Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits

27 June 2020

Mikolaj Sacha

Mikolaj Blaz

Piotr Byrski

Paweł Dąbrowski-Tumański

Mikołaj Chromiński

Rafał Loska

Pawel Wlodarczyk-Pruszynski

Stanislaw Jastrzebski

GNN

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Papers citing "Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits"

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Title
LLM-Augmented Chemical Synthesis and Design Decision Programs Haorui Wang Jeff Guo Lingkai Kong R. Ramprasad Philippe Schwaller Yuanqi Du Chao Zhang 74 0 0 11 May 2025
A User-Tunable Machine Learning Framework for Step-Wise Synthesis Planning Shivesh Prakash Viki Kumar Prasad Hans-Arno Jacobsen 79 0 0 03 Apr 2025
RetroGFN: Diverse and Feasible Retrosynthesis using GFlowNets Piotr Gaiñski Michał Koziarski Krzysztof Maziarz Marwin H. S. Segler Jacek Tabor Marek Śmieja 105 4 0 26 Jun 2024
DirectMultiStep: Direct Route Generation for Multistep Retrosynthesis Yu Shee Haote Li Anton Morgunov Victor S. Batista 69 3 0 22 May 2024
Decoding and Diversity in Machine Translation Nicholas Roberts Davis Liang Graham Neubig Zachary Chase Lipton 40 21 0 26 Nov 2020
RetroGNN: Approximating Retrosynthesis by Graph Neural Networks for De Novo Drug Design Cheng-Hao Liu Maksym Korablyov Stanislaw Jastrzebski Pawel Wlodarczyk-Pruszynski Yoshua Bengio Marwin H. S. Segler GNN 58 16 0 25 Nov 2020
RetroXpert: Decompose Retrosynthesis Prediction like a Chemist Chao-chao Yan Qianggang Ding P. Zhao Shuangjia Zheng Jinyu Yang Yang Yu Junzhou Huang 57 107 0 04 Nov 2020
Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning S. Gottipati B. Sattarov Sufeng Niu Yashaswi Pathak Haoran Wei ... Simon R. Blackburn Connor W. Coley Jian Tang Sarath Chandar Yoshua Bengio 43 109 0 26 Apr 2020
A Graph to Graphs Framework for Retrosynthesis Prediction Chence Shi Minkai Xu Hongyu Guo Ming Zhang Jian Tang 57 154 0 28 Mar 2020
The Synthesizability of Molecules Proposed by Generative Models Wenhao Gao Connor W. Coley 63 256 0 17 Feb 2020
Retrosynthesis Prediction with Conditional Graph Logic Network H. Dai Chengtao Li Connor W. Coley Bo Dai Le Song 59 182 0 06 Jan 2020
Learning to Make Generalizable and Diverse Predictions for Retrosynthesis Benson Chen T. Shen Tommi Jaakkola Regina Barzilay 56 46 0 21 Oct 2019
Insertion-based Decoding with automatically Inferred Generation Order Jiatao Gu Qi Liu Kyunghyun Cho 57 109 0 04 Feb 2019
Graph Transformation Policy Network for Chemical Reaction Prediction Kien Do T. Tran Svetha Venkatesh 107 162 0 22 Dec 2018
Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction P. Schwaller Teodoro Laino John McGuinness A. Horváth Constantine Bekas A. Lee 103 739 0 06 Nov 2018
Middle-Out Decoding Shikib Mehri Leonid Sigal 41 22 0 28 Oct 2018
Sequence to Sequence Mixture Model for Diverse Machine Translation Xuanli He Gholamreza Haffari Mohammad Norouzi 58 57 0 17 Oct 2018
Why are Sequence-to-Sequence Models So Dull? Understanding the Low-Diversity Problem of Chatbots Shaojie Jiang Maarten de Rijke 97 44 0 06 Sep 2018
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 287 902 0 07 Jun 2018
A Generative Model For Electron Paths John Bradshaw Matt J. Kusner Brooks Paige Marwin H. S. Segler José Miguel Hernández-Lobato 51 56 0 23 May 2018
GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models Jiaxuan You Rex Ying Xiang Ren William L. Hamilton J. Leskovec GNN BDL 116 849 0 24 Feb 2018
Deep Reinforcement Learning for De-Novo Drug Design Mariya Popova Olexandr Isayev Alexander Tropsha 85 1,031 0 29 Nov 2017
"Found in Translation": Predicting Outcomes of Complex Organic Chemistry Reactions using Neural Sequence-to-Sequence Models P. Schwaller T. Gaudin D. Lanyi C. Bekas Teodoro Laino 72 281 0 13 Nov 2017
Graph Attention Networks Petar Velickovic Guillem Cucurull Arantxa Casanova Adriana Romero Pietro Lio Yoshua Bengio GNN 479 20,138 0 30 Oct 2017
Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network Wengong Jin Connor W. Coley Regina Barzilay Tommi Jaakkola 68 276 0 13 Sep 2017
Learning Graph-Level Representation for Drug Discovery Junying Li Deng Cai Xiaofei He GNN AI4CE 64 116 0 12 Sep 2017
Learning to Plan Chemical Syntheses Marwin H. S. Segler Mike Preuss M. Waller 87 1,372 0 14 Aug 2017
Attention Is All You Need Ashish Vaswani Noam M. Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan Gomez Lukasz Kaiser Illia Polosukhin 3DV 701 131,652 0 12 Jun 2017
Retrosynthetic reaction prediction using neural sequence-to-sequence models Bowen Liu Bharath Ramsundar Prasad Kawthekar Jade Shi Joseph Gomes Quang Luu Nguyen Stephen Ho Jack L. Sloane P. Wender Vijay S. Pande 57 418 0 06 Jun 2017
Molecular De Novo Design through Deep Reinforcement Learning Marcus Olivecrona T. Blaschke Ola Engkvist Hongming Chen BDL 126 1,014 0 25 Apr 2017
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 161 2,932 0 07 Oct 2016
Modelling Chemical Reasoning to Predict Reactions Marwin H. S. Segler M. Waller LRM 51 120 0 25 Aug 2016
Neural networks for the prediction organic chemistry reactions Jennifer N. Wei David Duvenaud Alán Aspuru-Guzik 40 353 0 22 Aug 2016
Convolutional Networks on Graphs for Learning Molecular Fingerprints David Duvenaud D. Maclaurin J. Aguilera-Iparraguirre Rafael Gómez-Bombarelli Timothy D. Hirzel Alán Aspuru-Guzik Ryan P. Adams GNN 223 3,352 0 30 Sep 2015
Adam: A Method for Stochastic Optimization Diederik P. Kingma Jimmy Ba ODL 1.8K 150,115 0 22 Dec 2014
Sequence Transduction with Recurrent Neural Networks Alex Graves 191 1,870 0 14 Nov 2012