Table 1. Disease and fragment statistics.
Analysis of M and T chemical-disease annotations, ‘Total’ column refers to the union of both categories. When applicable, median values are shown for count data, while mean values are shown for performance metrics. Point performance metrics are taken with default 0.5 cutoff in the random forest classifier. The cutoff could be slid along the classifier’s outcome to get different point performances along the ROC space.
| M | T | Total | |
|---|---|---|---|
| Diseases | 934 | 835 | 1,176 |
| Molecules per disease | 36 | 25 | 30 |
| LC fragments | 23,135 | 28,325 | 37,809 |
| HC fragments | 910 | 1,107 | 1,550 |
| LC fragments per disease | 204.5 | 196.5 | 200.5 |
| HC fragments per disease | 5 | 6 | 6 |
| Liable (M) and privileged (T) fragments | 348 | 367 | 715 |
| Diseases with ≥ 1 HC fragment | 385 | 409 | 794 |
| AUC | 0.613 | 0.641 | 0.627 |
| Specificity | 0.878 | 0.882 | 0.880 |
| Sensitivity | 0.265 | 0.292 | 0.278 |
| Balanced accuracy | 0.571 | 0.588 | 0.579 |
| Positive predictive value | 0.032 | 0.023 | 0.029 |
| G-mean | 0.463 | 0.488 | 0.475 |
| F1-score | 0.053 | 0.044 | 0.049 |
| Diseases with AUC > 0.7 | 184 | 216 | 400 |