Table I. Comparison of different prediction approaches with F1 score.

The average true positive of the random network is calculated from 10 randomized networks. Precision represents predicted PPIs with experimental evidence/all predicted PPIs, and recall represents predicted PPIs with experimental evidence/all experimentally determined PPIs.

Method	Predicted PPIs with Experimental Evidence	All Predicted PPIs	All Experimentally Determined PPIs	Precision	Recall	F1 Score
Random network	348	316,747	21,282	0.001	0.016	0.002
AtPID	386	24,418	21,282	0.016	0.018	0.017
AtPIN	449	90,043	21,282	0.005	0.021	0.008
PAIR	1,995	145,355	21,282	0.014	0.094	0.024
AraPPINet	6,040	316,747	21,282	0.019	0.284	0.036