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 31 0 0 11 May 2025
A User-Tunable Machine Learning Framework for Step-Wise Synthesis Planning Shivesh Prakash Viki Kumar Prasad Hans-Arno Jacobsen 36 0 0 03 Apr 2025
Chemical knowledge-informed framework for privacy-aware retrosynthesis learning Guikun Chen Xu Zhang Y. Yang Wenguan Wang 47 0 0 26 Feb 2025
Challenging reaction prediction models to generalize to novel chemistry John Bradshaw Anji Zhang Babak Mahjour David E. Graff Marwin H. S. Segler Connor W. Coley 40 1 0 11 Jan 2025
Generative Model for Synthesizing Ionizable Lipids: A Monte Carlo Tree Search Approach Jingyi Zhao Yuxuan Ou Austin Tripp Morteza Rasoulianboroujeni José Miguel Hernández-Lobato 62 0 0 01 Dec 2024
Accelerating the inference of string generation-based chemical reaction models for industrial applications Mikhail Andronov Natalia Andronova Michael Wand Jürgen Schmidhuber Djork-Arné Clevert AI4CE 25 3 0 12 Jul 2024
Double-Ended Synthesis Planning with Goal-Constrained Bidirectional Search Kevin Yu Jihye Roh Ziang Li Wenhao Gao Runzhong Wang Connor W. Coley 34 5 0 08 Jul 2024
RetroGFN: Diverse and Feasible Retrosynthesis using GFlowNets Piotr Gaiñski Michał Koziarski Krzysztof Maziarz Marwin H. S. Segler Jacek Tabor Marek Śmieja 49 3 0 26 Jun 2024
Alignment is Key for Applying Diffusion Models to Retrosynthesis Najwa Laabid Severi Rissanen Markus Heinonen Arno Solin Vikas K. Garg DiffM 31 1 0 27 May 2024
ReactXT: Understanding Molecular "Reaction-ship" via Reaction-Contextualized Molecule-Text Pretraining Zhiyuan Liu Yaorui Shi An Zhang Sihang Li Enzhi Zhang Xiang Wang Kenji Kawaguchi Tat-Seng Chua 44 10 0 23 May 2024
DirectMultiStep: Direct Route Generation for Multistep Retrosynthesis Yu Shee Haote Li Anton Morgunov Victor S. Batista 48 1 0 22 May 2024
UAlign: Pushing the Limit of Template-free Retrosynthesis Prediction with Unsupervised SMILES Alignment Kaipeng Zeng Bo Yang Xin Zhao Yu Zhang Fan Nie Xiaokang Yang Yaohui Jin Yanyan Xu 20 6 0 25 Mar 2024
Retrosynthesis Prediction via Search in (Hyper) Graph Zixun Lan Binjie Hong Jiajun Zhu Zuo Zeng Zhenfu Liu Limin Yu Fei Ma 42 0 0 09 Feb 2024
T-Rex: Text-assisted Retrosynthesis Prediction Yifeng Liu Hanwen Xu Tangqi Fang Haocheng Xi Zixuan Liu Sheng Zhang Hoifung Poon Sheng Wang 29 1 0 26 Jan 2024
RetroOOD: Understanding Out-of-Distribution Generalization in Retrosynthesis Prediction Yemin Yu Luotian Yuan Ying Wei Hanyu Gao Xinhai Ye Zhihua Wang Fei Wu OOD 29 3 0 18 Dec 2023
Efficiently Predicting Protein Stability Changes Upon Single-point Mutation with Large Language Models Yijie Zhang Zhangyang Gao Cheng Tan Stan Z.Li 27 2 0 07 Dec 2023
RetroDiff: Retrosynthesis as Multi-stage Distribution Interpolation Yiming Wang Yuxuan Song Minkai Xu Rui Wang Hao Zhou Wei-Ying Ma 25 2 0 23 Nov 2023
Re-evaluating Retrosynthesis Algorithms with Syntheseus Krzysztof Maziarz Austin Tripp Guoqing Liu Megan Stanley Shufang Xie Piotr Gaiñski Philipp Seidl Marwin H. S. Segler ELM 29 13 0 30 Oct 2023
ReLM: Leveraging Language Models for Enhanced Chemical Reaction Prediction Yaorui Shi An Zhang Enzhi Zhang Zhiyuan Liu Xiang Wang AI4CE 16 24 0 20 Oct 2023
Retro-fallback: retrosynthetic planning in an uncertain world Austin Tripp Krzysztof Maziarz Sarah Lewis Marwin H. S. Segler José Miguel Hernández-Lobato 19 8 0 13 Oct 2023
Molecule-Edit Templates for Efficient and Accurate Retrosynthesis Prediction Mikolaj Sacha Michal Sadowski Piotr Kozakowski Ruard van Workum Stanislaw Jastrzebski 21 1 0 11 Oct 2023
Evolutionary Retrosynthetic Route Planning Yan Zhang Hao Hao Xiao He Shuanhu Gao Aimin Zhou 26 1 0 08 Oct 2023
Node-Aligned Graph-to-Graph (NAG2G): Elevating Template-Free Deep Learning Approaches in Single-Step Retrosynthesis Lin Yao Wentao Guo Zhen Wang Shang Xiang Wentan Liu Guolin Ke 43 12 0 27 Sep 2023
RetroBridge: Modeling Retrosynthesis with Markov Bridges Ilia Igashov Arne Schneuing Marwin H. S. Segler Michael M. Bronstein B. Correia 28 14 0 30 Aug 2023
