Levenshtein Augmentation Improves Performance of SMILES Based Deep-Learning Synthesis Prediction

06 July 2020, Version 2
This content is a preprint and has not undergone peer review at the time of posting.


SMILES randomization, a form of data augmentation, has previously been shown to increase the performance of deep learning models compared to non-augmented baselines. Here, we propose a novel data augmentation method we call “Levenshtein augmentation” which considers local SMILES sub-sequence similarity between reactants and their respective products when creating training pairs. The performance of Levenshtein augmentation was tested using two state of the art models - transformer and sequence-to-sequence based recurrent neural networks with attention. Levenshtein augmentation demonstrated an increase performance over non-augmented, and conventionally SMILES randomization augmented data when used for training of baseline models. Furthermore, Levenshtein augmentation seemingly results in what we define as attentional gain – an enhancement in the pattern recognition capabilities of the underlying network to molecular motifs.


molecular transformer
machine learning
reaction prediction
synthesis prediction
data augmentation

Supplementary weblinks


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