DRDB: A Machine Learning Platform to Predict Chemical-Protein Interactions towards Diabetic Retinopathy

Table 2

Performance summary of the test set external validation for 15 targets towards DR.

Target	Fingerprint	Random Forest					KNN					SVM					Neural networks
		AUC	SE	SP		MCC	AUC	SE	SP		MCC	AUC	SE	SP		MCC	AUC	SE	SP		MCC
ACE	MACCS	0.806	0.885	0.727	0.810	0.623	0.744	0.869	0.618	0.750	0.506	0.799	0.852	0.745	0.802	0.603	0.743	0.885	0.600	0.750	0.510
	ECFP6	0.814	0.902	0.727	0.819	0.642	0.790	0.852	0.727	0.793	0.586	0.842	0.902	0.782	0.845	0.691	0.784	0.787	0.782	0.784	0.568
AGTR1	MACCS	0.884	0.888	0.880	0.884	0.768	0.851	0.843	0.859	0.851	0.702	0.868	0.876	0.859	0.867	0.735	0.872	0.843	0.902	0.873	0.747
	ECFP6	0.862	0.876	0.848	0.862	0.724	0.885	0.921	0.848	0.884	0.770	0.863	0.910	0.815	0.862	0.728	0.856	0.865	0.848	0.856	0.713
AKR1B1	MACCS	0.746	0.768	0.724	0.745	0.491	0.660	0.623	0.697	0.662	0.321	0.745	0.754	0.737	0.745	0.490	0.718	0.739	0.697	0.717	0.436
	ECFP6	0.741	0.797	0.684	0.738	0.483	0.734	0.797	0.671	0.731	0.470	0.753	0.783	0.724	0.752	0.506	0.734	0.797	0.671	0.731	0.470
AR	MACCS	0.754	0.788	0.721	0.753	0.509	0.762	0.849	0.675	0.760	0.531	0.794	0.836	0.753	0.793	0.590	0.758	0.815	0.701	0.757	0.519
	ECFP6	0.824	0.856	0.792	0.823	0.649	0.811	0.856	0.766	0.810	0.624	0.831	0.863	0.799	0.830	0.662	0.769	0.726	0.812	0.770	0.540
FLT1	MACCS	0.791	0.773	0.809	0.791	0.582	0.757	0.693	0.820	0.757	0.518	0.791	0.761	0.820	0.791	0.583	0.729	0.693	0.764	0.729	0.458
	ECFP6	0.808	0.750	0.865	0.808	0.620	0.751	0.705	0.798	0.751	0.505	0.802	0.705	0.899	0.802	0.616	0.780	0.773	0.787	0.780	0.559
ICAM1	MACCS	0.712	0.778	0.647	0.714	0.429	0.855	0.944	0.765	0.857	0.723	0.797	0.889	0.706	0.800	0.607	0.799	0.833	0.765	0.800	0.600
	ECFP6	0.858	0.833	0.882	0.857	0.716	0.858	0.833	0.882	0.857	0.716	0.858	0.833	0.882	0.857	0.716	0.971	1.000	0.941	0.971	0.944
KDR	MACCS	0.788	0.812	0.764	0.788	0.576	0.765	0.800	0.730	0.765	0.531	0.799	0.821	0.777	0.799	0.599	0.756	0.816	0.696	0.757	0.516
	ECFP6	0.829	0.827	0.831	0.829	0.658	0.812	0.837	0.788	0.813	0.625	0.833	0.838	0.828	0.833	0.666	0.805	0.830	0.780	0.805	0.611
MAPT	MACCS	0.838	0.875	0.800	0.833	0.671	0.838	0.875	0.800	0.833	0.671	0.750	1.000	0.500	0.722	0.555	0.900	1.000	0.800	0.889	0.800
	ECFP6	0.750	1.000	0.500	0.722	0.555	0.750	1.000	0.500	0.722	0.555	0.750	1.000	0.500	0.722	0.555	0.900	1.000	0.800	0.889	0.800
NOS2	MACCS	0.762	0.829	0.694	0.761	0.527	0.775	0.800	0.750	0.775	0.550	0.832	0.886	0.778	0.831	0.667	0.762	0.829	0.694	0.761	0.527
	ECFP6	0.832	0.886	0.778	0.831	0.667	0.790	0.914	0.667	0.789	0.598	0.762	0.829	0.694	0.761	0.527	0.704	0.714	0.694	0.704	0.409
NOS3	MACCS	0.719	0.721	0.717	0.719	0.438	0.686	0.689	0.683	0.686	0.372	0.686	0.689	0.683	0.686	0.372	0.678	0.639	0.717	0.678	0.357
	ECFP6	0.817	0.902	0.733	0.818	0.645	0.792	0.902	0.683	0.793	0.600	0.826	0.869	0.783	0.826	0.655	0.818	0.836	0.800	0.818	0.637
PRKCB	MACCS	0.783	0.750	0.816	0.786	0.567	0.825	0.781	0.868	0.829	0.654	0.838	0.781	0.895	0.843	0.684	0.764	0.844	0.684	0.757	0.529
	ECFP6	0.882	0.844	0.921	0.886	0.770	0.803	0.844	0.763	0.800	0.605	0.869	0.844	0.895	0.871	0.741	0.869	0.844	0.895	0.871	0.741
SERPINE1	MACCS	0.762	0.846	0.677	0.754	0.526	0.778	0.846	0.710	0.772	0.556	0.746	0.846	0.645	0.737	0.496	0.762	0.846	0.677	0.754	0.526
	ECFP6	0.704	0.731	0.677	0.702	0.407	0.749	0.692	0.806	0.754	0.503	0.813	0.885	0.742	0.807	0.627	0.813	0.885	0.742	0.807	0.627
SLC2A1	MACCS	0.789	0.810	0.769	0.789	0.579	0.719	0.714	0.723	0.719	0.437	0.758	0.778	0.738	0.758	0.516	0.720	0.778	0.662	0.719	0.442
	ECFP6	0.704	0.778	0.631	0.703	0.413	0.711	0.746	0.677	0.711	0.424	0.727	0.762	0.692	0.727	0.455	0.688	0.730	0.646	0.688	0.377
TNF	MACCS	0.890	0.899	0.881	0.890	0.779	0.875	0.870	0.881	0.875	0.750	0.860	0.899	0.821	0.860	0.722	0.838	0.855	0.821	0.838	0.677
	ECFP6	0.889	0.928	0.851	0.890	0.781	0.889	0.913	0.866	0.890	0.780	0.874	0.913	0.836	0.875	0.752	0.845	0.855	0.836	0.846	0.691
VCAM1	MACCS	0.742	0.667	0.818	0.750	0.492	0.833	0.667	1.000	0.850	0.724	0.778	0.556	1.000	0.800	0.638	0.596	0.556	0.636	0.600	0.192
	ECFP6	0.732	0.556	0.909	0.750	0.504	0.778	0.556	1.000	0.800	0.638	0.778	0.556	1.000	0.800	0.638	0.732	0.556	0.909	0.750	0.504
PCM	MACCS_pro	0.788	0.808	0.769	0.788	0.577	0.77	0.8	0.741	0.77	0.542	0.799	0.8	0.798	0.799	0.597	0.758	0.726	0.79	0.758	0.518
	ECFP6_pro	0.821	0.836	0.806	0.821	0.643	0.803	0.842	0.764	0.803	0.608	0.818	0.823	0.813	0.818	0.636	0.795	0.814	0.775	0.795	0.59