A Unified View of Deep Learning for Reaction and Retrosynthesis Prediction: Current Status and Future Challenges Ziqiao Meng Peilin Zhao Yang Yu Irwin King 32 8 0 28 Jun 2023
Retrosynthesis Prediction with Local Template Retrieval Shufang Xie Rui Yan Junliang Guo Yingce Xia Lijun Wu Tao Qin 24 12 0 07 Jun 2023
Doubly Stochastic Graph-based Non-autoregressive Reaction Prediction Ziqiao Meng Peilin Zhao Yang Yu Irwin King 31 7 0 05 Jun 2023
MotifRetro: Exploring the Combinability-Consistency Trade-offs in retrosynthesis via Dynamic Motif Editing Zhangyang Gao Xingran Chen Cheng Tan Stan Z. Li 22 1 0 20 May 2023
Deep Learning Methods for Small Molecule Drug Discovery: A Survey Wenhao Hu Yingying Liu Xuanyu Chen Wenhao Chai Hangyue Chen Hongwei Wang Gaoang Wang 60 10 0 01 Mar 2023
Recent advances in artificial intelligence for retrosynthesis Zipeng Zhong Jie Song Zunlei Feng Tiantao Liu Lingxiang Jia Shaolun Yao Tingjun Hou Mingli Song 29 5 0 14 Jan 2023
Mind the Retrosynthesis Gap: Bridging the divide between Single-step and Multi-step Retrosynthesis Prediction Alan Kai Hassen Paula Torren-Peraire S. Genheden Jonas Verhoeven Mike Preuss Igor V. Tetko 22 9 0 12 Dec 2022
Proactive Robot Assistance via Spatio-Temporal Object Modeling Maithili Patel Sonia Chernova 29 26 0 28 Nov 2022
Bidirectional Generation of Structure and Properties Through a Single Molecular Foundation Model Jinho Chang Jong Chul Ye AI4CE 22 29 0 19 Nov 2022
ChemAlgebra: Algebraic Reasoning on Chemical Reactions Andrea Valenti D. Bacciu Antonio Vergari OOD LRM 32 0 0 05 Oct 2022
FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning Songtao Liu Zhengkai Tu Minkai Xu Zuobai Zhang Lu Lin Rex Ying Jian Tang Peilin Zhao Dinghao Wu 35 12 0 30 Sep 2022
MARS: A Motif-based Autoregressive Model for Retrosynthesis Prediction Jiahan Liu Chao-chao Yan Yang Yu Chan Lu Junzhou Huang Le Ou-Yang P. Zhao 43 13 0 27 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 45 20 0 12 Sep 2022
Modeling Diverse Chemical Reactions for Single-step Retrosynthesis via Discrete Latent Variables Huarui He Jie Wang Yunfei Liu Feng Wu BDL 30 6 0 10 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 42 370 0 05 Aug 2022
Root-aligned SMILES: A Tight Representation for Chemical Reaction Prediction Zipeng Zhong Jie Song Zunlei Feng Tiantao Liu Lingxiang Jia Shaolun Yao Min-Ying Wu Tingjun Hou Mingli Song 29 53 0 22 Mar 2022
SemiRetro: Semi-template framework boosts deep retrosynthesis prediction Zhangyang Gao Cheng Tan Lirong Wu Stan Z. Li 11 17 0 12 Feb 2022
Retroformer: Pushing the Limits of Interpretable End-to-end Retrosynthesis Transformer Yue Wan Ben Liao Chang-Yu Hsieh Shengyu Zhang 17 10 0 29 Jan 2022
RetroComposer: Composing Templates for Template-Based Retrosynthesis Prediction Chao-chao Yan P. Zhao Chan Lu Yang Yu Junzhou Huang 25 20 0 20 Dec 2021
Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction prediction Zhengkai Tu Connor W. Coley 22 90 0 19 Oct 2021
Non-Autoregressive Electron Redistribution Modeling for Reaction Prediction Hangrui Bi Hengyi Wang Chence Shi Connor W. Coley Jian Tang Hongyu Guo 11 19 0 08 Jun 2021
Modern Hopfield Networks for Few- and Zero-Shot Reaction Template Prediction Philipp Seidl Philipp Renz N. Dyubankova Paulo Neves Jonas Verhoeven Marwin H. S. Segler J. Wegner Sepp Hochreiter G. Klambauer 30 17 0 07 Apr 2021
Learning to Extend Molecular Scaffolds with Structural Motifs Krzysztof Maziarz Henry Jackson-Flux Pashmina Cameron F. Sirockin Nadine Schneider N. Stiefl Marwin H. S. Segler Marc Brockschmidt AI4CE 18 69 0 05 Mar 2021
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development Kexin Huang Tianfan Fu Wenhao Gao Yue Zhao Yusuf Roohani J. Leskovec Connor W. Coley Cao Xiao Jimeng Sun Marinka Zitnik OOD LM&MA 30 261 0 18 Feb 2021
Unassisted Noise Reduction of Chemical Reaction Data Sets A. Toniato P. Schwaller Antonio Cardinale Joppe Geluykens Teodoro Laino AAML 17 23 0 02 Feb 2021
Non-autoregressive electron flow generation for reaction prediction Hangrui Bi Hengyi Wang Chence Shi Jian Tang 12 0 0 16 Dec 2020