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Table 2 AUROC and AUPRC values obtained by NCBoost upon different configurations of the training and independent testing sets. The figures obtained by the six state-of-the-art methods evaluated on the same testing sets are shown together with NCBoost

From: NCBoost classifies pathogenic non-coding variants in Mendelian diseases through supervised learning on purifying selection signals in humans

Positive set used for NCBoost training Positive set used for testing AUROC AUPRC
Source # SNVs Source # SNVs CADD DeepSEA Eigen Eigen PC FunSeq2 ReMM NCBoost CADD DeepSEA Eigen Eigen PC FunSeq2 ReMM NCBoost
HGMD-DM 186 !HGMD-DM 97 0.67 0.76 0.78 0.70 0.67 0.74 0.82 0.16 0.24 0.23 0.13 0.15 0.26 0.36
CV 107 !CV 176 0.72 0.74 0.73 0.63 0.68 0.77 0.78 0.27 0.31 0.24 0.11 0.15 0.37 0.38
Smedley 78 !Smedley 205 0.69 0.72 0.73 0.65 0.66 0.75 0.78 0.24 0.25 0.21 0.11 0.14 0.31 0.36
≥ 2 sources 73 1 source 210 0.68 0.72 0.73 0.64 0.66 0.75 0.78 0.23 0.24 0.21 0.11 0.14 0.31 0.31
1 source 210 ≥ 2 sources 73 0.8 0.81 0.82 0.69 0.77 0.82 0.85 0.31 0.43 0.29 0.16 0.24 0.48 0.52