Junction Tree Variational Autoencoder for Molecular Graph Generation

12 February 2018

Papers citing "Junction Tree Variational Autoencoder for Molecular Graph Generation"

50 / 254 papers shown

Title
Stability and Generalization of lp-Regularized Stochastic Learning for GCN Shiyu Liu Linsen Wei Shaogao Lv Ming Li MLT 25 0 0 20 May 2023
Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB files Daniel Flam-Shepherd Alán Aspuru-Guzik 27 52 0 09 May 2023
High-Dimensional Bayesian Optimization via Semi-Supervised Learning with Optimized Unlabeled Data Sampling Y. Yin Yu Wang Gang Xu 32 4 0 04 May 2023
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design Zaixin Zhang Qi Liu Cheekong Lee Chang-Yu Hsieh Enhong Chen 29 18 0 12 Apr 2023
GraphGANFed: A Federated Generative Framework for Graph-Structured Molecules Towards Efficient Drug Discovery Daniel Manu Jingjing Yao Wuji Liu Xiang Sun FedML 38 6 0 11 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 72 141 0 11 Apr 2023
InstructBio: A Large-scale Semi-supervised Learning Paradigm for Biochemical Problems Fang Wu Huiling Qin Siyuan Li Stan Z. Li Xianyuan Zhan Jinbo Xu 24 5 0 08 Apr 2023
Utilizing Reinforcement Learning for de novo Drug Design Hampus Gummesson Svensson C. Tyrchan O. Engkvist M. Chehreghani 40 17 0 30 Mar 2023
Mind the Label Shift of Augmentation-based Graph OOD Generalization Junchi Yu Jian Liang Ran He 34 28 0 27 Mar 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 31 6 0 23 Feb 2023
Distributional GFlowNets with Quantile Flows Dinghuai Zhang L. Pan Ricky T. Q. Chen Aaron Courville Yoshua Bengio 32 25 0 11 Feb 2023
Generalization in Graph Neural Networks: Improved PAC-Bayesian Bounds on Graph Diffusion Haotian Ju Dongyue Li Aneesh Sharma Hongyang R. Zhang 31 40 0 09 Feb 2023
Proposing Novel Extrapolative Compounds by Nested Variational Autoencoders Yoshihiro Osakabe A. Asahara DRL 25 0 0 06 Feb 2023
Image To Tree with Recursive Prompting James Batten Matthew Sinclair Ben Glocker M. Schaap MedIm 20 1 0 01 Jan 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
Molecule optimization via multi-objective evolutionary in implicit chemical space Xin Xia Yansen Su Chunhou Zheng Xiangxiang Zeng 41 1 0 17 Dec 2022
Molecular Graph Generation by Decomposition and Reassembling Masatsugu Yamada M. Sugiyama 24 4 0 11 Dec 2022
Improving Molecule Properties Through 2-Stage VAE Chenghui Zhou Barnabás Póczós DRL 33 1 0 06 Dec 2022
GrannGAN: Graph annotation generative adversarial networks Yoann Boget Magda Gregorova Alexandros Kalousis GAN 23 0 0 01 Dec 2022
A Deep Learning Approach to the Prediction of Drug Side-Effects on Molecular Graphs P. Bongini Elisa Messori Niccolò Pancino Monica Bianchini GNN OOD 23 2 0 30 Nov 2022
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 33 51 0 28 Nov 2022
Proactive Robot Assistance via Spatio-Temporal Object Modeling Maithili Patel Sonia Chernova 34 26 0 28 Nov 2022
NVDiff: Graph Generation through the Diffusion of Node Vectors Xiaohui Chen Yukun Li Aonan Zhang Liping Liu DiffM 28 21 0 19 Nov 2022
Deep learning methods for drug response prediction in cancer: predominant and emerging trends A. Partin Thomas Brettin Yitan Zhu Oleksandr Narykov Austin R. Clyde Jamie Overbeek Department of Materials Science 13 54 0 18 Nov 2022
