Drug interactions prediction using a weighted drug-protein network
The primary files used for this research can be found in the root directory of this project. networks.ipynb is used to construct the weighted DTPPI network and calculates the network specific features. The weights for this network are created in text_embeddings.ipynb.
The main file, predictor.ipynb is used to run the various comparisons between network, traditional and combined features using an MLP.
Next to the jupyter notebook files there are data, embeddings and networks directories. The /data directory contains DDI, DPI, negative_fileted and PPI data used to in the construction of the DTPPI network and MLP comparisons. The actual constructed network is saved in /networks. The embeddings used to weight the network are found in /embeddings
To run this project python 3.9 is required to be installed on your local machine, newer versions can possibly not be supported. Create a venv by running:
python3.9 -m venv .venv
Activate the virtual environment by running
source .venv/bin/activate
And install the dependencies found in requirements.txt
pip install -r requirements.txt