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Table 1 Comparison of clustering algorithms on the Collins network. The populations in our method are initialized using spectral and random clusterings

From: Protein complexes predictions within protein interaction networks using genetic algorithms

Method

#Cls

CYC2008

MIPS

Discard

  

R

P

F-measure

R

P

F-measure

 

MCODE

54

0.66

0.59

0.63

0.27

0.48

0.35

40 %

MCL

75

0.65

0.45

0.54

0.27

0.34

0.30

19 %

ClusterOne

114

0.55

0.43

0.49

0.20

0.34

0.25

18 %

Our method using

        

spectral initialization

        

1) Density cut

162

0.74

0.60

0.66

0.32

0.45

0.37

14 %

2) Maxmin cut

180

0.71

0.47

0.60

0.38

0.40

0.39

15 %

3) Normalized cut

193

0.67

0.50

0.57

0.39

0.37

0.37

20 %

4) Ratio cut

161

0.73

0.38

0.50

0.39

0.33

0.36

17 %

Our method using

        

random initialization

        

5) Density cut

164

0.72

0.54

0.62

0.30

0.41

0.35

18 %

6) Maxmin cut

162

0.71

0.45

0.56

0.40

0.35

0.38

17 %

7) Normalized cut

138

0.66

0.57

0.61

0.36

0.44

0.41

19 %

8) Ratio cut

154

0.61

0.55

0.58

0.34

0.43

0.38

18 %