This repository contains Python scripts for "deepNF: Deep network fusion for protein function prediction" by V. Gligorijevic, M. Barot and R. Bonneau.
@article {Gligorijevic2017,
author = {Gligorijevi{\'c}, Vladimir and Barot, Meet and Bonneau, Richard},
title = {deepNF: Deep network fusion for protein function prediction},
year = {2018},
doi = {10.1093/bioinformatics/bty440},
pages = {bty440},
publisher = {Oxford},
URL = {http://dx.doi.org/10.1093/bioinformatics/bty440},
journal = {Bioinformatics}
}
To run deepNF run the following command from the project directory:
python2.7 main.py example_params.txt
deepNF is tested to work under Python 2.7.
The required dependencies for deepNF are Keras, TensorFlow, Numpy, and scikit-learn.
Data (PPMI matrices for human and yeast STRING networks as well as protein annotations) used for producing figures in the paper can be downloaded from:
https://users.flatironinstitute.org/vgligorijevic/public_www/deepNF_data/