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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