MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation

MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation

17 February 2023

Clément Vignac

Papers citing "MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation"

18 / 18 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
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
Geometric Representation Condition Improves Equivariant Molecule Generation Zian Li Cai Zhou Xiyuan Wang Xingang Peng Muhan Zhang 29 1 0 04 Oct 2024
3D Vessel Graph Generation Using Denoising Diffusion Chinmay Prabhakar Suprosanna Shit Fabio Musio Kaiyuan Yang Tamaz Amiranashvili Johannes C. Paetzold Hongwei Bran Li Bjoern H. Menze DiffM MedIm 34 2 0 08 Jul 2024
Cometh: A continuous-time discrete-state graph diffusion model Antoine Siraudin Fragkiskos D. Malliaros Christopher Morris 16 3 0 10 Jun 2024
MUDiff: Unified Diffusion for Complete Molecule Generation Chenqing Hua Sitao Luan Minkai Xu Rex Ying Jie Fu Stefano Ermon Doina Precup DiffM 33 34 0 28 Apr 2023
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 130 399 0 04 Oct 2022
Diffusion Models for Graphs Benefit From Discrete State Spaces K. Haefeli Karolis Martinkus Nathanael Perraudin Roger Wattenhofer DiffM 66 36 0 04 Oct 2022
Equivariant Energy-Guided SDE for Inverse Molecular Design Fan Bao Min Zhao Zhongkai Hao Pei‐Yun Li Chongxuan Li Jun Zhu DiffM 160 38 0 30 Sep 2022
Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs Yi-Lun Liao Tess E. Smidt 71 142 0 23 Jun 2022
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 106 294 0 07 Oct 2021
Top-N: Equivariant set and graph generation without exchangeability Clément Vignac P. Frossard BDL 50 34 0 05 Oct 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
MoleculeNet: A Benchmark for Molecular Machine Learning Zhenqin Wu Bharath Ramsundar Evan N. Feinberg Joseph Gomes C. Geniesse Aneesh S. Pappu K. Leswing Vijay S. Pande OOD 152 1,748 0 02 Mar 2017
Spatial Transformer Networks Max Jaderberg Karen Simonyan Andrew Zisserman Koray Kavukcuoglu 124 7,284 0 05 Jun 2015