ParticleGrid: Enabling Deep Learning using 3D Representation of Materials Shehtab Zaman E. Ferguson Cécile Pereira D. Akhiyarov Mauricio Araya-Polo Kenneth Chiu DiffM AI4CE 29 2 0 15 Nov 2022
Micro and Macro Level Graph Modeling for Graph Variational Auto-Encoders Kiarash Zahirnia Oliver Schulte Parmis Naddaf Ke Li 42 10 0 30 Oct 2022
An Empirical Evaluation of Zeroth-Order Optimization Methods on AI-driven Molecule Optimization Elvin Lo Pin-Yu Chen 37 0 0 27 Oct 2022
Boosting the Cycle Counting Power of Graph Neural Networks with I $^2$ -GNNs Yinan Huang Xingang Peng Jianzhu Ma Muhan Zhang 84 47 0 22 Oct 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 36 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
CLEAR: Generative Counterfactual Explanations on Graphs Jing Ma Ruocheng Guo Saumitra Mishra Aidong Zhang Jundong Li CML OOD 35 54 0 16 Oct 2022
Modular Flows: Differential Molecular Generation Yogesh Verma Samuel Kaski Markus Heinonen Vikas K. Garg 29 14 0 12 Oct 2022
Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design Keir Adams Connor W. Coley 39 25 0 06 Oct 2022
GFlowNets and variational inference Nikolay Malkin Salem Lahlou T. Deleu Xu Ji J. E. Hu Katie Everett Dinghuai Zhang Yoshua Bengio BDL 134 77 0 02 Oct 2022
Multi-objective Deep Data Generation with Correlated Property Control Shiyu Wang Xiaojie Guo Xuanyang Lin Bo Pan Yuanqi Du ... S. Alkhalifa K. Minbiole Bill Wuest Amarda Shehu Liang Zhao AI4CE 54 14 0 01 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
GLSO: Grammar-guided Latent Space Optimization for Sample-efficient Robot Design Automation Jiaheng Hu Julian Whiman Howie Choset 42 16 0 23 Sep 2022
Probabilistic Generative Transformer Language models for Generative Design of Molecules Lai Wei Nihang Fu Yuqi Song Qian Wang Jianjun Hu AI4CE 38 11 0 20 Sep 2022
Artificial Intelligence for In Silico Clinical Trials: A Review Zifeng Wang Chufan Gao Lucas Glass Jimeng Sun 41 12 0 16 Sep 2022
MDM: Molecular Diffusion Model for 3D Molecule Generation Lei Huang Hengtong Zhang Tingyang Xu Ka-Chun Wong DiffM 34 81 0 13 Sep 2022
A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language Bing-Huang Su Dazhao Du Zhao-Qing Yang Yujie Zhou Jiangmeng Li Anyi Rao Haoran Sun Zhiwu Lu Ji-Rong Wen 49 108 0 12 Sep 2022
Diffusion Models: A Comprehensive Survey of Methods and Applications Ling Yang Zhilong Zhang Yingxia Shao Shenda Hong Runsheng Xu Yue Zhao Wentao Zhang Bin Cui Ming-Hsuan Yang DiffM MedIm 224 1,311 0 02 Sep 2022
String-based Molecule Generation via Multi-decoder VAE Kisoo Kwon Kuhwan Jung Jung-Geun Park Hwidong Na Jinwoo Shin DRL 34 2 0 23 Aug 2022
Improving Small Molecule Generation using Mutual Information Machine Daniel A. Reidenbach M. Livne Rajesh Ilango M. Gill Johnny Israeli 28 14 0 18 Aug 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 50 374 0 05 Aug 2022
Controllable Data Generation by Deep Learning: A Review Shiyu Wang Yuanqi Du Xiaojie Guo Bo Pan Zhaohui Qin Liang Zhao 33 28 0 19 Jul 2022
Graph Neural Network Bandits Parnian Kassraie Andreas Krause Ilija Bogunovic 26 11 0 13 Jul 2022
GEMS: Scene Expansion using Generative Models of Graphs Rishi G. Agarwal Tirupati Saketh Chandra Vaidehi Patil Aniruddha Mahapatra K. Kulkarni Vishwa Vinay 30 4 0 08 Jul 2022
Dynamic-Group-Aware Networks for Multi-Agent Trajectory Prediction with Relational Reasoning Chenxin Xu Yuxin Wei Bohan Tang Sheng Yin Ya Zhang Siheng Chen AI4TS AI4CE 32 33 0 27 Jun 2022