Figure 2

Effect of network sparsification on ROC scores. For various sparsity levels of GeneMANIA and for the support vector machine (SVM), boxplot shows the following features of the distribution of the prediction errors as measured with 1 - area under the receiver operating characteristic (ROC) curve (1 - AUC): the median (red line), 25% and 75% percentile (blue box), and outliers of prediction errors more than 1.5 times the interquartile range away from the median (blue stars). The evaluations are based on 3-fold cross-validation on 992 GO categories with the Zhang and coworkers [12] mouse tissue expression data as input. The GeneMANIA experiments were run by creating an association network from the mouse tissue expression data where the number of neighbors for each gene is restricted to N. For example, when the number of neighbors = 5, each gene is associated with only five other genes. The settings for the SVM experiments are as described in [12].