I had a look at the GENTRL paper recently, wondering how they got from three-dimensional chemical structure space to a vector that could be fed into a machine learning algorithm... and even harder, how they made that mapping reversible. Couldn't figure it out.
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And I don't think that's my fault. They say approximately one word about how the transformation starts: SMILES. https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system …
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But from there, how they get to "a continous space of 50 dimensions" (i.e. a 50-element vector) is left almost completely undescribed, even in the supplementary information.
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