A model for the yeast cell cycle transcriptional regulatory network learned by our method. The text inside each dark node (ellipse or rounded rectangle) represents one or more regulatory rules. The position of a node, together with the green arc crossing it if there is one, represents the period during which the rules inside are functioning. The gray area on the top contains a module of rules that regulate late G1/S phase, and the one on the bottom encloses a module of rules that regulate G2/M phase. A solid red line represents that a set of regulatory rules regulates a TF outside the module, while a dashed blue line represents that a set of regulatory rules regulates a TF within the same module.