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
You Only Look One Step: Accelerating Backpropagation in Diffusion Sampling with Gradient Shortcuts Hongkun Dou Zeyu Li Xingyu Jiang Hao Li Lijun Yang Wen Yao Yue Deng DiffM 38 0 0 12 May 2025
Diffusion Model Quantization: A Review Qian Zeng Chenggong Hu Mingli Song Jie Song MQ 45 0 0 08 May 2025
GEOM-Drugs Revisited: Toward More Chemically Accurate Benchmarks for 3D Molecule Generation Filipp Nikitin Ian Dunn D. Koes Olexandr Isayev 130 0 0 30 Apr 2025
Clifford Group Equivariant Diffusion Models for 3D Molecular Generation Cong Liu Sharvaree P. Vadgama David Ruhe Erik J Bekkers Patrick Forré DiffM 22 0 0 22 Apr 2025
FLOWR: Flow Matching for Structure-Aware De Novo, Interaction- and Fragment-Based Ligand Generation Julian Cremer Ross Irwin Alessandro Tibot J. Janet Simon Olsson Djork-Arné Clevert 35 0 0 14 Apr 2025
Towards Unified Latent Space for 3D Molecular Latent Diffusion Modeling Yanchen Luo Zhiyuan Liu Yi Zhao Sihang Li Kenji Kawaguchi Tat-Seng Chua Xuben Wang MedIm 69 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 53 4 0 05 Mar 2025
Towards Hierarchical Rectified Flow Yichi Zhang Yici Yan A. Schwing Zhizhen Zhao 47 1 0 24 Feb 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Sihang Li Fan Zhang Yaorui Shi Xuben Wang Kenji Kawaguchi Tat-Seng Chua 100 3 0 18 Feb 2025
SymmCD: Symmetry-Preserving Crystal Generation with Diffusion Models Daniel Levy Siba Smarak Panigrahi Sékou-Oumar Kaba Qiang Zhu Kin Long Kelvin Lee Mikhail Galkin Santiago Miret Siamak Ravanbakhsh 211 12 0 05 Feb 2025
Text2Data: Low-Resource Data Generation with Textual Control Shiyu Wang Yihao Feng Tian Lan Ning Yu Yu Bai Ran Xu Hairu Wang Caiming Xiong Shri Kiran Srinivasan DiffM 82 0 0 03 Jan 2025
Efficient Diversity-Preserving Diffusion Alignment via Gradient-Informed GFlowNets Zhen Liu Tim Z. Xiao Weiyang Liu Yoshua Bengio Dinghuai Zhang 123 2 0 10 Dec 2024
ArtFormer: Controllable Generation of Diverse 3D Articulated Objects Jiayi Su Youhe Feng Zheng Li Jinhua Song Yangfan He Botao Ren Botian Xu AI4CE 91 2 0 10 Dec 2024
Schedule On the Fly: Diffusion Time Prediction for Faster and Better Image Generation Zilyu Ye Zhiyang Chen Tiancheng Li Zemin Huang Weijian Luo Guo-jun Qi DiffM 83 5 0 02 Dec 2024
TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models Kiwoong Yoo Owen Oertell Junhyun Lee Sanghoon Lee Jaewoo Kang 31 0 0 28 Oct 2024
Bio2Token: All-atom tokenization of any biomolecular structure with Mamba Andrew Liu Axel Elaldi Nathan Russell Olivia Viessmann Mamba 63 2 0 24 Oct 2024
Beyond Autoregression: Discrete Diffusion for Complex Reasoning and Planning Jiacheng Ye Jiahui Gao Shansan Gong Lin Zheng Xin Jiang Z. Li Lingpeng Kong DiffM LRM 51 15 0 18 Oct 2024
Training Neural Samplers with Reverse Diffusive KL Divergence Jiajun He Wenlin Chen Mingtian Zhang David Barber José Miguel Hernández-Lobato DiffM 37 4 0 16 Oct 2024
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning Peter Eckmann D. Wu G. Heinzelmann Michael K. Gilson Rose Yu AI4CE 42 0 0 15 Oct 2024
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 38 5 0 14 Oct 2024
NetDiff: Deep Graph Denoising Diffusion for Ad Hoc Network Topology Generation Félix Marcoccia C. Adjih P. Mühlethaler DiffM 16 0 0 09 Oct 2024
Chemistry-Inspired Diffusion with Non-Differentiable Guidance Yuchen Shen Chenhao Zhang Sijie Fu Chenghui Zhou Newell Washburn Barnabás Póczos 52 0 0 09 Oct 2024
Unsupervised Representation Learning from Sparse Transformation Analysis Yue Song Thomas Anderson Keller Yisong Yue Pietro Perona Max Welling DRL 29 0 0 07 Oct 2024
Geometric Representation Condition Improves Equivariant Molecule Generation Zian Li Cai Zhou Xiyuan Wang Xingang Peng Muhan Zhang 45 1 0 04 Oct 2024
