SELFIES and the future of molecular string representations

Mario Krenn , Qianxiang Ai , Senja Barthel , Nessa Carson , Angelo Frei , Nathan C. Frey , Pascal Friederich , Theophile Gaudin , Alberto Alexander Gayle , Kevin Maik Jablonka , Rafael F. Lameiro , Dominik Lemm , Alston Lo Seyed Mohamad Moosavi , Jos ́e Manuel Napoles-Duarte , AkshatKumar Nigam, Robert Pollice , Kohulan Rajan , Ulrich Schatzschneider , Philippe Schwaller Marta Skreta , Berend Smit , Felix Strieth-Kalthoff , Chong Sun , Gary Tom , Guido Falk von Rudorff , Andrew Wang , Andrew White Adamo Young , Rose Yu , and Alan Aspuru-Guzik
physics.chem-ph 31 Mar 2022.
Development Published: (Mar/2022)

Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad ap- plications to challenging tasks in chemistry and materials science. Examples include the prediction of properties, the discovery of new reaction pathways, or the design of new molecules. The ma- chine needs to read and write fluently in a chemical language for each of these tasks. Strings are a common tool to represent molecular graphs, and the most popular molecular string representation, SMILES, has powered cheminformatics since the late 1980s. However, in the context of AI and ML in chemistry, SMILES has several shortcomings – most pertinently, most combinations of symbols lead to invalid results with no valid chemical interpretation. To overcome this issue, a new language for molecules was introduced in 2020 that guarantees 100% robustness: SELFIES (SELF-referencIng Embedded Strings). SELFIES has since simplified and enabled numerous new applications in chem- istry. In this manuscript, we look to the future and discuss molecular string representations, along with their respective opportunities and challenges. We propose 16 concrete Future Projects for robust molecular representations. These involve the extension toward new chemical domains, ex- citing questions at the interface of AI and robust languages, and interpretability for both humans and machines. We hope that these proposals will inspire several follow-up works exploiting the full potential of molecular string representations for the future of AI in chemistry and materials science.

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