Leveraging conformal prediction to annotate enzyme function space with limited false positives
Fig 3
CPEC achieves FDR control for EC number prediction.
For FDR tolerance α from 0.1 to 0.9 with increments 0.1, we evaluated how well CPEC controls the FDR for EC number prediction. Observed FDR risks, precision averaged over samples, recall averaged over samples, F1 score averaged over samples, and nDCG were reported for each FDR tolerance on test proteins in (A-E). The black dotted line in (A) represents the theoretical upper bound of FDR over test proteins. Three thresholding strategies were assessed over PenLight2 as a comparison to CPEC, which includes 1) max-separation [30], 2) top-1, and 3) σ-threshold. The results of CPEC were averaged over five different seeds. DeepFRI was also included for comparison.