Complex System Ensemble Analysis
Open AccessA new measure for interaction network ensembles and their dynamics is presented: the ensemble transition matrix, T, the proportions of networks in an ensemble that support particular transitions. That presentation begins with generation of the ensemble and application of constraint perturbations to compute T, including estimating alternatives to accommodate cases where the problem size becomes computationally intractable. Then, T is used to predict ensemble dynamics properties in expected-value like calculations. Finally, analyses from the two complementary assumptions about T - that it represents uncertainty about a unique system or that it represents stochasticity around a unique constraint - are presented: entropy-based experiment selection and generalized potentials/heat dissipation of the system, respectively. Extension of these techniques to more general graph models is described, but not demonstrated. Future directions for research using T are proposed in the summary chapter. Throughout this work, the presentation of various calculations involving T are motivated by the Budding Yeast Cell Cycle example, with argument for the generality of the approaches presented by the results of their application to a database of pseudo-randomly generated dynamic constraints.
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