Table 3.
Best-performing numeric features, ordered by AUC
| Feature | AUC | max. ACC | SN (max. ACC) | SP (max. ACC) | max. FM | PR (max. FM) | RC (max. FM) |
|---|---|---|---|---|---|---|---|
| fraction-reactions-with-Enzymes | 0.902 | 0.878 | 0.662 | 0.935 | 0.715 | 0.641 | 0.807 |
| fraction-reactions-present | 0.899 | 0.879 | 0.618 | 0.948 | 0.699 | 0.612 | 0.815 |
| fraction-reactions-present-or-Orphaned | 0.899 | 0.879 | 0.619 | 0.948 | 0.7 | 0.69 | 0.709 |
| best-fraction-reactions-present-in-linear-path | 0.898 | 0.879 | 0.662 | 0.936 | 0.703 | 0.682 | 0.726 |
| evidence-info-content-norm-all | 0.894 | 0.866 | 0.638 | 0.927 | 0.689 | 0.617 | 0.781 |
| enzyme-info-content-norm | 0.89 | 0.855 | 0.69 | 0.899 | 0.69 | 0.584 | 0.844 |
| enzyme-info-content-unnorm | 0.88 | 0.847 | 0.665 | 0.895 | 0.683 | 0.556 | 0.887 |
| evidence-info-content-unnorm | 0.875 | 0.841 | 0.526 | 0.925 | 0.657 | 0.511 | 0.918 |
| num-reactions-with-enzymes | 0.873 | 0.838 | 0.635 | 0.892 | 0.681 | 0.543 | 0.914 |
| enzymes-per-reaction | 0.871 | 0.842 | 0.686 | 0.883 | 0.688 | 0.567 | 0.875 |
See section "Feature Extraction and Processing" and Section 1 of Additional file 2 for description of features.
Columns 2 through 8 correspond to various performance measures: AUC = area under the ROC curve; max. ACC = maximum thresholded accuracy; SN (max. ACC) = sensitivity at maximum-accuracy threshold; SP = specificity at maximum-accuracy threshold; max. FM = maximum thresholded F-measure; PR (max. FM) = precision at maximum-F-measure threshold; RC (max. FM) = recall at maximum-F-measure threshold.