Many biological networks have been labelled scale-free as their degree distribution can be approximately described by a powerlaw distribution. While the degree distribution does not summarize all aspects of a network it has often been suggested that its functional form contains important clues as to underlying evolutionary processes that have shaped the network. Generally determining the appropriate functional form for the degree distribution has been fitted in an ad-hoc fashion. Here we apply formal statistical model selection methods to determine which functional form best describes degree distributions of protein interaction and metabolic networks. We interpret the degree distribution as belonging to a class of probability models and determine which of these models provides the best description for the empirical data using maximum likelihood inference, composite likelihood methods, the Akaike information criterion and goodness-of-fit tests. The whole data is used in order to determine the parameter that best explains the data under a given model (e.g. scale-free or random graph). As we will show, present protein interaction and metabolic network data from different organisms suggests that simple scale-free models do not provide an adequate description of real network data.
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