Positive-unlabelled learning of glycosylation sites in the human proteome

Li, Fuyi; Zhang, Yang; Purcell, Anthony W.; Webb, Geoffrey I.; Chou, Kuo-Chen; Lithgow, Trevor; Li, Chen; Song, Jiangning

doi:10.1186/s12859-019-2700-1

BMC Bioinformatics

Table 3 Performance comparison of PU-learning, supervised-learning, and one-class classification algorithms on the benchmark datasets

From: Positive-unlabelled learning of glycosylation sites in the human proteome

Type	Algorithm	2007			2010			2013
Type	Algorithm	F1	ACC	AUC	F1	ACC	AUC	F1	ACC	AUC
C	PA2DE (V2.0)	0.917 ± 0.049	0.909 ± 0.041	0.975 ± 0.061	0.917 ± 0.147	0.917 ± 0.087	0.948 ± 0.074	0.917 ± 0.034	0.923 ± 0.073	0.941 ± 0.037
	PA2DE	0.910 ± 0.051	0.904 ± 0.055	0.966 ± 0.039	0.898 ± 0.049	0.890 ± 0.054	0.925 ± 0.055	0.915 ± 0.044	0.910 ± 0.049	0.937 ± 0.046
	PAODE	0.843 ± 0.082	0.843 ± 0.077	0.912 ± 0.071	0.826 ± 0.111	0.837 ± 0.086	0.902 ± 0.083	0.870 ± 0.083	0.870 ± 0.074	0.933 ± 0.060
	PNB	0.889 ± 0.047	0.872 ± 0.060	0.943 ± 0.048	0.906 ± 0.047	0.895 ± 0.057	0.923 ± 0.047	0.908 ± 0.046	0.899 ± 0.056	0.936 ± 0.043
	PTAN	0.861 ± 0.056	0.841 ± 0.070	0.932 ± 0.049	0.887 ± 0.053	0.875 ± 0.064	0.923 ± 0.053	0.918 ± 0.046	0.912 ± 0.052	0.951 ± 0.039
	PFBC	0.869 ± 0.049	0.846 ± 0.066	0.947 ± 0.042	0.882 ± 0.045	0.866 ± 0.058	0.935 ± 0.044	0.893 ± 0.054	0.879 ± 0.068	0.940 ± 0.046
	RF^[a]	0.847 ± 0.070	0.835 ± 0.075	0.922 ± 0.064	0.864 ± 0.058	0.856 ± 0.059	0.922 ± 0.056	0.883 ± 0.057	0.875 ± 0.062	0.941 ± 0.051
	SVM	0.810 ± 0.095	0.814 ± 0.080	0.814 ± 0.080	0.851 ± 0.083	0.853 ± 0.073	0.853 ± 0.073	0.847 ± 0.085	0.855 ± 0.068	0.855 ± 0.068
	O-SVM^[b]	0.365 ± 0.152	0.612 ± 0.065	0.612 ± 0.065	0.400 ± 0.151	0.613 ± 0.066	0.613 ± 0.066	0.366 ± 0.136	0.606 ± 0.055	0.606 ± 0.055
	O-Classifier^[c]	0.680 ± 0.142	0.760 ± 0.081	0.760 ± 0.081	0.662 ± 0.139	0.740 ± 0.082	0.740 ± 0.082	0.726 ± 0.122	0.785 ± 0.076	0.785 ± 0.076
N	PA2DE (V2.0)	0.933 ± 0.041	0.928 ± 0.051	0.929 ± 0.012	0.989 ± 0.011	0.985 ± 0.003	0.998 ± 0.013	0.990 ± 0.012	0.985 ± 0.003	0.998 ± 0.011
	PA2DE	0.916 ± 0.007	0.910 ± 0.008	0.914 ± 0.008	0.987 ± 0.003	0.983 ± 0.004	0.998 ± 0.002	0.988 ± 0.003	0.984 ± 0.004	0.998 ± 0.001
	PAODE	0.916 ± 0.009	0.910 ± 0.009	0.943 ± 0.026	0.940 ± 0.051	0.920 ± 0.049	0.928 ± 0.018	0.957 ± 0.004	0.938 ± 0.006	0.928 ± 0.015
	PNB	0.916 ± 0.009	0.910 ± 0.009	0.943 ± 0.026	0.948 ± 0.005	0.928 ± 0.007	0.923 ± 0.009	0.957 ± 0.004	0.938 ± 0.006	0.925 ± 0.009
