Data Each processed data set and its adjacency matrices representing gold standard networks are stored in one specific folder. The folders have the data set name. The process of obtaining the pairwise results and the evaluation metrics are divided into two main parts: 1. Pairwise results First, all the data set folders have to be placed in one main folder. Then run the script: RunAll_Matrices.R This script: Goes through each data set folder: reads the data set calculates for each method the resulting matrix Save in the data folder one file with all resulting matrices: file type RData 2. Evaluation After this first step, each data set folder has a file that contains all the resulting adjacency matrices. The second step is to run the script RunAll_Golds.R This script Goes through each folder: reads the data set reads the result adjacency matrices from RData files reads the gold networks Calculates all evaluation metrics for each result and each gold network type.