Equivariant Diffusion for Molecule Generation in 3D

31 March 2022

Emiel Hoogeboom

Victor Garcia Satorras

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

46 / 46 papers shown

Title
GEOM-Drugs Revisited: Toward More Chemically Accurate Benchmarks for 3D Molecule Generation Filipp Nikitin Ian Dunn D. Koes Olexandr Isayev 36 0 0 30 Apr 2025
FLOWR: Flow Matching for Structure-Aware De Novo, Interaction- and Fragment-Based Ligand Generation Julian Cremer Ross Irwin Alessandro Tibot J. Janet Simon Olsson Djork-Arné Clevert 19 0 0 14 Apr 2025
Towards Unified Latent Space for 3D Molecular Latent Diffusion Modeling Yanchen Luo Zhiyuan Liu Yi Zhao Sihang Li Kenji Kawaguchi Tat-Seng Chua X. Wang MedIm 57 0 0 19 Mar 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Sihang Li Junfeng Fang Yaorui Shi X. Wang Kenji Kawaguchi Tat-Seng Chua 84 3 0 18 Feb 2025
SymmCD: Symmetry-Preserving Crystal Generation with Diffusion Models Daniel Levy Siba Smarak Panigrahi Sékou-Oumar Kaba Qiang Zhu Kin Long Kelvin Lee Mikhail Galkin Santiago Miret Siamak Ravanbakhsh 79 11 0 05 Feb 2025
Text2Data: Low-Resource Data Generation with Textual Control Shiyu Wang Yihao Feng Tian Lan Ning Yu Yu Bai R. Xu H. Wang Caiming Xiong S. DiffM 73 0 0 03 Jan 2025
Efficient Diversity-Preserving Diffusion Alignment via Gradient-Informed GFlowNets Zhen Liu Tim Z. Xiao Weiyang Liu Yoshua Bengio Dinghuai Zhang 115 2 0 10 Dec 2024
ArtFormer: Controllable Generation of Diverse 3D Articulated Objects Jiayi Su Youhe Feng Zheng Li Jinhua Song Yangfan He Botao Ren Botian Xu AI4CE 81 2 0 10 Dec 2024
Schedule On the Fly: Diffusion Time Prediction for Faster and Better Image Generation Zilyu Ye Zhiyang Chen Tiancheng Li Zemin Huang Weijian Luo Guo-jun Qi DiffM 65 4 0 02 Dec 2024
TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models Kiwoong Yoo Owen Oertell Junhyun Lee Sanghoon Lee Jaewoo Kang 26 0 0 28 Oct 2024
Bio2Token: All-atom tokenization of any biomolecular structure with Mamba Andrew Liu Axel Elaldi Nathan Russell Olivia Viessmann Mamba 53 2 0 24 Oct 2024
Training Neural Samplers with Reverse Diffusive KL Divergence Jiajun He Wenlin Chen Mingtian Zhang David Barber José Miguel Hernández-Lobato DiffM 26 4 0 16 Oct 2024
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning Peter Eckmann D. Wu G. Heinzelmann Michael K. Gilson Rose Yu AI4CE 33 0 0 15 Oct 2024
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules Shikun Feng Yuyan Ni Yan Lu Zhi-Ming Ma Wei-Ying Ma Yanyan Lan 27 4 0 14 Oct 2024
Chemistry-Inspired Diffusion with Non-Differentiable Guidance Yuchen Shen Chenhao Zhang Sijie Fu Chenghui Zhou Newell Washburn Barnabás Póczos 38 0 0 09 Oct 2024
Geometric Representation Condition Improves Equivariant Molecule Generation Zian Li Cai Zhou Xiyuan Wang Xingang Peng Muhan Zhang 29 1 0 04 Oct 2024
Flow Matching with Gaussian Process Priors for Probabilistic Time Series Forecasting Marcel Kollovieh Marten Lienen David Ludke Leo Schwinn Stephan Günnemann AI4TS BDL DiffM 19 3 0 03 Oct 2024
Gen-Swarms: Adapting Deep Generative Models to Swarms of Drones Carlos Plou Pablo Pueyo Ruben Martinez-Cantin Mac Schwager Ana C. Murillo Eduardo Montijano 28 0 0 28 Aug 2024
Efficient Evolutionary Search Over Chemical Space with Large Language Models Haorui Wang Marta Skreta C. Ser Wenhao Gao Lingkai Kong ... Yanqiao Zhu Yuanqi Du Alán Aspuru-Guzik Kirill Neklyudov Chao Zhang 29 10 0 23 Jun 2024
Generative Topological Networks Alona Levy-Jurgenson Z. Yakhini 34 0 0 21 Jun 2024
Neural Approximate Mirror Maps for Constrained Diffusion Models Berthy T. Feng Ricardo Baptista Katherine L. Bouman MedIm DiffM 18 3 0 18 Jun 2024
