A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations

Table 4 Parameters of each algorithm on datasets

ID	Algorithms	Parameter
1	MCODE	(default setting)
2	MCL	inflation=2(default setting)
3	CFinder	k=3
4	DPClus	CP_in=0.5,d_in=0.6(default setting)
5	IPCA	S=3,P=2, T_in=0.6(default setting)
6	CMC	overlap thres = 0.5 merge thres= 0.5,
		size=3(author suggestions)
7	COACH	w=0.225(default setting)
8	HC-PIN	λ = 2.0(default setting)
9	SPICi	density = 0.5, support threshold = 0.5, graph mode = 0(default setting)
10	ClusterONE	s=3,density=auto(default setting)
11	WPNCA	lambda=0.3,size=3(author suggestions)
12	CALM	size=3,weighted= unweighted
		minimum support threshold=0.4,
		maximum support threshold= 0.05,
13	ClusterEPs	Maximum overlap threshold=0.9,
		Maximum size of the clusters = 100
		(author suggestions)
14	SE-DMTG	(default setting and no need parameters)

ISSN: 1471-2164