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SMILES strings are not necessarily unique; each molecule can be encoded multiple ways as a SMILES string. As a sanity check, you could pass multiple representat
by brilee 10y ago
SMILES strings are not necessarily unique; each molecule can be encoded multiple ways as a SMILES string. As a sanity check, you could pass multiple representations of a molecule into the autoencoder to see if they generate the same continuous representation. Otherwise, you may end up essentially training to the peculiarities of whatever algorithm generated your SMILES strings.
- deleted 10y ago[deleted]
- rgbombarelli 10y agoYou are right about SMILES. We trained on the canonical SMILES output by the RDKit, so as far as our AE is concerned, there is only one way to write SMILES for a given molecule (http://www.rdkit.org/docs/GettingStartedInPython.html#writing-molecules http://www.rdkit.org/docs/GettingStartedInPython.html#writin...). Of course, the choice of what the canonical SMILES is is somewhat arbitrary.