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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
DuoDiff: Accelerating Diffusion Models with a Dual-Backbone Approach Daniel Gallo Fernández Rǎzvan-Andrei Matişan Alejandro Monroy Muñoz Ana-Maria Vasilcoiu Janusz Partyka Tin Hadži Veljković Metod Jazbec DiffM 98 4 0 12 Oct 2024
nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder Maksim Kuznetsov Airat Valiev Alex Aliper Daniil Polykovskiy E. Tutubalina Rim Shayakhmetov Z. Miftahutdinov 59 0 0 11 Oct 2024
NetDiff: Deep Graph Denoising Diffusion for Ad Hoc Network Topology Generation Félix Marcoccia C. Adjih P. Mühlethaler DiffM 51 0 0 09 Oct 2024
DLGNet: Hyperedge Classification through Directed Line Graphs for Chemical Reactions Stefano Fiorini Giulia M. Bovolenta Stefano Coniglio Michele Ciavotta Pietro Morerio Michele Parrinello Alessio Del Bue GNN AI4CE 425 0 0 09 Oct 2024
Chemistry-Inspired Diffusion with Non-Differentiable Guidance Yuchen Shen Chenhao Zhang Sijie Fu Chenghui Zhou Newell Washburn Barnabás Póczos 103 2 0 09 Oct 2024
Molecular Dynamics and Machine Learning Unlock Possibilities in Beauty Design -- A Perspective Yuzhi Xu Haowei Ni Qinhui Gao Chia-Hua Chang Yanran Huo ... Yike Zhang Radu Grovu Min He John Z. H. Zhang Yuanqing Wang AI4CE 70 0 0 08 Oct 2024
Unsupervised Representation Learning from Sparse Transformation Analysis Yue Song Thomas Anderson Keller Yisong Yue Pietro Perona Max Welling DRL 71 0 0 07 Oct 2024
Latent Abstractions in Generative Diffusion Models Giulio Franzese Mattia Martini Giulio Corallo Paolo Papotti Pietro Michiardi DiffM 58 0 0 04 Oct 2024
Geometric Representation Condition Improves Equivariant Molecule Generation Zian Li Cai Zhou Xiyuan Wang Xingang Peng Muhan Zhang 104 2 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 150 8 0 03 Oct 2024
Equivariant score-based generative models provably learn distributions with symmetries efficiently Ziyu Chen Markos A. Katsoulakis Benjamin J. Zhang DiffM 72 2 0 02 Oct 2024
Physics-aligned Schrödinger bridge Zeyu Li Hongkun Dou Shen Fang Wang Han Yue Deng Lijun Yang AI4CE DiffM 52 0 0 26 Sep 2024
TFG: Unified Training-Free Guidance for Diffusion Models Haotian Ye Haowei Lin Jiaqi Han Minkai Xu Sheng Liu Yitao Liang Jianzhu Ma James Zou Stefano Ermon 70 28 0 24 Sep 2024
Improving generalisability of 3D binding affinity models in low data regimes Julia Buhmann Ward Haddadin Lukáš Pravda Alan Bilsland Hagen Triendl AI4CE 50 0 0 19 Sep 2024
XMOL: Explainable Multi-property Optimization of Molecules Aye Phyu Phyu Aung Jay Chaudhary Ji Wei Yoon Senthilnath Jayavelu 50 1 0 12 Sep 2024
Reward-Directed Score-Based Diffusion Models via q-Learning Xuefeng Gao Jiale Zha X. Zhou DiffM 75 3 0 07 Sep 2024
On the design space between molecular mechanics and machine learning force fields Yuanqing Wang Kenichiro Takaba Michael S. Chen Marcus Wieder Yuzhi Xu ... Kyunghyun Cho Joe G. Greener Peter K. Eastman Stefano Martiniani M. Tuckerman AI4CE 112 5 0 03 Sep 2024
Exploring Selective Layer Fine-Tuning in Federated Learning Yuchang Sun Yuexiang Xie Bolin Ding Yaliang Li Jun Zhang FedML 64 3 0 28 Aug 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 276 0 0 28 Aug 2024
Geometry Informed Tokenization of Molecules for Language Model Generation Xiner Li Limei Wang Youzhi Luo Carl Edwards Shurui Gui Yuchao Lin Heng Ji Shuiwang Ji 98 7 0 19 Aug 2024
What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much? Rafał Karczewski Samuel Kaski Markus Heinonen Vikas Garg 114 0 0 12 Aug 2024
CloudFixer: Test-Time Adaptation for 3D Point Clouds via Diffusion-Guided Geometric Transformation Hajin Shim Changhun Kim Eunho Yang TTA 64 7 0 23 Jul 2024
Understanding Reinforcement Learning-Based Fine-Tuning of Diffusion Models: A Tutorial and Review Masatoshi Uehara Yulai Zhao Tommaso Biancalani Sergey Levine 144 32 0 18 Jul 2024
Pre-training with Fractional Denoising to Enhance Molecular Property Prediction Yuyan Ni Shikun Feng Xin Hong Yuancheng Sun Wei-Ying Ma Zhiming Ma Qiwei Ye Yanyan Lan AI4CE 78 18 0 14 Jul 2024
NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries E. Nowara Pedro H. O. Pinheiro Sai Pooja Mahajan Omar Mahmood Andrew Watkins Saeed Saremi Michael R. Maser BDL DiffM 66 2 0 03 Jul 2024
Equivariant Diffusion Policy Dian Wang Stephen M. Hart David Surovik Tarik Kelestemur Haojie Huang Haibo Zhao Mark Yeatman Jiuguang Wang Robin Walters Robert Platt DiffM 129 29 0 01 Jul 2024
EquiBot: SIM(3)-Equivariant Diffusion Policy for Generalizable and Data Efficient Learning Jingyun Yang Zi-ang Cao Congyue Deng Rika Antonova Shuran Song Jeannette Bohg DiffM 118 38 0 01 Jul 2024
Diffusion Models and Representation Learning: A Survey Michael Fuest Pingchuan Ma Ming Gui Johannes S. Fischer Vincent Tao Hu Bjorn Ommer DiffM 98 24 0 30 Jun 2024
Molecular Diffusion Models with Virtual Receptors Matan Halfon Eyal Rozenberg Ehud Rivlin Daniel Freedman 87 0 0 26 Jun 2024
General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design Yue Jian Curtis Wu Danny Reidenbach Aditi S. Krishnapriyan 74 1 0 24 Jun 2024
TimeAutoDiff: Combining Autoencoder and Diffusion model for time series tabular data synthesizing Namjoon Suh Yuning Yang Din-Yin Hsieh Qitong Luan Shirong Xu Shixiang Zhu Guang Cheng 127 7 0 23 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 137 19 0 23 Jun 2024
Generative Topological Networks Alona Levy-Jurgenson Z. Yakhini 137 0 0 21 Jun 2024
Transferable Boltzmann Generators Leon Klein Frank Noé 142 19 0 20 Jun 2024
Neural Approximate Mirror Maps for Constrained Diffusion Models Berthy Feng Ricardo Baptista Katherine Bouman MedIm DiffM 132 4 0 18 Jun 2024
Unfolding Time: Generative Modeling for Turbulent Flows in 4D Abdullah Saydemir Marten Lienen Stephan Günnemann AI4CE DiffM 131 3 0 17 Jun 2024
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph Haitao Lin Guojiang Zhao Odin Zhang Yufei Huang Lirong Wu Zicheng Liu Siyuan Li Cheng Tan Zhifeng Gao Stan Z. Li 80 4 0 16 Jun 2024
Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Space Mohamed Amine Ketata Nicholas Gao Johanna Sommer Tom Wollschlager Stephan Günnemann DiffM 100 2 0 15 Jun 2024
Generative Inverse Design of Crystal Structures via Diffusion Models with Transformers Izumi Takahara Kiyou Shibata Teruyasu Mizoguchi DiffM AI4CE 55 2 0 13 Jun 2024
Equivariance via Minimal Frame Averaging for More Symmetries and Efficiency Yuchao Lin Jacob Helwig Shurui Gui Shuiwang Ji 86 11 0 11 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 146 10 0 09 Jun 2024
Mean-field Chaos Diffusion Models S. Park Dongjun Kim Ahmed Alaa DiffM 63 1 0 08 Jun 2024
Large Generative Graph Models Yu Wang Ryan Rossi Namyong Park Huiyuan Chen Nesreen K. Ahmed Puja Trivedi Franck Dernoncourt Danai Koutra Hanyu Wang AI4CE 100 4 0 07 Jun 2024
Variational Flow Matching for Graph Generation Floor Eijkelboom Grigory Bartosh C. A. Naesseth Max Welling Jan-Willem van de Meent 102 18 0 07 Jun 2024
FlowMM: Generating Materials with Riemannian Flow Matching Benjamin Kurt Miller Ricky T. Q. Chen Anuroop Sriram Brandon M. Wood 97 42 0 07 Jun 2024
$Diffusion Models in $\textit{De Novo}$ Drug Design$ Diffusion Models in $\textit{De Novo}$ Drug Design Amira Alakhdar Barnabas Poczos Newell Washburn MedIm 94 27 0 07 Jun 2024
BindGPT: A Scalable Framework for 3D Molecular Design via Language Modeling and Reinforcement Learning Artem Zholus Maksim Kuznetsov Roman Schutski Rim Shayakhmetov Daniil Polykovskiy Sarath Chandar Alex Zhavoronkov DiffM AI4CE 79 6 0 06 Jun 2024
TAGMol: Target-Aware Gradient-guided Molecule Generation Vineeth Dorna Subhalingam D Keshav Kolluru Shreshth Tuli Mrityunjay Singh Saurabh Singal N. M. A. Krishnan Sayan Ranu 105 3 0 03 Jun 2024
Constraint-Aware Diffusion Models for Trajectory Optimization Anjian Li Zihan Ding Adji Bousso Dieng Ryne T. Beeson 109 5 0 03 Jun 2024
Unlocking Guidance for Discrete State-Space Diffusion and Flow Models Hunter Nisonoff Junhao Xiong Stephan Allenspach Jennifer Listgarten 161 44 0 03 Jun 2024