correia DiffM 32 84 0 11 Oct 2022
Learned Force Fields Are Ready For Ground State Catalyst Discovery Michael Schaarschmidt M. Rivière A. Ganose J. Spencer Alex Gaunt J. Kirkpatrick Simon Axelrod Peter W. Battaglia Jonathan Godwin 8 10 0 26 Sep 2022
MDM: Molecular Diffusion Model for 3D Molecule Generation Lei Huang Hengtong Zhang Tingyang Xu Ka-Chun Wong DiffM 18 81 0 13 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 41 20 0 12 Sep 2022
A Survey on Generative Diffusion Model Hanqun Cao Cheng Tan Zhangyang Gao Yilun Xu Guangyong Chen Pheng-Ann Heng Stan Z. Li MedIm 37 206 0 06 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
TarGF: Learning Target Gradient Field to Rearrange Objects without Explicit Goal Specification Min-Yu Wu Fangwei Zhong Yulong Xia Hao Dong OOD 28 17 0 02 Sep 2022
Diffusion Models: A Comprehensive Survey of Methods and Applications Ling Yang Zhilong Zhang Yingxia Shao Shenda Hong Runsheng Xu Yue Zhao Wentao Zhang Bin Cui Ming-Hsuan Yang DiffM MedIm 224 1,300 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
Energy-Motivated Equivariant Pretraining for 3D Molecular Graphs Rui Jiao Jiaqi Han Wenbing Huang Yu Rong Yang Liu AI4CE 28 45 0 18 Jul 2022