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Awesome Diffusion Models for Science

Awesome License: MIT

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.

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Contents

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

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