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Table 1 Cross-validated prediction of genes associated with HPO terms of the Organ, Inheritance and Onset sub-ontology

From: Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods

  AUROC F max Precision Recall
Organ sub-ontology
TPR-W-RANKS 0.89 0.40 0.34 0.48
TPR-W-SVM 0.77 0.44 0.38 0.51
HTD-RANKS 0.88 0.37 0.30 0.49
HTD-SVM 0.75 0.43 0.37 0.49
PHENOstruct 0.73 0.42 0.35 0.56
Clus-HMC-Ens 0.65 0.41 0.39 0.43
PhenoPPIOrth 0.52 0.20 0.27 0.15
SSVM →Dis→HPO 0.49 0.23 0.16 0.41
RANKS 0.87 0.30 0.23 0.43
SVM 0.74 0.42 0.36 0.50
Inheritance sub-ontology
TPR-W-RANKS 0.91 0.57 0.45 0.80
TPR-W-SVMs 0.82 0.69 0.59 0.82
HTD-RANKS 0.90 0.57 0.44 0.81
HTD-SVMs 0.81 0.69 0.59 0.82
PHENOstruct 0.74 0.74 0.68 0.81
Clus-HMC-Ens 0.73 0.73 0.64 0.84
PhenoPPIOrth 0.55 0.12 0.16 0.10
SSVM →Dis→HPO 0.46 0.11 0.07 0.25
RANKS 0.90 0.56 0.43 0.81
SVMs 0.82 0.69 0.59 0.82
Onset sub-ontology
TPR-RANKS 0.86 0.44 0.33 0.70
TPR-SVMs 0.75 0.48 0.38 0.66
HTD-RANKS 0.86 0.42 0.30 0.69
HTD-SVMs 0.74 0.46 0.37 0.67
PHENOstruct 0.64 0.39 0.31 0.52
Clus-HMC-Ens 0.58 0.35 0.27 0.48
PhenoPPIOrth 0.53 0.25 0.25 0.24
SSVM →Dis→HPO 0.49 0.07 0.06 0.10
RANKS 0.83 0.41 0.30 0.67
SVMs 0.74 0.47 0.37 0.63
  1. Average AUROC across terms and average F max , Precision and Recall across genes of HTD, TPR-W ensembles and state-of-the-art methods. Best results for each metric are highlighted in bold