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Recent advances in the Self-Referencing Embedding Strings (SELFIES) library

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arxiv 2302.03620 v1 pith:4I3E5SDD submitted 2023-02-07 physics.chem-ph cs.LG

classification physics.chem-phcs.LG
keywords selfiesadvanceslearningrepresentationrepresentationsself-referencingselfieslibsemantic
verification ladder T0 review T1 audit T2 compute T3 formal
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String-based molecular representations play a crucial role in cheminformatics applications, and with the growing success of deep learning in chemistry, have been readily adopted into machine learning pipelines. However, traditional string-based representations such as SMILES are often prone to syntactic and semantic errors when produced by generative models. To address these problems, a novel representation, SELF-referencIng Embedded Strings (SELFIES), was proposed that is inherently 100% robust, alongside an accompanying open-source implementation. Since then, we have generalized SELFIES to support a wider range of molecules and semantic constraints and streamlined its underlying grammar. We have implemented this updated representation in subsequent versions of \selfieslib, where we have also made major advances with respect to design, efficiency, and supported features. Hence, we present the current status of \selfieslib (version 2.1.1) in this manuscript.

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