This repository contains a collection of resources and papers on Diffusion Models for Science😆. We are pleased to see that more and more efforts have been devoted to employing diffusion models in tackling essential scientific problems since 2022. For a more comprehensive overview of diffusion-baed models, please refer to Awesome-Diffusion-Models.
If you have any relevant paper or codes to update the list, please pull a request or report an issue.
Structure-based Drug Design with Equivariant Diffusion Models
Arne Schneuing1, Yuanqi Du1, Charles Harris, Arian Jamasb, Ilia Igashov, Weitao Du, Tom Blundell, Pietro Lió, Carla Gomes, Max Welling, Michael Bronstein, Bruno Correia
arXiv 2022. [Paper] [Github]
24 Oct 2022
Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design
Ilia Igashov, Hannes Stärk, Clément Vignac, Victor Garcia Satorras, Pascal Frossard, Max Welling, Michael Bronstein, Bruno Correia
arXiv 2022. [Paper]
11 Oct 2022
Equivariant Energy-Guided SDE for Inverse Molecular Design
Fan Bao1, Min Zhao1, Zhongkai Hao, Peiyao Li, Chongxuan Li, Jun Zhu
arXiv 2022. [Paper]
30 Sep 2022
MDM: Molecular Diffusion Model for 3D Molecule Generation
Lei Huang, Hengtong Zhang, Tingyang Xu, Ka-Chun Wong
arXiv 2022. [Paper]
13 Sep 2022
Diffusion-based Molecule Generation with Informative Prior Bridges
Lemeng Wu1, Chengyue Gong1, Xingchao Liu, Mao Ye, Qiang Liu
NeurIPS 2022. [Paper]
2 Sep 2022
Equivariant Diffusion for Molecule Generation in 3D
Emiel Hoogeboom1, Victor Garcia Satorras1, Clément Vignac, Max Welling
ICML 2022. [Paper] [Github]
31 Mar 2022
Torsional Diffusion for Molecular Conformer Generation
Bowen Jing, Gabriele Corso, Regina Barzilay, Tommi S. Jaakkola
ICLR Workshop 2022. [Paper] [Github]
1 Jun 2022
Predicting Molecular Conformation via Dynamic Graph Score Matching
Shitong Luo, Chence Shi, Minkai Xu, Jian Tang
NeurIPS 2021. [Paper]
22 May 2021
GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation
Minkai Xu, Lantao Yu, Yang Song, Chence Shi, Stefano Ermon, Jian Tang
ICLR 2022 oral. [Paper] [Github]
6 Mar 2022
DiffMD: A Diffusion-based Geometric Model for Molecular Dynamics Simulations
Fang Wu1, Qiang Zhang1, Xurui Jin, Yinghui Jiang, Stan Z. Li
AAAI 2023. [Paper]
19 Apr 2022
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin K. Yang, Rianne van den Berg, James Y. Zou, Alex X. Lu, Ava P. Amini
arXiv 2022. [Paper] [Github]
30 Sep 2022
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem
Brian L. Trippe1, Jason Yim1, Doug Tischer, Tamara Broderick, David Baker, Regina Barzilay, Tommi Jaakkola
CoRR 2022. [Paper]
8 Jun 2022'
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models
Namrata Anand, Tudor Achim
arXiv 2022. [Paper] [Project] [Github]
26 May 2022
Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models
Shitong Luo1, Yufeng Su1, Xingang Peng, Sheng Wang, Jian Peng, Jianzhu Ma
NeurIPS 2022. [Paper][Github]
11 July 2022
Dynamic-Backbone Protein-Ligand Structure Prediction with Multiscale Generative Diffusion Models
Zhuoran Qiao, Weili Nie, Arash Vahdat, Thomas F. Miller III, Anima Anandkumar
arXiv 2022. [Paper]
30 Sep 2022
Crystal Diffusion Variational Autoencoder for Periodic Material Generation
Tian Xie1, Xiang Fu1, Octavian-Eugen Ganea1, Regina Barzilay, Tommi Jaakkola
ICLR 2022. [Paper] [Github]
12 Oct 2021
Data-driven discovery of novel 2D materials by deep generative models
Peder Lyngby, Kristian Sommer Thygesen
arXiv 2022. [Paper]
24 Jun 2022
Score-based Generative Models for Calorimeter Shower Simulation
Vinicius Mikuni, Benjamin Nachman
arXiv 2022. [Paper]
17 Jun 2022