performance measures morten nielsen, cbs, department of systems biology, dtu

Performance measures

Morten Nielsen,CBS, Department of Systems

Biology, DTU

Performance measures

Meas Pred0.4050 0.83440.9373 1.00000.8161 0.63880.6752 0.98410.0253 0.00000.3196 0.53880.6764 0.62470.1872 0.19210.4220 0.65460.6545 0.65460.7917 0.13420.4405 0.35510.1548 0.00000.2740 0.19930.4399 0.64610.1725 0.39160.0539 0.00000.3795 0.56230.2242 0.19680.3108 0.21140.2260 0.03360.2780 0.56470.0198 0.12240.5890 0.55380.5120 0.43490.7266 1.00000.1136 0.00000.0456 0.21280.0069 0.41000.4502 0.3848

Pearsons’ correlation coefficient

Performance measures

• Accuracy of prediction method

Sort

Evaluation of prediction accuracy

TPFN AP

ANTN FP

Matthews correlation- Threshold of 0.5

False positive

True positive

True negative

False negative

Matthews correlation- Threshold of 0.5

5 9

8 5

Performance measure – Roc curve

False positive

True positive

True negative

False negative

Performance measure – Roc curve

False positive

True positive

True negative

False negative

Threshold TP FN

TP/(TP+FN) FP TN FP/(FP+TN)

>0.8  4  10  0.29  1  12  0.08

>0.6 8  6  0.57  3  10  0.23 

>0.4 11  3  0.79  6  7  0.46 

>0.2 13 1  0.93  9  4  0.69 

>0 14  0  1  13  0  1 

AUC = 0.5AUC = 1.0

ROC curves

AUC (area under the ROC curve)

Summary

• MCC and PCC• Random = 0.0• Perfect = 1.0 (or -1)

• ROC (AUC)• Random = 0.5• Perfect = 1 (or 0)