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A Microbial Screening in Silico Method for the Fitness Step Evaluation in Evolutionary Algorithms

Department of Biodiversity, Ecology and Evolution (Biomathematics), Faculty of Biological Sciences c/Jose Antonio Novais 2, Complutense University of Madrid, 28040 Madrid, Spain
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Appl. Sci. 2020, 10(11), 3936; https://doi.org/10.3390/app10113936
Received: 20 April 2020 / Revised: 15 May 2020 / Accepted: 22 May 2020 / Published: 5 June 2020
(This article belongs to the Section Computing and Artificial Intelligence)
One of the most delicate stages of an evolutionary algorithm is the evaluation of the goodness of the solutions by some procedure providing a fitness value. However, although there are general rules, it is not always easy to find an appropriate evaluation function for a given problem. In the biological realm, today, there is a variety of experimental methods under the name of microbial screening to identify and select bacteria from their traits, as well as to obtain their fitness. In this paper, we show how given an optimization problem, a colony of synthetic bacteria or bacterial agents is able to evaluate the fitness of candidate solutions by building an evaluation function. The evaluation function is obtained simulating, in silico, a bacterial colony conducting the laboratory methods used in microbiology, biotechnology and synthetic biology to measure microbial fitness. Once the evaluation function is built, it is included in the code of the genetic algorithm as part of the fitness routine. The practical use of this approach is illustrated in two classic optimization problems. In silico routines have been programmed in Gro, a cell programming language oriented to synthetic biology, and can easily be customized to many other optimization problems. View Full-Text
Keywords: evolutionary computing; fitness function evaluation; bioinspired algorithms; synthetic biology evolutionary computing; fitness function evaluation; bioinspired algorithms; synthetic biology
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Gargantilla Becerra, A.; Lahoz-Beltra, R. A Microbial Screening in Silico Method for the Fitness Step Evaluation in Evolutionary Algorithms. Appl. Sci. 2020, 10, 3936.

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