Reagent prediction with a molecular transformer improves reaction data quality

Mikhail Andronov, Varvara Voinarovska, Natalia Andronova, Michael Wand, Djork-Arné Clevert, Juergen Schmidhuber

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Automated synthesis planning is key for efficient generative chemistry. Since reactions of given reactants may yield different products depending on conditions such as the chemical context imposed by specific reagents, computer-aided synthesis planning should benefit from recommendations of reaction conditions. Traditional synthesis planning software, however, typically proposes reactions without specifying such conditions, relying on human organic chemists who know the conditions to carry out suggested reactions. In particular, reagent prediction for arbitrary reactions, a crucial aspect of condition recommendation, has been largely overlooked in cheminformatics until recently. Here we employ the Molecular Transformer, a state-of-the-art model for reaction prediction and single-step retrosynthesis, to tackle this problem. We train the model on the US patents dataset (USPTO) and test it on Reaxys to demonstrate its out-of-distribution generalization capabilities. Our reagent prediction model also improves the quality of product prediction: the Molecular Transformer is able to substitute the reagents in the noisy USPTO data with reagents that enable product prediction models to outperform those trained on plain USPTO. This makes it possible to improve upon the state-of-the-art in reaction product prediction on the USPTO MIT benchmark.
Original languageEnglish (US)
JournalChemical Science
StatePublished - Mar 1 2023

Bibliographical note

KAUST Repository Item: Exported on 2023-03-07
Acknowledgements: This study was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions, grant agreement “Advanced machine learning for Innovative Drug Discovery (AIDD)” No. 956832.

ASJC Scopus subject areas

  • General Chemistry


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