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 / 331 papers shown

Title
On Calibrating Diffusion Probabilistic Models Tianyu Pang Cheng Lu Chao Du Min Lin Shuicheng Yan Zhijie Deng DiffM 50 2 0 21 Feb 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 57 52 0 17 Feb 2023
DIFUSCO: Graph-based Diffusion Solvers for Combinatorial Optimization Zhiqing Sun Yiming Yang DiffM 48 123 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 98 40 0 14 Feb 2023
PrefixMol: Target- and Chemistry-aware Molecule Design via Prefix Embedding Zhangyang Gao Yuqi Hu Cheng Tan Stan Z. Li 51 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 57 16 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 61 22 0 13 Feb 2023
Lorentz Equivariant Model for Knowledge-Enhanced Hyperbolic Collaborative Filtering Bosong Huang Weihao Yu Ruzhong Xie Jing Xiao Jin Huang 47 0 0 09 Feb 2023
Geometry-Complete Diffusion for 3D Molecule Generation and Optimization Alex Morehead Jianlin Cheng DiffM 32 27 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 55 160 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 57 141 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 47 60 0 07 Feb 2023
DDM $^2$ : Self-Supervised Diffusion MRI Denoising with Generative Diffusion Models Tiange Xiang Mahmut Yurt Ali B. Syed Kawin Setsompop Akshay S. Chaudhari MedIm DiffM 50 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 44 59 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 28 203 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 57 45 0 02 Feb 2023
Stable Target Field for Reduced Variance Score Estimation in Diffusion Models Yilun Xu Shangyuan Tong Tommi Jaakkola DiffM 28 26 0 01 Feb 2023
End-to-End Full-Atom Antibody Design Xiangzhe Kong Wenbing Huang Yang Liu 48 51 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 37 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 40 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 45 1 0 20 Jan 2023
Diffusion Probabilistic Models for Scene-Scale 3D Categorical Data Jumin Lee Woobin Im Sebin Lee Sung-eui Yoon DiffM 51 15 0 02 Jan 2023
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation Han Huang Leilei Sun Bowen Du Weifeng Lv 58 42 0 01 Jan 2023
Dynamic Molecular Graph-based Implementation for Biophysical Properties Prediction C. Knutson G. Panapitiya R. Varikoti Neeraj Kumar AI4CE 48 0 0 20 Dec 2022
How to Backdoor Diffusion Models? Sheng-Yen Chou Pin-Yu Chen Tsung-Yi Ho DiffM SILM 41 99 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 40 343 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 46 32 0 07 Dec 2022
Improving Molecule Properties Through 2-Stage VAE Chenghui Zhou Barnabás Póczós DRL 53 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 47 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 51 186 0 02 Dec 2022
Diffusion Generative Models in Infinite Dimensions Gavin Kerrigan Justin Ley Padhraic Smyth DiffM 71 29 0 01 Dec 2022
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 47 53 0 28 Nov 2022
Latent Space Diffusion Models of Cryo-EM Structures Karsten Kreis Tim Dockhorn Zihao Li Ellen D. Zhong DiffM 35 15 0 25 Nov 2022
Fast Sampling of Diffusion Models via Operator Learning Hongkai Zheng Weili Nie Arash Vahdat Kamyar Azizzadenesheli Anima Anandkumar DiffM 70 138 0 24 Nov 2022
HouseDiffusion: Vector Floorplan Generation via a Diffusion Model with Discrete and Continuous Denoising M. Shabani Sepidehsadat Hosseini Yasutaka Furukawa DiffM 36 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 41 62 0 21 Nov 2022
DiffusionDet: Diffusion Model for Object Detection Shoufa Chen Pei Sun Yibing Song Ping Luo 68 446 0 17 Nov 2022
Few-shot Image Generation with Diffusion Models Jin Zhu Huimin Ma Jiansheng Chen Jian Yuan DiffM 58 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 86 811 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 87 569 0 02 Nov 2022
Diffusion models for missing value imputation in tabular data Shuhan Zheng Nontawat Charoenphakdee VLM DiffM 51 68 0 31 Oct 2022
MagicMix: Semantic Mixing with Diffusion Models Jun Hao Liew Hanshu Yan Daquan Zhou Jiashi Feng DiffM 192 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 Lio Carla P. Gomes Max Welling Michael M. Bronstein B. Correia DiffM 59 204 0 24 Oct 2022
Protein Sequence and Structure Co-Design with Equivariant Translation Chence Shi Chuanrui Wang Jiarui Lu Bozitao Zhong Jian Tang DiffM 35 47 0 17 Oct 2022
Unifying Diffusion Models' Latent Space, with Applications to CycleDiffusion and Guidance Chen Henry Wu Fernando de la Torre DiffM 64 67 0 11 Oct 2022
GENIE: Higher-Order Denoising Diffusion Solvers Tim Dockhorn Arash Vahdat Karsten Kreis DiffM 56 106 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 59 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 42 502 0 06 Oct 2022
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 162 422 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 195 66 0 30 Sep 2022