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Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation

1 January 2023

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Papers citing "Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation"

39 / 39 papers shown

Title
Graph ODEs and Beyond: A Comprehensive Survey on Integrating Differential Equations with Graph Neural Networks Ziqiang Liu Xiaoda Wang Bohan Wang Zijie Huang Carl Yang Wei Jin AI4TS AI4CE 509 1 0 29 Mar 2025
Towards Unified and Lossless Latent Space for 3D Molecular Latent Diffusion Modeling Yanchen Luo Zhiyuan Liu Yi Zhao Changhao Nai Kenji Kawaguchi Tat-Seng Chua Xiang Wang Yang Zhang Xiang Wang MedIm 134 0 0 19 Mar 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Changhao Nai Sihang Li Yaorui Shi Xiang Wang Kenji Kawaguchi Tat-Seng Chua 170 3 0 18 Feb 2025
DiffGAD: A Diffusion-based Unsupervised Graph Anomaly Detector Jinghan Li Yuan Gao Jinda Lu Sihang Li Congcong Wen Hui Lin Xiang Wang 113 3 0 09 Oct 2024
Discrete Copula Diffusion Hoang Trung-Dung Oliver Broadrick Mathias Niepert Guy Van den Broeck DiffM 151 12 0 02 Oct 2024
DPM-Solver: A Fast ODE Solver for Diffusion Probabilistic Model Sampling in Around 10 Steps Cheng Lu Yuhao Zhou Fan Bao Jianfei Chen Chongxuan Li Jun Zhu DiffM 217 1,449 0 02 Jun 2022
Torsional Diffusion for Molecular Conformer Generation Bowen Jing Gabriele Corso Jeffrey Chang Regina Barzilay Tommi Jaakkola DiffM BDL 91 272 0 01 Jun 2022
Equivariant Diffusion for Molecule Generation in 3D Emiel Hoogeboom Victor Garcia Satorras Clément Vignac Max Welling DiffM 127 618 0 31 Mar 2022
GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation Minkai Xu Lantao Yu Yang Song Chence Shi Stefano Ermon Jian Tang BDL DiffM 160 516 0 06 Mar 2022
Pseudo Numerical Methods for Diffusion Models on Manifolds Luping Liu Yi Ren Zhijie Lin Zhou Zhao DiffM 97 647 0 20 Feb 2022
Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations Jaehyeong Jo Seul Lee Sung Ju Hwang DiffM 65 225 0 05 Feb 2022
On Evaluation Metrics for Graph Generative Models Rylee Thompson Boris Knyazev Elahe Ghalebi Jungtaek Kim Graham W. Taylor EGVM 83 43 0 24 Jan 2022
Top-N: Equivariant set and graph generation without exchangeability Clément Vignac P. Frossard BDL 114 34 0 05 Oct 2021
Structured Denoising Diffusion Models in Discrete State-Spaces Jacob Austin Daniel D. Johnson Jonathan Ho Daniel Tarlow Rianne van den Berg DiffM 176 941 0 07 Jul 2021
Variational Diffusion Models Diederik P. Kingma Tim Salimans Ben Poole Jonathan Ho DiffM 181 1,130 0 01 Jul 2021
Do Transformers Really Perform Bad for Graph Representation? Chengxuan Ying Tianle Cai Shengjie Luo Shuxin Zheng Guolin Ke Di He Yanming Shen Tie-Yan Liu GNN 95 442 0 09 Jun 2021
Rethinking Graph Transformers with Spectral Attention Devin Kreuzer Dominique Beaini William L. Hamilton Vincent Létourneau Prudencio Tossou 99 542 0 07 Jun 2021
GraphDF: A Discrete Flow Model for Molecular Graph Generation Youzhi Luo Keqiang Yan Shuiwang Ji DRL 230 199 0 01 Feb 2021
