Synthetic data generation with probabilistic Bayesian Networks

Abstract Bayesian Network (BN) modeling is a prominent and increasingly popular computational systems biology method. It aims to construct probabilistic networks from the large heterogeneous biological datasets that reflect the underlying networks of biological relationships. Currently, a variety of strategies exist for evaluating BN methodology performance, ranging from utilizing artificial benchmark datasets and models, to specialized biological benchmark datasets, to simulation studies that generate synthetic data from predefined network models. The latter is arguably the most comprehensive approach; however, existing implementations are typically limited by their reliance on the SEM (structural equation modeling) framework, which includes many explicit and implicit assumptions that may be unrealistic in a typical biological data analysis scenario. In this study, we develop an alternative, purely probabilistic, simulation framework that more appropriately fits with real biological data and biological network models. In conjunction, we also expand on our current understanding of the theoretical notions of causality and dependence / conditional independence in BNs and the Markov Blankets within.