Junction Tree Variational Autoencoder for Molecular Graph Generation

12 February 2018

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

50 / 200 papers shown

Title
Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks Xinyu Wang Jinbo Bi Minghu Song CLL 62 0 0 01 May 2025
MetaMolGen: A Neural Graph Motif Generation Model for De Novo Molecular Design Zimo Yan Jie Zhang Zheng Xie Chang-rui Liu Y. Liu Yiping Song 34 0 0 22 Apr 2025
Latent Bayesian Optimization via Autoregressive Normalizing Flows Seunghun Lee Jinyoung Park Jaewon Chu Minseo Yoon H. Kim BDL 30 1 0 21 Apr 2025
Towards Unified Latent Space for 3D Molecular Latent Diffusion Modeling Yanchen Luo Zhiyuan Liu Yi Zhao Sihang Li Kenji Kawaguchi Tat-Seng Chua X. Wang MedIm 59 0 0 19 Mar 2025
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation Mohit Pandey G. Subbaraj Artem Cherkasov Martin Ester Emmanuel Bengio AI4CE 74 1 0 08 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 X. Wang Kenji Kawaguchi Tat-Seng Chua 100 3 0 18 Feb 2025
Towards Efficient Molecular Property Optimization with Graph Energy Based Models Luca Miglior Lorenzo Simone Marco Podda Davide Bacciu AI4CE 67 0 0 17 Feb 2025
HOG-Diff: Higher-Order Guided Diffusion for Graph Generation Yiming Huang Tolga Birdal DiffM 76 0 0 06 Feb 2025
Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization N. Maus Kyurae Kim Yimeng Zeng Haydn Jones Fangping Wan Marcelo Der Torossian Torres Cesar de la Fuente-Nunez J. Gardner 80 0 0 31 Jan 2025
Graph Representation Learning with Diffusion Generative Models Daniel Wesego DiffM 41 0 0 22 Jan 2025
Text2Data: Low-Resource Data Generation with Textual Control Shiyu Wang Yihao Feng Tian Lan Ning Yu Yu Bai R. Xu H. Wang Caiming Xiong S. DiffM 80 0 0 03 Jan 2025
Conditional Latent Space Molecular Scaffold Optimization for Accelerated Molecular Design O. Boyar Hiroyuki Hanada I. Takeuchi BDL 40 0 0 03 Nov 2024
GraphXForm: Graph transformer for computer-aided molecular design Jonathan Pirnay Jan G. Rittig Alexander B. Wolf Martin Grohe Jakob Burger Alexander Mitsos D. G. Grimm AI4CE 51 1 0 03 Nov 2024
Chemical Language Model Linker: blending text and molecules with modular adapters Yifan Deng Spencer S. Ericksen Anthony Gitter 21 1 0 26 Oct 2024
Optimizing Backward Policies in GFlowNets via Trajectory Likelihood Maximization Timofei Gritsaev Nikita Morozov S. Samsonov D. Tiapkin 16 0 0 20 Oct 2024
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning Peter Eckmann D. Wu G. Heinzelmann Michael K. Gilson Rose Yu AI4CE 40 0 0 15 Oct 2024
Chemistry-Inspired Diffusion with Non-Differentiable Guidance Yuchen Shen Chenhao Zhang Sijie Fu Chenghui Zhou Newell Washburn Barnabás Póczos 50 0 0 09 Oct 2024
Signed Graph Autoencoder for Explainable and Polarization-Aware Network Embeddings Nikolaos Nakis Chrysoula Kosma Giannis Nikolentzos Michalis Chatzianastasis Iakovos Evdaimon Michalis Vazirgiannis 44 1 0 16 Sep 2024
MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs Zhixiang Cheng Hongxin Xiang Pengsen Ma Li Zeng Xin Jin ... Yang Deng Bosheng Song Xinxin Feng Changhui Deng Xiangxiang Zeng 24 0 0 02 Sep 2024
Repurformer: Transformers for Repurposing-Aware Molecule Generation Changhun Lee Gyumin Lee 47 0 0 16 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 43 7 0 01 Jul 2024
Efficient Evolutionary Search Over Chemical Space with Large Language Models Haorui Wang Marta Skreta C. Ser Wenhao Gao Lingkai Kong ... Yanqiao Zhu Yuanqi Du Alán Aspuru-Guzik Kirill Neklyudov Chao Zhang 37 12 0 23 Jun 2024
Graph Neural Thompson Sampling Shuang Wu Arash A. Amini 43 0 0 15 Jun 2024
