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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 / 404 papers shown

Title
De Novo Drug Design with Joint Transformers Adam Izdebski Ewelina Węglarz-Tomczak Ewa Szczurek Jakub M. Tomczak ViT 66 3 0 03 Oct 2023
Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation Tuan Le Julian Cremer Frank Noé Djork-Arné Clevert Kristof T. Schütt DiffM 131 31 0 29 Sep 2023
Flow Factorized Representation Learning Yue Song Thomas Anderson Keller N. Sebe Max Welling DRL OOD 125 3 0 22 Sep 2023
Deep Quantum Graph Dreaming: Deciphering Neural Network Insights into Quantum Experiments Tareq Jaouni Sören Arlt Carlos Ruiz-Gonzalez Ebrahim Karimi Xuemei Gu Mario Krenn GNN 85 6 0 13 Sep 2023
InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation Xingchao Liu Xiwen Zhang Jianzhu Ma Jian Peng Qiang Liu 191 223 0 12 Sep 2023
Molecular Conformation Generation via Shifting Scores Zihan Zhou Ruiying Liu Chaolong Ying Ruimao Zhang Tianshu Yu DiffM 63 2 0 12 Sep 2023
DiffHPE: Robust, Coherent 3D Human Pose Lifting with Diffusion Cédric Rommel Eduardo Valle Mickaël Chen Souhaiel Khalfaoui Renaud Marlet Matthieu Cord Patrick Pérez 91 15 0 04 Sep 2023
RetroBridge: Modeling Retrosynthesis with Markov Bridges Ilia Igashov Arne Schneuing Marwin H. S. Segler Michael M. Bronstein B. Correia 111 16 0 30 Aug 2023
Objective-Agnostic Enhancement of Molecule Properties via Multi-Stage VAE Chenghui Zhou Barnabás Póczós 66 2 0 24 Aug 2023
Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models Ziqi Chen Bo Peng Srinivas Parthasarathy Xia Ning DiffM 72 12 0 23 Aug 2023
Diffusion Language Models Can Perform Many Tasks with Scaling and Instruction-Finetuning Jiasheng Ye Zaixiang Zheng Yu Bao Lihua Qian Quanquan Gu DiffM 185 19 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 181 27 0 20 Aug 2023
Synthesizing Long-Term Human Motions with Diffusion Models via Coherent Sampling Zhaohui Yang Fuchun Sun Ji-Rong Wen DiffM 109 16 0 03 Aug 2023
Leveraging Side Information for Ligand Conformation Generation using Diffusion-Based Approaches Nhat-Khang Ngô Truong-Son Hy Yuan Yao DiffM 62 0 0 02 Aug 2023
Crystal Structure Prediction by Joint Equivariant Diffusion Rui Jiao Wen-bing Huang Peijia Lin Jiaqi Han Pin Chen Yutong Lu Yang Liu DiffM 93 70 0 30 Jul 2023
AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodies Karolis Martinkus J. Ludwiczak Kyunghyun Cho Weishao Lian J. Lafrance-Vanasse ... A. Rajpal Yongpeng Wu Richard Bonneau Vladimir Gligorijević Andreas Loukas DiffM 111 45 0 28 Jul 2023
Learned Gridification for Efficient Point Cloud Processing P. A. V. D. Linden David W. Romero Erik J. Bekkers 3DPC 62 2 0 22 Jul 2023
Patch-Wise Point Cloud Generation: A Divide-and-Conquer Approach Cheng Wen Baosheng Yu Rao Fu Dacheng Tao 3DPC 67 1 0 22 Jul 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 109 29 0 20 Jul 2023
Complexity Matters: Rethinking the Latent Space for Generative Modeling Tianyang Hu Fei Chen Hong Wang Jiawei Li Wei Cao Jiacheng Sun Zechao Li DiffM 118 10 0 17 Jul 2023
Geometric Constraints in Probabilistic Manifolds: A Bridge from Molecular Dynamics to Structured Diffusion Processes Justin S. Diamond M. Lill DiffM AI4CE 95 1 0 10 Jul 2023
Enhancing Adversarial Robustness via Score-Based Optimization Boya Zhang Weijian Luo Zhihua Zhang DiffM 77 14 0 10 Jul 2023
Towards Symmetry-Aware Generation of Periodic Materials Youzhi Luo Chengkai Liu Shuiwang Ji DiffM 96 25 0 06 Jul 2023
SwinGNN: Rethinking Permutation Invariance in Diffusion Models for Graph Generation Qi Yan Zhen-Long Liang Yang Song Renjie Liao Lele Wang DiffM 82 18 0 04 Jul 2023
Graph Denoising Diffusion for Inverse Protein Folding Kai Yi Bingxin Zhou Yiqing Shen Pietro Lio Yu Guang Wang DiffM 98 46 0 29 Jun 2023
Equivariant flow matching Leon Klein Andreas Krämer Frank Noé 105 79 0 26 Jun 2023
