Table 3.
The prediction accuracies of RF and SVM algorithms on PFGE patterns standardized by the BioNumerics fixed-band method and NCTR fixed-band method using either the group 1 or group 2 band class as the standard
| Algorithm and S. enterica serotype group and name | % Accuracy by method and groupa |
|||||
|---|---|---|---|---|---|---|
| BioNumerics fixed-band method |
NCTR fixed-band method |
|||||
| G1 as the standard | G2 as the standard | Avg of the serotypes | G1 as the standard | G2 as the standard | Avg of the serotypes | |
| RF algorithm | ||||||
| Most frequent serotypes (n = 20) | ||||||
| I 4,[5],12:i:− | 90.1 | 90.5 | 90.3 | 91.7 | 91.0 | 91.3 |
| Agona | 99.9 | 99.7 | 99.8 | 99.9 | 99.7 | 99.8 |
| Braenderup | 98.9 | 98.7 | 98.8 | 99.7 | 99.8 | 99.7 |
| Enteritidis | 99.6 | 99.5 | 99.5 | 99.7 | 99.8 | 99.7 |
| Hadar | 99.4 | 99.0 | 99.2 | 99.0 | 98.5 | 98.7 |
| Heidelberg | 99.5 | 99.8 | 99.6 | 99.9 | 99.7 | 99.8 |
| Infantis | 98.5 | 98.7 | 98.6 | 99.8 | 99.9 | 99.8 |
| Javiana | 99.7 | 99.5 | 99.6 | 99.9 | 99.0 | 99.4 |
| Mississippi | 99.4 | 99.1 | 99.3 | 99.4 | 99.4 | 99.4 |
| Montevideo | 96.2 | 97.2 | 96.7 | 99.8 | 99.6 | 99.7 |
| Muenchen | 98.3 | 98.7 | 98.5 | 98.9 | 99.3 | 99.1 |
| Newport | 98.0 | 98.1 | 98.1 | 99.3 | 99.5 | 99.4 |
| Oranienburg | 98.5 | 98.3 | 98.4 | 99.4 | 99.2 | 99.3 |
| Paratyphi B var. L(+) tartrate+ | 98.3 | 97.6 | 97.9 | 99.7 | 99.6 | 99.6 |
| Poona | 98.9 | 98.7 | 98.8 | 97.8 | 98.1 | 98.0 |
| Saintpaul | 99.7 | 99.6 | 99.6 | 99.6 | 99.2 | 99.4 |
| Thompson | 98.2 | 98.0 | 98.1 | 100.0 | 99.4 | 99.7 |
| Typhi | 99.9 | 99.8 | 99.8 | 99.6 | 99.7 | 99.6 |
| Typhimurium | 66.6 | 64.8 | 65.7 | 70.9 | 68.5 | 69.7 |
| Typhimurium var. 5− | 70.9 | 72.1 | 71.5 | 72.8 | 72.0 | 72.4 |
| Less frequent serotypes (n = 12) | ||||||
| Anatum | 75.9 | 78.3 | 77.0 | 96.6 | 96.2 | 96.4 |
| Bareilly | 82.2 | 72.0 | 77.1 | 75.2 | 52.0 | 63.6 |
| Berta | 95.0 | 97.2 | 96.2 | 94.0 | 99.1 | 96.7 |
| Derby | 91.6 | 91.4 | 91.5 | 88.8 | 88.6 | 88.7 |
| Hartford | 97.3 | 97.1 | 97.2 | 98.2 | 95.2 | 96.8 |
| Litchfield | 98.1 | 94.8 | 96.2 | 97.1 | 97.0 | 97.0 |
| Mbandaka | 99.1 | 96.2 | 97.4 | 100.0 | 99.4 | 99.6 |
| Panama | 90.4 | 90.3 | 90.4 | 91.3 | 81.5 | 86.0 |
