Prediction of Chemical Reaction Yields using Deep Learning

05 August 2020, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Artificial intelligence is driving one of the most important revolutions in organic chemistry.
Multiple platforms, including tools for reaction prediction and synthesis planning based on machine learning, successfully became part of the organic chemists' daily laboratory, assisting in domain-specific synthetic problems. Unlike reaction prediction and retrosynthetic models, reaction yields models have been less investigated, despite the enormous potential of accurately predicting them. Reaction yields models, describing the percentage of the reactants that is converted to the desired products, could guide chemists and help them select high-yielding reactions and score synthesis routes, reducing the number of attempts. So far, yield predictions have been predominantly performed for high-throughput experiments using a categorical (one-hot) encoding of reactants, concatenated molecular fingerprints, or computed chemical descriptors. Here, we extend the application of natural language processing architectures to predict reaction properties given a text-based representation of the reaction, using an encoder transformer model combined with a regression layer. We demonstrate outstanding prediction performance on two high-throughput experiment reactions sets. An analysis of the yields reported in the open-source USPTO data set shows that their distribution differs depending on the mass scale, limiting the dataset applicability in reaction yields predictions.


SMILES-Encoded Molecular Structures
Deep Learning
Chemical Reactions


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