Optimal parameter identification of synthetic gene networks using harmony search algorithm

Wei Zhang, Wenchao Li, Jianming Zhang and Ning Wang

PLOS ONE, 2019, vol. 14, issue 3, 1-28

Abstract: Computational modeling of engineered gene circuits is an important while challenged task in systems biology. In order to describe and predict the response behaviors of genetic circuits using reliable model parameters, this paper applies an optimal experimental design(OED) method to obtain input signals. In order to obtain informative observations, this study focuses on maximizing Fisher information matrix(FIM)-based optimal criteria and to provide optimal inputs. Furthermore, this paper designs a two-stage optimization with the modified E-optimal criteria and applies harmony search(HS)-based OED algorithm to minimize estimation errors. The proposed optimal identification methodology involves estimation errors and the sample size to pursue a trade-off between estimation accuracy and measurement cost in modeling gene networks. The designed cost function takes two major factors into account, in which experimental costs are proportional to the number of time points. Experiments select two types of synthetic genetic networks to validate the effectiveness of the proposed HS-OED approach. Identification outcomes and analysis indicate the proposed HS-OED method outperforms two candidate OED approaches, with reduced computational effort.

Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0213977

DOI: 10.1371/journal.pone.0213977

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