NWE: Node-weighted expansion for protein complex prediction using random walk distances

Table 1 Optimal parameter sets of algorithms

Algorithm	Parameter	Search range	Optimal value
NWE	restart probability	0.6,0.7,0.8	0.6
	early cutoff	0.5, 0.6, 0.7	0.5
	overlap ratio	0.1, 0.2, 0.3	0.3
	minimum cluster size	4	4
	maximum cluster size	11, 50, 100	100
RRW	restart probability	0.6,0.7,0.8	0.6
	early cutoff	0.5, 0.6, 0.7	0.5
	overlap ratio	0.1, 0.2, 0.3	0.3
	minimum cluster size	4	4
	maximum cluster size	11, 50, 100	100
MCL	inflation	1.1, 1, 2, ⋯ , 3.0	1.6

The search spaces of parameter sets of NWE and RRW are determined based on the default parameter set of RRW [17]. MCL is optimized in the inflation parameter, whose default value is 2.0. All the combination of values of the parameters listed is evaluated.

ISSN: 1477-5956