Equivariant Diffusion for Molecule Generation in 3D

31 March 2022

Emiel Hoogeboom

Victor Garcia Satorras

Papers citing "Equivariant Diffusion for Molecule Generation in 3D"

50 / 122 papers shown

Title
STRIDE: Structure-guided Generation for Inverse Design of Molecules Shehtab Zaman D. Akhiyarov Mauricio Araya-Polo Kenneth Chiu 26 1 0 06 Nov 2023
Purify++: Improving Diffusion-Purification with Advanced Diffusion Models and Control of Randomness Boya Zhang Weijian Luo Zhihua Zhang 34 10 0 28 Oct 2023
Closed-Form Diffusion Models Christopher Scarvelis Haitz Sáez de Ocáriz Borde Justin Solomon DiffM 95 9 0 19 Oct 2023
Diffusion Language Models Can Perform Many Tasks with Scaling and Instruction-Finetuning Jiasheng Ye Zaixiang Zheng Yu Bao Lihua Qian Quanquan Gu DiffM 54 14 0 23 Aug 2023
SE(3) Equivariant Augmented Coupling Flows Laurence I. Midgley Vincent Stimper Javier Antorán Emile Mathieu Bernhard Schölkopf José Miguel Hernández-Lobato 38 22 0 20 Aug 2023
Learned Gridification for Efficient Point Cloud Processing P. A. V. D. Linden David W. Romero Erik J. Bekkers 3DPC 25 2 0 22 Jul 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 47 25 0 20 Jul 2023
Enhancing Adversarial Robustness via Score-Based Optimization Boya Zhang Weijian Luo Zhihua Zhang DiffM 29 12 0 10 Jul 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 22 13 0 02 Jun 2023
Statistical Guarantees of Group-Invariant GANs Ziyu Chen M. Katsoulakis Luc Rey-Bellet Wei-wei Zhu 45 2 0 22 May 2023
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation Han Huang Leilei Sun Bowen Du Weifeng Lv DiffM 26 16 0 21 May 2023
SILVR: Guided Diffusion for Molecule Generation Nicholas T. Runcie A. Mey 24 16 0 21 Apr 2023
Semi-Equivariant Conditional Normalizing Flows Eyal Rozenberg Daniel Freedman 27 0 0 13 Apr 2023
Accurate transition state generation with an object-aware equivariant elementary reaction diffusion model Chenru Duan Yuanqi Du Haojun Jia Heather J. Kulik DiffM 29 46 0 12 Apr 2023
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design Zaixin Zhang Qi Liu Cheekong Lee Chang-Yu Hsieh Enhong Chen 19 18 0 12 Apr 2023
A Comprehensive Survey on Deep Graph Representation Learning Wei Ju Zheng Fang Yiyang Gu Zequn Liu Qingqing Long ... Jingyang Yuan Yusheng Zhao Yifan Wang Xiao Luo Ming Zhang GNN AI4TS 54 141 0 11 Apr 2023
A Comprehensive Survey on Knowledge Distillation of Diffusion Models Weijian Luo DiffM MedIm 52 33 0 09 Apr 2023
A new perspective on building efficient and expressive 3D equivariant graph neural networks Weitao Du Yuanqi Du Limei Wang Dieqiao Feng Guifeng Wang Shuiwang Ji Carla P. Gomes Zhixin Ma AI4CE 32 33 0 07 Apr 2023
ChiroDiff: Modelling chirographic data with Diffusion Models Ayan Das Yongxin Yang Timothy M. Hospedales Tao Xiang Yi-Zhe Song DiffM 29 10 0 07 Apr 2023
GenPhys: From Physical Processes to Generative Models Ziming Liu Di Luo Yilun Xu Tommi Jaakkola M. Tegmark AI4CE 22 14 0 05 Apr 2023
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 41 0 0 05 Apr 2023
DiffTAD: Temporal Action Detection with Proposal Denoising Diffusion Sauradip Nag Xiatian Zhu Jiankang Deng Yi-Zhe Song Tao Xiang DiffM VGen 41 21 0 27 Mar 2023
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction Jiaqi Guan Wesley Wei Qian Xingang Peng Yufeng Su Jian-wei Peng Jianzhu Ma DiffM 31 162 0 06 Mar 2023
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow Fangce Sun Zhihao Zhan Hongyu Guo Ming Zhang Jian Tang 26 6 0 23 Feb 2023
