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

Table 1

Performance summary of the 5-fold cross-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	0.821	0.863	0.779	0.823	0.646	0.817	0.909	0.725	0.821	0.648	0.813	0.838	0.788	0.814	0.628	0.823	0.822	0.824	0.823	0.646
	ECFP6	0.808	0.855	0.761	0.810	0.620	0.809	0.822	0.797	0.810	0.619	0.816	0.871	0.761	0.819	0.638	0.797	0.846	0.748	0.799	0.598
AGTR1	MACCS	0.858	0.870	0.846	0.858	0.716	0.861	0.876	0.846	0.860	0.722	0.864	0.879	0.848	0.863	0.727	0.840	0.834	0.846	0.840	0.679
	ECFP6	0.879	0.885	0.873	0.878	0.757	0.876	0.910	0.843	0.876	0.754	0.879	0.899	0.859	0.878	0.758	0.862	0.870	0.854	0.862	0.724
AKR1B1	MACCS	0.716	0.736	0.696	0.715	0.432	0.719	0.696	0.743	0.720	0.439	0.734	0.733	0.736	0.734	0.468	0.714	0.692	0.736	0.715	0.429
	ECFP6	0.778	0.791	0.766	0.778	0.556	0.736	0.766	0.706	0.734	0.471	0.769	0.773	0.766	0.769	0.538	0.740	0.755	0.726	0.740	0.480
AR	MACCS	0.767	0.769	0.765	0.767	0.534	0.754	0.788	0.721	0.754	0.509	0.778	0.773	0.783	0.778	0.555	0.738	0.740	0.735	0.738	0.475
	ECFP6	0.767	0.788	0.747	0.767	0.535	0.763	0.805	0.721	0.762	0.527	0.768	0.798	0.739	0.768	0.537	0.756	0.766	0.747	0.756	0.512
FLT1	MACCS	0.770	0.778	0.762	0.770	0.540	0.753	0.755	0.751	0.753	0.506	0.770	0.769	0.771	0.770	0.540	0.741	0.735	0.748	0.741	0.483
	ECFP6	0.754	0.732	0.776	0.754	0.509	0.749	0.724	0.773	0.749	0.498	0.763	0.701	0.824	0.763	0.529	0.737	0.726	0.748	0.737	0.474
ICAM1	MACCS	0.754	0.797	0.710	0.754	0.509	0.739	0.812	0.667	0.739	0.483	0.775	0.855	0.696	0.775	0.558	0.783	0.812	0.754	0.783	0.566
	ECFP6	0.790	0.870	0.710	0.790	0.587	0.768	0.884	0.652	0.768	0.551	0.812	0.870	0.754	0.812	0.627	0.775	0.812	0.739	0.775	0.552
KDR	MACCS	0.787	0.801	0.773	0.787	0.574	0.777	0.791	0.763	0.777	0.554	0.800	0.800	0.800	0.800	0.600	0.762	0.775	0.748	0.762	0.524
	ECFP6	0.824	0.839	0.809	0.824	0.649	0.804	0.841	0.768	0.805	0.611	0.830	0.835	0.825	0.830	0.660	0.797	0.815	0.779	0.797	0.595
MAPT	MACCS	0.702	0.667	0.737	0.704	0.404	0.711	0.606	0.816	0.718	0.433	0.667	0.545	0.789	0.676	0.347	0.687	0.636	0.737	0.690	0.375
	ECFP6	0.783	0.697	0.868	0.789	0.577	0.770	0.697	0.842	0.775	0.547	0.743	0.697	0.789	0.746	0.489	0.754	0.667	0.842	0.761	0.519
NOS2	MACCS	0.812	0.818	0.807	0.812	0.624	0.830	0.825	0.834	0.830	0.659	0.820	0.847	0.793	0.819	0.640	0.794	0.796	0.793	0.794	0.589
	ECFP6	0.823	0.832	0.814	0.823	0.646	0.817	0.883	0.752	0.816	0.639	0.830	0.832	0.828	0.830	0.660	0.815	0.803	0.828	0.816	0.631
NOS3	MACCS	0.720	0.710	0.730	0.720	0.440	0.714	0.718	0.710	0.714	0.427	0.734	0.714	0.755	0.734	0.469	0.730	0.710	0.751	0.730	0.461
	ECFP6	0.741	0.763	0.718	0.741	0.482	0.718	0.788	0.647	0.718	0.440	0.745	0.776	0.714	0.745	0.491	0.726	0.730	0.722	0.726	0.452
PRKCB	MACCS	0.785	0.791	0.780	0.785	0.569	0.784	0.822	0.747	0.781	0.567	0.805	0.744	0.867	0.810	0.618	0.791	0.783	0.800	0.792	0.582
	ECFP6	0.828	0.829	0.827	0.828	0.655	0.816	0.891	0.740	0.810	0.633	0.839	0.845	0.833	0.839	0.677	0.823	0.806	0.840	0.824	0.647
SERPINE1	MACCS	0.801	0.819	0.783	0.800	0.601	0.780	0.810	0.750	0.778	0.558	0.820	0.848	0.792	0.818	0.638	0.804	0.800	0.808	0.804	0.608
	ECFP6	0.800	0.800	0.800	0.800	0.599	0.792	0.810	0.775	0.791	0.583	0.819	0.838	0.800	0.818	0.637	0.811	0.838	0.783	0.809	0.620
SLC2A1	MACCS	0.707	0.741	0.673	0.706	0.415	0.685	0.689	0.681	0.685	0.370	0.723	0.753	0.692	0.722	0.446	0.695	0.697	0.692	0.695	0.389
	ECFP6	0.733	0.797	0.669	0.732	0.469	0.731	0.769	0.692	0.730	0.462	0.746	0.769	0.723	0.746	0.492	0.736	0.765	0.708	0.736	0.473
TNF	MACCS	0.832	0.827	0.836	0.831	0.663	0.824	0.842	0.806	0.824	0.648	0.848	0.886	0.810	0.848	0.698	0.817	0.820	0.813	0.817	0.633
	ECFP6	0.859	0.846	0.873	0.859	0.719	0.863	0.875	0.851	0.863	0.726	0.859	0.879	0.840	0.859	0.719	0.842	0.864	0.821	0.843	0.686
VCAM1	MACCS	0.774	0.595	0.953	0.787	0.596	0.813	0.649	0.977	0.825	0.673	0.786	0.595	0.977	0.800	0.629	0.679	0.568	0.791	0.688	0.369
	ECFP6	0.788	0.622	0.953	0.800	0.619	0.799	0.622	0.977	0.812	0.651	0.813	0.649	0.977	0.825	0.673	0.735	0.703	0.767	0.738	0.471
PCM	MACCS_pro	0.776	0.784	0.767	0.776	0.552	0.769	0.783	0.755	0.769	0.539	0.787	0.776	0.797	0.787	0.573	0.75	0.743	0.757	0.75	0.501
	ECFP6_pro	0.810	0.821	0.799	0.810	0.619	0.788	0.832	0.743	0.788	0.578	0.805	0.810	0.800	0.805	0.610	0.781	0.800	0.762	0.781	0.562