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Completing and Balancing Database Excerpted Chemical Reactions with a Hybrid Mechanistic-Machine Learning Approach.

Published version
Peer-reviewed

Repository DOI


Change log

Authors

Zhang, Chonghuan 
Arun, Adarsh 

Abstract

Computer-aided synthesis planning (CASP) development of reaction routes requires an understanding of complete reaction structures. However, most reactions in the current databases are missing reaction coparticipants. Although reaction prediction and atom mapping tools can predict major reaction participants and trace atom rearrangements in reactions, they fail to identify the missing molecules to complete reactions. This is because these approaches are data-driven models trained on the current reaction databases, which comprise incomplete reactions. In this work, a workflow was developed to tackle the reaction completion challenge. This includes a heuristic-based method to identify balanced reactions from reaction databases and complete some imbalanced reactions by adding candidate molecules. A machine learning masked language model (MLM) was trained to learn from simplified molecular input line entry system (SMILES) sentences of these completed reactions. The model predicted missing molecules for the incomplete reactions, a workflow analogous to predicting missing words in sentences. The model is promising for the prediction of small- and middle-sized missing molecules in incomplete reaction records. The workflow combining both the heuristic and machine learning methods completed more than half of the entire reaction space.

Description

Publication status: Published

Keywords

3403 Macromolecular and Materials Chemistry, 34 Chemical Sciences, 3406 Physical Chemistry, Machine Learning and Artificial Intelligence, Networking and Information Technology R&D (NITRD)

Journal Title

ACS Omega

Conference Name

Journal ISSN

2470-1343
2470-1343

Volume Title

9

Publisher

American Chemical Society (ACS)
Sponsorship
National Research Foundation Singapore (NA)
Cambridge Trust (NA)
Chemical Data Intelligence Pte Ltd (NA)