Table 4. Results obtained for the classification of the external validation sequence dataset for each predictor, where TP corresponds to the number of true positives, TN to the number of true negatives, FP to the number of false positives and FN to the number of false negatives.
The values of sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy, with corresponding 95% confidence intervals, were obtained using bootstrap replicates. The p-value corresponds to the p-value obtained for the comparison of the accuracy values between the APPNN and each given predictor using the Wilcoxon-Nemenyi-McDonald-Thompson post-hoc test performed after 10-fold stratified resampling.
| TP | TN | FP | FN | Sensitivity [95% CI] | Specificity [95% CI] | PPV [95% CI] | NPV [95% CI] | Accuracy [95% CI] | p-value | |
|---|---|---|---|---|---|---|---|---|---|---|
| APPNN | 298 | 112 | 30 | 43 | 87.4 [83.4, 90.6] | 78.9 [70.9, 85.0] | 90.9 [87.2, 93.6] | 72.3 [64.9, 78.8] | 84.9 [81.2, 87.6] | - |
| Aggrescan | 284 | 97 | 45 | 57 | 83.3 [78.9, 87.0] | 68.3 [59.7, 75.7] | 86.3 [82.1, 89.7] | 63.0 [55.1, 70.6] | 78.9 [74.9, 82.4] | 0.90 |
| Amylpred | 248 | 120 | 22 | 93 | 72.7 [68.1, 77.3] | 84.5 [77.9, 89.9] | 91.9 [88.2, 94.7] | 56.3 [49.3, 63.0] | 76.2 [72.3, 79.7] | 0.51 |
| Amylpred2 | 271 | 122 | 20 | 70 | 79.5 [75.3, 83.7] | 85.9 [79.6, 90.9] | 93.1 [89.9, 95.7] | 63.5 [56.4, 70.3] | 81.4 [77.6, 84.7] | 1.00 |
| Foldamyloid | 306 | 74 | 68 | 35 | 89.7 [86.3, 92.5] | 52.1 [43.9, 60.0] | 81.8 [77.6, 85.5] | 67.9 [58.7, 76.2] | 78.7 [74.9, 82.0] | 0.73 |
| Metamyl | 296 | 107 | 35 | 45 | 86.8 [82.9, 90.1] | 75.4 [67.9, 81.7] | 89.4 [85.5, 92.4] | 70.4 [62.5, 77.2] | 83.4 [79.5, 86.3] | 1.00 |
| Pafig | 331 | 68 | 74 | 10 | 97.1 [94.8, 98.6] | 47.9 [40.2, 56.3] | 81.7 [77.3, 85.3] | 87.2 [78.4, 93.8] | 82.6 [78.7, 85.7] | 1.00 |
| Pasta | 224 | 124 | 18 | 117 | 65.7 [60.8, 70.6] | 87.3 [81.1, 91.9] | 92.6 [88.6, 95.3] | 51.5 [45.2, 57.9] | 72.0 [67.7, 75.6] | 0.03 |
| Pasta2 | 208 | 129 | 13 | 133 | 61.0 [55.7, 65.7] | 90.8 [85.1, 94.7] | 94.1 [90.5, 96.8] | 49.2 [43.2, 55.6] | 69.8 [65.4, 73.5] | 2.32E-03 |
| Tango | 191 | 132 | 10 | 150 | 56.0 [50.4, 60.9] | 93.0 [87.7, 96.5] | 95.0 [91.1, 97.5] | 46.8 [41.1, 53.0] | 66.9 [62.3, 70.8] | 4.07E-05 |
| Waltz | 168 | 132 | 10 | 173 | 49.3 [43.8, 54.5] | 93.0 [87.7, 96.5] | 94.4 [90.2, 97.1] | 43.3 [37.7, 49.2] | 62.1 [57.3, 66.0] | 2.42E-07 |
| Zyggregator | 228 | 116 | 26 | 113 | 66.9 [62.0, 72.0] | 81.7 [74.8, 87.5] | 89.8 [85.4, 93.0] | 50.7 [44.4, 57.5] | 71.2 [67.2, 75.4] | 0.01 |