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deepchem / deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
https://deepchem.io/
MIT License
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Drug Response VAE #620

Open rbharath opened 7 years ago

rbharath commented 7 years ago

https://arxiv.org/abs/1706.08203

Looks interesting. We should add an implementation to DeepChem

LRParser commented 7 years ago

Agreed, it doesn't look like any of their code is open source though. Would a Keras implementation be the desired way to go? Ref: https://github.com/fchollet/keras/blob/master/examples/variational_autoencoder.py

rbharath commented 7 years ago

We dropped Keras support a while ago due the rapidly changing API which broke the build a few times. Has the Keras API stabilized now?

It might also be straightforward to do this in TensorGraph (cc @lilleswing)

lilleswing commented 7 years ago

The main network topology is described in this paper -- https://papers.nips.cc/paper/6581-improved-variational-inference-with-inverse-autoregressive-flow.pdf

selection_039

I had trouble following their semi-supervised learning scheme so I don't know if I can comment on how easy it would be to port.

@LRParser the code you linked is already ported into deepchem here Gene Expressions are expressed in a bitvector really easily -- but small molecules are not. This is the main challenge for creating a molecular autoencoder.

https://github.com/deepchem/deepchem/tree/master/deepchem/models/autoencoder_models

lilleswing commented 7 years ago

Their semi-supervised learning scheme works because they can train both x_1 and x_2 over the encoder without training the gene expression changes as shown here.

selection_040

This should be doable to port to Tensorgraph. Getting our hands on the datasets to prove that it worked might be the trickiest part.

rbharath commented 7 years ago

I'd love to get some gene expression data in DeepChem. There are some very impressive results here, notably:

http://stm.sciencemag.org/content/3/96/96ra77

If we could get that implemented in DeepChem, would be amazing!

LRParser commented 6 years ago

Ok, this one is over my head for the moment, but I'll do my best to follow along and learn Tensorgraph.

rbharath commented 6 years ago

This would be a good intermediate level contribution, especially for those with prior deep learning experience.