Tutorial on chemical properties using SMILE about deeplearning4j-docs HOT 4 OPEN

50 million ~ 1 billion compounds in SMILE format: http://gdb.unibe.ch/downloads/

from deeplearning4j-docs.

20 million compounds, perhaps also useful: https://github.com/isayev/ANI1_dataset

from deeplearning4j-docs.

Did we consult @AlexDBlack on this? He likely has strong opinions about it, some war stories about the SMILES data, and maybe some code we can repurpose?

from deeplearning4j-docs.

Yeah, @crockpotveggies and I discussed this privately on gitter.
tl;dr data in just about any format would work for a basic demo, as we can convert it to SMILES or whatever as required.
As for the net, I was suggesting perhaps an MLP using ECFP4, and maybe (depending on the task) also a bidirectional RNN directly on SMILES. I'm happy to do the ECFP4 conversion if required to produce a 'clean' dataset.
If we go the RNN route, it might make sense to finally build a proper character sequence record reader in DataVec.

from deeplearning4j-docs.