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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
ERA-Solver: Error-Robust Adams Solver for Fast Sampling of Diffusion Probabilistic Models Shengmeng Li Luping Liu Zenghao Chai Runnan Li Xuejiao Tan DiffM 86 12 0 30 Jan 2023
Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction Zuobai Zhang Minghao Xu A. Lozano Vijil Chenthamarakshan Payel Das Jian Tang DiffM 88 21 0 28 Jan 2023
Bipartite Graph Diffusion Model for Human Interaction Generation Baptiste Chopin Hao Tang Mohamed Daoudi DiffM 64 12 0 24 Jan 2023
DiffSDS: A language diffusion model for protein backbone inpainting under geometric conditions and constraints Zhangyang Gao Cheng Tan Stan Z. Li DiffM 76 19 0 22 Jan 2023
t-SMILES: A Scalable Fragment-based Molecular Representation Framework for De Novo Molecule Generation Juan-Ni Wu Tong Wang Yue (Eleanor) Chen Li-Juan Tang Hai-Long Wu Ru-Qin Yu 47 0 0 04 Jan 2023
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation Han Huang Leilei Sun Bowen Du Weifeng Lv 127 43 0 01 Jan 2023
Structure-based drug discovery with deep learning Rıza Özçelik D. V. Tilborg José Jiménez-Luna F. Grisoni AI4CE 72 38 0 26 Dec 2022
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 75 68 0 22 Dec 2022
Improving Molecule Properties Through 2-Stage VAE Chenghui Zhou Barnabás Póczós DRL 78 1 0 06 Dec 2022
Latent Space Diffusion Models of Cryo-EM Structures Karsten Kreis Tim Dockhorn Zihao Li Ellen D. Zhong DiffM 64 16 0 25 Nov 2022
HouseDiffusion: Vector Floorplan Generation via a Diffusion Model with Discrete and Continuous Denoising M. Shabani Sepidehsadat Hosseini Yasutaka Furukawa DiffM 85 66 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 112 67 0 21 Nov 2022
DiffusionDet: Diffusion Model for Object Detection Shoufa Chen Pei Sun Yibing Song Ping Luo 130 471 0 17 Nov 2022
Physics-Informed Machine Learning: A Survey on Problems, Methods and Applications Zhongkai Hao Songming Liu Yichi Zhang Chengyang Ying Yao Feng Hang Su Jun Zhu PINN AI4CE 127 99 0 15 Nov 2022
Semi-Equivariant Continuous Normalizing Flows for Target-Aware Molecule Generation Eyal Rozenberg Daniel Freedman 74 0 0 09 Nov 2022
Few-shot Image Generation with Diffusion Models Jin Zhu Huimin Ma Jiansheng Chen Jian Yuan DiffM 109 21 0 07 Nov 2022
DPM-Solver++: Fast Solver for Guided Sampling of Diffusion Probabilistic Models Cheng Lu Yuhao Zhou Fan Bao Jianfei Chen Chongxuan Li Jun Zhu DiffM 247 616 0 02 Nov 2022
Predicting Protein-Ligand Binding Affinity with Equivariant Line Graph Network Yi Yi Xu Wan Kangfei Zhao Ou-Yang Le Pei-Ying Zhao 65 1 0 27 Oct 2022
Categorical SDEs with Simplex Diffusion Pierre Harvey Richemond Sander Dieleman Arnaud Doucet DiffM 72 26 0 26 Oct 2022
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 153 227 0 24 Oct 2022
Graphically Structured Diffusion Models Christian D. Weilbach William Harvey Frank Wood DiffM 87 7 0 20 Oct 2022
Structure-based drug design with geometric deep learning Clemens Isert Kenneth Atz G. Schneider 95 110 0 19 Oct 2022
Protein Sequence and Structure Co-Design with Equivariant Translation Chence Shi Chuanrui Wang Jiarui Lu Bozitao Zhong Jian Tang DiffM 81 48 0 17 Oct 2022
Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design Ilia Igashov Hannes Stärk Clément Vignac Victor Garcia Satorras P. Frossard Max Welling Michael M. Bronstein B. Correia DiffM 102 85 0 11 Oct 2022
Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design Keir Adams Connor W. Coley 93 27 0 06 Oct 2022
