The evolution of higher-level biochemical reaction models

Computational tools for analyzing biochemical phenomena are becoming increasingly important. Recently, high-level formal languages for modeling and simulating biochemical reactions have been proposed. These languages make the formal modeling of complex reactions accessible to domain specialists outside of theoretical computer science. This research explores the use of genetic programming to automate the construction of models written in one such language. Given a description of desired time-course data, the goal is for genetic programming to construct a model that might generate the data. The language investigated is Kahramanoğullari’s and Cardelli’s Programming Interface for Modeling (PIM) language. The PIM syntax is defined in a grammar-guided genetic programming system. All time series generated during simulations are described by statistical feature tests, and the fitness evaluation compares feature proximity between the target and candidate solutions. PIM models of varying complexity were used as target expressions for genetic programming, and were successfully reconstructed in all cases. This shows that the compositional nature of PIM models is amenable to genetic program search.