| Paratyphi A | 100.0 | 96.5 | 97.0 | 100.0 | 88.7 | 90.4 |
| Schwarzengrund | 93.4 | 95.8 | 94.7 | 97.2 | 95.0 | 96.0 |
| Senftenberg | 81.5 | 74.2 | 77.8 | 92.4 | 86.6 | 89.4 |
| Stanley | 93.1 | 91.5 | 92.2 | 92.2 | 91.5 | 91.8 |
| Total for the group | 95.1 | 95.9 | ||||
| SVM algorithm | ||||||
| Most frequent serotypes (n = 20) | ||||||
| I 4,[5],12:i:− | 91.5 | 91.2 | 91.3 | 93.0 | 92.3 | 92.6 |
| Agona | 99.5 | 99.7 | 99.6 | 100.0 | 100.0 | 100.0 |
| Braenderup | 98.6 | 98.5 | 98.5 | 99.8 | 99.7 | 99.7 |
| Enteritidis | 99.3 | 98.9 | 99.1 | 99.8 | 99.8 | 99.8 |
| Hadar | 99.1 | 99.1 | 99.1 | 99.1 | 98.5 | 98.8 |
| Heidelberg | 99.5 | 99.7 | 99.6 | 99.8 | 99.9 | 99.8 |
| Infantis | 98.4 | 98.0 | 98.2 | 99.8 | 99.8 | 99.8 |
| Javiana | 99.8 | 99.5 | 99.6 | 99.9 | 99.6 | 99.7 |
| Mississippi | 99.6 | 99.6 | 99.6 | 99.6 | 99.2 | 99.4 |
| Montevideo | 97.3 | 97.9 | 97.6 | 100.0 | 99.6 | 99.8 |
| Muenchen | 99.5 | 99.0 | 99.3 | 99.6 | 99.6 | 99.6 |
| Newport | 98.4 | 98.6 | 98.5 | 99.6 | 99.6 | 99.6 |
| Oranienburg | 97.2 | 98.1 | 97.6 | 99.4 | 99.6 | 99.5 |
| Paratyphi B var. L(+) tartrate+ | 98.1 | 97.9 | 98.0 | 99.5 | 99.4 | 99.5 |
| Poona | 99.5 | 99.7 | 99.6 | 99.3 | 99.3 | 99.3 |
| Saintpaul | 99.1 | 99.6 | 99.4 | 99.5 | 99.2 | 99.3 |
| Thompson | 98.0 | 98.2 | 98.1 | 99.8 | 99.1 | 99.5 |
| Typhi | 100.0 | 100.0 | 100.0 | 99.8 | 99.9 | 99.8 |
| Typhimurium | 65.5 | 64.8 | 65.2 | 67.9 | 66.0 | 67.0 |
| Typhimurium var. 5− | 72.1 | 70.3 | 71.2 | 72.8 | 71.3 | 72.0 |
| Less frequent serotypes (n = 12) | ||||||
| Anatum | 50.9 | 68.9 | 59.5 | 98.3 | 95.3 | 96.8 |
| Bareilly | 93.1 | 85.0 | 89.0 | 91.1 | 66.0 | 78.5 |
| Berta | 94.0 | 96.3 | 95.2 | 95.0 | 96.3 | 95.7 |
| Derby | 88.8 | 91.4 | 90.1 | 86.0 | 89.5 | 87.7 |
| Hartford | 96.5 | 95.2 | 95.9 | 95.6 | 95.2 | 95.4 |
| Litchfield | 92.2 | 90.3 | 91.1 | 94.2 | 94.8 | 94.5 |
| Mbandaka | 97.3 | 95.6 | 96.3 | 99.1 | 98.7 | 98.9 |
| Panama | 92.3 | 96.0 | 94.3 | 90.4 | 88.7 | 89.5 |
| Paratyphi A | 100.0 | 92.2 | 93.3 | 100.0 | 90.4 | 91.9 |
| Schwarzengrund | 92.5 | 93.3 | 92.9 | 99.1 | 95.0 | 96.9 |
| Senftenberg | 91.3 | 85.6 | 88.4 | 91.3 | 89.7 | 90.5 |
| Stanley | 94.1 | 94.0 | 94.1 | 95.1 | 95.7 | 95.4 |
| Total for the group | 95.1 | 96.1 | ||||