	PTAN	0.985 ± 0.004	0.985 ± 0.004	0.996 ± 0.002	0.929 ± 0.010	0.899 ± 0.015	0.915 ± 0.010	0.939 ± 0.010	0.909 ± 0.015	0.920 ± 0.009
	PFBC	0.916 ± 0.008	0.910 ± 0.009	0.945 ± 0.029	0.949 ± 0.005	0.929 ± 0.007	0.937 ± 0.022	0.957 ± 0.004	0.938 ± 0.006	0.937 ± 0.021
	RF^[a]	0.980 ± 0.005	0.980 ± 0.005	0.994 ± 0.003	0.984 ± 0.004	0.978 ± 0.005	0.997 ± 0.002	0.985 ± 0.003	0.979 ± 0.004	0.997 ± 0.002
	SVM	0.916 ± 0.007	0.910 ± 0.008	0.910 ± 0.008	0.948 ± 0.005	0.928 ± 0.007	0.912 ± 0.009	0.957 ± 0.004	0.938 ± 0.006	0.916 ± 0.009
	O-SVM^[b]	0.551 ± 0.125	0.695 ± 0.695	0.695 ± 0.061	0.553 ± 0.108	0.585 ± 0.069	0.695 ± 0.051	0.567 ± 0.097	0.570 ± 0.066	0.701 ± 0.046
	O-Classifier^[c]	0.868 ± 0.052	0.850 ± 0.045	0.894 ± 0.045	0.871 ± 0.037	0.855 ± 0.043	0.897 ± 0.036	0.923 ± 0.042	0.896 ± 0.051	0.904 ± 0.038
O	PA2DE (V2.0)	0.979 ± 0.007	0.979 ± 0.011	0.995 ± 0.007	0.986 ± 0.007	0.986 ± 0.010	0.997 ± 0.006	0.982 ± 0.013	0.982 ± 0.007	0.996 ± 0.012
	PA2DE	0.977 ± 0.011	0.978 ± 0.011	0.996 ± 0.012	0.983 ± 0.008	0.983 ± 0.008	0.997 ± 0.002	0.977 ± 0.013	0.977 ± 0.013	0.996 ± 0.005
	PAODE	0.968 ± 0.012	0.968 ± 0.013	0.994 ± 0.004	0.980 ± 0.010	0.980 ± 0.009	0.998 ± 0.002	0.967 ± 0.011	0.968 ± 0.010	0.995 ± 0.005
	PNB	0.984 ± 0.007	0.984 ± 0.007	0.997 ± 0.002	0.967 ± 0.010	0.966 ± 0.011	0.998 ± 0.001	0.980 ± 0.009	0.980 ± 0.008	0.997 ± 0.002
	PTAN	0.938 ± 0.016	0.936 ± 0.017	0.987 ± 0.007	0.942 ± 0.013	0.940 ± 0.014	0.988 ± 0.006	0.935 ± 0.014	0.932 ± 0.015	0.987 ± 0.006
	PFBC	0.967 ± 0.012	0.966 ± 0.013	0.998 ± 0.002	0.965 ± 0.011	0.965 ± 0.011	0.995 ± 0.003	0.963 ± 0.010	0.962 ± 0.010	0.993 ± 0.004
	RF^[a]	0.979 ± 0.016	0.979 ± 0.016	0.994 ± 0.006	0.980 ± 0.016	0.981 ± 0.015	0.996 ± 0.004	0.967 ± 0.011	0.968 ± 0.010	0.995 ± 0.005
	SVM	0.977 ± 0.011	0.978 ± 0.011	0.996 ± 0.012	0.974 ± 0.014	0.974 ± 0.013	0.996 ± 0.005	0.981 ± 0.014	0.981 ± 0.013	0.994 ± 0.005
	O-SVM^[b]	0.582 ± 0.053	0.691 ± 0.026	0.691 ± 0.026	0.575 ± 0.575	0.681 ± 0.028	0.681 ± 0.028	0.578 ± 0.045	0.666 ± 0.027	0.666 ± 0.027
	O-Classifier^[c]	0.695 ± 0.039	0.593 ± 0.080	0.593 ± 0.080	0.665 ± 0.026	0.535 ± 0.059	0.535 ± 0.059	0.702 ± 0.026	0.621 ± 0.059	0.621 ± 0.059

[a] RF – Random Forest; [b] O-SVM – One-class SVM; [c] O-Classifier – One-class Classifier

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