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)