A genetic algorithm for multiple sequence alignment

Multiple sequence alignment is an important tool in molecular sequence analysis. This paper presents genetic algorithms to solve multiple sequence alignments. Several data sets are tested and the experimental results are compared with other methods. We find our approach could obtain good performance in the data sets with high similarity and long sequences.The software can be found in http://rsdb.csie.ncu.edu.tw/tools/msa.htm.     

基于遗传算法的一种生物序列比对方法

生物序列比对是对DNA（或RNA,蛋白质）序列,寻找和确定它们的相似部分或稳定区域.二重序列比对问题可采用动态规划方法求得其最优解;多重序列比对问题是一个NP完全的组合优化问题,有待进一步探索与研究.通过合理的编码表示,采用相应的遗传算子,设计了一种求生物序列比对的遗传算法.并对几组DNA序列进行了测试.     

基于遗传算法的多序列比对算法研究

本文使用遗传算法解决多序列比对问题,并进一步研究了各种遗传算子在比对过程中所起的作用,对算法进行了改进。最后实现了一个多序列比对程序,对实验结果进行分析。     

一种优化的生物序列比对算法

序列比对是生物信息学中一种基本的信息处理方法,在序列比对所使用的算法中当前重点解决的问题是如何降低算法的时间和空间复杂度。在介绍基本动态规划原理的基础上,提出了一种基于动态规划思想的优化序列比对算法。对3种算法对比实验表明,该算法在保证其生物敏感性的基础上,有效地降低了时间和空间复杂度。     

Optimizing reliability-based robust design model using multi-objective genetic algorithm

Reliability-based robust design optimization (RBRDO) is one of the most important tools developed in recent years to improve both quality and reliability of the products at an early design stage. This paper presents a comparative study of different formulation approaches of RBRDO models and their performances. The paper also proposes an evolutionary multi-objective genetic algorithm (MOGA) to one of the promising hybrid quality loss functions (HQLF)-based RBRDO model. The enhanced effectiveness of the HQLF-based RBRDO model is demonstrated by optimizing suitable examples.     

一种求解MSA问题的自适应遗传算法

多序列比对(MSA)在生物信息学研究中占有重要地位,MSA问题是一个典型的NP问题,遗传算法是求解NP完全问题的一种有效方法。文章针对MSA问题,提出了一种新型自适应遗传算法,根据群体的多样性自适应调节变异概率,有效消除了算法中的欺骗性条件,使用突变算子来确保算法的搜索能力。整个算法模拟了自然界进化的周期性,较好的解决了群体的多样性和收敛深度的矛盾。算法的分析和测试表明,该算法是有效的。     

Dijkstra算法在蛋白质序列比对中的研究

提出一种基于Dijkstra算法的序列比对方法,该算法主要用于求最短路径,而序列比对可以转化为在有向无环图中寻找最短路径问题。对于少量序列比对,使用该算法可以求出最优解。对于多序列比对,可将在N维空间求解最短路径问题转化为在二维空间求解最短路径。该算法可以简化问题复杂度,能求得相对最优解。     

A multi-objective genetic algorithm approach to rule mining for affective product design

A novel multi-objective genetic algorithm (GA)-based rule-mining method for affective product design is proposed to discover a set of rules relating design attributes with customer evaluation based on survey data. The proposed method can generate approximate rules to consider the ambiguity of customer assessments. The generated rules can be used to determine the lower and upper limits of the affective effect of design patterns. For a rule-mining problem, the proposed multi-objective GA approach could simultaneously consider the accuracy, comprehensibility, and definability of approximate rules. In addition, the proposed approach can deal with categorical attributes and quantitative attributes, and determine the interval of quantitative attributes. Categorical and quantitative attributes in affective product design should be considered because they are commonly used to define the design profile of a product. In this paper, a two-stage rule-mining approach is proposed to generate rules with a simple chromosome design in the first stage of rule mining. In the second stage of rule mining, entire rule sets are refined to determine solutions considering rule interaction. A case study on mobile phones is used to demonstrate and validate the performance of the proposed rule-mining method. The method can discover rule sets with good support and coverage rates from the survey data.     

