A Petri net representation of Bayesian message flows: importance of Bayesian networks for biological applications

Abstract

This article combines Bayes’ theorem with flows of probabilities, flows of evidences (likelihoods), and fundamental concepts for learning Bayesian networks as biological models from data. There is a huge amount of biological applications of Bayesian networks. For example in the fields of protein modeling, pathway modeling, gene expression analysis, DNA sequence analysis, protein–protein interaction, or protein–DNA interaction. Usually, the Bayesian networks have to be learned (statistically constructed) from array data. Then they are considered as an executable and analyzable model of the data source. To improve that, this work introduces a Petri net representation for the propagation of probabilities and likelihoods in Bayesian networks. The reason for doing so is to exploit the structural and dynamic properties of Petri nets for increasing the transparency of propagation processes. Consequently the novel Petri nets are called “probability propagation nets”. By means of examples it is shown that the understanding of the Bayesian propagation algorithm is improved. This is of particular importance for an exact visualization of biological systems by Bayesian networks.