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Equivariant Diffusion for Molecule Generation in 3D

31 March 2022

Emiel Hoogeboom

Victor Garcia Satorras

Papers citing "Equivariant Diffusion for Molecule Generation in 3D"

50 / 404 papers shown

Title
Full-Atom Peptide Design based on Multi-modal Flow Matching Jiahan Li Chaoran Cheng Zuofan Wu Ruihan Guo Shitong Luo Zhizhou Ren Jian-wei Peng Jianzhu Ma 115 18 0 02 Jun 2024
Neural Polarization: Toward Electron Density for Molecules by Extending Equivariant Networks Bumju Kwak Jeonghee Jo 87 0 0 01 Jun 2024
Diffusion On Syntax Trees For Program Synthesis Shreyas Kapur Erik Jenner Stuart J. Russell DiffM 100 5 0 30 May 2024
A Recipe for Charge Density Prediction Xiang Fu Andrew S. Rosen Kyle Bystrom Rui Wang Albert Musaelian Boris Kozinsky Tess E. Smidt Tommi Jaakkola 89 6 0 29 May 2024
Equivariant Denoisers Cannot Copy Graphs: Align Your Graph Diffusion Models Najwa Laabid Severi Rissanen Markus Heinonen Arno Solin Vikas Garg DiffM 87 1 0 27 May 2024
Reflected Flow Matching Tianyu Xie Yu Zhu Longlin Yu Tong Yang Ziheng Cheng Shiyue Zhang Xiangyu Zhang Cheng Zhang 84 6 0 26 May 2024
Nonlinear denoising score matching for enhanced learning of structured distributions Jeremiah Birrell Markos A. Katsoulakis Luc Rey-Bellet Benjamin J. Zhang Wei-wei Zhu DiffM 58 1 0 24 May 2024
Learning to Discretize Denoising Diffusion ODEs Vinh Tong Hoang Trung-Dung Anji Liu Guy Van den Broeck Mathias Niepert DiffM 136 6 0 24 May 2024
Lorentz-Equivariant Geometric Algebra Transformers for High-Energy Physics Jonas Spinner Victor Bresó P. D. Haan Tilman Plehn Jesse Thaler Johann Brehmer AI4CE 96 19 0 23 May 2024
Fisher Flow Matching for Generative Modeling over Discrete Data Oscar Davis Samuel Kessler Mircea Petrache .Ismail .Ilkan Ceylan Michael M. Bronstein A. Bose 103 21 0 23 May 2024
Regressor-free Molecule Generation to Support Drug Response Prediction Kun Li Xiuwen Gong Shirui Pan Hongzhi Zhang Bo Du Wenbin Hu 68 1 0 23 May 2024
Multi-Type Point Cloud Autoencoder: A Complete Equivariant Embedding for Molecule Conformation and Pose Michael Kilgour Mark Tuckerman Jutta Rogal 112 0 0 22 May 2024
Discrete-state Continuous-time Diffusion for Graph Generation Zhe Xu Ruizhong Qiu Yuzhong Chen Huiyuan Chen Xiran Fan Menghai Pan Zhichen Zeng Mahashweta Das Hanghang Tong 122 23 0 19 May 2024
Response Matching for generating materials and molecules Bingqing Cheng DiffM 58 1 0 15 May 2024
SubGDiff: A Subgraph Diffusion Model to Improve Molecular Representation Learning Jiying Zhang Zijing Liu Yu Wang Yu-Feng Li DiffM 80 1 0 09 May 2024
A Review on Fragment-based De Novo 2D Molecule Generation Sergei Voloboev VLM 63 2 0 08 May 2024
AdsorbDiff: Adsorbate Placement via Conditional Denoising Diffusion Adeesh Kolluru John R. Kitchin DiffM 83 5 0 07 May 2024
Structure-based drug design by denoising voxel grids Pedro H. O. Pinheiro Arian R. Jamasb Omar Mahmood Vishnu Sresht Saeed Saremi DiffM 54 9 0 07 May 2024
Synthetic Data from Diffusion Models Improve Drug Discovery Prediction Bing Hu Ashish Saragadam Anita Layton Helen Chen DiffM 59 1 0 06 May 2024
Data-Efficient Molecular Generation with Hierarchical Textual Inversion Seojin Kim Jaehyun Nam Sihyun Yu Younghoon Shin Jinwoo Shin 110 3 0 05 May 2024
CogDPM: Diffusion Probabilistic Models via Cognitive Predictive Coding Kaiyuan Chen Xingzhuo Guo Yu Zhang Jianmin Wang Mingsheng Long DiffM 56 1 0 03 May 2024
SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints M. Cretu Charles Harris Julien Roy Emmanuel Bengio Pietro Lio Bruno Correia Julien Roy Emmanuel Bengio Pietro Liò 91 5 0 02 May 2024
Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation Ian Dunn D. Koes BDL DiffM 95 15 0 30 Apr 2024
ControlMol: Adding Substruture Control To Molecule Diffusion Models Zhengyang Qi Zijing Liu Jiying Zhang He Cao Yu-Feng Li 73 2 0 22 Apr 2024
MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space Yanru Qu Keyue Qiu Yuxuan Song Jingjing Gong Jiawei Han Mingyue Zheng Hao Zhou Wei-Ying Ma 109 20 0 18 Apr 2024
