Table 4.
Top variant statistics. This table shows the ranking performance statistics for all methods evaluated on our test set (same order as Table 3)
| Ranking System | Percentage in Top X Variants - X=(1, 10, 20) | |||
|---|---|---|---|---|
| All (n=189) | VUS (n=111) | LP (n=42) | Path. (n=36) | |
| CADD Scaled | 4, 17, 24 | 0, 9, 15 | 7, 21, 30 | 13, 41, 47 |
| HPO-cosine | 7, 32, 47 | 7, 31, 48 | 7, 28, 40 | 8, 38, 50 |
| Exomiser(hiPhive) | 7, 29, 36 | 6, 30, 36 | 2, 16, 28 | 16, 38, 44 |
| Exomiser(hiPhive, human only) | 7, 28, 37 | 6, 28, 36 | 2, 16, 30 | 16, 38, 50 |
| Phen-Gen | 4, 21, 30 | 5, 20, 27 | 4, 16, 26 | 2, 27, 44 |
| DeepPVP | 11, 42, 52 | 4, 36, 47 | 16, 42, 50 | 27, 61, 72 |
| RandomForest(sklearn) | 16, 53, 65 | 9, 45, 55 | 19, 61, 76 | 36, 69, 80 |
| LogisticRegression(sklearn) | 23, 58, 72 | 13, 44, 62 | 26, 71, 80 | 52, 88, 94 |
| BalancedRandomForest(imblearn) | 16, 55, 67 | 9, 44, 57 | 23, 66, 76 | 33, 77, 86 |
| EasyEnsembleClassifier(imblearn) | 17, 58, 70 | 12, 43, 60 | 14, 71, 78 | 36, 88, 94 |
The “Percentage in Top X Variants” columns show the percentage of reported variants that were found in the top 1, 10, and 20 variants in a case after ranking by the corresponding method