Parameter estimation of biological pathways
Independent thesis Advanced level (degree of Magister), 20 points / 30 hpStudent thesis
To determine parameter values for models of reactions in the human body, like the glycolysis, good methods of parameter estimation are needed. Those models are often non-linear and estimation of the parameters can be very time consuming if it is possible at all. The goal of this work is to test different methods to improve the calculation speed of the parameter estimation of an example system. If the parameter estimation speed for the example system can be improved it is likely that the method could also be useful for systems similar to the example system.
One approach to improve the calculation speed is to construct a new cost function whose evaluation does not require any simulation of the system. Simulation free parameter estimation can be much quicker than using simulations to evaluate the cost function since the cost function is evaluated many times. Also a modication of the simulated annealing optimization method has been implemented and tested.
It turns out that some of the methods significantly reduced the time needed for the parameter estimations. However the quick methods have disadvantages in the form of reduced robustness. The most successful method was using a spline approximation together with a separation of the model into several submodels, and repeated use of the simulated annealing optimization algorithm to estimate the parameters.
Place, publisher, year, edition, pages
Institutionen för systemteknik , 2007. , 67 p.
parameter estimation, biolocical pathways, global optimization
IdentifiersURN: urn:nbn:se:liu:diva-8430ISRN: LITH-ISY-EX--06/3845--seOAI: oai:DiVA.org:liu-8430DiVA: diva2:23223
2007-02-12, Algoritmen, B-huset, LiTH, Linköping, 13:15