Table 1.

Summaries of the evaluated network inference methods

Category	Methods	Cor-based	MI-based	Ref.
Deal with indirect edges explicitly	RLowPC	Yes
	PC	Yes		[2, 45]
	PCIT	Yes	Yes	[33, 38, 50, 51]
	MRNET		Yes	[29, 33, 39, 50]
	MRNETB		Yes	[27, 29, 33, 50]
	ARACNE		Yes	[28, 33, 50]
Not deal with indirect edges	Cor	Yes
	CLR		Yes	[33, 48, 50]
	Random

Nine correlation-based, MI-based and random network inference methods have been compared and evaluated in this study. The methods are classified into two main groups: Deal with indirect edges explicitly and Not deal with indirect edges