Decoupling regularization from the action space Sobhan Mohammadpour Emma Frejinger Pierre-Luc Bacon 27 0 0 10 Jun 2024
MAGE: Model-Level Graph Neural Networks Explanations via Motif-based Graph Generation Zhaoning Yu Hongyang Gao 37 3 0 21 May 2024
Discrete-state Continuous-time Diffusion for Graph Generation Zhe Xu Ruizhong Qiu Yuzhong Chen Huiyuan Chen Xiran Fan Menghai Pan Zhichen Zeng Mahashweta Das Hanghang Tong 32 8 0 19 May 2024
Leveraging Active Subspaces to Capture Epistemic Model Uncertainty in Deep Generative Models for Molecular Design A. N. M. N. Abeer Sanket R. Jantre Nathan M. Urban Byung-Jun Yoon 42 1 0 30 Apr 2024
GP-MoLFormer: A Foundation Model For Molecular Generation Jerret Ross Brian M. Belgodere Samuel C. Hoffman Vijil Chenthamarakshan Youssef Mroueh Payel Das Payel Das 36 5 0 04 Apr 2024
Molecular Generative Adversarial Network with Multi-Property Optimization Huidong Tang Chen Li Sayaka Kamei Yoshihiro Yamanishi Yasuhiko Morimoto 37 0 0 29 Mar 2024
Overcoming Order in Autoregressive Graph Generation Edo Cohen-Karlik Eyal Rozenberg Daniel Freedman 30 1 0 04 Feb 2024
Graph Fairness Learning under Distribution Shifts Yibo Li Xiao Wang Yujie Xing Shaohua Fan Ruijia Wang Yaoqi Liu Chuan Shi OOD 31 7 0 30 Jan 2024
GraphMaker: Can Diffusion Models Generate Large Attributed Graphs? Mufei Li Eleonora Kreacic Vamsi K. Potluru Pan Li DiffM 32 7 0 20 Oct 2023
Genetic algorithms are strong baselines for molecule generation Austin Tripp José Miguel Hernández-Lobato 32 16 0 13 Oct 2023
Neural Relational Inference with Fast Modular Meta-learning Ferran Alet Erica Weng Tomás Lozano Pérez L. Kaelbling 52 55 0 10 Oct 2023
MHG-GNN: Combination of Molecular Hypergraph Grammar with Graph Neural Network Akihiro Kishimoto Hiroshi Kajino Masataka Hirose Junta Fuchiwaki Indra Priyadarsini Lisa Hamada Hajime Shinohara D. Nakano Seiji Takeda AI4CE 20 4 0 28 Sep 2023
An Empirical Study of the Effectiveness of Using a Replay Buffer on Mode Discovery in GFlowNets Nikhil Vemgal Elaine Lau Doina Precup 26 11 0 15 Jul 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 20 13 0 02 Jun 2023
Inverse Protein Folding Using Deep Bayesian Optimization N. Maus Yimeng Zeng Daniel A. Anderson Phillip M. Maffettone Aaron C. Solomon Peyton Greenside Osbert Bastani Jacob R. Gardner 15 2 0 25 May 2023
Learning Subpocket Prototypes for Generalizable Structure-based Drug Design Zaixin Zhang Qi Liu 25 34 0 22 May 2023
MotifRetro: Exploring the Combinability-Consistency Trade-offs in retrosynthesis via Dynamic Motif Editing Zhangyang Gao Xingran Chen Cheng Tan Stan Z. Li 19 1 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 19 51 0 09 May 2023
High-Dimensional Bayesian Optimization via Semi-Supervised Learning with Optimized Unlabeled Data Sampling Y. Yin Yu Wang Gang Xu 24 4 0 04 May 2023
GraphGANFed: A Federated Generative Framework for Graph-Structured Molecules Towards Efficient Drug Discovery Daniel Manu Jingjing Yao Wuji Liu Xiang Sun FedML 30 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 31 141 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 16 5 0 08 Apr 2023
Mind the Label Shift of Augmentation-based Graph OOD Generalization Junchi Yu Jian Liang R. He 34 27 0 27 Mar 2023
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow Fangce Sun Zhihao Zhan Hongyu Guo Ming Zhang Jian Tang 21 6 0 23 Feb 2023
Distributional GFlowNets with Quantile Flows Dinghuai Zhang L. Pan Ricky T. Q. Chen Aaron Courville Yoshua Bengio 26 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 23 40 0 09 Feb 2023
Proposing Novel Extrapolative Compounds by Nested Variational Autoencoders Yoshihiro Osakabe A. Asahara DRL 22 0 0 06 Feb 2023