Table 2

The number of functional class whose F1 = NaN for four algorithms and four functional groups

algorithms

< 60

60-100

100-300

> 300


twoclass

31

8

3

1

twoclassbal

0

0

0

0

PSoL

22

6

0

1

SPE-RNE

0

0

0

0


When the number of negative examples is far more than positive examples, imbalanced problem occurs and the algorithm can not recall any true positive examples for some functional classes. As a result, P = 0 and R = 0 result in F1 = NaN (Not a Number) in matlab. Table 2 shows the number of NaN for each functional group.

Chen et al. BMC Genomics 2010 11(Suppl 2):S11   doi:10.1186/1471-2164-11-S2-S11

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