Table 5. Performance Comparison of ConsMM, EvoIndMM, and Existing Predictors on the Blind Test Set.

repeated	predictor name	recall/sen	Spe	Pre	NPV	F1	ACC	MCC
repeated protein (consisting of 488 proteins with 2593 variants)	VEST4	0.9407	0.7541	0.8256	0.9114	0.8794	0.8573	0.7156
	PROVEAN	0.8159	0.7368	0.7932	0.7639	0.8044	0.7806	0.5549
	LIST-S2	0.8173	0.7170	0.7813	0.7603	0.7989	0.7725	0.5379
	gMVP	0.9135	0.6471	0.7621	0.8581	0.8310	0.7944	0.5897
	MetaSVM	0.9407	0.6264	0.7570	0.8952	0.8389	0.8002	0.6082
	MetaLR	0.9268	0.6264	0.7543	0.8736	0.8317	0.7925	0.5894
	M-CAP	0.9596	0.8136	0.8643	0.9421	0.9095	0.8943	0.7896
	DEOGEN2	0.9191	0.5876	0.7339	0.8545	0.8161	0.7709	0.5460
	InMeRF	0.8954	0.7843	0.8370	0.8584	0.8652	0.8457	0.6875
	VARITY	0.8375	0.7921	0.8329	0.7976	0.8352	0.8172	0.6300
	MetaRNN	0.8961	0.9974	0.9977	0.8858	0.9442	0.9414	0.8885
	MVP	0.9693	0.5789	0.7401	0.9385	0.8394	0.7948	0.6100
	ConsMM	0.9296	0.8878	0.9111	0.9106	0.9203	0.9109	0.8196
	EvoIndMM	0.9150	0.9617	0.9719	0.8866	0.9426	0.9341	0.8675
nonrepeated protein (consisting of 420 proteins with 3365 variants)	VEST4	0.9539	0.7864	0.8028	0.9492	0.8719	0.8663	0.7461
	PROVEAN	0.8249	0.7625	0.7600	0.8269	0.7912	0.7923	0.5872
	LIST-S2	0.8399	0.6909	0.7125	0.8255	0.7709	0.7620	0.5344
	gMVP	0.9221	0.6625	0.7136	0.9032	0.8046	0.7863	0.6005
	MetaSVM	0.9402	0.5807	0.6716	0.9141	0.7835	0.7522	0.5523
	MetaLR	0.9327	0.6091	0.6851	0.9085	0.7900	0.7634	0.5671
	M-CAP	0.9483	0.8540	0.8555	0.9477	0.8995	0.8990	0.8027
	DEOGEN2	0.9333	0.5608	0.6596	0.9022	0.7730	0.7385	0.5269
	InMeRF	0.9115	0.8295	0.8298	0.9114	0.8688	0.8686	0.7411
	VARITY	0.8704	0.8261	0.8203	0.8748	0.8446	0.8473	0.6959
	MetaRNN	0.9016	0.9972	0.9966	0.9174	0.9467	0.9516	0.9063
	MVP	0.9483	0.5830	0.6746	0.9252	0.7884	0.7572	0.5645
	ConsMM	0.9283	0.9364	0.9301	0.9348	0.9292	0.9325	0.8648
	EvoIndMM	0.9261	0.9840	0.9851	0.9213	0.9547	0.9532	0.9082