MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure

Table 14 Relative ranking of complex detection algorithms on unscored and affinity-scored networks

PPI network		Wodak		MIPS		Aloy
	Method	F1	Norm	F1	Norm	F1	Norm	Total	Norm
G+K	CMC	0.407	1.000	0.283	1.000	0.455	1.000	3.000	1.000
	HACO	0.351	0.862	0.216	0.761	0.333	0.731	2.355	0.785
	MCL-CAw	0.313	0.768	0.218	0.770	0.270	0.592	2.130	0.710
	CORE	0.292	0.718	0.210	0.741	0.256	0.561	2.020	0.673
	MCL	0.271	0.665	0.175	0.619	0.271	0.595	1.879	0.626
	MCL-CA	0.244	0.601	0.212	0.749	0.278	0.610	1.960	0.653
	COACH	0.183	0.450	0.137	0.486	0.194	0.426	1.361	0.454
ICD(G+K)	MCL-CAw	0.567	1.000	0.450	1.000	0.578	0.976	2.976	1.000
	HACO	0.565	0.995	0.378	0.841	0.593	1.000	2.837	0.953
	MCLO	0.533	0.939	0.412	0.916	0.572	0.965	2.820	0.947
	CMC	0.531	0.936	0.403	0.897	0.480	0.810	2.642	0.888
	MCL	0.498	0.879	0.370	0.822	0.543	0.916	2.616	0.879
FSW(G+K)	MCL-CAw	0.576	0.992	0.423	1.000	0.625	1.000	2.992	1.000
	HACO	0.581	1.000	0.396	0.935	0.609	0.974	2.910	0.972
	MCL	0.541	0.931	0.393	0.929	0.585	0.935	2.795	0.934
	MCLO	0.513	0.884	0.376	0.888	0.612	0.979	2.750	0.919
	CMC	0.484	0.833	0.338	0.798	0.465	0.744	2.375	0.794
Cons_3.19	MCL-CAw	0.614	1.000	0.487	1.000	0.576	0.979	2.979	1.000
	MCLO	0.606	0.986	0.471	0.967	0.575	0.977	2.930	0.984
	CMC	0.604	0.982	0.479	0.983	0.588	1.000	2.965	0.995
	MCL	0.573	0.932	0.407	0.836	0.567	0.964	2.732	0.917
	HACO	0.475	0.774	0.379	0.777	0.502	0.854	2.405	0.807
Boot_0.094	HACO	0.572	0.991	0.380	1.000	0.585	1.000	2.991	1.000
	CMC	0.577	1.000	0.367	0.965	0.515	0.881	2.846	0.952
	MCL-CAw	0.447	0.776	0.282	0.742	0.416	0.711	2.229	0.745
	MCL	0.426	0.738	0.299	0.785	0.400	0.683	2.207	0.738
	MCLO	0.424	0.736	0.267	0.701	0.392	0.670	2.108	0.705

Ranking obtained from normalized F1 values. The G+K network is unscored, while the remaining are scored using affinity scoring schemes.

ISSN: 1471-2105