Table 2.

Scores for assessment of predictions. Tau, Kendall’s tau coefficient (Tau-b); spearman, Spearman’s rank correlation coefficient; dele roc, area under ROC for detecting deleterious variants; wild roc, area under ROC for detecting benign variants; rmsd, root-mean-square deviation; pearson, Pearson correlation coefficient; value diff, area under curve of percentage of variants against the absolute difference between experimental score and predicted score of variants; mcc_dele, matthew correlation coefficient for deleterious variants; mcc_wild, matthew correlation coefficient for benign variants; f1, F-score for three classes (deleterious, mildly deleterious, benign) of variants. baseline: baseline predictor; positive: positive control.

group id	rank based scores				original value based						rescaled value based
	Tau	spearman	dele roc	wild roc	rmsd	pearson	value diff	mcc_dele	mcc_wild	f1	rmsd	pearson	value diff	mcc_dele	mcc_wild	f1
baseline	0.15	0.23	0.63	0.61	0.37	0.24	0.73	0.16	0.17	0.5	0.37	0.24	0.73	0.16	0.17	0.5
positive	0.85	0.98	0.99	0.98	0.07	0.97	0.95	0.85	0.92	0.92	0.07	0.97	0.96	0.85	0.92	0.92
1–1	0.15	0.22	0.63	0.61	0.38	0.22	0.73	0.11	0.16	0.48	0.38	0.22	0.73	0.11	0.16	0.48
1–2	0.15	0.22	0.63	0.6	0.38	0.23	0.73	0.11	0.16	0.48	0.38	0.23	0.73	0.11	0.16	0.48
2–1	0.17	0.25	0.65	0.61	0.4	0.24	0.66	0.13	0.1	0.29	0.38	0.24	0.73	0.11	0.17	0.48
2–2	0.15	0.23	0.64	0.6	0.37	0.22	0.69	0.1	0.09	0.34	0.38	0.22	0.72	0.09	0.17	0.47
3–1	0.07	0.108	0.58	0.57	0.35	0.17	0.75	0.09	0.1	0.51	0.4	0.17	0.71	0.14	0.08	0.46
4–1	−0.02	−0.03	0.45	0.48	0.51	−0.04	0.61	−0.05	−0.02	0.4	0.43	−0.04	0.67	−0.05	−0.03	0.4
4–2	−0.01	−0.02	0.49	0.49	0.5	−0.03	0.61	−0.03	−0.01	0.34	0.43	−0.03	0.67	−0.05	−0.03	0.4