Extraction of organic chemistry grammar from unsupervised learning of chemical reactions

Humans use different domain languages to represent, explore, and communicate scientific concepts. During the last few hundred years, chemists compiled the language of chemical synthesis inferring a series of "reaction rules" from knowing how atoms rearrange during a chemical transformation, a process called atom-mapping. Atom-mapping is a laborious experimental task and, when tackled with computational methods, requires continuous annotation of chemical reactions and the extension of logically consistent directives. Here, we demonstrate that Transformer Neural Networks learn atom-mapping information between products and reactants without supervision or human labeling. Using the Transformer attention weights, we build a chemically agnostic, attention-guided reaction mapper and extract coherent chemical grammar from unannotated sets of reactions. Our method shows remarkable performance in terms of accuracy and speed, even for strongly imbalanced and chemically complex reactions with nontrivial atom-mapping. It provides the missing link between data-driven and rule-based approaches for numerous chemical reaction tasks.