Table 3.
XGBoost classifier performance on 13 known antibiotic classes.
| Antibiotic target class | precision | recall | F1-score | #test data | #training data | #total data |
|---|---|---|---|---|---|---|
|
| ||||||
| 30S ribosomal subunit | 0.82 | 1.00 | 0.90 | 14 | 55 | 69 |
| 50S ribosomal subunit | 0.94 | 0.84 | 0.89 | 19 | 75 | 94 |
| DNA | 1.00 | 1.00 | 1.00 | 1 | 3 | 4 |
| DNA gyrase | 1.00 | 0.94 | 0.97 | 16 | 16 | 32 |
| DNA-directed RNA polymerase subunit β | 1.00 | 1.00 | 1.00 | 2 | 6 | 8 |
| Lipopolysaccharide UDP-N-acetylglucosamine | 1.00 | 1.00 | 1.00 | 1 | 3 | 4 |
| 1-carboxyvinyltransferase | 0.00 | 0.00 | 0.00 | 1 | 3 | 4 |
| β-lactamases | 1.00 | 0.50 | 0.67 | 2 | 10 | 12 |
| Dihydrofolate reductase | 1.00 | 1.00 | 1.00 | 2 | 8 | 10 |
| Dihydrofolate synthase | 1.00 | 1.00 | 1.00 | 9 | 37 | 46 |
| Enoyl-[acyl-carrier-protein] reductase (NADH) | 0 | 3 | 3 | |||
| Penicillin binding protein | 0.93 | 1.00 | 0.97 | 28 | 111 | 139 |
| Peptidoglycan (D-Ala-D-Ala) | 1.00 | 1.00 | 1.00 | 2 | 8 | 10 |
| Average | 0.93 | 0.94 | 91 | |||
Individual values are given for known antibiotics classes curated from the KEGG database. UDP-N-acetylglucosamine 1-carboxyvinyltransferase only had one representative molecule in the test data, which was misclassified.