Junction Tree Variational Autoencoder for Molecular Graph Generation

12 February 2018

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

50 / 248 papers shown

Title
A Comprehensive Benchmarking Platform for Deep Generative Models in Molecular Design Adarsh Singh ELM 18 0 0 19 May 2025
Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks Xinyu Wang Jinbo Bi Minghu Song CLL 69 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 Yong-Jin Liu Yiping Song 42 0 0 22 Apr 2025
Latent Bayesian Optimization via Autoregressive Normalizing Flows Seunghun Lee Jinyoung Park Jaewon Chu Minseo Yoon H. Kim BDL 38 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 Xuben Wang MedIm 69 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 81 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 Xuben Wang Kenji Kawaguchi Tat-Seng Chua 102 3 0 18 Feb 2025
Towards Efficient Molecular Property Optimization with Graph Energy Based Models Luca Miglior Lorenzo Simone Marco Podda Davide Bacciu AI4CE 71 0 0 17 Feb 2025
HOG-Diff: Higher-Order Guided Diffusion for Graph Generation Yiming Huang Tolga Birdal DiffM 78 0 0 06 Feb 2025
Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization Natalie Maus Kyurae Kim Yimeng Zeng Haydn Thomas Jones Fangping Wan Marcelo Der Torossian Torres Cesar de la Fuente-Nunez Jacob R. Gardner 85 0 0 31 Jan 2025
Graph Representation Learning with Diffusion Generative Models Daniel Wesego DiffM 43 0 0 22 Jan 2025
Text2Data: Low-Resource Data Generation with Textual Control Shiyu Wang Yihao Feng Tian Lan Ning Yu Yu Bai Ran Xu Han Wang Caiming Xiong Shri Kiran Srinivasan DiffM 88 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 58 1 0 03 Nov 2024
Chemical Language Model Linker: blending text and molecules with modular adapters Yifan Deng Spencer S. Ericksen Anthony Gitter 30 1 0 26 Oct 2024
Optimizing Backward Policies in GFlowNets via Trajectory Likelihood Maximization Timofei Gritsaev Nikita Morozov S. Samsonov D. Tiapkin 21 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 42 0 0 15 Oct 2024
Chemistry-Inspired Diffusion with Non-Differentiable Guidance Yuchen Shen Chenhao Zhang Sijie Fu Chenghui Zhou Newell Washburn Barnabás Póczos 55 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 46 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 28 0 0 02 Sep 2024
Repurformer: Transformers for Repurposing-Aware Molecule Generation Changhun Lee Gyumin Lee 57 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 48 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 47 12 0 23 Jun 2024
Graph Neural Thompson Sampling Shuang Wu Arash A. Amini 51 0 0 15 Jun 2024
Decoupling regularization from the action space Sobhan Mohammadpour Emma Frejinger Pierre-Luc Bacon 34 0 0 10 Jun 2024
A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences Miguel González Duque Richard Michael Simon Bartels Yevgen Zainchkovskyy Søren Hauberg Wouter Boomsma 44 4 0 07 Jun 2024
MAGE: Model-Level Graph Neural Networks Explanations via Motif-based Graph Generation Zhaoning Yu Hongyang Gao 47 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 48 10 0 19 May 2024
ACEGEN: Reinforcement learning of generative chemical agents for drug discovery Albert Bou Morgan Thomas Sebastian Dittert Carles Navarro Ramírez Maciej Majewski ... Mazen Ahmad Vincent Moens Woody Sherman Simone Sciabola Gianni De Fabritiis 50 6 0 07 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 52 1 0 30 Apr 2024
Graph Reinforcement Learning for Combinatorial Optimization: A Survey and Unifying Perspective Victor-Alexandru Darvariu Stephen Hailes Mirco Musolesi AI4CE 50 6 0 09 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 38 5 0 04 Apr 2024
Molecular Generative Adversarial Network with Multi-Property Optimization Huidong Tang Chen Li Sayaka Kamei Yoshihiro Yamanishi Yasuhiko Morimoto 45 0 0 29 Mar 2024
Overcoming Order in Autoregressive Graph Generation Edo Cohen-Karlik Eyal Rozenberg Daniel Freedman 34 1 0 04 Feb 2024
PF-GNN: Differentiable particle filtering based approximation of universal graph representations Mohammed Haroon Dupty Yanfei Dong W. Lee 26 13 0 31 Jan 2024
Graph Fairness Learning under Distribution Shifts Yibo Li Xiao Wang Yujie Xing Shaohua Fan Ruijia Wang Yaoqi Liu Chuan Shi OOD 39 7 0 30 Jan 2024
STRIDE: Structure-guided Generation for Inverse Design of Molecules Shehtab Zaman D. Akhiyarov Mauricio Araya-Polo Kenneth Chiu 29 1 0 06 Nov 2023
Synthetic Data as Validation Qixing Hu Alan L. Yuille Zongwei Zhou SyDa OOD 26 8 0 24 Oct 2023
Rethinking Tokenizer and Decoder in Masked Graph Modeling for Molecules Zhiyuan Liu Yaorui Shi An Zhang Enzhi Zhang Kenji Kawaguchi Xiang Wang Tat-Seng Chua AI4CE 39 36 0 23 Oct 2023
GraphMaker: Can Diffusion Models Generate Large Attributed Graphs? Mufei Li Eleonora Kreacic Vamsi K. Potluru Pan Li DiffM 42 7 0 20 Oct 2023
Genetic algorithms are strong baselines for molecule generation Austin Tripp José Miguel Hernández-Lobato 43 16 0 13 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
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 34 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 41 11 0 15 Jul 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 25 13 0 02 Jun 2023
Inverse Protein Folding Using Deep Bayesian Optimization Natalie Maus Yimeng Zeng Daniel A. Anderson Phillip M. Maffettone Aaron C. Solomon Peyton Greenside Osbert Bastani Jacob R. Gardner 28 2 0 25 May 2023
Learning Subpocket Prototypes for Generalizable Structure-based Drug Design Zaixin Zhang Qi Liu 33 34 0 22 May 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
MotifRetro: Exploring the Combinability-Consistency Trade-offs in retrosynthesis via Dynamic Motif Editing Zhangyang Gao Xingran Chen Cheng Tan Stan Z. Li 33 1 0 20 May 2023
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