Table 6.

Clustering performance of MCODE, MCL and MRF: comparison with the MIPS annotations. We use all proteins in the experiment with annotation.

Dataset		MCODE	MCL	MCL with inter. prob.	MRF (spoke)	MRF (matrix)
Gavin02	CO	29.0	61.5	62.6	64.4	66.4
	PPV	73.6	71.3	71.7	73.5	66.9
	Acc	46.2	66.2	67.0	68.8	66.6
	All pairs
	SN	2.3	68.6	68.9	66.7	62.6
	SP	92.5	78.7	82.4	87.9	64.7
	Geo. average	14.7	73.0	75.4	76.6	63.6
Gavin06	CO	33.7	64.0	65.7	66.0	67.7
	PPV	79.0	62.6	68.6	70.4	67.3
	Acc	51.6	63.3	67.2	68.2	67.5
	All pairs
	SN	4.9	44.1	44.7	37.2	38.2
	SP	79.6	18.0	22.5	70.0	66.1
	Geo. average	19.7	28.2	31.7	51.0	50.2