Chemical reactant recommendation using a network of organic chemistry

This paper focuses on the task of recommending to the chemist candidate molecules (reactants) necessary to synthesize a given target molecule (product), which is a novel application as well as an important step for the chemist to find a synthesis route to generate the product. We formulate this task as a link-prediction problem over a so-called Network of Organic Chemistry (NOC) that we have constructed from 8 million chemical reactions described in the US patent literature between 1976 and 2013. We leverage state-of-the-art factorization algorithms for recommender systems to solve this task. Our empirical evaluation demonstrates that Factorization Machines, trained with chemistry-specific knowledge, outperforms current methods based on similarity of chemical structures.