GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation

6 March 2022

Jian Tang

Papers citing "GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation"

50 / 330 papers shown

Title
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 53 50 0 17 Feb 2023
DIFUSCO: Graph-based Diffusion Solvers for Combinatorial Optimization Zhiqing Sun Yiming Yang DiffM 33 118 0 16 Feb 2023
Score-based Diffusion Models in Function Space Jae Hyun Lim Nikola B. Kovachki Ricardo Baptista Christopher Beckham Kamyar Azizzadenesheli ... Karsten Kreis Jan Kautz Christopher Pal Arash Vahdat Anima Anandkumar DiffM 77 37 0 14 Feb 2023
PrefixMol: Target- and Chemistry-aware Molecule Design via Prefix Embedding Zhangyang Gao Yuqi Hu Cheng Tan Stan Z. Li 34 13 0 14 Feb 2023
Do Deep Learning Methods Really Perform Better in Molecular Conformation Generation? G. Zhou Zhifeng Gao Zhewei Wei Hang Zheng Guolin Ke OOD AI4CE BDL 33 15 0 14 Feb 2023
Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action Zhiye Guo Jian Liu Yanli Wang Mengrui Chen Duolin Wang Dong Xu Jianlin Cheng MedIm AI4CE DiffM 46 22 0 13 Feb 2023
Lorentz Equivariant Model for Knowledge-Enhanced Hyperbolic Collaborative Filtering Bosong Huang Weihao Yu Ruzhong Xie Jing Xiao Jin Huang 38 0 0 09 Feb 2023
Geometry-Complete Diffusion for 3D Molecule Generation and Optimization Alex Morehead Jianlin Cheng DiffM 14 23 0 08 Feb 2023
Q-Diffusion: Quantizing Diffusion Models Xiuyu Li Yijia Liu Long Lian Hua Yang Zhen Dong Daniel Kang Shanghang Zhang Kurt Keutzer DiffM MQ 38 152 0 08 Feb 2023
Machine Learning for Synthetic Data Generation: A Review Ying-Cheng Lu Minjie Shen Huazheng Wang Xiao Wang Capucine Van Rechem Tianfan Fu Wenqi Wei SyDa 42 140 0 08 Feb 2023
HumanMAC: Masked Motion Completion for Human Motion Prediction Ling-Hao Chen Jiawei Zhang Ye-rong Li Yiren Pang Xiaobo Xia Tongliang Liu DiffM VGen 32 56 0 07 Feb 2023
DDM $^2$ : Self-Supervised Diffusion MRI Denoising with Generative Diffusion Models Tiange Xiang Mahmut Yurt Ali B. Syed K. Setsompop Akshay S. Chaudhari MedIm DiffM 33 54 0 06 Feb 2023
Generative Diffusion Models on Graphs: Methods and Applications Junfeng Fang Wenqi Fan Yunqing Liu Jiatong Li Hang Li Hui Liu Jiliang Tang Qing Li MedIm DiffM 34 58 0 06 Feb 2023
SE(3) diffusion model with application to protein backbone generation Jason Yim Brian L. Trippe Valentin De Bortoli Emile Mathieu Arnaud Doucet Regina Barzilay Tommi Jaakkola DiffM 20 195 0 05 Feb 2023
Timewarp: Transferable Acceleration of Molecular Dynamics by Learning Time-Coarsened Dynamics Leon Klein Andrew Y. K. Foong T. E. Fjelde Bruno Mlodozeniec Marc Brockschmidt Sebastian Nowozin Frank Noé Ryota Tomioka AI4CE 37 42 0 02 Feb 2023
Stable Target Field for Reduced Variance Score Estimation in Diffusion Models Yilun Xu Shangyuan Tong Tommi Jaakkola DiffM 20 26 0 01 Feb 2023
End-to-End Full-Atom Antibody Design Xiangzhe Kong Wenbing Huang Yang Liu 22 49 0 01 Feb 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 19 19 0 28 Jan 2023
DiffSDS: A language diffusion model for protein backbone inpainting under geometric conditions and constraints Zhangyang Gao Cheng Tan Stan Z. Li DiffM 29 19 0 22 Jan 2023
Domain-agnostic and Multi-level Evaluation of Generative Models G. Tadesse Jannis Born C. Cintas William Ogallo Dmitry Zubarev Matteo Manica Komminist Weldemariam ELM 29 1 0 20 Jan 2023