Aligned Diffusion Schrödinger Bridges Vignesh Ram Somnath Matteo Pariset Ya-Ping Hsieh María Rodríguez Martínez Andreas Krause Charlotte Bunne DiffM 117 30 0 22 Feb 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 50 50 0 17 Feb 2023
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability Zhiqiang Zhong A. Barkova Davide Mottin 24 8 0 16 Feb 2023
DIFUSCO: Graph-based Diffusion Solvers for Combinatorial Optimization Zhiqing Sun Yiming Yang DiffM 33 118 0 16 Feb 2023
A Reparameterized Discrete Diffusion Model for Text Generation Lin Zheng Jianbo Yuan Lei Yu Lingpeng Kong DiffM 38 57 0 11 Feb 2023
How to Trust Your Diffusion Model: A Convex Optimization Approach to Conformal Risk Control Jacopo Teneggi Matthew Tivnan J. W. Stayman Jeremias Sulam DiffM 35 28 0 07 Feb 2023
ERA-Solver: Error-Robust Adams Solver for Fast Sampling of Diffusion Probabilistic Models Shengmeng Li Luping Liu Zenghao Chai Runnan Li Xuejiao Tan DiffM 35 11 0 30 Jan 2023
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation Han Huang Leilei Sun Bowen Du Weifeng Lv 45 40 0 01 Jan 2023
Text Generation with Diffusion Language Models: A Pre-training Approach with Continuous Paragraph Denoise Zheng-Wen Lin Yeyun Gong Yelong Shen Tong Wu Zhihao Fan Chen Lin Nan Duan Weizhu Chen AI4CE DiffM VLM 35 61 0 22 Dec 2022
Improving Molecule Properties Through 2-Stage VAE Chenghui Zhou Barnabás Póczós DRL 28 1 0 06 Dec 2022
Latent Space Diffusion Models of Cryo-EM Structures Karsten Kreis Tim Dockhorn Zihao Li Ellen D. Zhong DiffM 30 15 0 25 Nov 2022
HouseDiffusion: Vector Floorplan Generation via a Diffusion Model with Discrete and Continuous Denoising M. Shabani Sepidehsadat Hosseini Yasutaka Furukawa DiffM 23 58 0 23 Nov 2022
DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding Haitao Lin Yufei Huang Odin Zhang Siqi Ma Meng Liu X. Li Lirong Wu Shuiwang Ji Tingjun Hou Stan Z. Li DiffM 26 60 0 21 Nov 2022
DiffusionDet: Diffusion Model for Object Detection Shoufa Chen Pei Sun Yibing Song Ping Luo 63 443 0 17 Nov 2022
Semi-Equivariant Continuous Normalizing Flows for Target-Aware Molecule Generation Eyal Rozenberg Daniel Freedman 21 0 0 09 Nov 2022
Few-shot Image Generation with Diffusion Models Jin Zhu Huimin Ma Jiansheng Chen Jian Yuan DiffM 37 20 0 07 Nov 2022
Predicting Protein-Ligand Binding Affinity with Equivariant Line Graph Network Yi Yi Xu Wan Kangfei Zhao Ou-Yang Le Pei-Ying Zhao 24 1 0 27 Oct 2022
Structure-based Drug Design with Equivariant Diffusion Models Arne Schneuing Yuanqi Du Charles Harris Arian R. Jamasb Ilia Igashov ... Pietro Lió Carla P. Gomes Max Welling Michael M. Bronstein B. Correia DiffM 42 195 0 24 Oct 2022
Graphically Structured Diffusion Models Christian Weilbach William Harvey Frank D. Wood DiffM 35 7 0 20 Oct 2022
Structure-based drug design with geometric deep learning Clemens Isert Kenneth Atz G. Schneider 53 104 0 19 Oct 2022
Protein Sequence and Structure Co-Design with Equivariant Translation Chence Shi Chuanrui Wang Jiarui Lu Bozitao Zhong Jian Tang DiffM 30 47 0 17 Oct 2022
Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design Keir Adams Connor W. Coley 34 25 0 06 Oct 2022
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 139 410 0 04 Oct 2022
Protein structure generation via folding diffusion Kevin E. Wu Kevin Kaichuang Yang Rianne van den Berg James Zou Alex X. Lu Ava P. Amini DiffM 30 192 0 30 Sep 2022
TabDDPM: Modelling Tabular Data with Diffusion Models Akim Kotelnikov Dmitry Baranchuk Ivan Rubachev Artem Babenko DiffM 60 239 0 30 Sep 2022
Equivariant Energy-Guided SDE for Inverse Molecular Design Fan Bao Min Zhao Zhongkai Hao Pei‐Yun Li Chongxuan Li Jun Zhu DiffM 187 64 0 30 Sep 2022