A hybrid of differential search algorithm and flux balance analysis to: Identify knockout strategies for in silico optimization of metabolites production

An increasing demand of naturally producing metabolites has gained the attention of researchers to develop better algorithms for predicting the effects of reaction knockouts. With the success of genome sequencing, in silico metabolic engineering has aided the researchers in modifying the genome-scale metabolic network. However, the complexities of the metabolic networks, have led to difficulty in obtaining a set of knockout reactions, which eventually lead to increase in computational time. Hence, many computational algorithms have been developed. Nevertheless, most of these algorithms are hindered by the solution being trapped in the local optima. In this paper, we proposed a hybrid of Differential Search Algorithm (DSA) and Flux Balance Analysis (FBA), to identify knockout reactions for enhancing the production of desired metabolites. Two organisms namely Escherichia coli and Zymomonas mobilis were tested by targeting the production rate of succinic acid, acetic acid, and ethanol. From this experiment, we obtained the list of knockout reactions and production rate. The results show that our proposed hybrid algorithm is capable of identifying knockout reactions with above 70% of production rate from the wild-type

Decomposition-Based Multiobjective Optimization for Constrained Evolutionary Optimization

Pareto dominance-based multiobjective optimization has been successfully applied to constrained evolutionary optimization during the last two decades. However, as another famous multiobjective optimization framework, decomposition-based multiobjective optimization has not received sufficient attention from constrained evolutionary optimization. In this paper, we make use of decomposition-based multiobjective optimization to solve constrained optimization problems (COPs). In our method, first of all, a COP is transformed into a biobjective optimization problem (BOP). Afterward, the transformed BOP is decomposed into a number of scalar optimization subproblems. After generating an offspring for each subproblem by differential evolution, the weighted sum method is utilized for selection. In addition, to make decomposition-based multiobjective optimization suit the characteristics of constrained evolutionary optimization, weight vectors are elaborately adjusted. Moreover, for some extremely complicated COPs, a restart strategy is introduced to help the population jump out of a local optimum in the infeasible region. Extensive experiments on three sets of benchmark test functions, namely, 24 test functions from IEEE CEC2006, 36 test functions from IEEE CEC2010, and 56 test functions from IEEE CEC2017, have demonstrated that the proposed method shows better or at least competitive performance against other state-of-the-art methods

An exact penalty function-based differential search algorithm for constrained global optimization

Differential search (DS) is a recently developed derivative-free global heuristic optimization algorithm for solving unconstrained optimization problems. In this paper, by applying the idea of exact penalty function approach, a DS algorithm, where an S-type dynamical penalty factor is introduced so as to achieve a better balance between exploration and exploitation, is developed for constrained global optimization problems. To illustrate the applicability and effectiveness of the proposed approach, a comparison study is carried out by applying the proposed algorithm and other widely used evolutionary methods on 24 benchmark problems. The results obtained clearly indicate that the proposed method is more effective and efficient over the other widely used evolutionary methods for most these benchmark problems

Improved differential search algorithms for metabolic network optimization

The capabilities of Escherichia coli and Zymomonas mobilis to efficiently converting substrate into valuable metabolites have caught the attention of many industries. However, the production rates of these metabolites are still below the maximum threshold. Over the years, the organism strain design was improvised through the development of metabolic network that eases the process of exploiting and manipulating organism to maximize its growth rate and to maximize metabolites production. Due to the complexity of metabolic networks and multiple objectives, it is difficult to identify near-optimal knockout reactions that can maximize both objectives. This research has developed two improved modelling-optimization methods. The first method introduces a Differential Search Algorithm and Flux Balance Analysis (DSAFBA) to identify knockout reactions that maximize the production rate of desired metabolites. The latter method develops a non-dominated searching DSAFBA (ndsDSAFBA) to investigate the trade-off relationship between production rate and its growth rate by identifying knockout reactions that maximize both objectives. These methods were assessed against three metabolic networks – E.coli core model, iAF1260 and iEM439 for production of succinic acid, acetic acid and ethanol. The results revealed that the improved methods are superior to the other state-of-the-art methods in terms of production rate, growth rate and computation time. The study has demonstrated that the two improved modelling-optimization methods could be used to identify near-optimal knockout reactions that maximize production of desired metabolites as well as the organism’s growth rate within a shorter computation time

SYNTHESIS OF ANALOG FILTER USING EVOLUTIONARY STRATEGIES

This project is designed to mimic automation of analog filter analysis to examine some efficient algorithm useful in filter synthesis. The process involves formation of MNA matrix to create symbolic transfer functions in s domain, continuous and discrete sizing of LC components using evolutionary algorithms; and finally, the performance of each algorithm is studied based on fixed error criterion and adaptability to discrete problem. Efficiency of the clever algorithms in optimizing piecewise filter response is ultimately dependent on the quality of the fitness function. A unique measure of error called Sum of Maximum Deviation (SMD) is implemented which evaluates the performance of global optimizer by weighing important details per unit sampled frequency. From global optimization point of view, it is certain that discrete evolutionary algorithms lacks the absoluteness of brute force analysis; however, the general continuous optimization is stretched to accommodate a new proximity estimator alongside its elementary constraint