Table 3.

The PC-LogicNet performance is evaluated for different values of c = α + β, i.e. c = 500, 750, 1000 and 1250. The PC-LogicNet is applied to reconstruct the directed network and logic functions among the regulatory genes in the E. coli, by using 10 gene expression samples and 100 repeats of the whole simulation study. Reported values for the TP, FP, TN, FN are the total of the corresponding values over 100 repeats of the whole simulation study

	Graph	TP	FP	TN	FN	TPR	FPR	PPV	ACC	MCC	F-measure
c = 500	Undirected a	716	165	2835	784	0.48	0.06	0.81	0.79	0.50	0.60
	Directed b	616	592	6908	884	0.41	0.08	0.51	0.84	0.36	0.45
	Directed logical c	614	592	–	885	0.41	–	0.51	–	–	0.45
c = 750	Undirected	720	155	2845	780	0.48	0.05	0.82	0.79	0.51	0.61
	Directed	620	590	6910	880	0.41	0.08	0.51	0.84	0.37	0.46
	Directed logical	605	590	–	899	0.40	–	0.51	–	–	0.45
c = 1000	Undirected	724	157	2843	776	0.48	0.05	0.82	0.79	0.51	0.61
	Directed	624	588	6912	876	0.42	0.08	0.51	0.84	0.37	0.46
	Directed logical	625	588	–	868	0.42	–	0.52	–	–	0.46
c = 1250	Undirected	758	147	2853	742	0.51	0.05	0.84	0.80	0.54	0.63
	Directed	658	571	6929	842	0.44	0.08	0.54	0.84	0.39	0.48
	Directed logical	632	571	–	845	0.43	–	0.53	–	–	0.47

^a The edge direction is not taken into account in calculating the performance

^b The edge direction is taken into account in calculating the performance

^c The integrative performance of the LogicNet in reconstructing both the edge direction and logic function among regulatory genes is evaluated