This is the repository of the paper "D'or: Deep orienter of protein-protein interaction networks"
This project is 100% implemented in python. Authors used python 3.8 but it should run with similar versions as well.
Please see that you clone the repository together with the gene translator submodule by running:
git clone --recursive https://github.com/pirakd/DeepOrienter.git
To instaell required packages run:
pip install -r path/to/project/requirements.txt
- Datasets used in the paper: Can be found in input folder.
- Deep learning model: found in deep_learning/models.py
- Example of a parameter configuration: in presets.py
- Train example script in scripts/main.py and model load and inference example script in scripts/inference.py. For this purpose we also added a pre computed propagation scores file generated using 5 AML patients and a deep model trained using these propgation scores and KPI interactions.
- Implementations of two previous methods mentioned in the paper: D2D.py and Vinayagam.py
DeepOrienter is MIT licensed, as found in the LICENSE file.