Constrained Graph Variational Autoencoders for Molecule Design

23 May 2018

Qi Liu

Papers citing "Constrained Graph Variational Autoencoders for Molecule Design"

50 / 89 papers shown

Title
Towards Unified Latent Space for 3D Molecular Latent Diffusion Modeling Yanchen Luo Zhiyuan Liu Yi Zhao Sihang Li Kenji Kawaguchi Tat-Seng Chua Xuben Wang MedIm 69 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 Sihang Li Junfeng Fang Yaorui Shi Xuben Wang Kenji Kawaguchi Tat-Seng Chua 102 3 0 18 Feb 2025
Sub-graph Based Diffusion Model for Link Prediction Hang Li Wei Jin Geri Skenderi Harry Shomer Wenzhuo Tang Wenqi Fan Jiliang Tang DiffM 33 0 0 13 Sep 2024
Any-Property-Conditional Molecule Generation with Self-Criticism using Spanning Trees Alexia Jolicoeur-Martineau A. Baratin Kisoo Kwon Boris Knyazev Yan Zhang 40 1 0 12 Jul 2024
Interpreting Equivariant Representations Andreas Abildtrup Hansen Anna Calissano Aasa Feragen 53 1 0 23 Jan 2024
GraphMaker: Can Diffusion Models Generate Large Attributed Graphs? Mufei Li Eleonora Kreacic Vamsi K. Potluru Pan Li DiffM 42 7 0 20 Oct 2023
Neural Relational Inference with Fast Modular Meta-learning Ferran Alet Erica Weng Tomás Lozano Pérez L. Kaelbling 59 55 0 10 Oct 2023
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation Han Huang Leilei Sun Bowen Du Weifeng Lv DiffM 32 16 0 21 May 2023
Cross-Gate MLP with Protein Complex Invariant Embedding is A One-Shot Antibody Designer Cheng Tan Zhangyang Gao Lirong Wu Jun Xia Jiangbin Zheng Xihong Yang Yue Liu Bozhen Hu Stan Z. Li 37 14 0 21 Apr 2023
A Comprehensive Survey on Deep Graph Representation Learning Wei Ju Zheng Fang Yiyang Gu Zequn Liu Qingqing Long ... Jingyang Yuan Yusheng Zhao Yifan Wang Xiao Luo Ming Zhang GNN AI4TS 64 141 0 11 Apr 2023
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction Jiaqi Guan Wesley Wei Qian Xingang Peng Yufeng Su Jian-wei Peng Jianzhu Ma DiffM 34 162 0 06 Mar 2023
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow Fangce Sun Zhihao Zhan Hongyu Guo Ming Zhang Jian Tang 26 6 0 23 Feb 2023
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
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability Zhiqiang Zhong A. Barkova Davide Mottin 24 8 0 16 Feb 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
SchNetPack 2.0: A neural network toolbox for atomistic machine learning Kristof T. Schütt Stefaan S. P. Hessmann Niklas W. A. Gebauer Jonas Lederer M. Gastegger 25 59 0 11 Dec 2022
Improving Molecule Properties Through 2-Stage VAE Chenghui Zhou Barnabás Póczós DRL 28 1 0 06 Dec 2022
GraphGDP: Generative Diffusion Processes for Permutation Invariant Graph Generation Han Huang Leilei Sun Bowen Du Yanjie Fu Weifeng Lv DiffM 32 42 0 04 Dec 2022
Multi-view deep learning based molecule design and structural optimization accelerates the SARS-CoV-2 inhibitor discovery Chao Pang Yu Wang Yi Jiang Ruheng Wang R. Su Leyi Wei 21 1 0 03 Dec 2022
NVDiff: Graph Generation through the Diffusion of Node Vectors Xiaohui Chen Yukun Li Aonan Zhang Liping Liu DiffM 23 21 0 19 Nov 2022
An efficient graph generative model for navigating ultra-large combinatorial synthesis libraries Aryan Pedawi P. Gniewek Chao-Ling Chang Brandon M. Anderson H. V. D. Bedem 34 5 0 19 Oct 2022
Machine Learning for a Sustainable Energy Future Zhenpeng Yao Yanwei Lum Andrew K. Johnston L. M. Mejia-Mendoza Xiaoxia Zhou Yonggang Wen Alán Aspuru-Guzik E. Sargent Z. Seh 32 210 0 19 Oct 2022
Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design Keir Adams Connor W. Coley 34 25 0 06 Oct 2022
Equivariant Energy-Guided SDE for Inverse Molecular Design Fan Bao Min Zhao Zhongkai Hao Pei‐Yun Li Chongxuan Li Jun Zhu DiffM 193 64 0 30 Sep 2022