Diffusion Probabilistic Models for Scene-Scale 3D Categorical Data Jumin Lee Woobin Im Sebin Lee Sung-eui Yoon DiffM 27 15 0 02 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
Dynamic Molecular Graph-based Implementation for Biophysical Properties Prediction C. Knutson G. Panapitiya R. Varikoti Neeraj Kumar AI4CE 28 0 0 20 Dec 2022
How to Backdoor Diffusion Models? Sheng-Yen Chou Pin-Yu Chen Tsung-Yi Ho DiffM SILM 19 95 0 11 Dec 2022
Executing your Commands via Motion Diffusion in Latent Space Xin Chen Biao Jiang Wen Liu Zilong Huang Bin-Bin Fu Tao Chen Jingyi Yu Gang Yu VGen DiffM 25 337 0 08 Dec 2022
Integration of Pre-trained Protein Language Models into Geometric Deep Learning Networks Fang Wu Yujun Tao Dragomir R. Radev Jinbo Xu Stan Z. Li AI4CE 33 32 0 07 Dec 2022
Improving Molecule Properties Through 2-Stage VAE Chenghui Zhou Barnabás Póczós DRL 28 1 0 06 Dec 2022
Score-based denoising for atomic structure identification Tim Hsu Babak Sadigh N. Bertin Cheol Woo Park James Chapman Vasily V. Bulatov Fei Zhou DiffM 40 6 0 05 Dec 2022
DiffRF: Rendering-Guided 3D Radiance Field Diffusion Norman Muller Yawar Siddiqui Lorenzo Porzi Samuel Rota Buló Peter Kontschieder Matthias Nießner 46 185 0 02 Dec 2022
Diffusion Generative Models in Infinite Dimensions Gavin Kerrigan Justin Ley Padhraic Smyth DiffM 48 27 0 01 Dec 2022
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 33 51 0 28 Nov 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
Fast Sampling of Diffusion Models via Operator Learning Hongkai Zheng Weili Nie Arash Vahdat Kamyar Azizzadenesheli Anima Anandkumar DiffM 65 131 0 24 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
Few-shot Image Generation with Diffusion Models Jin Zhu Huimin Ma Jiansheng Chen Jian Yuan DiffM 40 20 0 07 Nov 2022
eDiff-I: Text-to-Image Diffusion Models with an Ensemble of Expert Denoisers Yogesh Balaji Seungjun Nah Xun Huang Arash Vahdat Jiaming Song ... Timo Aila S. Laine Bryan Catanzaro Tero Karras Xuan Li VLM MoE 29 803 0 02 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 56 555 0 02 Nov 2022
Diffusion models for missing value imputation in tabular data Shuhan Zheng Nontawat Charoenphakdee VLM DiffM 32 67 0 31 Oct 2022
MagicMix: Semantic Mixing with Diffusion Models Jun Hao Liew Hanshu Yan Daquan Zhou Jiashi Feng DiffM 187 60 0 28 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
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
Unifying Diffusion Models' Latent Space, with Applications to CycleDiffusion and Guidance Chen Henry Wu Fernando de la Torre DiffM 28 66 0 11 Oct 2022
GENIE: Higher-Order Denoising Diffusion Solvers Tim Dockhorn Arash Vahdat Karsten Kreis DiffM 49 104 0 11 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 41 84 0 11 Oct 2022
On Distillation of Guided Diffusion Models Chenlin Meng Robin Rombach Ruiqi Gao Diederik P. Kingma Stefano Ermon Jonathan Ho Tim Salimans VLM DiffM 33 491 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
Equivariant Energy-Guided SDE for Inverse Molecular Design Fan Bao Min Zhao Zhongkai Hao Pei‐Yun Li Chongxuan Li Jun Zhu DiffM 190 64 0 30 Sep 2022
State-specific protein-ligand complex structure prediction with a multi-scale deep generative model Zhuoran Qiao Weili Nie Arash Vahdat Thomas F. Miller Anima Anandkumar DiffM 36 84 0 30 Sep 2022