These files contain implementation of experimental evaluation in the following paper:

@article{fakharei2014network,
title={Network-Based Drug-Target Interaction Prediction with Probabilistic Soft Logic},
author={Fakhraei, Shobeir and Huang, Bert and Raschid, Louiqa and Getoor, Lise},
journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
year={2014},
}

To run the files you need to install Probabilistic Soft Logic (PSL) prerequisites first. Please read the instructions here for details: https://github.com/linqs/psl/wiki

You can then run the first experiment using 'run.sh'. Please change that file to run the other experiments.

PSL models are located here: /src/main/java/edu/umd/cs/psl/fakhraei_tcbb2014

Perlman's method is implemented in matlab and is located here: /src/main/matlab/Perlmans_method

The full dataset in .mat format is located here: /src/main/matlab/Perlmans_method/data

A copy of the paper can be found here: https://shobeir.github.io/papers/fakhraei_tcbb_2014.pdf