Dataset Information

Genetic Optimization Algorithm for Metabolic Engineering Revisited.

ABSTRACT: To date, several independent methods and algorithms exist for exploiting constraint-based stoichiometric models to find metabolic engineering strategies that optimize microbial production performance. Optimization procedures based on metaheuristics facilitate a straightforward adaption and expansion of engineering objectives, as well as fitness functions, while being particularly suited for solving problems of high complexity. With the increasing interest in multi-scale models and a need for solving advanced engineering problems, we strive to advance genetic algorithms, which stand out due to their intuitive optimization principles and the proven usefulness in this field of research. A drawback of genetic algorithms is that premature convergence to sub-optimal solutions easily occurs if the optimization parameters are not adapted to the specific problem. Here, we conducted comprehensive parameter sensitivity analyses to study their impact on finding optimal strain designs. We further demonstrate the capability of genetic algorithms to simultaneously handle (i) multiple, non-linear engineering objectives; (ii) the identification of gene target-sets according to logical gene-protein-reaction associations; (iii) minimization of the number of network perturbations; and (iv) the insertion of non-native reactions, while employing genome-scale metabolic models. This framework adds a level of sophistication in terms of strain design robustness, which is exemplarily tested on succinate overproduction in Escherichia coli.

SUBMITTER: Alter TB

PROVIDER: S-EPMC6027426 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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Genetic Optimization Algorithm for Metabolic Engineering Revisited.

Alter Tobias B TB Blank Lars M LM Ebert Birgitta E BE

Metabolites 20180516 2

To date, several independent methods and algorithms exist for exploiting constraint-based stoichiometric models to find metabolic engineering strategies that optimize microbial production performance. Optimization procedures based on metaheuristics facilitate a straightforward adaption and expansion of engineering objectives, as well as fitness functions, while being particularly suited for solving problems of high complexity. With the increasing interest in multi-scale models and a need for sol ...[more]

PMID: 29772713

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Project description:Metaheuristic optimization algorithms manage the search process to explore search domains efficiently and are used efficiently in large-scale, complex problems. Transient Search Algorithm (TSO) is a recently proposed physics-based metaheuristic method inspired by the transient behavior of switched electrical circuits containing storage elements such as inductance and capacitance. TSO is still a new metaheuristic method; it tends to get stuck with local optimal solutions and offers solutions with low precision and a sluggish convergence rate. In order to improve the performance of metaheuristic methods, different approaches can be integrated and methods can be hybridized to achieve faster convergence with high accuracy by balancing the exploitation and exploration stages. Chaotic maps are effectively used to improve the performance of metaheuristic methods by escaping the local optimum and increasing the convergence rate. In this study, chaotic maps are included in the TSO search process to improve performance and accelerate global convergence. In order to prevent the slow convergence rate and the classical TSO algorithm from getting stuck in local solutions, 10 different chaotic maps that generate chaotic values instead of random values in TSO processes are proposed for the first time. Thus, ergodicity and non-repeatability are improved, and convergence speed and accuracy are increased. The performance of Chaotic Transient Search Algorithm (CTSO) in global optimization was investigated using the IEEE Congress on Evolutionary Computation (CEC)'17 benchmarking functions. Its performance in real-world engineering problems was investigated for speed reducer, tension compression spring, welded beam design, pressure vessel, and three-bar truss design problems. In addition, the performance of CTSO as a feature selection method was evaluated on 10 different University of California, Irvine (UCI) standard datasets. The results of the simulation showed that Gaussian and Sinusoidal maps in most of the comparison functions, Sinusoidal map in most of the real-world engineering problems, and finally the generally proposed CTSOs in feature selection outperform standard TSO and other competitive metaheuristic methods. Real application results demonstrate that the suggested approach is more effective than standard TSO.

Dataset Information

Genetic Optimization Algorithm for Metabolic Engineering Revisited.

Publications

Genetic Optimization Algorithm for Metabolic Engineering Revisited.

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