Table 2.

The performance of four symmetric representing schemes for protein pairs

Organism	Methods	Benchmark negatives					Random negatives
		AUC	Acc	Sn	Sp	Pre	AUC	Acc	Sn	Sp	Pre
E. coli	AG-CTF	0.996	0.968	0.997	0.941	0.893	0.886	0.797	0.794	0.799	0.798
	SM-CTF	0.988	0.948	0.985	0.929	0.879	0.876	0.788	0.785	0.789	0.789
	Sker-CTF	0.998	0.947	0.995	0.940	0.839	0.880	0.795	0.791	0.798	0.797
	Dist-CTF	0.955	0.892	0.842	0.899	0.786	0.769	0.702	0.704	0.699	0.701
S. cerevisiae	AG-CTF	0.991	0.968	0.991	0.959	0.786	0.948	0.880	0.879	0.928	0.919
	SM-CTF	0.990	0.964	0.984	0.958	0.766	0.939	0.868	0.837	0.899	0.893
	Sker-CTF	0.985	0.909	0.978	0.900	0.564	0.929	0.867	0.818	0.919	0.911
	Dist-CTF	0.946	0.891	0.826	0.900	0.523	0.849	0.788	0.764	0.799	0.792

Cutoff for each method was set according to the maximal F-measure statistic which is a community-standard procedure. Acc: accuracy; Sn: sensitivity; Sp: Specificity; Pre: precision.