Squeeze-and-Breathe Evolutionary Monte Carlo Optimisation with Local Search Acceleration and its application to parameter fitting

Details Squeeze-and-Breathe Evolutionary Monte Carlo Optimisation with Local Search Acceleration and its application to parameter fitting Squeeze-and-Breathe Evolutionary Monte Carlo Optimisation with Local Search Acceleration and its application to parameter fitting

2011-07-14

arxiv.org/abs/1107.2879v3

Biology

Quantitative Biology

Quantitative Methods

15 Pages, 3 Figures, 6 Tables; Availability: Matlab code available from the authors upon request

Scientific paper

Motivation: Estimating parameters from data is a key stage of the modelling process, particularly in biological systems where many parameters need to be estimated from sparse and noisy data sets. Over the years, a variety of heuristics have been proposed to solve this complex optimisation problem, with good results in some cases yet with limitations in the biological setting. Results: In this work, we develop an algorithm for model parameter fitting that combines ideas from evolutionary algorithms, sequential Monte Carlo and direct search optimisation. Our method performs well even when the order of magnitude and/or the range of the parameters is unknown. The method refines iteratively a sequence of parameter distributions through local optimisation combined with partial resampling from a historical prior defined over the support of all previous iterations. We exemplify our method with biological models using both simulated and real experimental data and estimate the parameters efficiently even in the absence of a priori knowledge about the parameters.

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