Graph neural networks for materials science and chemistry Patrick Reiser Marlen Neubert André Eberhard Luca Torresi Chen Zhou ... Houssam Metni Clint van Hoesel Henrik Schopmans T. Sommer Pascal Friederich GNN AI4CE 50 373 0 05 Aug 2022
Graph Learning based Generative Design for Resilience of Interdependent Network Systems Jiaxin Wu Pingfeng Wang AI4CE 31 6 0 03 Jul 2022
Exploring Chemical Space with Score-based Out-of-distribution Generation Seul Lee Jaehyeong Jo Sung Ju Hwang OODD 30 75 0 06 Jun 2022
An Empirical Study of Retrieval-enhanced Graph Neural Networks Dingmin Wang Shengchao Liu Hanchen Wang Bernardo Cuenca Grau Linfeng Song Jian Tang Song Le Qi Liu 21 0 0 01 Jun 2022
Tyger: Task-Type-Generic Active Learning for Molecular Property Prediction Kuangqi Zhou Kaixin Wang Jiashi Feng Jian Tang Tingyang Xu Xinchao Wang 29 1 0 23 May 2022
3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design Yinan Huang Xing Peng Jianzhu Ma Muhan Zhang BDL 30 48 0 15 May 2022
SPECTRE: Spectral Conditioning Helps to Overcome the Expressivity Limits of One-shot Graph Generators Karolis Martinkus Andreas Loukas Nathanael Perraudin Roger Wattenhofer 42 67 0 04 Apr 2022
SELFIES and the future of molecular string representations Mario Krenn Qianxiang Ai Senja Barthel Nessa Carson Angelo Frei ... Andrew Wang Andrew D. White Adamo Young Rose Yu A. Aspuru‐Guzik 38 149 0 31 Mar 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 36 86 0 28 Mar 2022
A Survey on Deep Graph Generation: Methods and Applications Yanqiao Zhu Yuanqi Du Yinkai Wang Yichen Xu Jieyu Zhang Qiang Liu Shu Wu 3DV GNN 31 67 0 13 Mar 2022
Interpretable Molecular Graph Generation via Monotonic Constraints Yuanqi Du Xiaojie Guo Amarda Shehu Liang Zhao 65 19 0 28 Feb 2022
MGCVAE: Multi-objective Inverse Design via Molecular Graph Conditional Variational Autoencoder Myeong-Sung Lee K. Min 33 41 0 14 Feb 2022
Deconfounding to Explanation Evaluation in Graph Neural Networks Yingmin Wu Xiang Wang An Zhang Xia Hu Fuli Feng Xiangnan He Tat-Seng Chua FAtt CML 17 14 0 21 Jan 2022
Structure-aware generation of drug-like molecules Pavol Drotár Arian R. Jamasb Ben Day Cătălina Cangea Pietro Lio 34 17 0 07 Nov 2021
Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design Wengong Jin Jeremy Wohlwend Regina Barzilay Tommi Jaakkola 22 136 0 09 Oct 2021
CCGG: A Deep Autoregressive Model for Class-Conditional Graph Generation Yassaman Ommi Matin Yousefabadi Faezeh Faez Amirmojtaba Sabour M. Baghshah Hamid R. Rabiee GNN CML BDL 42 4 0 07 Oct 2021
Top-N: Equivariant set and graph generation without exchangeability Clément Vignac P. Frossard BDL 71 34 0 05 Oct 2021
Vitruvion: A Generative Model of Parametric CAD Sketches Ari Seff Wenda Zhou Nick Richardson Ryan P. Adams 27 64 0 29 Sep 2021
Local Augmentation for Graph Neural Networks Songtao Liu Rex Ying Hanze Dong Lanqing Li Tingyang Xu Yu Rong P. Zhao Junzhou Huang Dinghao Wu 45 91 0 08 Sep 2021
Unconditional Scene Graph Generation Sarthak Garg Helisa Dhamo Azade Farshad Sabrina Musatian Nassir Navab F. Tombari 18 23 0 12 Aug 2021
Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction Jiahua Rao Shuangjia Zheng Yuedong Yang 21 46 0 01 Jul 2021
Geometric learning of the conformational dynamics of molecules using dynamic graph neural networks Michael Ashby Jenna A. Bilbrey 25 4 0 24 Jun 2021
Artificial Intelligence in Drug Discovery: Applications and Techniques Jianyuan Deng Zhibo Yang Iwao Ojima Dimitris Samaras Fusheng Wang AI4TS 35 100 0 09 Jun 2021
JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Design AkshatKumar Nigam R. Pollice Alán Aspuru-Guzik 32 51 0 07 Jun 2021
GraphDF: A Discrete Flow Model for Molecular Graph Generation Youzhi Luo Keqiang Yan Shuiwang Ji DRL 185 188 0 01 Feb 2021
Neural representation and generation for RNA secondary structures Zichao Yan William L. Hamilton Mathieu Blanchette 40 2 0 01 Feb 2021