Grounding Continuous Representations in Geometry: Equivariant Neural Fields David R. Wessels David M. Knigge Samuele Papa Riccardo Valperga Sharvaree P. Vadgama E. Gavves Erik J. Bekkers 28 7 0 09 Jun 2024
Unlocking Guidance for Discrete State-Space Diffusion and Flow Models Hunter Nisonoff Junhao Xiong Stephan Allenspach Jennifer Listgarten 31 29 0 03 Jun 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 24 5 0 29 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 16 8 0 19 May 2024
Physics-Informed Diffusion Models Jan-Hendrik Bastek WaiChing Sun D. Kochmann DiffM AI4CE 41 10 0 21 Mar 2024
Iterated Denoising Energy Matching for Sampling from Boltzmann Densities Tara Akhound-Sadegh Jarrid Rector-Brooks A. Bose Sarthak Mittal Pablo Lemos ... Siamak Ravanbakhsh Gauthier Gidel Yoshua Bengio Nikolay Malkin Alexander Tong DiffM 16 41 0 09 Feb 2024
Reflected Schrödinger Bridge for Constrained Generative Modeling Wei Deng Yu Chen Nicole Tianjiao Yang Hengrong Du Qi Feng Ricky T. Q. Chen 16 7 0 06 Jan 2024
Continuous Diffusion for Mixed-Type Tabular Data Markus Mueller Kathrin Gruber Dennis Fok DiffM 41 5 0 16 Dec 2023
Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure Ian Dunn D. Koes DiffM GNN 6 3 0 22 Nov 2023
Closed-Form Diffusion Models Christopher Scarvelis Haitz Sáez de Ocáriz Borde Justin Solomon DiffM 86 9 0 19 Oct 2023
Diffusion Language Models Can Perform Many Tasks with Scaling and Instruction-Finetuning Jiasheng Ye Zaixiang Zheng Yu Bao Lihua Qian Quanquan Gu DiffM 42 14 0 23 Aug 2023
SE(3) Equivariant Augmented Coupling Flows Laurence I. Midgley Vincent Stimper Javier Antorán Emile Mathieu Bernhard Schölkopf José Miguel Hernández-Lobato 15 22 0 20 Aug 2023
Learned Gridification for Efficient Point Cloud Processing P. A. V. D. Linden David W. Romero Erik J. Bekkers 3DPC 6 2 0 22 Jul 2023
Enhancing Adversarial Robustness via Score-Based Optimization Boya Zhang Weijian Luo Zhihua Zhang DiffM 8 11 0 10 Jul 2023
Statistical Guarantees of Group-Invariant GANs Ziyu Chen M. Katsoulakis Luc Rey-Bellet Wei-wei Zhu 15 1 0 22 May 2023
Accurate transition state generation with an object-aware equivariant elementary reaction diffusion model Chenru Duan Yuanqi Du Haojun Jia Heather J. Kulik DiffM 6 44 0 12 Apr 2023
A Comprehensive Survey on Deep Graph Representation Learning Wei Ju Zheng Fang Yiyang Gu Zequn Liu Qingqing Long ... Jingyang Yuan Yusheng Zhao Yifan Wang Xiao Luo Ming Zhang GNN AI4TS 17 138 0 11 Apr 2023
ChiroDiff: Modelling chirographic data with Diffusion Models Ayan Das Yongxin Yang Timothy M. Hospedales Tao Xiang Yi-Zhe Song DiffM 9 10 0 07 Apr 2023
Few-Shot Diffusion Models Giorgio Giannone Didrik Nielsen Ole Winther DiffM 162 49 0 30 May 2022
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 60 176 0 20 Mar 2022
Top-N: Equivariant set and graph generation without exchangeability Clément Vignac P. Frossard BDL 50 34 0 05 Oct 2021
Inverse design of 3d molecular structures with conditional generative neural networks Niklas W. A. Gebauer M. Gastegger Stefaan S. P. Hessmann Klaus-Robert Muller Kristof T. Schütt AI4CE 170 125 0 10 Sep 2021
Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions Emiel Hoogeboom Didrik Nielsen P. Jaini Patrick Forré Max Welling DiffM 191 392 0 10 Feb 2021
Learning a Continuous Representation of 3D Molecular Structures with Deep Generative Models Matthew Ragoza Tomohide Masuda D. Koes DiffM MedIm 56 25 0 17 Oct 2020
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 181 878 0 07 Jun 2018