Improved Parameter Estimation for Completely Observed Ordinary Differential Equations with Application to Biological Systems

Authors:
Peter Gennemark;Dag Wedelin
Affiliations:
University of Göteborg, Göteborg, Sweden SE-412 96 and Uppsala University, Uppsala, Sweden SE-751 06;Chalmers University of Technology, Göteborg, Sweden SE-412 96
Venue:
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Year:
2009

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Abstract

We consider parameter estimation in ordinary differential equations (ODEs) from completely observed systems, and describe an improved version of our previously reported heuristic algorithm (IET Syst. Biol. , 2007). Basically, in that method, estimation based on decomposing the problem to simulation of one ODE, is followed by estimation based on simulation of all ODEs of the system. The main algorithmic improvement compared to the original version, is that we decompose not only to single ODEs, but also to arbitrary subsets of ODEs, as a complementary intermediate step. The subsets are selected based on an analysis of the interaction between the variables and possible common parameters. We evaluate our algorithm on a number of well-known hard test problems from the biological literature. The results show that our approach is more accurate and considerably faster compared to other reported methods on these problems. Additionally, we find that the algorithm scales favourably with problem size.