Learning Gradient Fields for Molecular Conformation Generation

9 May 2021

Jian Tang

Papers citing "Learning Gradient Fields for Molecular Conformation Generation"

35 / 135 papers shown

Title
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 54 67 0 14 Jul 2022
Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching Shengchao Liu Hongyu Guo Jian Tang 18 77 0 27 Jun 2022
Stochastic Optimal Control for Collective Variable Free Sampling of Molecular Transition Paths Lars Holdijk Yuanqi Du F. Hooft P. Jaini B. Ensing Max Welling 6 23 0 27 Jun 2022
Data Augmentation vs. Equivariant Networks: A Theory of Generalization on Dynamics Forecasting Rui Wang Robin G. Walters Rose Yu 22 13 0 19 Jun 2022
A Flexible Diffusion Model Weitao Du Tao Yang Heidi Zhang Yuanqi Du DiffM 25 11 0 17 Jun 2022
Long Range Graph Benchmark Vijay Prakash Dwivedi Ladislav Rampášek Mikhail Galkin Alipanah Parviz Guy Wolf A. Luu Dominique Beaini 26 193 0 16 Jun 2022
Exploring Chemical Space with Score-based Out-of-distribution Generation Seul Lee Jaehyeong Jo S. Hwang OODD 28 75 0 06 Jun 2022
Torsional Diffusion for Molecular Conformer Generation Bowen Jing Gabriele Corso Jeffrey Chang Regina Barzilay Tommi Jaakkola DiffM BDL 22 259 0 01 Jun 2022
Pre-training via Denoising for Molecular Property Prediction Sheheryar Zaidi Michael Schaarschmidt James Martens Hyunjik Kim Yee Whye Teh Alvaro Sanchez-Gonzalez Peter W. Battaglia Razvan Pascanu Jonathan Godwin DiffM AI4CE 15 121 0 31 May 2022
3D Graph Contrastive Learning for Molecular Property Prediction Kisung Moon Sunyoung Kwon 13 17 0 31 May 2022
Simulate Time-integrated Coarse-grained Molecular Dynamics with Multi-Scale Graph Networks Xiang Fu T. Xie Nathan J. Rebello B. Olsen Tommi Jaakkola AI4CE 12 13 0 21 Apr 2022
Generating 3D Molecules for Target Protein Binding Meng Liu Youzhi Luo Kanji Uchino Koji Maruhashi Shuiwang Ji 11 112 0 19 Apr 2022
DiffMD: A Geometric Diffusion Model for Molecular Dynamics Simulations Fang Wu Stan Z. Li DiffM 19 31 0 19 Apr 2022
Equivariant Diffusion for Molecule Generation in 3D Emiel Hoogeboom Victor Garcia Satorras Clément Vignac Max Welling DiffM 26 570 0 31 Mar 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 23 86 0 28 Mar 2022
Equivariant Graph Mechanics Networks with Constraints Wen-bing Huang J. Han Yu Rong Tingyang Xu Fuchun Sun Junzhou Huang AI4CE 25 78 0 12 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 14 494 0 06 Mar 2022
Learning Neural Set Functions Under the Optimal Subset Oracle Zijing Ou Tingyang Xu Qinliang Su Yingzhen Li P. Zhao Yatao Bian BDL 16 9 0 03 Mar 2022
How to Fill the Optimum Set? Population Gradient Descent with Harmless Diversity Chengyue Gong Lemeng Wu Qiang Liu 22 3 0 16 Feb 2022
TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery Zhaocheng Zhu Chence Shi Zuobai Zhang Shengchao Liu Minghao Xu ... Chang Ma Runcheng Liu Louis-Pascal Xhonneux Meng Qu Jian Tang OOD VLM MedIm 14 70 0 16 Feb 2022
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Hannes Stärk O. Ganea L. Pattanaik Regina Barzilay Tommi Jaakkola 8 260 0 07 Feb 2022
Direct Molecular Conformation Generation Jinhua Zhu Yingce Xia Chang-Shu Liu Lijun Wu Shufang Xie ... Tao Qin Wen-gang Zhou Houqiang Li Haiguang Liu Tie-Yan Liu 24 41 0 03 Feb 2022
Generative Coarse-Graining of Molecular Conformations Wujie Wang Minkai Xu Chen Cai Benjamin Kurt Miller Tess E. Smidt Yusu Wang Jian Tang Rafael Gómez-Bombarelli 16 34 0 28 Jan 2022
Deep Molecular Representation Learning via Fusing Physical and Chemical Information Shuwen Yang Ziyao Li Guojie Song Lingsheng Cai AI4CE 21 28 0 28 Nov 2021
Towards Conditional Generation of Minimal Action Potential Pathways for Molecular Dynamics J. Cava J. Vant Nicholas Ho Ankita Shulka P. Turaga Ross Maciejewski A. Singharoy AI4CE 18 2 0 28 Nov 2021
SE(3) Equivariant Graph Neural Networks with Complete Local Frames Weitao Du He Zhang Yuanqi Du Qi Meng Wei-Neng Chen Bin Shao Tie-Yan Liu 48 79 0 26 Oct 2021
Crystal Diffusion Variational Autoencoder for Periodic Material Generation Tian Xie Xiang Fu O. Ganea Regina Barzilay Tommi Jaakkola DiffM BDL 204 227 0 12 Oct 2021
Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design Wengong Jin Jeremy Wohlwend Regina Barzilay Tommi Jaakkola 6 136 0 09 Oct 2021
3D Infomax improves GNNs for Molecular Property Prediction Hannes Stärk Dominique Beaini Gabriele Corso Prudencio Tossou Christian Dallago Stephan Günnemann Pietro Lió AI4CE 25 203 0 08 Oct 2021
Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs Zhao Xu Youzhi Luo Xuan Zhang Xinyi Xu Yaochen Xie Meng Liu Kaleb Dickerson Cheng Deng Maho Nakata Shuiwang Ji 33 39 0 30 Sep 2021
Physics-Guided Deep Learning for Dynamical Systems: A Survey Rui Wang Rose Yu AI4CE PINN 28 64 0 02 Jul 2021
EBM-Fold: Fully-Differentiable Protein Folding Powered by Energy-based Models Jiaxiang Wu Shitong Luo Tao Shen Haidong Lan Sheng Wang Junzhou Huang DiffM 19 8 0 11 May 2021
Autoregressive Score Matching Chenlin Meng Lantao Yu Yang Song Jiaming Song Stefano Ermon DiffM 180 12 0 24 Oct 2020
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 189 885 0 07 Jun 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 219 1,332 0 12 Feb 2018