We compared IRAP with IG1/2 with the enriched GO term comparison method instead of the exact GO term matching. By considering the GO term relationships, IRAP outperforms IG1 and IG2.
We also tested the top 10% PPIs in the first 5 iterations of the repurification process (we select 5 because IRAP* to over-fit after 5 iterations). Results are shown in the figure below. The "increasing of functional homology" refers to the increase of similarity score based on the enriched GO term in the whole network after removing the bottom 10% interactions according to IRAP* or IG1/IG2. We see that IRAP* is consistently better than IG1 and IG2 in detecting false positives.