Stochastic simulation and modelling of metabolic networks in a machine learning framework

Metabolomics is increasingly becoming an important field. The fundamental task in this area is to measure and interpret complex time and condition dependent parameters such as the activity or flux of metabolites in cells, their concentration, tissues elements and other biosamples. The careful study of all these elements has led to important insights in the functioning of metabolism. Recently, however, there is a growing interest towards an integrated approach to studying biological systems. This is the main goal in Systems Biology where a combined investigation of several components of a biological system is thought to produce a thorough understanding of such systems. Biological circuits are complex to model and simulate and many efforts are being made to develop models that can handle their intrinsic complexity. A significant part of biological networks still remains unknown even though recent technological developments allow simultaneous acquisition of many metabolite measurements. Metabolic networks are not only structurally complex but behave also in a stochastic fashion. Therefore, it is necessary to express structure and handle uncertainty to construct complete dynamics of these networks. In this paper we describe how stochastic modeling and simulation can be performed in a symbolic-statistical machine learning (ML) framework. We show that symbolic ML deal with structural and relational complexity while statistical ML provides principled approaches to uncertainty modeling. Learning is used to analyze traces of biochemical reactions and model the dynamicity through parameter learning, while inference is used to produce stochastic simulation of the network.