Encoding representations

[hkmztrk]

Hello,

I'm pretty new to autoencoders and I know we can use utilize them for unsupervised learning. Is it possible to use this model to create representations (with encoding) for a set of SMILES?

If so, I guess first I had to preprocess my data set, then use sample.py ?

Thanks!

[pechersky]

That's exactly right. Have you taken a look at the Gomez-Bombarelli paper linked in the README?

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On Wed, May 17, 2017 at 6:54 AM, hkmztrk ***@***.***> wrote: Hello, I'm pretty new to autoencoders and I know we can use utilize them for unsupervised learning. Is it possible to use this model to create representations (with encoding) for a set of SMILES? If so, I guess first I had to preprocess my data set, then usesample.py ? Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#64>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFGDhslq3v_TLfGwwvU9PtNIjZdSQbkZks5r6tHTgaJpZM4NdshN> .

[hkmztrk]

Yes, it was that paper led me to here. Thanks!

[liamnaka]

Last time I checked the VAE encodings were pretty substantial in size, so if you're trying to learn from a large set of SMILES it might be more feasible to generate them on the fly.

[hkmztrk]

Hello, thanks for your suggestion. Sorry for my asking but, how do we generate them on the fly? Aren't we supposed to learn the model first? How do we do that?

[pechersky]

Those reasons are why we developed `sample_gen.py` and `train_gen.py`, which generate the one-hot representations on the fly and can train the model using the `fit_generator` functionality of Keras. To train the model in such a way, run `python train_gen.py structures.h5 model.h5`, where `structures.h5` is an h5 file containing structures under the 'structure' key. Check out the source for `train_gen.py` for more details.

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On Thu, May 25, 2017 at 3:01 AM, hkmztrk ***@***.***> wrote: Hello, thanks for your suggestion. Sorry for my asking but, how do we generate them on the fly? Aren't we supposed to learn the model first? How do we do that? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#64 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFGDhp7WKoES35uWL3zu54DUfSzIf7Upks5r9SdagaJpZM4NdshN> .