Novel Molecular Representations using Neumann-Cayley Orthogonal Gated Recurrent Unit

• Full Code is going to be available soon

Implementation of the Paper "Novel Molecular Representations using Neumann-Cayley Orthogonal Gated Recurrent Unit" by Edison Mucllari, Vasily Zadorozhnyy, Qiang Ye and Duc Nguyen

Installing

Conda

Create a new ncgru_fp enviorment:

git clone https://github.com/Edison1994/NC-GRU-molecular-representation.git
conda env create -f env.yml
source activate ncgru_fp

Install tensorflow with GPU support:

pip install tensorflow-gpu==1.10.0

Install additional zmq package:

pip install zmq

Getting Data (from Google Drive)

The google_drive_data.zip file can also be downloaded manualy under https://drive.google.com/file/d/1pXBp7Jvf9iS6reQbv5MxJ5z4f0lpwWaD/view?usp=share_link

After unzipping the folder, chembl_28 corresponds to the AutoEncoder train/test data and prediction_data is the folder containing the data for the inference model

Train AutoEncoder from scratch

Run the script run.sh :

bash run.sh