Protein-protein interaction prediction using a hybrid feature representation and a stacked generalization scheme

Chen, Kuan-Hsi; Wang, Tsai-Feng; Hu, Yuh-Jyh

doi:10.1186/s12859-019-2907-1

BMC Bioinformatics

Table 7 Performance results in 10-fold CV of PPI-MetaGO with different feature combinations

From: Protein-protein interaction prediction using a hybrid feature representation and a stacked generalization scheme

	TPR	FPR	Prec	ACC	F-score	MCC	AUC
HS1
F₁	0.917	0.016	0.983	0.951	0.949	0.903	0.981
F₂	0.872	0.101	0.897	0.886	0.884	0.772	0.901
F₃	0.686	0.637	0.521	0.525	0.588	0.053	0.534
F₁&F₂	0.894	0.031	0.966	0.931	0.929	0.865	0.977
F₁&F₃	0.926	0.028	0.971	0.949	0.948	0.899	0.987
F₂&F₃	0.885	0.089	0.909	0.898	0.896	0.796	0.915
F₁&F₂&F₃	0.964	0.013	0.987	0.975	0.975	0.951	0.993
DM1
F₁	0.978	0.001	0.999	0.988	0.988	0.977	0.997
F₂	0.664	0.237	0.727	0.714	0.644	0.449	0.787
F₃	0.690	0.604	0.417	0.543	0.497	0.132	0.538
F₁&F₂	0.933	0.005	0.995	0.964	0.963	0.930	0.995
F₁&F₃	0.977	0.001	0.999	0.988	0.988	0.976	0.998
F₂&F₃	0.740	0.253	0.728	0.743	0.705	0.501	0.765
F₁&F₂&F₃	0.966	0.010	0.990	0.978	0.978	0.956	0.996
HS3
F₁	0.812	0.215	0.790	0.798	0.801	0.597	0.862
F₂	0.730	0.244	0.750	0.743	0.740	0.487	0.788
F₃	0.626	0.235	0.731	0.695	0.672	0.397	0.733
F₁&F₂	0.809	0.206	0.797	0.801	0.803	0.602	0.870
F₁&F₃	0.812	0.191	0.809	0.811	0.811	0.621	0.883
F₂&F₃	0.720	0.202	0.781	0.759	0.749	0.520	0.810
F₁&F₂&F₃	0.826	0.187	0.816	0.820	0.821	0.639	0.897
SC2
F₁	0.747	0.261	0.741	0.743	0.744	0.486	0.812
F₂	0.805	0.133	0.858	0.836	0.831	0.673	0.871
F₃	0.796	0.063	0.927	0.866	0.856	0.740	0.885
F₁&F₂	0.809	0.145	0.848	0.832	0.828	0.665	0.908
F₁&F₃	0.841	0.070	0.923	0.885	0.880	0.774	0.933
F₂&F₃	0.858	0.065	0.930	0.897	0.893	0.796	0.934
F₁&F₂&F₃	0.858	0.059	0.936	0.899	0.895	0.802	0.952
EC2
F₁	0.763	0.169	0.821	0.797	0.790	0.598	0.845
F₂	0.810	0.089	0.902	0.860	0.853	0.725	0.913
F₃	0.878	0.075	0.922	0.902	0.899	0.805	0.938
F₁&F₂	0.793	0.141	0.850	0.826	0.820	0.655	0.895
F₁&F₃	0.901	0.069	0.929	0.916	0.914	0.832	0.956
F₂&F₃	0.915	0.046	0.952	0.934	0.933	0.870	0.973
F₁&F₂&F₃	0.913	0.048	0.950	0.933	0.931	0.866	0.960

F₁ physicochemical features, F₂ LCA-indexed GO-term features, F₃ network-based features
TPR true positive rate, FPR false positive rate, Prec precision, ACC accuracy, MCC Matthews correlation coefficient, AUC area under ROC
EC Escherichia coli, HS Homo sapiens, SC Saccharomyces cerevisiae, DM Drosophila melanogaster

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ISSN: 1471-2105

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