"Found in Translation": Predicting Outcomes of Complex Organic Chemistry Reactions using Neural Sequence-to-Sequence Models

13 November 2017

Papers citing ""Found in Translation": Predicting Outcomes of Complex Organic Chemistry Reactions using Neural Sequence-to-Sequence Models"

29 / 29 papers shown

Title
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
Smirk: An Atomically Complete Tokenizer for Molecular Foundation Models Alexius Wadell Anoushka Bhutani Venkatasubramanian Viswanathan 127 0 0 19 Sep 2024
Aligning Transformers with Continuous Feedback via Energy Rank Alignment Shriram Chennakesavalu Frank Hu Sebastian Ibarraran Grant M. Rotskoff 33 3 0 21 May 2024
Holistic chemical evaluation reveals pitfalls in reaction prediction models Victor Sabanza Gil Andres M Bran Malte Franke Remi Schlama J. Luterbacher Philippe Schwaller ELM 25 1 0 14 Dec 2023
Language models in molecular discovery Chaoqi Wang Yibo Jiang Chenghao Yang Han Liu Yuxin Chen 23 7 0 28 Sep 2023
MolXPT: Wrapping Molecules with Text for Generative Pre-training Zequn Liu Wei Zhang Yingce Xia Lijun Wu Shufang Xie Tao Qin M. Zhang Tie-Yan Liu 22 66 0 18 May 2023
Unifying Molecular and Textual Representations via Multi-task Language Modelling Dimitrios Christofidellis Giorgio Giannone Jannis Born Ole Winther Teodoro Laino Matteo Manica AI4CE 19 79 0 29 Jan 2023
BARTSmiles: Generative Masked Language Models for Molecular Representations Gayane Chilingaryan Hovhannes Tamoyan Ani Tevosyan N. Babayan L. Khondkaryan Karen Hambardzumyan Zaven Navoyan Hrant Khachatrian Armen Aghajanyan SSL 29 25 0 29 Nov 2022
MOFormer: Self-Supervised Transformer model for Metal-Organic Framework Property Prediction Zhonglin Cao Rishikesh Magar Yuyang Wang A. Farimani AI4CE 23 88 0 25 Oct 2022
TransPolymer: a Transformer-based language model for polymer property predictions Changwen Xu Yuyang Wang A. Farimani 24 86 0 03 Sep 2022
Learning from flowsheets: A generative transformer model for autocompletion of flowsheets Gabriel Vogel Lukas Schulze Balhorn Artur M. Schweidtmann AI4CE 35 33 0 01 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
Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction prediction Zhengkai Tu Connor W. Coley 30 90 0 19 Oct 2021
Automated and Explainable Ontology Extension Based on Deep Learning: A Case Study in the Chemical Domain A. Memariani Martin Glauer Fabian Neuhaus Till Mossakowski Janna Hastings 28 5 0 19 Sep 2021
Geometric Deep Learning on Molecular Representations Kenneth Atz F. Grisoni G. Schneider AI4CE 34 287 0 26 Jul 2021
Dataset Bias in the Natural Sciences: A Case Study in Chemical Reaction Prediction and Synthesis Design Ryan-Rhys Griffiths P. Schwaller Alpha A. Lee AI4CE 34 19 0 06 May 2021
TITAN: T Cell Receptor Specificity Prediction with Bimodal Attention Networks Anna Weber Jannis Born María Rodríguez Martínez 11 129 0 21 Apr 2021
Barking up the right tree: an approach to search over molecule synthesis DAGs John Bradshaw Brooks Paige Matt J. Kusner Marwin H. S. Segler José Miguel Hernández-Lobato 51 56 0 21 Dec 2020
RetroXpert: Decompose Retrosynthesis Prediction like a Chemist Chao-chao Yan Qianggang Ding P. Zhao Shuangjia Zheng Jinyu Yang Yang Yu Junzhou Huang 25 107 0 04 Nov 2020
Drug discovery with explainable artificial intelligence José Jiménez-Luna F. Grisoni G. Schneider 30 625 0 01 Jul 2020
Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits Mikolaj Sacha Mikolaj Blaz Piotr Byrski Paweł Dąbrowski-Tumański Mikołaj Chromiński Rafał Loska Pawel Wlodarczyk-Pruszynski Stanislaw Jastrzebski GNN 25 142 0 27 Jun 2020
A Graph to Graphs Framework for Retrosynthesis Prediction Chence Shi Minkai Xu Hongyu Guo Ming Zhang Jian Tang 19 151 0 28 Mar 2020
Retrosynthesis Prediction with Conditional Graph Logic Network H. Dai Chengtao Li Connor W. Coley Bo Dai Le Song 26 177 0 06 Jan 2020
SMILES-X: autonomous molecular compounds characterization for small datasets without descriptors G. Lambard Ekaterina Gracheva 27 20 0 20 Jun 2019
Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction P. Schwaller Teodoro Laino John McGuinness A. Horváth Constantine Bekas A. Lee 25 719 0 06 Nov 2018
Compressing physical properties of atomic species for improving predictive chemistry John E. Herr Kevin J Koh Kun Yao John A. Parkhill AI4CE 14 20 0 31 Oct 2018
A Generative Model For Electron Paths John Bradshaw Matt J. Kusner Brooks Paige Marwin H. S. Segler José Miguel Hernández-Lobato 14 55 0 23 May 2018
Constrained Bayesian Optimization for Automatic Chemical Design Ryan-Rhys Griffiths José Miguel Hernández-Lobato BDL 39 76 0 16 Sep 2017
Effective Approaches to Attention-based Neural Machine Translation Thang Luong Hieu H. Pham Christopher D. Manning 218 7,926 0 17 Aug 2015