Methods and systems for displaying dependencies within data and illustrating differences between a plurality of data sets are disclosed. In accordance with one such method, a plurality of data sets are received for the generation of a plurality of dependency networks in accordance with a graphical modeling scheme. The method further includes receiving a selection of a value of a parameter that adjusts a number of differences between the dependency networks in accordance with the graphical modeling scheme. In addition, at least one version of the dependency networks is generated based on the selected value of the parameter. Further, the one or more versions of the dependency networks is output to permit a user to analyze distinctions between the dependency networks.