GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation

6 March 2022

Jian Tang

Papers citing "GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation"

50 / 331 papers shown

Title
Distribution Shift Inversion for Out-of-Distribution Prediction Runpeng Yu Songhua Liu Xingyi Yang Xinchao Wang OODD 33 19 0 14 Jun 2023
Hyperbolic Graph Diffusion Model Lingfeng Wen Xuan Tang Mingjie Ouyang Xiangxiang Shen Jian Yang Daxin Zhu Mingsong Chen Xian Wei 53 2 0 13 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 43 22 0 13 Jun 2023
Von Mises Mixture Distributions for Molecular Conformation Generation K. Swanson Jake Williams Eric Jonas 45 6 0 13 Jun 2023
On the Design Fundamentals of Diffusion Models: A Survey Ziyi Chang George Alex Koulieris Hubert P. H. Shum DiffM 34 56 0 07 Jun 2023
Detector Guidance for Multi-Object Text-to-Image Generation Luping Liu Zijian Zhang Yi Ren Rongjie Huang Xiang Yin Zhou Zhao DiffM 44 9 0 04 Jun 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 47 14 0 02 Jun 2023
DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing Yang Zhang Zuobai Zhang Bozitao Zhong Sanchit Misra Jian Tang DiffM 37 34 0 01 Jun 2023
Improving Protein-peptide Interface Predictions in the Low Data Regime Justin S. Diamond M. Lill ViT 35 0 0 31 May 2023
Spontaneous Symmetry Breaking in Generative Diffusion Models G. Raya L. Ambrogioni DiffM 25 30 0 31 May 2023
Unsupervised Statistical Feature-Guided Diffusion Model for Sensor-based Human Activity Recognition Si Zuo Vitor Fortes Rey Sungho Suh S. Sigg P. Lukowicz DiffM 50 4 0 30 May 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 40 24 0 30 May 2023
Implicit Transfer Operator Learning: Multiple Time-Resolution Surrogates for Molecular Dynamics Mathias Jacob Schreiner Ole Winther Simon Olsson OOD AI4CE 77 13 0 29 May 2023
Aligning Optimization Trajectories with Diffusion Models for Constrained Design Generation Giorgio Giannone Akash Srivastava Ole Winther Faez Ahmed DiffM AI4CE 42 28 0 29 May 2023
Alteration-free and Model-agnostic Origin Attribution of Generated Images Zhenting Wang Chen Chen Yi Zeng Lingjuan Lyu Shiqing Ma 37 5 0 29 May 2023
Parallel Sampling of Diffusion Models Andy Shih Suneel Belkhale Stefano Ermon Dorsa Sadigh Nima Anari DiffM 57 52 0 25 May 2023
Manifold Diffusion Fields Ahmed A. A. Elhag Yuyang Wang J. Susskind Miguel Angel Bautista DiffM AI4CE 41 6 0 24 May 2023
Equivariant Neural Simulators for Stochastic Spatiotemporal Dynamics Koen Minartz Y. Poels Simon Koop Vlado Menkovski 35 6 0 23 May 2023
Training Diffusion Models with Reinforcement Learning Kevin Black Michael Janner Yilun Du Ilya Kostrikov Sergey Levine EGVM 51 333 0 22 May 2023
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation Han Huang Leilei Sun Bowen Du Weifeng Lv DiffM 53 16 0 21 May 2023
Efficient Cross-Lingual Transfer for Chinese Stable Diffusion with Images as Pivots Jinyi Hu Xu Han Xiaoyuan Yi Yutong Chen Wenhao Li Zhiyuan Liu Maosong Sun DiffM 33 4 0 19 May 2023
Generation of 3D Molecules in Pockets via Language Model Wei Feng L. Wang Zaiyun Lin Yanhao Zhu Han Wang ... Huting Wang Jielong Zhou Wei Peng Bo Huang Wenbiao Zhou 38 30 0 17 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 42 6 0 14 May 2023
MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation Xingang Peng Jiaqi Guan Qiang Liu Jianzhu Ma DiffM 33 43 0 11 May 2023
A Latent Diffusion Model for Protein Structure Generation Cong Fu Keqiang Yan Limei Wang Wing Yee Au Michael McThrow Tao Komikado Koji Maruhashi Kanji Uchino Xiaoning Qian Shuiwang Ji DiffM 31 31 0 06 May 2023
Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D Yiran Zhou Yuxuan Song Minkai Xu Jingjing Gong B. Gao Hao Zhou Weiying Ma Yanyan Lan DiffM 55 18 0 05 May 2023
MolKD: Distilling Cross-Modal Knowledge in Chemical Reactions for Molecular Property Prediction Liang Zeng Lanqing Li Jian Li 45 3 0 03 May 2023
Geometric Latent Diffusion Models for 3D Molecule Generation Minkai Xu Alexander Powers R. Dror Stefano Ermon J. Leskovec DiffM AI4CE 75 142 0 02 May 2023
MUDiff: Unified Diffusion for Complete Molecule Generation Chenqing Hua Sitao Luan Minkai Xu Rex Ying Jie Fu Stefano Ermon Doina Precup DiffM 66 35 0 28 Apr 2023
Contrastive Energy Prediction for Exact Energy-Guided Diffusion Sampling in Offline Reinforcement Learning Cheng Lu Huayu Chen Jianfei Chen Hang Su Chongxuan Li Jun Zhu DiffM OffRL 40 62 0 25 Apr 2023
Diffusion-based Generative AI for Exploring Transition States from 2D Molecular Graphs Seonghwan Kim Jeheon Woo Woo Youn Kim DiffM 55 25 0 20 Apr 2023
Two-stage Denoising Diffusion Model for Source Localization in Graph Inverse Problems Bosong Huang Weihao Yu Ruzhong Xie Jing Xiao Jin Huang DiffM 36 3 0 18 Apr 2023
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design Zaixin Zhang Qi Liu Cheekong Lee Chang-Yu Hsieh Enhong Chen 35 18 0 12 Apr 2023
Reflected Diffusion Models Aaron Lou Stefano Ermon 38 53 0 10 Apr 2023
Harnessing the Spatial-Temporal Attention of Diffusion Models for High-Fidelity Text-to-Image Synthesis Qiucheng Wu Yujian Liu Handong Zhao T. Bui Zhe Lin Yang Zhang Shiyu Chang DiffM 47 46 0 07 Apr 2023
ChiroDiff: Modelling chirographic data with Diffusion Models Ayan Das Yongxin Yang Timothy M. Hospedales Tao Xiang Yi-Zhe Song DiffM 52 10 0 07 Apr 2023
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 125 0 0 05 Apr 2023
EigenFold: Generative Protein Structure Prediction with Diffusion Models Bowen Jing Ezra Erives Peter Pao-Huang Gabriele Corso Bonnie Berger Tommi Jaakkola DiffM 41 69 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 48 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 47 6 0 28 Mar 2023
DiffTAD: Temporal Action Detection with Proposal Denoising Diffusion Sauradip Nag Xiatian Zhu Jiankang Deng Yi-Zhe Song Tao Xiang DiffM VGen 52 21 0 27 Mar 2023
EDGI: Equivariant Diffusion for Planning with Embodied Agents Johann Brehmer Joey Bose P. D. Haan Taco S. Cohen DiffM 40 34 0 22 Mar 2023
Affordance Diffusion: Synthesizing Hand-Object Interactions Yufei Ye Xueting Li Abhi Gupta Shalini De Mello Stan Birchfield Jiaming Song Shubham Tulsiani Sifei Liu DiffM 52 76 0 21 Mar 2023
Efficient Diffusion Training via Min-SNR Weighting Strategy Tiankai Hang Shuyang Gu Chen Li Jianmin Bao Dong Chen Han Hu Xin Geng B. Guo 33 152 0 16 Mar 2023
Automatic Geo-alignment of Artwork in Children's Story Books Jakub J Dylag V. Suarez James Wald Aneesha Amodini Uvara DiffM 51 0 0 16 Mar 2023
Infinite Physical Monkey: Do Deep Learning Methods Really Perform Better in Conformation Generation? Haotian Zhang Jintu Zhang Huifeng Zhao Dejun Jiang Yafeng Deng 27 1 0 08 Mar 2023
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction Jiaqi Guan Wesley Wei Qian Xingang Peng Yufeng Su Jian-wei Peng Jianzhu Ma DiffM 39 166 0 06 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 76 11 0 01 Mar 2023
GNNDelete: A General Strategy for Unlearning in Graph Neural Networks Jiali Cheng George Dasoulas Huan He Chirag Agarwal Marinka Zitnik MU 60 37 0 26 Feb 2023
Aligned Diffusion Schrödinger Bridges Vignesh Ram Somnath Matteo Pariset Ya-Ping Hsieh María Rodríguez Martínez Andreas Krause Charlotte Bunne DiffM 123 34 0 22 Feb 2023