Advancing drug–target interaction prediction: a comprehensive graph-based approach integrating knowledge graph embedding and ProtBert pretraining

Djeddi, Warith Eddine; Hermi, Khalil; Ben Yahia, Sadok; Diallo, Gayo

doi:10.1186/s12859-023-05593-6

Table 10 Comparison of DTIOG variants versus other DTI competitor prediction methods

From: Advancing drug–target interaction prediction: a comprehensive graph-based approach integrating knowledge graph embedding and ProtBert pretraining

Classifiers	AUPR	AUC	ACC	MCC	F1
GPCR
DTIOG-DT-PRTB-COS	0.948	0.978	0.968	0.926	0.945
DTIOG-DT-PRTB-ED	0.963	0.985	0.978	0.948	0.961
DTIOG-DT-PRTB-MD	0.959	0.983	0.976	0.943	0.958
DTIOG-DT-PRTB-JCC	0.958	0.983	0.975	0.941	0.956
DTIOG-DT-PRTB-PCC	0.956	0.982	0.974	0.938	0.954
DTIOG-DT-KGE-COS	0.968	0.987	0.981	0.955	0.967
DTIOG-DT-KGE-ED	0.967	0.987	0.981	0.954	0.966
DTIOG-DT-KGE-MD	0.966	0.986	0.980	0.952	0.965
DTIOG-DT-KGE-JCC	0.966	0.986	0.980	0.953	0.965
DTIOG-DT-KGE-PCC	0.965	0.986	0.980	0.951	0.964
DTIOG-DT-FP-COS	0.953	0.980	0.971	0.933	0.950
DTIOG-DT-FP-ED	0.951	0.980	0.971	0.931	0.949
DTIOG-DT-FP-MD	0.953	0.981	0.972	0.934	0.951
DTIOG-DT-FP-JCC	0.954	0.981	0.972	0.933	0.951
DTIOG-DT-FP-PCC	0.957	0.982	0.974	0.940	0.955
iGRLDTI	0.954	0.979	0.944	0.850	0.885
DTI-HeNE	0.948	0.945	0.972	0.923	0.939
ALADIN	0.516	0.795	0.970	0.381	0.298
BLM-NII	0.476	0.834	0.970	0.297	0.189
IC
DTIOG-DT-PRTB-COS	0.965	0.983	0.976	0.948	0.963
DTIOG-DT-PRTB-ED	0.972	0.986	0.981	0.959	0.971
DTIOG-DT-PRTB-MD	0.973	0.987	0.982	0.961	0.972
DTIOG-DT-PRTB-JCC	0.969	0.985	0.979	0.954	0.968
DTIOG-DT-PRTB-PCC	0.968	0.985	0.979	0.953	0.967
DTIOG-DT-KGE-COS	0.972	0.987	0.982	0.959	0.971
DTIOG-DT-KGE-ED	0.977	0.989	0.985	0.967	0.977
DTIOG-DT-KGE-MD	0.976	0.988	0.984	0.965	0.975
DTIOG-DT-KGE-JCC	0.973	0.987	0.982	0.961	0.973
DTIOG-DT-KGE-PCC	0.972	0.986	0.982	0.959	0.971
DTIOG-DT-FP-COS	0.959	0.980	0.973	0.940	0.958
DTIOG-DT-FP-ED	0.962	0.981	0.974	0.944	0.960
DTIOG-DT-FP-MD	0.961	0.981	0.973	0.942	0.959
DTIOG-DT-FP-JCC	0.960	0.981	0.973	0.941	0.959
DTIOG-DT-FP-PCC	0.962	0.982	0.975	0.944	0.961
iGRLDTI	0.973	0.980	0.931	0.861	0.921
DTI-HeNE	0.981	0.978	0.986	0.964	0.973
ALADIN	0.803	0.913	0.965	0.757	0.751
BLM-NII	0.786	0.930	0.965	0.763	0.762
ENZ
DTIOG-DT-PRTB-COS	0.963	0.994	0.990	0.957	0.961
DTIOG-DT-PRTB-ED	0.971	0.996	0.993	0.967	0.970
DTIOG-DT-PRTB-MD	0.973	0.996	0.993	0.969	0.972
DTIOG-DT-PRTB-JCC	0.962	0.994	0.990	0.956	0.961
DTIOG-DT-PRTB-PCC	0.962	0.994	0.990	0.956	0.961
DTIOG-DT-KGE-COS	0.976	0.996	0.994	0.972	0.975
DTIOG-DT-KGE-ED	0.976	0.996	0.994	0.973	0.976
DTIOG-DT-KGE-MD	0.976	0.996	0.994	0.972	0.975
DTIOG-DT-KGE-JCC	0.975	0.996	0.993	0.971	0.974
DTIOG-DT-KGE-PCC	0.975	0.996	0.994	0.971	0.974
DTIOG-DT-FP-COS	0.954	0.993	0.988	0.947	0.952
DTIOG-DT-FP-ED	0.951	0.992	0.987	0.943	0.948
DTIOG-DT-FP-MD	0.956	0.993	0.989	0.949	0.954
DTIOG-DT-FP-JCC	0.955	0.993	0.988	0.948	0.953
DTIOG-DT-FP-PCC	0.955	0.993	0.988	0.948	0.953
iGRLDTI	0.949	0.940	0.885	0.760	0.906
DTI-HeNE	0.963	0.962	0.992	0.954	0.957
ALADIN	0.757	0.896	0.990	0.665	0.620
BLM-NII	0.769	0.925	0.990	0.702	0.666

The best results are indicated in bold concerning each row

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ISSN: 1471-2105

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