"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"

50 / 74 papers shown

Title
Predicting Chemical Reaction Outcomes Based on Electron Movements Using Machine Learning Shuan Chen Kye Sung Park Taewan Kim Sunkyu Han Yousung Jung 50 0 0 13 Mar 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
SMI-Editor: Edit-based SMILES Language Model with Fragment-level Supervision Kangjie Zheng Siyue Liang Junwei Yang Bin Feng Zequn Liu Wei Ju Zhiping Xiao Ming Zhang 73 1 0 07 Dec 2024
Smirk: An Atomically Complete Tokenizer for Molecular Foundation Models Alexius Wadell Anoushka Bhutani Venkatasubramanian Viswanathan 159 0 0 19 Sep 2024
Accurate and efficient structure elucidation from routine one-dimensional NMR spectra using multitask machine learning Frank Hu Michael S Chen Grant M. Rotskoff M. Kanan T. Markland 33 3 0 15 Aug 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
Aligning Transformers with Continuous Feedback via Energy Rank Alignment Shriram Chennakesavalu Frank Hu Sebastian Ibarraran Grant M. Rotskoff 41 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 33 1 0 14 Dec 2023
Large Language Models on Graphs: A Comprehensive Survey Bowen Jin Gang Liu Chi Han Meng Jiang Heng Ji Jiawei Han AI4CE 37 138 0 05 Dec 2023
AI for Interpretable Chemistry: Predicting Radical Mechanistic Pathways via Contrastive Learning Mohammadamin Tavakoli Y. T. T. Chiu Alexander Shmakov Ann Marie Carlton David Van Vranken Pierre Baldi 25 2 0 02 Nov 2023
MLAgentBench: Evaluating Language Agents on Machine Learning Experimentation Qian Huang Jian Vora Percy Liang J. Leskovec ELM LLMAG 27 70 0 05 Oct 2023
Language models in molecular discovery Chaoqi Wang Yibo Jiang Chenghao Yang Han Liu Yuxin Chen 25 7 0 28 Sep 2023
14 Examples of How LLMs Can Transform Materials Science and Chemistry: A Reflection on a Large Language Model Hackathon Kevin Maik Jablonka Qianxiang Ai Alexander H Al-Feghali S. Badhwar Joshua D. Bocarsly Andres M Bran ... Aristana Scourtas K. J. Schmidt Ian Foster Andrew D. White Ben Blaiszik 46 101 0 09 Jun 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 28 67 0 18 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 66 10 0 01 Mar 2023
Unifying Molecular and Textual Representations via Multi-task Language Modelling Dimitrios Christofidellis Giorgio Giannone Jannis Born Ole Winther Teodoro Laino Matteo Manica AI4CE 24 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 35 25 0 29 Nov 2022
Towards automatic generation of Piping and Instrumentation Diagrams (P&IDs) with Artificial Intelligence Edwin Hirtreiter Lukas Schulze Balhorn Artur M. Schweidtmann AI4CE 14 14 0 26 Oct 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 27 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 40 33 0 01 Aug 2022
Pre-training Transformers for Molecular Property Prediction Using Reaction Prediction J. Broberg Maria Bånkestad Erik Ylipää AI4CE 21 5 0 06 Jul 2022
Root-aligned SMILES: A Tight Representation for Chemical Reaction Prediction Zipeng Zhong Mingli 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 13 17 0 12 Feb 2022
Regression Transformer: Concurrent sequence regression and generation for molecular language modeling Jannis Born Matteo Manica 13 91 0 01 Feb 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
Chemical-Reaction-Aware Molecule Representation Learning Hongwei Wang Weijian Li Xiaomeng Jin Kyunghyun Cho Heng Ji Jiawei Han Martin D. Burke 107 56 0 21 Sep 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 36 5 0 19 Sep 2021
Hybrid quantum-classical machine learning for generative chemistry and drug design A. I. Gircha A. S. Boev K. Avchaciov P. Fedichev A. Fedorov AI4CE BDL 25 27 0 26 Aug 2021
Geometric Deep Learning on Molecular Representations Kenneth Atz F. Grisoni G. Schneider AI4CE 34 287 0 26 Jul 2021
Self-Improved Retrosynthetic Planning Junsup Kim Sungsoo Ahn Hankook Lee Jinwoo Shin 15 26 0 09 Jun 2021
Non-Autoregressive Electron Redistribution Modeling for Reaction Prediction Hangrui Bi Hengyi Wang Chence Shi Connor W. Coley Jian Tang Hongyu Guo 16 19 0 08 Jun 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 40 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
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 33 17 0 07 Apr 2021
Using Molecular Embeddings in QSAR Modeling: Does it Make a Difference? María Virginia Sabando I. Ponzoni E. Milios Axel J. Soto 33 26 0 20 Mar 2021
Gemini: Dynamic Bias Correction for Autonomous Experimentation and Molecular Simulation Riley J. Hickman Florian Hase L. Roch Alán Aspuru-Guzik 18 4 0 05 Mar 2021
Robust PDF Document Conversion Using Recurrent Neural Networks Nikolaos Livathinos Cesar Berrospi Maksym Lysak Viktor Kuropiatnyk Ahmed Nassar A. Carvalho Michele Dolfi Christoph Auer K. Dinkla Peter W. J. Staar 20 22 0 18 Feb 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
Non-autoregressive electron flow generation for reaction prediction Hangrui Bi Hengyi Wang Chence Shi Jian Tang 16 0 0 16 Dec 2020
Mapping the Space of Chemical Reactions Using Attention-Based Neural Networks P. Schwaller Daniel Probst Alain C. Vaucher Vishnu H. Nair D. Kreutter Teodoro Laino J. Reymond 147 225 0 09 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
Graph-Aware Transformer: Is Attention All Graphs Need? Sang-yong Yoo Young-Seok Kim Kang Lee Kuhwan Jeong Junhwi Choi Hoshik Lee Y. S. Choi GNN 22 11 0 09 Jun 2020
Autonomous discovery in the chemical sciences part I: Progress Connor W. Coley Natalie S. Eyke K. Jensen 26 213 0 30 Mar 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
State-of-the-Art Augmented NLP Transformer models for direct and single-step retrosynthesis Igor V. Tetko Pavel Karpov R. V. Deursen Guillaume Godin 19 6 0 05 Mar 2020
Exploring Chemical Space using Natural Language Processing Methodologies for Drug Discovery Hakime Öztürk Arzucan Özgür P. Schwaller Teodoro Laino Elif Özkirimli 27 116 0 10 Feb 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