Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation

29 September 2023

Frank Noé

Papers citing "Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation"

31 / 31 papers shown

Title
Towards Unified and Lossless Latent Space for 3D Molecular Latent Diffusion Modeling Yanchen Luo Zhiyuan Liu Yi Zhao Changhao Nai Kenji Kawaguchi Tat-Seng Chua Xiang Wang Yang Zhang Xiang Wang MedIm 111 0 0 19 Mar 2025
All-atom Diffusion Transformers: Unified generative modelling of molecules and materials Chaitanya K. Joshi Xiang Fu Yi-Lun Liao Vahe Gharakhanyan Benjamin Kurt Miller Anuroop Sriram Zachary W. Ulissi DiffM 146 7 0 05 Mar 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Changhao Nai Sihang Li Yaorui Shi Xiang Wang Kenji Kawaguchi Tat-Seng Chua 150 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 72 6 0 14 Oct 2024
Geometric Representation Condition Improves Equivariant Molecule Generation Zian Li Cai Zhou Xiyuan Wang Xingang Peng Muhan Zhang 57 2 0 04 Oct 2024
Structure-based Drug Design with Equivariant Diffusion Models Arne Schneuing Yuanqi Du Charles Harris Arian R. Jamasb Ilia Igashov ... Pietro Lio Carla P. Gomes Max Welling Michael M. Bronstein B. Correia DiffM 79 215 0 24 Oct 2022
Diffusion-based Molecule Generation with Informative Prior Bridges Lemeng Wu Chengyue Gong Xingchao Liu Mao Ye Qiang Liu DiffM 69 113 0 02 Sep 2022
MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields Ilyes Batatia D. P. Kovács G. Simm Christoph Ortner Gábor Csányi 66 476 0 15 Jun 2022
Elucidating the Design Space of Diffusion-Based Generative Models Tero Karras M. Aittala Timo Aila S. Laine DiffM 156 1,952 0 01 Jun 2022
Torsional Diffusion for Molecular Conformer Generation Bowen Jing Gabriele Corso Jeffrey Chang Regina Barzilay Tommi Jaakkola DiffM BDL 73 270 0 01 Jun 2022
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets Xingang Peng Shitong Luo Jiaqi Guan Qi Xie Jian-wei Peng Jianzhu Ma 54 187 0 15 May 2022
Equivariant Diffusion for Molecule Generation in 3D Emiel Hoogeboom Victor Garcia Satorras Clément Vignac Max Welling DiffM 94 606 0 31 Mar 2022
GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation Minkai Xu Lantao Yu Yang Song Chence Shi Stefano Ermon Jian Tang BDL DiffM 125 511 0 06 Mar 2022
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Hannes Stärk O. Ganea L. Pattanaik Regina Barzilay Tommi Jaakkola 66 267 0 07 Feb 2022
TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials Philipp Thölke Gianni De Fabritiis AI4CE 70 194 0 05 Feb 2022
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 211 174 0 10 Sep 2021
Structured Denoising Diffusion Models in Discrete State-Spaces Jacob Austin Daniel D. Johnson Jonathan Ho Daniel Tarlow Rianne van den Berg DiffM 122 924 0 07 Jul 2021
Diffusion Schrödinger Bridge with Applications to Score-Based Generative Modeling Valentin De Bortoli James Thornton J. Heng Arnaud Doucet DiffM OT 93 461 0 01 Jun 2021
Grad-TTS: A Diffusion Probabilistic Model for Text-to-Speech Vadim Popov Ivan Vovk Vladimir Gogoryan Tasnima Sadekova Mikhail Kudinov DiffM 92 532 0 13 May 2021
Diffusion Models Beat GANs on Image Synthesis Prafulla Dhariwal Alex Nichol 178 7,765 0 11 May 2021
Improved Denoising Diffusion Probabilistic Models Alex Nichol Prafulla Dhariwal DiffM 285 3,648 0 18 Feb 2021
Equivariant message passing for the prediction of tensorial properties and molecular spectra Kristof T. Schütt Oliver T. Unke M. Gastegger 92 530 0 05 Feb 2021
Score-Based Generative Modeling through Stochastic Differential Equations Yang Song Jascha Narain Sohl-Dickstein Diederik P. Kingma Abhishek Kumar Stefano Ermon Ben Poole DiffM SyDa 292 6,409 0 26 Nov 2020
Denoising Diffusion Implicit Models Jiaming Song Chenlin Meng Stefano Ermon VLM DiffM 208 7,294 0 06 Oct 2020
DiffWave: A Versatile Diffusion Model for Audio Synthesis Zhifeng Kong Ming-Yu Liu Jiaji Huang Kexin Zhao Bryan Catanzaro DiffM BDL 110 1,449 0 21 Sep 2020
Learning from Protein Structure with Geometric Vector Perceptrons Bowen Jing Stephan Eismann Patricia Suriana Raphael J. L. Townshend R. Dror GNN 3DV 59 480 0 03 Sep 2020
GEOM: Energy-annotated molecular conformations for property prediction and molecular generation Simon Axelrod Rafael Gómez-Bombarelli 3DV AI4CE 72 216 0 09 Jun 2020
A Generative Model for Molecular Distance Geometry G. Simm José Miguel Hernández-Lobato GAN 75 107 0 25 Sep 2019
Generative Modeling by Estimating Gradients of the Data Distribution Yang Song Stefano Ermon SyDa DiffM 213 3,870 0 12 Jul 2019
Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules Niklas W. A. Gebauer M. Gastegger Kristof T. Schütt 104 208 0 02 Jun 2019
Deep Unsupervised Learning using Nonequilibrium Thermodynamics Jascha Narain Sohl-Dickstein Eric A. Weiss Niru Maheswaranathan Surya Ganguli SyDa DiffM 255 6,887 0 12 Mar 2015