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"

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Title
Warped Diffusion: Solving Video Inverse Problems with Image Diffusion Models Giannis Daras Weili Nie Karsten Kreis A. Dimakis Morteza Mardani Nikola B. Kovachki Arash Vahdat DiffM 35 5 0 21 Oct 2024
Beyond Autoregression: Discrete Diffusion for Complex Reasoning and Planning Jiacheng Ye Jiahui Gao Shansan Gong Lin Zheng Xin Jiang Z. Li Lingpeng Kong DiffM LRM 54 15 0 18 Oct 2024
Geometric Trajectory Diffusion Models Jiaqi Han Minkai Xu Aaron Lou Haotian Ye Stefano Ermon DiffM 54 4 0 16 Oct 2024
Off-dynamics Conditional Diffusion Planners Wen Zheng Terence Ng Jianda Chen Tianwei Zhang DiffM OffRL 35 0 0 16 Oct 2024
Are High-Degree Representations Really Unnecessary in Equivariant Graph Neural Networks? Jiacheng Cen Anyi Li Ning Lin Yuxiang Ren Zihe Wang Wenbing Huang 46 2 0 15 Oct 2024
Physical Consistency Bridges Heterogeneous Data in Molecular Multi-Task Learning Yuxuan Ren Dihan Zheng Chang-Shu Liu Peiran Jin Yu Shi Lin Huang Jiyan He Shengjie Luo Tao Qin Tie-Yan Liu AI4CE 38 1 0 14 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 27 0 0 11 Oct 2024
Physics-Informed Regularization for Domain-Agnostic Dynamical System Modeling Zijie Huang Wanjia Zhao Jingdong Gao Ziniu Hu Xiao Luo Yadi Cao Yuanzhou Chen Yizhou Sun Wei Wang PINN AI4CE 27 1 0 08 Oct 2024
MOFFlow: Flow Matching for Structure Prediction of Metal-Organic Frameworks N. Kim Seongsu Kim Minsu Kim Jinkyoo Park Sungsoo Ahn AI4CE 41 0 0 07 Oct 2024
REBIND: Enhancing ground-state molecular conformation via force-based graph rewiring Taewon Kim Hyunjin Seo Sungsoo Ahn Eunho Yang AI4CE 37 1 0 04 Oct 2024
Text-guided Diffusion Model for 3D Molecule Generation Yanchen Luo Junfeng Fang Sihang Li Zhiyuan Liu Jiancan Wu An Zhang Wenjie Du Xiang Wang 36 6 0 04 Oct 2024
How Discrete and Continuous Diffusion Meet: Comprehensive Analysis of Discrete Diffusion Models via a Stochastic Integral Framework Yinuo Ren Haoxuan Chen Grant M. Rotskoff Lexing Ying 47 3 0 04 Oct 2024
Geometric Representation Condition Improves Equivariant Molecule Generation Zian Li Cai Zhou Xiyuan Wang Xingang Peng Muhan Zhang 45 1 0 04 Oct 2024
Simple and Fast Distillation of Diffusion Models Zhenyu Zhou Defang Chen Can Wang Chun Chen Siwei Lyu DiffM 43 5 0 29 Sep 2024
Physics-aligned Schrödinger bridge Zeyu Li Hongkun Dou Shen Fang Wang Han Yue Deng Lijun Yang AI4CE DiffM 30 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 39 14 0 24 Sep 2024
Mitigating Exposure Bias in Score-Based Generation of Molecular Conformations Sijia Wang Chen Wang Zhenhao Zhao Jiqiang Zhang Weiran Cai 26 0 0 21 Sep 2024
XMOL: Explainable Multi-property Optimization of Molecules Aye Phyu Phyu Aung Jay Chaudhary Ji Wei Yoon Senthilnath Jayavelu 32 0 0 12 Sep 2024
Generating Physical Dynamics under Priors Zihan Zhou Xiaoxue Wang Tianshu Yu DiffM AI4CE 69 0 0 01 Sep 2024
Exploring Selective Layer Fine-Tuning in Federated Learning Yuchang Sun Yuexiang Xie Bolin Ding Yaliang Li Jun Zhang FedML 38 2 0 28 Aug 2024
Geometry Informed Tokenization of Molecules for Language Model Generation Xiner Li Limei Wang Youzhi Luo Carl N. Edwards Shurui Gui Yuchao Lin Heng Ji Shuiwang Ji 39 6 0 19 Aug 2024
Instruction-Based Molecular Graph Generation with Unified Text-Graph Diffusion Model Yuran Xiang Haiteng Zhao Chang Ma Zhi-Hong Deng 29 0 0 19 Aug 2024
Attacks and Defenses for Generative Diffusion Models: A Comprehensive Survey V. T. Truong Luan Ba Dang Long Bao Le DiffM MedIm 56 16 0 06 Aug 2024
RCDM: Enabling Robustness for Conditional Diffusion Model Weifeng Xu Xiang Zhu Xiaoyong Li AAML 23 0 0 05 Aug 2024
Self-Supervision Improves Diffusion Models for Tabular Data Imputation Yixin Liu Thalaiyasingam Ajanthan Hisham Husain Vu-Linh Nguyen 47 9 0 25 Jul 2024
