Table 4.

SAP achieves the highest F_max scores across all bacteria for all three GO categories on the full SwissProt experiment set, except for S. typhimurium where DeepGOPlus performs in BPO and MFO. F_max scores on the full SwissProt experiment set are tabulated in three parts for separate GO categories, BPO, MFO and CCO respectively, and each column is a different bacteria found in our SwissProt experiments

Method	EC	MT	BS	PA	ST
Biological process
BLAST	0.570	0.543	0.639	0.683	0.852
Pfam	0.610	0.513	0.582	0.579	0.579
knn	0.646	0.636	0.828	0.797	0.880
SAP-operon	0.872	0.837	0.915	0.928	0.903
SAP	0.876	0.838	0.915	0.929	0.902
DeepGOPlus	0.648	0.669	0.857	0.824	0.928
Molecular function
BLAST	0.613	0.593	0.625	0.699	0.814
Pfam	0.650	0.549	0.571	0.534	0.559
knn	0.675	0.723	0.814	0.854	0.837
SAP-operon	0.880	0.869	0.893	0.938	0.878
SAP	0.885	0.869	0.893	0.938	0.877
DeepGOPlus	0.686	0.755	0.841	0.883	0.911
Cellular component
BLAST	0.569	0.397	0.638	0.700	0.871
Pfam	0.625	0.541	0.608	0.560	0.616
knn	0.731	0.500	0.898	0.900	0.917
SAP-operon	0.920	0.847	0.943	0.945	0.918
SAP	0.922	0.847	0.943	0.945	0.917
DeepGOPlus	0.745	0.567	0.885	0.887	0.936