Molecular AutoEncoder in PyTorch

Related tags

Deep Learningpythondeep-learningpytorchcomputational-chemistryautoencoder
Overview

MolEncoder

Molecular AutoEncoder in PyTorch

Install

$ git clone https://github.com/cxhernandez/molencoder.git && cd molencoder
$ python setup.py install

Download Dataset

$ molencoder download --dataset chembl22

Train

$ molencoder train --dataset data/chembl22.h5

Add --cuda flag to enable CUDA. Add --cont to continue training a model from a checkpoint file.

Pre-Trained Model

A pre-trained reference model is available in the ref/ directory. Currently, it performs with ~98% accuracy on the validation set after 100 epochs of training. However, if you succeed at training a better model, feel free to submit a pull request!

TODO

  • Implement encoder
  • Implement decoder
  • Add download command
  • Add train command
  • Add encode command
  • Add decode command
  • Add pre-trained model

Shoutouts

Owner
Carlos Hernández
Research Scientist @facebookresearch
Carlos Hernández
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