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 % |