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arXiv · 2003.12725

A Graph to Graphs Framework for Retrosynthesis Prediction

Chence Shi·Minkai Xu·Hongyu Guo·Ming Zhang·Jian Tang
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Abstract

A fundamental problem in computational chemistry is to find a set of reactants to synthesize a target molecule, a.k.a. retrosynthesis prediction. Existing state-of-the-art methods rely on matching the target molecule with a large set of reaction templates, which are very computationally expensive and also suffer from the problem of coverage. In this paper, we propose a novel template-free approach called G2Gs by transforming a target molecular graph into a set of reactant molecular graphs. G2Gs first splits the target molecular graph into a set of synthons by identifying the reaction centers, and then translates the synthons to the final reactant graphs via a variational graph translation framework. Experimental results show that G2Gs significantly outperforms existing template-free approaches by up to 63% in terms of the top-1 accuracy and achieves a performance close to that of state-of-the-art template based approaches, but does not require domain knowledge and is much more scalable.

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Chence Shi, Minkai Xu, Hongyu Guo, Ming Zhang, Jian Tang. 2020-03-28. A Graph to Graphs Framework for Retrosynthesis Prediction. https://arxiv.org/abs/2003.12725

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