Awesome Diffusion Models for Science

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.

Contents

• Small Molecules
  • Drug Design
  • Molecule Conformation Prediction
  • Molecular Dynamics Simulations
• Proteins
  • Protein Structure Prediction
  • Protein Design
  • Antibody Design
• Complex
  • Complex Structure Prediction
• Materials
  • Materials Design
• Physics

Papers

Small Molecules

Drug Design

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

Molecule Conformation Prediction

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

Molecular Dynamics Simulations

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

Proteins

Protein Structure Prediction

EigenFold: Generative Protein Structure Prediction with Diffusion Models

Bowen Jing, Ezra Erives, Peter Pao-Huang, Gabriele Corso, Bonnie Berger, Tommi Jaakkola
MLDD Workshop, ICLR 2023. [Paper] [Github]
4 Apr 2023

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

Protein Design

Score-based generative modeling for de novo protein design

Lee, Jin Sub, Jisun Kim, and Philip M. Kim
Nature Commutational Science 2023. [Paper]
4 Feb 2023

DiffSDS: A language diffusion model for protein backbone inpainting under geometric conditions and constraints

Zhangyang Gao, Cheng Tan, Stan Z. Li
arXiv 2023. [Paper]
22 Jan 2023

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

Antibody Design

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

Complex

Complex Structure Prediction

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

Materials

Materials Design

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

Physics

Score-based Generative Models for Calorimeter Shower Simulation

Vinicius Mikuni, Benjamin Nachman
arXiv 2022. [Paper]
17 Jun 2022