Implementation of our Junction Tree Variational Autoencoder https://arxiv.org/abs/1802.04364
- Linux (We only tested on Ubuntu)
- RDKit (version >= 2017.09)
- Python (version >= 3.5)
- PyTorch (version >= 0.2)
To install RDKit, please follow the instructions here http://www.rdkit.org/docs/Install.html
We highly recommend you to use conda for package management.
This repository contains the following directories:
jtnn/bo/
includes scripts for Bayesian optimization experiments. Please readjtnn/bo/README.md
for details.jtnn/molvae/
includes scripts for training our VAE model only. Please readjtnn/molvae/README.md
for training our VAE model.jtnn/molopt/
includes scripts for jointly training our VAE and property predictors. Please readjtnn/molopt/README.md
for details.jtnn/jtnn/
contains codes for model formulation.
Wengong Jin ([email protected])