Table 2

Performance statistics of classification models and other existing programs based on independent test set

Method

Promoters = 2980, NonPromoters = 11481


# of true positive

# of false negative

# of true negative

# of false positive

Sensitivity (%)

Positive predictive value (PPV)%

Mathew correlation coefficient

True positive cost


Bagging

2593

387

11385

96

87.01

96.43

0.9

0.04


LogitBoost

2594

386

11356

125

87.05

95.4

0.89

0.05


Random Forest

2599

381

11349

132

87.21

95.17

0.89

0.05


Rotational Forest

2391

589

11332

149

80.23

94.13

0.84

0.06


EP3 Program

2493

487

11064

417

86.91

85.67

0.81

0.17


Eponine Program

2581

399

9633

1848

87.01

58.28

0.62

0.72


ProSOM

2563

417

8817

2664

86.01

49.03

0.53

1.04


FirstEF

1714

1226

11402

79

57.52

95.6

0.70

0.05


Gupta et al. BMC Bioinformatics 2010 11(Suppl 1):S65   doi:10.1186/1471-2105-11-S1-S65

Open Data