Understanding Reinforcement Learning-Based Fine-Tuning of Diffusion Models: A Tutorial and Review Masatoshi Uehara Yulai Zhao Tommaso Biancalani Sergey Levine 66 22 0 18 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 57 21 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 56 30 0 01 Jul 2024
An Expectation-Maximization Algorithm for Training Clean Diffusion Models from Corrupted Observations Weimin Bai Yifei Wang Wenzheng Chen He Sun 44 9 0 01 Jul 2024
Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization Siyi Gu Minkai Xu Alexander Powers Weili Nie Tomas Geffner Karsten Kreis J. Leskovec Arash Vahdat Stefano Ermon 48 7 0 01 Jul 2024
General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design Yue Jian Curtis Wu Danny Reidenbach Aditi S. Krishnapriyan 34 1 0 24 Jun 2024
LatentExplainer: Explaining Latent Representations in Deep Generative Models with Multimodal Large Language Models Mengdan Zhu Raasikh Kanjiani Jiahui Lu Andrew Choi Qirui Ye Liang Zhao DiffM 42 1 0 21 Jun 2024
Transferable Boltzmann Generators Leon Klein Frank Noé 49 12 0 20 Jun 2024
Neural Approximate Mirror Maps for Constrained Diffusion Models Berthy Feng Ricardo Baptista Katherine Bouman MedIm DiffM 48 3 0 18 Jun 2024
Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Space Mohamed Amine Ketata Nicholas Gao Johanna Sommer Tom Wollschlager Stephan Günnemann DiffM 40 1 0 15 Jun 2024
Alleviating Distortion in Image Generation via Multi-Resolution Diffusion Models Qihao Liu Zhanpeng Zeng Ju He Qihang Yu Xiaohui Shen Liang-Chieh Chen 53 19 0 13 Jun 2024
$Diffusion Models in $\textit{De Novo}$ Drug Design$ Diffusion Models in $\textit{De Novo}$ Drug Design Amira Alakhdar Barnabás Póczos Newell Washburn MedIm 38 13 0 07 Jun 2024
CLoG: Benchmarking Continual Learning of Image Generation Models Haotian Zhang Junting Zhou Haowei Lin Hang Ye Jianhua Zhu Zihao Wang Liangcai Gao Yizhou Wang Yitao Liang DiffM VLM 37 1 0 07 Jun 2024
Using GNN property predictors as molecule generators Felix Therrien Edward H. Sargent Oleksandr Voznyy 48 1 0 05 Jun 2024
Cross-Domain Graph Data Scaling: A Showcase with Diffusion Models Wenzhuo Tang Haitao Mao Danial Dervovic Ivan Brugere Saumitra Mishra Yuying Xie Jiliang Tang 50 3 0 04 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 40 2 0 03 Jun 2024
Unlocking Guidance for Discrete State-Space Diffusion and Flow Models Hunter Nisonoff Junhao Xiong Stephan Allenspach Jennifer Listgarten 63 31 0 03 Jun 2024
Full-Atom Peptide Design based on Multi-modal Flow Matching Jiahan Li Chaoran Cheng Zuofan Wu Ruihan Guo Shitong Luo Zhizhou Ren Jian-wei Peng Jianzhu Ma 45 15 0 02 Jun 2024
Graph Neural Networks for Brain Graph Learning: A Survey Xuexiong Luo Jia Wu Jian Yang Shan Xue Amin Beheshti Quan Z. Sheng David Mcalpine Paul F. Sowman Alexis Giral Philip S. Yu AI4CE 26 4 0 01 Jun 2024
Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules Trevor Norton Debswapna Bhattacharya MedIm DiffM 50 2 0 31 May 2024
A Recipe for Charge Density Prediction Xiang Fu Andrew S. Rosen Kyle Bystrom Rui Wang Albert Musaelian Boris Kozinsky Tess E. Smidt Tommi Jaakkola 53 5 0 29 May 2024
MemControl: Mitigating Memorization in Diffusion Models via Automated Parameter Selection Raman Dutt Pedro Sanchez Ondrej Bohdal Sotirios A. Tsaftaris Timothy M. Hospedales MedIm 36 2 0 29 May 2024
EM Distillation for One-step Diffusion Models Sirui Xie Zhisheng Xiao Diederik P. Kingma Tingbo Hou Ying Nian Wu Kevin Patrick Murphy Tim Salimans Ben Poole Ruiqi Gao VLM DiffM 42 24 0 27 May 2024
Reflected Flow Matching Tianyu Xie Yu Zhu Longlin Yu Tong Yang Ziheng Cheng Shiyue Zhang Xiangyu Zhang Cheng Zhang 41 5 0 26 May 2024
Accelerating Diffusion Models with Parallel Sampling: Inference at Sub-Linear Time Complexity Haoxuan Chen Yinuo Ren Lexing Ying Grant M. Rotskoff 50 16 0 24 May 2024