A hybrid genetic algorithm for multi-objective product plan selection problem with ASP and ALB

Facing current environment full of a variety of small quantity customized requests, enterprises must provide diversified products for speedy and effective responses to customers’ requests. Among multiple plans of product, both assembly sequence planning (ASP) and assembly line balance (ALB) must be taken into consideration for the selection of optimal product plan because assembly sequence and assembly line balance have significant impact on production efficiency. Considering different setup times among different assembly tasks, this issue is an NP-hard problem which cannot be easily solved by general method. In this study the multi-objective optimization mathematical model for the selection of product plan integrating ASP and ALB has been established. Introduced cases will be solved by the established model connecting to database statistics. The results show that the proposed Guided-modified weighted Pareto-based multi-objective genetic algorithm (G-WPMOGA) can effectively solve this difficult problem. The results of comparison among three different kinds of hybrid algorithms show that in terms of the issues of ASP and ALB for multiple plans, G-WPMOGA shows better problem-solving capability for four-objective optimization.     

An optimal image watermarking approach based on a multi-objective genetic algorithm

In accordance with the multi-objective nature of image watermarking, an optimal image watermarking approach using a multi-objective genetic algorithm is presented in this paper. Both watermarking parameters and embedding positions are often important factors affecting the performance of watermarking systems. The proposed multi-objective watermarking method can automatically optimize system parameters, and a variable-length mechanism is specially designed to search the most suitable positions for embedding watermarks. The method can also remove the difficult issue of determining optimal watermarking parameters from previous watermarking algorithms. The proposed multi-objective watermarking method directly deals with the problem of optimizing watermarking under non-dominated meaning, thus it can effectively avoid the difficulty of determining the optimally weighted factor in existing single-objective watermarking schemes. In addition, a Pareto-optimal set generated by multi-objective optimization can provide flexibility in selecting the most suitable watermarking parameters according to practical requirements.     

Energy efficient coverage control in wireless sensor networks based on multi-objective genetic algorithm

Due to the constrained energy and computational resources available to sensor nodes, the number of nodes deployed to cover the whole monitored area completely is often higher than if a deterministic procedure were used. Activating only the necessary number of sensor nodes at any particular moment is an efficient way to save the overall energy of the system. A novel coverage control scheme based on multi-objective genetic algorithm is proposed in this paper. The minimum number of sensors is selected in a densely deployed environment while preserving full coverage. As opposed to the binary detection sensor model in the previous work, a more precise detection model is applied in combination with the coverage control scheme. Simulation results show that our algorithm can achieve balanced performance on different types of detection sensor models while maintaining high coverage rate. With the same number of deployed sensors, our scheme compares favorably with the existing schemes.     

Extraction and optimization of fuzzy association rules using multi-objective genetic algorithm

Association Rule Mining is one of the important data mining activities and has received substantial attention in the literature. Association rule mining is a computationally and I/O intensive task. In this paper, we propose a solution approach for mining optimized fuzzy association rules of different orders. We also propose an approach to define membership functions for all the continuous attributes in a database by using clustering techniques. Although single objective genetic algorithms are used extensively, they degenerate the solution. In our approach, extraction and optimization of fuzzy association rules are done together using multi-objective genetic algorithm by considering the objectives such as fuzzy support, fuzzy confidence and rule length. The effectiveness of the proposed approach is tested using computer activity dataset to analyze the performance of a multi processor system and network audit data to detect anomaly based intrusions. Experiments show that the proposed method is efficient in many scenarios.

Medical image reconstruction using a multi-objective genetic local search algorithm

Image reconstruction from projections is a key problem in medical image analysis. In this paper, we cast image reconstruction from projections as a multi-objective problem. It is essential to choose some proper objective functions of the problem. We choose the square error, smoothness of the reconstructed image, and the maximum entropy as our objective functions of the problem. Then we introduce a hybrid algorithm comprising of multi-objective genetic and local search algorithms to reconstruct the image. Our algorithm has remarkable global performance. Our experiments show that we can get different results when we give different weights to different objective functions. We can also control the noise by giving different weights on different objective function. At the same time, we can adjust the parameter to let it have good local performance. Though the computation demands of the hybrid algorithm tends to be larger because of the random search of the GA, it is really a common feature of the global optimization method. Our results show that the hybrid algorithm is a more effective than the conventional method. We think our method is very promising for the medical imaging field.     

A multi-objective approach to facility layout problem by genetic search algorithm and Electre method

Classical approaches to layout design problem tend to maximise the efficiency of layout, measured by the handling cost related to the interdepartmental flow and to the distance among the departments. However, the actual problem involves several conflicting objectives hence requiring a multi-objective formulation. Multi-objective approaches, recently proposed, in most cases lead to the maximisation of a weighted sum of score functions. The poor practicability of such an approach is due to the difficulty of normalising these functions and of quantifying the weights. In this paper, this difficulty is overcome by approaching the problem in two subsequent steps: in the first step, the Pareto-optimal solutions are determined by employing a multi-objective constrained genetic algorithm and the subsequent selection of the optimal solution is carried out by means of the multi-criteria decision-making procedure Electre. This procedure allows the decision maker to express his preferences on the basis of the knowledge of candidate solution set. Quantitative (handling cost) and qualitative (adjacency and distance requests between departments) objectives are considered referring to a bay structure-based layout model, that allows to take into account also practical constraints such as the aspect ratio of departments. Results obtained confirm the effectiveness of the proposed procedure as a practicable support tool for layout designers.     

