Performance of the MIM using MSA-COV. In the upper left is a precision-recall (PR) plot and in the upper right is a receiver operating characteristic (ROC) plot. Blue triangles and orange squares represent data points for the WTM and the MIM, respectively. The labels for the data points are as follows: E = ectoderm module; M = mesoderm module; P = targets of PAL-1; Overall = entire model. A parenthetical “s” for “module s ubnetwork” indicates performance of the subgraph generated by genes within a module; that is, edges incident to genes outside of the module are not counted. A parenthetical “w” for “module in w hole network” indicates performance of the subgraph induced by those edges incident to genes within a module; note that genes outside the module may be included in the subgraph. A good value lies in the upper right-hand corner of the PR graph and in the upper left-hand corner of the ROC graph. In either case, values that lie on the dashed line are considered to be no better than random guesses and values below the line are considered to be poor. In the bottom row are the distances of the points in the upper plots from the dashed lines.