"Found in Translation": predicting outcomes of complex organic chemistry reactions using neural sequence-to-sequence models. Issue 28 (27th June 2018)

• Record Type: Journal Article
• Authors: Schwaller, Philippe; Gaudin, Théophile; Lányi, Dávid; Bekas, Costas; Laino, Teodoro
• Is Part Of: Chemical science. Volume 9:Issue 28(2018)
• Page Start: 6091
• Page End: 6098
• Publication Date: 2018-06-27
• Subjects: Chemistry -- Periodicals; 540.5
• DOI: 10.1039/c8sc02339e
• Languages: English
• ISSNs: 2041-6520

Abstract

Abstract : Using a text-based representation of molecules, chemical reactions are predicted with a neural machine translation model borrowed from language processing. Abstract : There is an intuitive analogy of an organic chemist's understanding of a compound and a language speaker's understanding of a word. Based on this analogy, it is possible to introduce the basic concepts and analyze potential impacts of linguistic analysis to the world of organic chemistry. In this work, we cast the reaction prediction task as a translation problem by introducing a template-free sequence-to-sequence model, trained end-to-end and fully data-driven. We propose a tokenization, which is arbitrarily extensible with reaction information. Using an attention-based model borrowed from human language translation, we improve the state-of-the-art solutions in reaction prediction on the top-1 accuracy by achieving 80.3% without relying on auxiliary knowledge, such as reaction templates or explicit atomic features. Also, a top-1 accuracy of 65.4% is reached on a larger and noisier dataset.