Tuning of Metaheuristics for Systems Biology Applications

University essay from Linköpings universitet/Institutionen för systemteknik

Abstract:

In the field of systems biology the task of finding optimal model parameters is a common procedure. The optimization problems encountered are often multi-modal, i.e., with several local optima. In this thesis, a class of algorithms for multi-modal problems called metaheuristics are studied. A downside of metaheuristic algorithms is that they are dependent on algorithm settings in order to yield ideal performance.This thesis studies an approach to tune these algorithm settings using user constructed test functions which are faster to evaluate than an actual biological model. A statistical procedure is constructed in order to distinguish differences in performance between different configurations. Three optimization algorithms are examined closer, namely, scatter search, particle swarm optimization, and simulated annealing. However, the statistical procedure used can be applied to any algorithm that has configurable options.The results are inconclusive in the sense that performance advantages between configurations in the test functions are not necessarily transferred onto real biological models. However, of the algorithms studied a scatter search implementation was the clear top performer in general. The set of test functions used must be studied if any further work is to be made following this thesis.In the field of systems biology the task of finding optimal model parameters is a common procedure. The optimization problems encountered are often multi-modal, i.e., with several local optima. In this thesis, a class of algorithms for multi-modal problems called metaheuristics are studied. A downside of metaheuristic algorithms is that they are dependent on algorithm settings in order to yield ideal performance.

This thesis studies an approach to tune these algorithm settings using user constructed test functions which are faster to evaluate than an actual biological model. A statistical procedure is constructed in order to distinguish differences in performance between different configurations. Three optimization algorithms are examined closer, namely, scatter search, particle swarm optimization, and simulated annealing. However, the statistical procedure used can be applied to any algorithm that has configurable options.

The results are inconclusive in the sense that performance advantages between configurations in the test functions are not necessarily transferred onto real biological models. However, of the algorithms studied a scatter search implementation was the clear top performer in general. The set of test functions used must be studied if any further work is to be made following this thesis.

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