Flow Matching with Gaussian Process Priors for Probabilistic Time Series Forecasting Marcel Kollovieh Marten Lienen David Lüdke Leo Schwinn Stephan Günnemann AI4TS BDL DiffM 42 4 0 03 Oct 2024
Gen-Swarms: Adapting Deep Generative Models to Swarms of Drones Carlos Plou Pablo Pueyo Ruben Martinez-Cantin Mac Schwager Ana C. Murillo Eduardo Montijano 133 0 0 28 Aug 2024
Molecular Diffusion Models with Virtual Receptors Matan Halfon Eyal Rozenberg Ehud Rivlin Daniel Freedman 53 0 0 26 Jun 2024
Efficient Evolutionary Search Over Chemical Space with Large Language Models Haorui Wang Marta Skreta C. Ser Wenhao Gao Lingkai Kong ... Yanqiao Zhu Yuanqi Du Alán Aspuru-Guzik Kirill Neklyudov Chao Zhang 47 12 0 23 Jun 2024
Generative Topological Networks Alona Levy-Jurgenson Z. Yakhini 43 0 0 21 Jun 2024
Neural Approximate Mirror Maps for Constrained Diffusion Models Berthy T. Feng Ricardo Baptista Katherine L. Bouman MedIm DiffM 48 3 0 18 Jun 2024
Generative Inverse Design of Crystal Structures via Diffusion Models with Transformers Izumi Takahara Kiyou Shibata Teruyasu Mizoguchi DiffM AI4CE 34 2 0 13 Jun 2024
Grounding Continuous Representations in Geometry: Equivariant Neural Fields David R. Wessels David M. Knigge Samuele Papa Riccardo Valperga Sharvaree P. Vadgama E. Gavves Erik J. Bekkers 47 7 0 09 Jun 2024
Unlocking Guidance for Discrete State-Space Diffusion and Flow Models Hunter Nisonoff Junhao Xiong Stephan Allenspach Jennifer Listgarten 60 31 0 03 Jun 2024
Diffusion On Syntax Trees For Program Synthesis Shreyas Kapur Erik Jenner Stuart J. Russell DiffM 37 5 0 30 May 2024
A Recipe for Charge Density Prediction Xiang Fu Andrew S. Rosen Kyle Bystrom Rui Wang Albert Musaelian Boris Kozinsky Tess E. Smidt Tommi Jaakkola 53 5 0 29 May 2024
Discrete-state Continuous-time Diffusion for Graph Generation Zhe Xu Ruizhong Qiu Yuzhong Chen Huiyuan Chen Xiran Fan Menghai Pan Zhichen Zeng Mahashweta Das Hanghang Tong 43 10 0 19 May 2024
AdsorbDiff: Adsorbate Placement via Conditional Denoising Diffusion Adeesh Kolluru John R. Kitchin DiffM 47 4 0 07 May 2024
Quantum State Generation with Structure-Preserving Diffusion Model Yuchen Zhu Tianrong Chen Evangelos A. Theodorou Xie Chen Molei Tao DiffM 37 6 0 09 Apr 2024
Physics-Informed Diffusion Models Jan-Hendrik Bastek WaiChing Sun D. Kochmann DiffM AI4CE 47 11 0 21 Mar 2024
Understanding and Improving Training-free Loss-based Diffusion Guidance Yifei Shen Xinyang Jiang Yezhen Wang Yifan Yang Dongqi Han Dongsheng Li FaML 26 6 0 19 Mar 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 34 20 0 01 Mar 2024
Generative AI and Process Systems Engineering: The Next Frontier Benjamin Decardi-Nelson Abdulelah S. Alshehri Akshay Ajagekar Fengqi You AI4CE LLMAG 26 24 0 15 Feb 2024
Iterated Denoising Energy Matching for Sampling from Boltzmann Densities Tara Akhound-Sadegh Jarrid Rector-Brooks A. Bose Sarthak Mittal Pablo Lemos ... Siamak Ravanbakhsh Gauthier Gidel Yoshua Bengio Nikolay Malkin Alexander Tong DiffM 37 41 0 09 Feb 2024
Pard: Permutation-Invariant Autoregressive Diffusion for Graph Generation Lingxiao Zhao Xueying Ding L. Akoglu DiffM 23 8 0 06 Feb 2024
Equivariant Symmetry Breaking Sets YuQing Xie Tess E. Smidt 25 4 0 05 Feb 2024
Overcoming Order in Autoregressive Graph Generation Edo Cohen-Karlik Eyal Rozenberg Daniel Freedman 34 1 0 04 Feb 2024
Reflected Schrödinger Bridge for Constrained Generative Modeling Wei Deng Yu Chen Nicole Tianjiao Yang Hengrong Du Qi Feng Ricky T. Q. Chen 29 7 0 06 Jan 2024
Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion Alex Morehead Jeffrey A. Ruffolo Aadyot Bhatnagar Ali Madani DiffM 24 9 0 21 Dec 2023
Continuous Diffusion for Mixed-Type Tabular Data Markus Mueller Kathrin Gruber Dennis Fok DiffM 53 5 0 16 Dec 2023
Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure Ian Dunn D. Koes DiffM GNN 19 3 0 22 Nov 2023