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Table 5: Running times of the programs on 3 data sets of yeast protein interactions on a Pentium IV 3.0 GHz processor with 512 MB memory.

Program MIPS data (4874 nodes 15660 edges) DIP data (4932 nodes 17491 edges) BOND data (18692 nodes 59516 edges) Our program 10.06 s 13.06 s 1 m 06.63 s CFinder 17.45 s 24.33 s 2 m 22.46 s

MIPS data: PPI_180105.tab from MIPS (1/18/2005). DIP data: yeast20071104.lst from DIP (11/04/2007). BOND data: data from BOND (11/9/2007).