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

Peter Gennemark (Institutionen för matematiska vetenskaper) ; Dag Wedelin (Institutionen för data- och informationsteknik, Datavetenskap (Chalmers))
LEcture Notes in Computer Science: 7th International Conference on Computational Methods in Systems Biology, CMSB 2009; Bologna; Italy; 31 August 2009 through 1 September 2009 (1611-3349). Vol. LNCS 5688 (2009), p. 205-217.
[Konferensbidrag, refereegranskat]

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.

Nyckelord: Decomposition; Ordinary differential equations; Parameter estimation



Denna post skapades 2009-09-22. Senast ändrad 2016-07-11.
CPL Pubid: 98474

 

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Institutioner (Chalmers)

Institutionen för matematiska vetenskaperInstitutionen för matematiska vetenskaper (GU)
Institutionen för data- och informationsteknik, Datavetenskap (Chalmers)

Ämnesområden

Tillämpad matematik
Datavetenskap (datalogi)

Chalmers infrastruktur