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
Swallowing the Bitter Pill: Simplified Scalable Conformer Generation Yuyang Wang Ahmed A. A. Elhag Navdeep Jaitly J. Susskind Miguel Angel Bautista DiffM 27 20 0 27 Nov 2023
Synthetic Shifts to Initial Seed Vector Exposes the Brittle Nature of Latent-Based Diffusion Models Poyuan Mao Shashank Kotyan Tham Yik Foong Danilo Vasconcellos Vargas 26 5 0 24 Nov 2023
RetroDiff: Retrosynthesis as Multi-stage Distribution Interpolation Yiming Wang Yuxuan Song Minkai Xu Rui Wang Hao Zhou Wei-Ying Ma 25 2 0 23 Nov 2023
UFOGen: You Forward Once Large Scale Text-to-Image Generation via Diffusion GANs Yanwu Xu Yang Zhao Zhisheng Xiao Tingbo Hou 134 107 0 14 Nov 2023
Gradual Optimization Learning for Conformational Energy Minimization Artem Tsypin L. Ugadiarov Kuzma Khrabrov Alexander Telepov Egor Rumiantsev Alexey Skrynnik Aleksandr I. Panov Dmitry Vetrov E. Tutubalina Artur Kadurin 24 1 0 05 Nov 2023
Diffusion Models for Reinforcement Learning: A Survey Zhengbang Zhu Hanye Zhao Haoran He Yichao Zhong Shenyu Zhang Haoquan Guo Tingting Chen Weinan Zhang 41 60 0 02 Nov 2023
Towards equilibrium molecular conformation generation with GFlowNets Alexandra Volokhova Michal Koziarski Alex Hernández-García Cheng-Hao Liu Santiago Miret Pablo Lemos Luca Thiede Zichao Yan Alán Aspuru-Guzik Yoshua Bengio 32 9 0 20 Oct 2023
Particle Guidance: non-I.I.D. Diverse Sampling with Diffusion Models Gabriele Corso Yilun Xu Valentin De Bortoli Regina Barzilay Tommi Jaakkola DiffM 19 20 0 19 Oct 2023
Scalable Diffusion for Materials Generation Mengjiao Yang KwangHwan Cho Amil Merchant Pieter Abbeel Dale Schuurmans Igor Mordatch E. D. Cubuk 29 39 0 18 Oct 2023
Reflection-Equivariant Diffusion for 3D Structure Determination from Isotopologue Rotational Spectra in Natural Abundance Austin H. Cheng Alston Lo Santiago Miret Brooks H Pate Alán Aspuru-Guzik 38 6 0 17 Oct 2023
BayesDiff: Estimating Pixel-wise Uncertainty in Diffusion via Bayesian Inference Siqi Kou Lei Gan Dequan Wang Chongxuan Li Zhijie Deng BDL DiffM 23 7 0 17 Oct 2023
MOFDiff: Coarse-grained Diffusion for Metal-Organic Framework Design Xiang Fu Tian Xie Andrew S. Rosen Tommi Jaakkola Jake A. Smith DiffM 42 9 0 16 Oct 2023
Data-Driven Score-Based Models for Generating Stable Structures with Adaptive Crystal Cells Arsen Sultanov J. Crivello Tabea Rebafka Nataliya Sokolovska DiffM 32 6 0 16 Oct 2023
Score Regularized Policy Optimization through Diffusion Behavior Huayu Chen Cheng Lu Zhengyi Wang Hang Su Jun Zhu 31 20 0 11 Oct 2023
DockGame: Cooperative Games for Multimeric Rigid Protein Docking Vignesh Ram Somnath Pier Giuseppe Sessa María Rodríguez Martínez Andreas Krause 37 2 0 09 Oct 2023
Crystal-GFN: sampling crystals with desirable properties and constraints Mila AI4Science Alex Hernandez-Garcia Alexandre Duval Alexandra Volokhova Yoshua Bengio Divya Sharma P. Carrier Yasmine Benabed Michal Koziarski Victor Schmidt 141 18 0 07 Oct 2023
On Accelerating Diffusion-based Molecular Conformation Generation in SE(3)-invariant Space Zihan Zhou Ruiying Liu Tianshu Yu DiffM 30 0 0 07 Oct 2023
Fast, Expressive SE $(n)$ Equivariant Networks through Weight-Sharing in Position-Orientation Space Erik J. Bekkers Sharvaree P. Vadgama Rob D. Hesselink P. A. V. D. Linden David W. Romero 21 24 0 04 Oct 2023
SE(3)-Stochastic Flow Matching for Protein Backbone Generation A. Bose Tara Akhound-Sadegh Guillaume Huguet Kilian Fatras Jarrid Rector-Brooks Cheng-Hao Liu A. Nica Maksym Korablyov Michael M. Bronstein Alexander Tong DiffM 47 74 0 03 Oct 2023
Score dynamics: scaling molecular dynamics with picoseconds timestep via conditional diffusion model Tim Hsu Babak Sadigh Vasily V. Bulatov Fei Zhou 28 11 0 02 Oct 2023
Generative Design of inorganic compounds using deep diffusion language models Rongzhi Dong Nihang Fu dirisuriya M. D. Siriwardane Jianjun Hu DiffM 35 1 0 30 Sep 2023
Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation Tuan Le Julian Cremer Frank Noé Djork-Arné Clevert Kristof T. Schütt DiffM 29 25 0 29 Sep 2023
Exploiting the Signal-Leak Bias in Diffusion Models Martin Nicolas Everaert Athanasios Fitsios Marco Bocchio Sami Arpa Sabine Süsstrunk R. Achanta DiffM 32 25 0 27 Sep 2023
InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation Xingchao Liu Xiwen Zhang Jianzhu Ma Jian Peng Qiang Liu 96 194 0 12 Sep 2023
Molecular Conformation Generation via Shifting Scores Zihan Zhou Ruiying Liu Chaolong Ying Ruimao Zhang Tianshu Yu DiffM 29 2 0 12 Sep 2023
3D Denoisers are Good 2D Teachers: Molecular Pretraining via Denoising and Cross-Modal Distillation Sungjun Cho Dae-Woong Jeong Sung Moon Ko Jinwoo Kim Sehui Han Seunghoon Hong Honglak Lee Moontae Lee AI4CE DiffM 35 1 0 08 Sep 2023
NADiffuSE: Noise-aware Diffusion-based Model for Speech Enhancement Wen Wang Dongchao Yang Qichen Ye Bowen Cao Yuexian Zou DiffM 37 3 0 03 Sep 2023
AI-Generated Content (AIGC) for Various Data Modalities: A Survey Lin Geng Foo Hossein Rahmani Xiaozhong Liu 78 31 0 27 Aug 2023
Sampling with flows, diffusion and autoregressive neural networks: A spin-glass perspective Davide Ghio Yatin Dandi Florent Krzakala Lenka Zdeborová DiffM 30 26 0 27 Aug 2023
Objective-Agnostic Enhancement of Molecule Properties via Multi-Stage VAE Chenghui Zhou Barnabás Póczós 33 0 0 24 Aug 2023
SE(3) Equivariant Augmented Coupling Flows Laurence I. Midgley Vincent Stimper Javier Antorán Emile Mathieu Bernhard Schölkopf José Miguel Hernández-Lobato 38 22 0 20 Aug 2023
U-Turn Diffusion Hamidreza Behjoo Michael Chertkov 24 3 0 14 Aug 2023
ChatGPT in Drug Discovery: A Case Study on Anti-Cocaine Addiction Drug Development with Chatbots Rui Wang Hongsong Feng Guo-Wei Wei 11 28 0 14 Aug 2023
3D Scene Diffusion Guidance using Scene Graphs Mohammad Naanaa Katharina Schmid Y. Nie DiffM 24 0 0 08 Aug 2023
Nearly $d$ -Linear Convergence Bounds for Diffusion Models via Stochastic Localization Joe Benton Valentin De Bortoli Arnaud Doucet George Deligiannidis DiffM 47 102 0 07 Aug 2023
Diffusion probabilistic models enhance variational autoencoder for crystal structure generative modeling T. Pakornchote Natthaphon Choomphon-anomakhun Sorrjit Arrerut C. Atthapak S. Khamkaeo Thiparat Chotibut T. Bovornratanaraks DiffM 29 17 0 04 Aug 2023
Improved Order Analysis and Design of Exponential Integrator for Diffusion Models Sampling Qinsheng Zhang Jiaming Song Yongxin Chen DiffM 30 10 0 04 Aug 2023
Synthesizing Long-Term Human Motions with Diffusion Models via Coherent Sampling Zhaohui Yang Bing-Huang Su Ji-Rong Wen DiffM 36 14 0 03 Aug 2023
Leveraging Side Information for Ligand Conformation Generation using Diffusion-Based Approaches Nhat-Khang Ngô Truong-Son Hy Yuan Yao DiffM 41 0 0 02 Aug 2023
Crystal Structure Prediction by Joint Equivariant Diffusion Rui Jiao Wen-bing Huang Peijia Lin Jiaqi Han Pin Chen Yutong Lu Yang Liu DiffM 27 60 0 30 Jul 2023
Towards Symmetry-Aware Generation of Periodic Materials Youzhi Luo Chengkai Liu Shuiwang Ji DiffM 29 22 0 06 Jul 2023
SwinGNN: Rethinking Permutation Invariance in Diffusion Models for Graph Generation Qi Yan Zhen-Long Liang Yang Song Renjie Liao Lele Wang DiffM 55 18 0 04 Jul 2023
SaGess: Sampling Graph Denoising Diffusion Model for Scalable Graph Generation Stratis Limnios Praveen Selvaraj Mihai Cucuringu Carsten Maple Gesine Reinert Andrew Elliott DiffM 24 7 0 29 Jun 2023
Equivariant flow matching Leon Klein Andreas Krämer Frank Noé 16 60 0 26 Jun 2023
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation Danny Reidenbach Aditi S. Krishnapriyan 29 7 0 26 Jun 2023
DomainStudio: Fine-Tuning Diffusion Models for Domain-Driven Image Generation using Limited Data Jin Zhu Huimin Ma Jiansheng Chen Jian Yuan DiffM 24 10 0 25 Jun 2023
StrainTensorNet: Predicting crystal structure elastic properties using SE(3)-equivariant graph neural networks T. Pakornchote A. Ektarawong Thiparat Chotibut 31 4 0 22 Jun 2023
InfoDiffusion: Representation Learning Using Information Maximizing Diffusion Models Yingheng Wang Yair Schiff Aaron Gokaslan Weishen Pan Fei Wang Chris De Sa Volodymyr Kuleshov DiffM 14 40 0 14 Jun 2023
A generative artificial intelligence framework based on a molecular diffusion model for the design of metal-organic frameworks for carbon capture Hyun Park Xiaoli Yan Ruijie Zhu Eliu A. Huerta Santanu Chaudhuri Donny Cooper Ian Foster E. Tajkhorshid AI4CE 30 19 0 14 Jun 2023
Distribution Shift Inversion for Out-of-Distribution Prediction Runpeng Yu Songhua Liu Xingyi Yang Xinchao Wang OODD 18 18 0 14 Jun 2023