Prediction and Interpretable Visualization of Synthetic Reactions Using Graph Convolutional Networks

01 July 2019, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Recently, many research groups have been addressing data-driven approaches for reaction prediction and retrosynthetic analysis. Although the performances of the data-driven approach have progressed due to recent advances of machine learning and deep learning techniques, problems such as improving capability of reaction prediction and the black-box problem of neural networks still persist for practical use by chemists. To expand data-driven approaches to chemists, we focused on two challenges: improvement of reaction prediction and interpretability of the prediction. In this paper, we propose an interpretable prediction framework using Graph Convolutional Networks (GCN) for reaction prediction and Integrated Gradients (IGs) for visualization of contributions to the prediction to address these challenges. As a result, our model showed better performances than the approach using Extended-Connectivity Fingerprint (ECFP). Furthermore, IGs based visualization of the GCN prediction successfully highlighted reaction-related atoms.

Keywords

Retrosynthesis
Reaction prediction
deep learning
graph convolutional networks
Integrated Gradients
Visualization
Interpretability

Supplementary materials

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Prediction and Interpretable Visualization sup 2019
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