DomainStudio: Fine-Tuning Diffusion Models for Domain-Driven Image Generation using Limited Data Jin Zhu Huimin Ma Jiansheng Chen Jian Yuan DiffM 102 11 0 25 Jun 2023
DiffDTM: A conditional structure-free framework for bioactive molecules generation targeted for dual proteins Lei Huang Zheng Yuan Huihui Yan Rong Sheng Linjing Liu ... Nanjun Chen Fei Huang Songfang Huang Ka-Chun Wong Yaoyun Zhang 52 1 0 24 Jun 2023
A generative artificial intelligence framework based on a molecular diffusion model for the design of metal-organic frameworks for carbon capture Hyun Park Xiaoli Yan Ruijie Zhu Eliu A. Huerta Santanu Chaudhuri Donny Cooper Ian Foster E. Tajkhorshid AI4CE 81 21 0 14 Jun 2023
Distribution Shift Inversion for Out-of-Distribution Prediction Runpeng Yu Songhua Liu Xingyi Yang Xinchao Wang OODD 100 19 0 14 Jun 2023
Discrete Graph Auto-Encoder Yoann Boget Magda Gregorova Alexandros Kalousis 44 4 0 13 Jun 2023
Hyperbolic Graph Diffusion Model Lingfeng Wen Xuan Tang Mingjie Ouyang Xiangxiang Shen Jian Yang Daxin Zhu Mingsong Chen Xian Wei 90 4 0 13 Jun 2023
3D molecule generation by denoising voxel grids Pedro H. O. Pinheiro Joshua Rackers J. Kleinhenz Michael R. Maser Omar Mahmood Andrew Watkins Stephen Ra Vishnu Sresht Saeed Saremi DiffM 106 25 0 13 Jun 2023
Efficient Approximations of Complete Interatomic Potentials for Crystal Property Prediction Yu-Ching Lin Keqiang Yan Youzhi Luo Yi Liu Xiaoning Qian Shuiwang Ji 182 37 0 12 Jun 2023
A Crystal-Specific Pre-Training Framework for Crystal Material Property Prediction Haomin Yu Yanru Song Jilin Hu Chenjuan Guo B. Yang AI4CE 61 4 0 08 Jun 2023
On the Design Fundamentals of Diffusion Models: A Survey Ziyi Chang George Alex Koulieris Hyung Jin Chang Hubert P. H. Shum DiffM 183 56 0 07 Jun 2023
Conditional Generation from Unconditional Diffusion Models using Denoiser Representations Alexandros Graikos Srikar Yellapragada Dimitris Samaras DiffM AI4CE 72 6 0 02 Jun 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 156 15 0 02 Jun 2023
Extracting Reward Functions from Diffusion Models Felipe Nuti Tim Franzmeyer João F. Henriques 87 15 0 01 Jun 2023
DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing Yang Zhang Zuobai Zhang Bozitao Zhong Sanchit Misra Jian Tang DiffM 101 35 0 01 Jun 2023
Spontaneous Symmetry Breaking in Generative Diffusion Models G. Raya L. Ambrogioni DiffM 92 37 0 31 May 2023
Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration Haitao Lin Yufei Huang Haotian Zhang Lirong Wu Siyuan Li Zhiyuan Chen Stan Z. Li DiffM 109 27 0 30 May 2023
Aligning Optimization Trajectories with Diffusion Models for Constrained Design Generation Giorgio Giannone Akash Srivastava Ole Winther Faez Ahmed DiffM AI4CE 91 36 0 29 May 2023
Diff-Instruct: A Universal Approach for Transferring Knowledge From Pre-trained Diffusion Models Weijian Luo Tianyang Hu Shifeng Zhang Jiacheng Sun Zhenguo Li Zhihua Zhang 124 137 0 29 May 2023
DiffusionNAG: Predictor-guided Neural Architecture Generation with Diffusion Models Sohyun An Hayeon Lee Jaehyeong Jo Seanie Lee Sung Ju Hwang DiffM 83 11 0 26 May 2023
Trans-Dimensional Generative Modeling via Jump Diffusion Models Andrew Campbell William Harvey Christian D. Weilbach Valentin De Bortoli Tom Rainforth Arnaud Doucet DiffM 122 13 0 25 May 2023
Statistical Guarantees of Group-Invariant GANs Ziyu Chen Markos A. Katsoulakis Luc Rey-Bellet Wei-wei Zhu 248 2 0 22 May 2023
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation Han Huang Leilei Sun Bowen Du Weifeng Lv DiffM 97 16 0 21 May 2023
Generation of 3D Molecules in Pockets via Language Model Wei Feng L. Wang Zaiyun Lin Yanhao Zhu Han Wang ... Huting Wang Jielong Zhou Wei Peng Bo Huang Wenbiao Zhou 66 35 0 17 May 2023
MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation Xingang Peng Jiaqi Guan Qiang Liu Jianzhu Ma DiffM 82 47 0 11 May 2023