Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation — mentioned by dekhn

Wed, 05 Nov 2025 23:31:54 GMT

Let me start with an example- some time ago I worked on a VAE that encoded and decoded SMILES strings. The idea is that you should be able to encode a SMILES into an embedding space, do all the normal things you would do in that space, and then convert the resulting embedding vector back to a valid molecule. The VAE is trained with a very large number of valid SMILES strings, typically tokenized at the character level (so "C" is a token, and "Br" is "B" then "r"). I and others have observed that VAEs trained like this produce large number of embedding vectors that do not decode to valid…

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Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation · HackerPapers discussions

Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation — mentioned by dekhn