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Performance measures
Morten Nielsen,CBS, Department of Systems
Biology, DTU
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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
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Pearsons’ correlation coefficient
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Performance measures
• Accuracy of prediction method
Sort
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Evaluation of prediction accuracy
TPFN AP
ANTN FP
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Matthews correlation- Threshold of 0.5
False positive
True positive
True negative
False negative
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Matthews correlation- Threshold of 0.5
5 9
8 5
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Performance measure – Roc curve
False positive
True positive
True negative
False negative
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Performance measure – Roc curve
False positive
True positive
True negative
False negative
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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
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AUC (area under the ROC curve)
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Summary
• MCC and PCC• Random = 0.0• Perfect = 1.0 (or -1)
• ROC (AUC)• Random = 0.5• Perfect = 1 (or 0)