The Bridge Builders

This repo houses an academic project for the seminar course at Leiden University, Advances in Deep Learning (2021).

Members

• Alessandro Palma
• Heleen Severin
• Julius Cathalina
• Laurens Engwegen
• Stijn Oudshoorn*

Getting started

• Make sure you have conda (compatible with python 3.7) installed on your machine. You can download it here
• Install the conda environment by running conda env create -f env.yml
• Install the rest of the packages by running poetry install
• Install torch with cudatoolkit for version 11 using poe get-torch-cuda
• Get gxx for linux (for rdkit support) in conda by running poe get-gxx
• Install seaborn via pip install seaborn

References

• The original repo that our project is based on can be found here along with its paper [1].

1. Wu, Y., Gao, M., Zeng, M., Chen, F., Li, M. and Zhang, J., 2021. BridgeDPI: A Novel Graph Neural Network for Predicting Drug-Protein Interactions. arXiv preprint arXiv:2101.12547.