Parameter optimization of methods. Comparison of unsupervised GRNI (gene regulatory network inference) methods using the DREAM4 multifactorial dataset. Each boxplot represents variation in prediction accuracy over the different parameter values used for optimization. With GENIE (Gene Network Inference with Ensemble of Trees), no parameter was found useful for optimization, so it was used with default settings. For information on the complete parameter sweep see Figure S1 in Additional file 3.