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Junction Tree VAE - example for training

This is a direct modification from https://github.com/wengong-jin/icml18-jtnn

Dependencies

  • PyTorch 0.4.1+
  • RDKit=2018.09.3.0
  • requests

How to run

To run the model, use

python3 vaetrain_dgl.py

The script will automatically download the data, which is the same as the one in the original repository.

To disable CUDA, run with NOCUDA variable set:

NOCUDA=1 python3 vaetrain_dgl.py

To decode for new molecules, run

python3 vaetrain_dgl.py -T

Currently, decoding involves encoding a training example, sampling from the posterior distribution, and decoding a molecule from that.