GraphEBM: Molecular Graph Generation with Energy-Based Models Meng Liu Keqiang Yan Bora Oztekin Shuiwang Ji 75 88 0 31 Jan 2021
A Generalization of Transformer Networks to Graphs Vijay Prakash Dwivedi Xavier Bresson AI4CE 105 749 0 17 Dec 2020
Score-Based Generative Modeling through Stochastic Differential Equations Yang Song Jascha Narain Sohl-Dickstein Diederik P. Kingma Abhishek Kumar Stefano Ermon Ben Poole DiffM SyDa 344 6,480 0 26 Nov 2020
MoFlow: An Invertible Flow Model for Generating Molecular Graphs Chengxi Zang Fei Wang BDL 127 294 0 17 Jun 2020
GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation Chence Shi Minkai Xu Zhaocheng Zhu Weinan Zhang Ming Zhang Jian Tang 173 438 0 26 Jan 2020
Efficient Graph Generation with Graph Recurrent Attention Networks Renjie Liao Yujia Li Yang Song Shenlong Wang C. Nash William L. Hamilton David Duvenaud R. Urtasun R. Zemel GNN 138 335 0 02 Oct 2019
Generative Modeling by Estimating Gradients of the Data Distribution Yang Song Stefano Ermon SyDa DiffM 258 3,916 0 12 Jul 2019
Strategies for Pre-training Graph Neural Networks Weihua Hu Bowen Liu Joseph Gomes Marinka Zitnik Percy Liang Vijay S. Pande J. Leskovec SSL AI4CE 116 1,409 0 29 May 2019
DEFactor: Differentiable Edge Factorization-based Probabilistic Graph Generation Rim Assouel Mohamed Ahmed Marwin H. S. Segler Amir Saffari Yoshua Bengio 70 55 0 24 Nov 2018
Neural Ordinary Differential Equations T. Chen Yulia Rubanova J. Bettencourt David Duvenaud AI4CE 417 5,111 0 19 Jun 2018
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 293 902 0 07 Jun 2018
Constrained Graph Variational Autoencoders for Molecule Design Qi Liu Miltiadis Allamanis Marc Brockschmidt Alexander L. Gaunt BDL 77 456 0 23 May 2018
Fréchet ChemNet Distance: A metric for generative models for molecules in drug discovery Kristina Preuer Philipp Renz Thomas Unterthiner Sepp Hochreiter Günter Klambauer MedIm 96 338 0 26 Mar 2018
Syntax-Directed Variational Autoencoder for Structured Data H. Dai Yingtao Tian Bo Dai Steven Skiena Le Song 102 329 0 24 Feb 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 352 1,368 0 12 Feb 2018
GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders M. Simonovsky N. Komodakis GNN BDL 117 851 0 09 Feb 2018
Modeling Relational Data with Graph Convolutional Networks Michael Schlichtkrull Thomas Kipf Peter Bloem Rianne van den Berg Ivan Titov Max Welling GNN 191 4,828 0 17 Mar 2017
Grammar Variational Autoencoder Matt J. Kusner Brooks Paige José Miguel Hernández-Lobato BDL DRL 85 844 0 06 Mar 2017
Variational Graph Auto-Encoders Thomas Kipf Max Welling GNN BDL SSL CML 151 3,586 0 21 Nov 2016
Automatic chemical design using a data-driven continuous representation of molecules Rafael Gómez-Bombarelli Jennifer N. Wei David Duvenaud José Miguel Hernández-Lobato Benjamín Sánchez-Lengeling Dennis Sheberla J. Aguilera-Iparraguirre Timothy D. Hirzel Ryan P. Adams Alán Aspuru-Guzik 3DV 171 2,939 0 07 Oct 2016
Deep Unsupervised Learning using Nonequilibrium Thermodynamics Jascha Narain Sohl-Dickstein Eric A. Weiss Niru Maheswaranathan Surya Ganguli SyDa DiffM 306 7,005 0 12 Mar 2015