Table 1.

Performance comparison result

Tools	#Matched complexes	#Total complexes	#Matched known complexes	Precision	Recall	F-measure
Human
NEOComplex	538	1154	1100	0.47	0.47	0.47
MCL	153	389	391	0.39	0.17	0.23
MCODE	33	63	115	0.52	0.05	0.09
CMC	1402	5417	1673	0.26	0.71	0.38
COACH	1024	4274	1150	0.24	0.49	0.32
ClusterONE	271	495	609	0.55	0.26	0.35
Yeast
NEOComplex	334	777	519	0.43	0.41	0.42
MCL	27	46	72	0.59	0.06	0.10
MCODE	17	18	41	0.94	0.03	0.06
CMC	367	2316	520	0.16	0.41	0.23
COACH	341	1517	333	0.22	0.26	0.24
ClusterONE	184	259	359	0.71	0.28	0.40
Fly
NEOComplex	191	483	468	0.40	0.29	0.33
MCL	113	324	292	0.35	0.18	0.23
MCODE	45	90	97	0.5	0.06	0.11
CMC	167	445	453	0.38	0.28	0.32
COACH	274	701	484	0.39	0.30	0.33
ClusterONE	131	224	317	0.58	0.19	0.29

Note:^#Matched complexes is the number of predicted complexes that match at least a known complex. #Total complexes is the total number of predicted complexes generated by each approach. #Matched known complexes is the number of known complexes in a reference set matched with the complexes derived by each approach. Note that the number of the known complexes in human, yeast and fly are 2351, 1278 and 1637, respectively.