Table 4 Performance comparison of different methods based on the balanced subset of the independent test set in which benign variants were randomly selected from the full negative independent test set. We repeated this process 5 times with different random subsets of benign variants and averaged the results
Method | Recall | Precision | F-measure (β = 1) | AUC | P-value |
|---|---|---|---|---|---|
IDSV | 0.765 ± 0.000 | 0.781 ± 0.022 | 0.772 ± 0.011 | 0.868 ± 0.008 | * |
CADD | 0.320 ± 0.000 | 0.760 ± 0.041 | 0.450 ± 0.007 | 0.698 ± 0.018 | 9.452e-07 |
FATHMM-MKL | 0.712 ± 0.000 | 0.660 ± 0.026 | 0.685 ± 0.014 | 0.753 ± 0.019 | 0.0007962 |
SilVA | 0.490 ± 0.000 | 0.977 ± 0.017 | 0.653 ± 0.004 | 0.844 ± 0.017 | 3.211e-05 |
DDIG-SN | 0.298 ± 0.000 | 0.996 ± 0.010 | 0.459 ± 0.001 | 0.853 ± 0.006 | 5.957e-07 |
TraP | 0.575 ± 0.000 | 0.971 ± 0.012 | 0.723 ± 0.003 | 0.848 ± 0.043 | 0.001015 |