Bridging chemistry and artificial intelligence by a reaction description language

Abstract

With the fast-paced development of artificial intelligence, large language models are increasingly used to tackle various scientific challenges. A critical step in this process is converting domain-specific data into a sequence of tokens for language modelling. In chemistry, molecules are often represented by molecular linear notations, and chemical reactions are depicted as sequence pairs of reactants and products. However, this approach does not capture atomic and bond changes during reactions. Here, we present ReactSeq, a reaction description language that defines molecular editing operations for step-by-step chemical transformation. Based on ReactSeq, language models for retrosynthesis prediction may consistently excel in all benchmark tests, and demonstrate promising emergent abilities in the human-in-the-loop and explainable artificial intelligence. Moreover, ReactSeq has allowed us to obtain universal and reliable representations of chemical reactions, which enable navigation of the reaction space and aid in the recommendation of experimental procedures and prediction of reaction yields. We foresee that ReactSeq can serve as a bridge to narrow the gap between chemistry and artificial intelligence.