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 260 449 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 123 206 0 30 Sep 2022
Holographic-(V)AE: an end-to-end SO(3)-Equivariant (Variational) Autoencoder in Fourier Space Gian Marco Visani Michael N. Pun Arman Angaji Armita Nourmohammad BDL 50 3 0 30 Sep 2022
TabDDPM: Modelling Tabular Data with Diffusion Models Akim Kotelnikov Dmitry Baranchuk Ivan Rubachev Artem Babenko DiffM 126 268 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 272 67 0 30 Sep 2022
MDM: Molecular Diffusion Model for 3D Molecule Generation Lei Huang Hengtong Zhang Tingyang Xu Ka-Chun Wong DiffM 106 87 0 13 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 154 28 0 12 Sep 2022
Soft Diffusion: Score Matching for General Corruptions Giannis Daras M. Delbracio Hossein Talebi A. Dimakis P. Milanfar DiffM 144 111 0 12 Sep 2022
A Survey on Generative Diffusion Model Hanqun Cao Cheng Tan Zhangyang Gao Yilun Xu Guangyong Chen Pheng-Ann Heng Stan Z. Li MedIm 242 238 0 06 Sep 2022
Diffusion-based Molecule Generation with Informative Prior Bridges Lemeng Wu Chengyue Gong Xingchao Liu Mao Ye Qiang Liu DiffM 106 116 0 02 Sep 2022
Diffusion Models: A Comprehensive Survey of Methods and Applications Ling Yang Zhilong Zhang Yingxia Shao Shenda Hong Runsheng Xu Yue Zhao Wentao Zhang Tengjiao Wang Ming-Hsuan Yang DiffM MedIm 485 1,420 0 02 Sep 2022
Ab-initio quantum chemistry with neural-network wavefunctions J. Hermann J. Spencer Kenny Choo Antonio Mezzacapo W. Foulkes David Pfau Giuseppe Carleo Frank Noé AI4CE 72 86 0 26 Aug 2022
Thermal half-lives of azobenzene derivatives: virtual screening based on intersystem crossing using a machine learning potential Simon Axelrod E. Shakhnovich Rafael Gómez-Bombarelli 76 20 0 23 Jul 2022
Controllable Data Generation by Deep Learning: A Review Shiyu Wang Yuanqi Du Xiaojie Guo Bo Pan Zhaohui Qin Liang Zhao 97 28 0 19 Jul 2022
Accelerating Material Design with the Generative Toolkit for Scientific Discovery Matteo Manica Jannis Born Joris Cadow Dimitrios Christofidellis A. Dave ... Lauren N. McHugh Alexy Khrabrov Payel Das Seiji Takeda John Smith 93 27 0 08 Jul 2022
Diffusion models as plug-and-play priors Alexandros Graikos Nikolay Malkin Nebojsa Jojic Dimitris Samaras DiffM 141 224 0 17 Jun 2022
Cluster Generation via Deep Energy-Based Model A. Y. Artsukevich S. Lepeshkin 58 0 0 17 Jun 2022
A Flexible Diffusion Model Weitao Du Tao Yang Heidi Zhang Yuanqi Du DiffM 75 12 0 17 Jun 2022
ComENet: Towards Complete and Efficient Message Passing for 3D Molecular Graphs Limei Wang Yi Liu Yu-Ching Lin Hao Liu Shuiwang Ji GNN 111 95 0 17 Jun 2022
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem Brian L. Trippe Jason Yim D. Tischer D. Baker Tamara Broderick Regina Barzilay Tommi Jaakkola DiffM 90 242 0 08 Jun 2022
Neural Diffusion Processes Vincent Dutordoir Alan D. Saul Zoubin Ghahramani F. Simpson DiffM 112 42 0 08 Jun 2022
Exploring Chemical Space with Score-based Out-of-distribution Generation Seul Lee Jaehyeong Jo Sung Ju Hwang OODD 129 81 0 06 Jun 2022
Pre-training via Denoising for Molecular Property Prediction Sheheryar Zaidi Michael Schaarschmidt James Martens Hyunjik Kim Yee Whye Teh Alvaro Sanchez-Gonzalez Peter W. Battaglia Razvan Pascanu Jonathan Godwin DiffM AI4CE 129 127 0 31 May 2022
Few-Shot Diffusion Models Giorgio Giannone Didrik Nielsen Ole Winther DiffM 231 51 0 30 May 2022
A Continuous Time Framework for Discrete Denoising Models Andrew Campbell Joe Benton Valentin De Bortoli Tom Rainforth George Deligiannidis Arnaud Doucet DiffM 290 168 0 30 May 2022