Molecular relaxation by reverse diffusion with time step prediction Khaled Kahouli Stefaan S. P. Hessmann Klaus-Robert Muller Shinichi Nakajima Stefan Gugler Niklas W. A. Gebauer DiffM 72 6 0 16 Apr 2024
Diffusion Models Meet Remote Sensing: Principles, Methods, and Perspectives Yidan Liu Jun Yue Shaobo Xia Pedram Ghamisi Weiying Xie Leyuan Fang DiffM 97 17 0 13 Apr 2024
Quantum State Generation with Structure-Preserving Diffusion Model Yuchen Zhu Tianrong Chen Evangelos A. Theodorou Xie Chen Molei Tao DiffM 84 8 0 09 Apr 2024
AUTODIFF: Autoregressive Diffusion Modeling for Structure-based Drug Design Xinze Li Penglei Wang Tianfan Fu Wenhao Gao Chengtao Li Leilei Shi Junhong Liu 104 3 0 02 Apr 2024
Jailbreaking Prompt Attack: A Controllable Adversarial Attack against Diffusion Models Jiachen Ma Anda Cao Zhiqing Xiao Jie Zhang Chaonan Ye Chao Ye Junbo Zhao 135 33 0 02 Apr 2024
Diffusion-Driven Domain Adaptation for Generating 3D Molecules Haokai Hong Wanyu Lin Kay Chen Tan DiffM 74 2 0 01 Apr 2024
Manifold-Guided Lyapunov Control with Diffusion Models Amartya Mukherjee Thanin Quartz Jun Liu 88 0 0 26 Mar 2024
Diffusion-based Negative Sampling on Graphs for Link Prediction Trung-Kien Nguyen Yuan Fang DiffM 76 11 0 25 Mar 2024
Physics-Informed Diffusion Models Jan-Hendrik Bastek WaiChing Sun D. Kochmann DiffM AI4CE 190 20 0 21 Mar 2024
A Practical Guide to Statistical Distances for Evaluating Generative Models in Science Sebastian Bischoff Alana Darcher Michael Deistler Richard Gao Franziska Gerken ... Auguste Schulz Zinovia Stefanidi Shoji Toyota Linda Ulmer Julius Vetter SyDa 52 14 0 19 Mar 2024
Understanding and Improving Training-free Loss-based Diffusion Guidance Yifei Shen Xinyang Jiang Yezhen Wang Yifan Yang Dongqi Han Dongsheng Li FaML 86 14 0 19 Mar 2024
Diffusion-Based Environment-Aware Trajectory Prediction Theodor Westny Björn Olofsson Erik Frisk 87 12 0 18 Mar 2024
Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks Yuxuan Song Jingjing Gong Yanru Qu Hao Zhou Mingyue Zheng Jingjing Liu Wei-Ying Ma 89 13 0 17 Mar 2024
Multi-conditioned Graph Diffusion for Neural Architecture Search Rohan Asthana Joschua Conrad Youssef Dawoud M. Ortmanns Vasileios Belagiannis GNN AI4CE 70 6 0 09 Mar 2024
Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion Bowen Gao Minsi Ren Yuyan Ni Yanwen Huang Yiran Zhou Zhiming Ma Wei-Ying Ma Yanyan Lan 73 6 0 04 Mar 2024
Neural Graph Generator: Feature-Conditioned Graph Generation using Latent Diffusion Models Iakovos Evdaimon Giannis Nikolentzos Michail Chatzianastasis Hadi Abdine Michalis Vazirgiannis DiffM 61 4 0 03 Mar 2024
Bespoke Non-Stationary Solvers for Fast Sampling of Diffusion and Flow Models Neta Shaul Uriel Singer Ricky T. Q. Chen Matt Le Ali K. Thabet Albert Pumarola Y. Lipman DiffM 82 4 0 02 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 168 25 0 01 Mar 2024
Retrieval-Augmented Generation for AI-Generated Content: A Survey Penghao Zhao Hailin Zhang Qinhan Yu Zhengren Wang Yunteng Geng Fangcheng Fu Ling Yang Wentao Zhang Jie Jiang Tengjiao Wang 3DV 290 286 0 29 Feb 2024
Extended Flow Matching: a Method of Conditional Generation with Generalized Continuity Equation Noboru Isobe Masanori Koyama Jinzhe Zhang Kohei Hayashi Kenji Fukumizu 144 10 0 29 Feb 2024
Structure Preserving Diffusion Models Haoye Lu S. Szabados Yaoliang Yu DiffM 85 3 0 29 Feb 2024
Structure-Guided Adversarial Training of Diffusion Models Ling Yang Haotian Qian Zhilong Zhang Jingwei Liu Tengjiao Wang 89 12 0 27 Feb 2024
TrustMol: Trustworthy Inverse Molecular Design via Alignment with Molecular Dynamics Kevin Tirta Wijaya Navid Ansari Hans-Peter Seidel Vahid Babaei 60 0 0 26 Feb 2024
DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design Jiaqi Guan Xiangxin Zhou Yuwei Yang Yu Bao Jian-wei Peng Jianzhu Ma Qiang Liu Liang Wang Quanquan Gu 99 75 0 26 Feb 2024
An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning Rui Jiao Xiangzhe Kong Ziyang Yu Wenbing Huang Fangyuan Ren Wenjuan Tan Wenbing Huang Yang Liu 41 2 0 20 Feb 2024