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Pytorch implementation of the paper "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules"

License: MIT License

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cheminformatics pytorch materials-science materials-informatics python deep-learning variational-autoencoder molecular-structures machine-learning drug-discovery

molecular-vae's Introduction

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

MIT license made-with-python

Pytorch implementation of the paper Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules by:

  • Rafa Gómez-Bombarelli
  • David Duvenaud
  • José Miguel Hernández-Lobato
  • Jorge Aguilera-Iparraguirre
  • Timothy Hirzel
  • Ryan P. Adams
  • Alán Aspuru-Guzik

References

Portions of the code have been re-used from the following repositories:

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molecular-vae's Issues

Mention code contribution and a potential bug fix.

Hi

want to point out that this repo should cite the original code contribution from topazape/molecular-VAE and also cxhernandez/molencoder so that their contributions are clearly stated because what you did is essentially just reusing their code. I think this project is better started as a fork as supposed to a fresh repo.

I have also fixed a bug on conv1d layer that existed in topazape/molecular-VAE that is also carried over to this repo, you can check it out here: topazape/molecular-VAE#2. That should also help you with further minimizing the loss.

How to prepare data

Hi, thanks for putting this together. In your notebook with an example, I see that you are using the dataset you already processed. I wondered if you could list what the procedure to follow is. I would like to use your implementation.

Best,

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