Improving multi-objective genetic algorithms with adaptive design of experiments and online metamodeling

Applications of multi-objective genetic algorithms (MOGAs) in engineering optimization problems often require numerous function calls. One way to reduce the number of function calls is to use an approximation in lieu of function calls. An approximation involves two steps: design of experiments (DOE) and metamodeling. This paper presents a new approach where both DOE and metamodeling are integrated with a MOGA. In particular, the DOE method reduces the number of generations in a MOGA, while the metamodeling reduces the number of function calls in each generation. In the present approach, the DOE locates a subset of design points that is estimated to better sample the design space, while the metamodeling assists in estimating the fitness of design points. Several numerical and engineering examples are used to demonstrate the applicability of this new approach. The results from these examples show that the proposed improved approach requires significantly fewer function calls and obtains similar solutions compared to a conventional MOGA and a recently developed metamodeling-assisted MOGA.     

A genetic algorithm approach for multi-objective optimization of supply chain networks

Supply chain network (SCN) design is to provide an optimal platform for efficient and effective supply chain management. It is an important and strategic operations management problem in supply chain management, and usually involves multiple and conflicting objectives such as cost, service level, resource utilization, etc. This paper proposes a new solution procedure based on genetic algorithms to find the set of Pareto-optimal solutions for multi-objective SCN design problem. To deal with multi-objective and enable the decision maker for evaluating a greater number of alternative solutions, two different weight approaches are implemented in the proposed solution procedure. An experimental study using actual data from a company, which is a producer of plastic products in Turkey, is carried out into two stages. While the effects of weight approaches on the performance of proposed solution procedure are investigated in the first stage, the proposed solution procedure and simulated annealing are compared according to quality of Pareto-optimal solutions in the second stage.     

A hybrid multi-objective shuffled frog-leaping algorithm for a mixed-model assembly line sequencing problem

In this paper, a mixed-model assembly line (MMAL) sequencing problem is studied. This type of production system is used to manufacture multiple products along a single assembly line while maintaining the least possible inventories. With the growth in customers’ demand diversification, mixed-model assembly lines have gained increasing importance in the field of management. Among the available criteria used to judge a sequence in MMAL, the following three are taken into account: the minimization of total utility work, total production rate variation, and total setup cost. Due to the complexity of the problem, it is very difficult to obtain optimum solution for this kind of problems by means of traditional approaches. Therefore, a hybrid multi-objective algorithm based on shuffled frog-leaping algorithm (SFLA) and bacteria optimization (BO) are deployed. The performance of the proposed hybrid algorithm is then compared with three well-known genetic algorithms, i.e. PS-NC GA, NSGA-II, and SPEA-II. The computational results show that the proposed hybrid algorithm outperforms the existing genetic algorithms, significantly in large-sized problems.     

A new particle swarm algorithm for a multi-objective mixed-model assembly line sequencing problem

The sequencing of products for mixed-model assembly line in Just-in-Time manufacturing systems is sometimes based on multiple criteria. In this paper, three major goals are to be simultaneously minimized: total utility work, total production rate variation, and total setup cost. A multi-objective sequencing problem and its mathematical formulation are described. Due to the NP-hardness of the problem, a new multi-objective particle swarm (MOPS) is designed to search locally Pareto-optimal frontier for the problem. To validate the performance of the proposed algorithm, various test problems are solved and the reliability of the proposed algorithm, based on some comparison metrics, is compared with three distinguished multi-objective genetic algorithms (MOGAs), i.e. PS-NC GA, NSGA-II, and SPEA-II. Comparison shows that MOPS provides superior results to MOGAs.     

An elitist non-dominated sorting genetic algorithm enhanced with a neural network applied to the multi-objective optimization of a polysiloxane synthesis process

This paper presents an original software implementation of the elitist non-dominated sorting genetic algorithm (NSGA-II) applied and adapted to the multi-objective optimization of a polysiloxane synthesis process. An optimized feed-forward neural network, modeling the variation in time of the main parameters of the process, was used to calculate the vectorial objective function of NSGA-II, as an enhancement to the multi-objective optimization procedure. An original technique was utilized in order to find the most appropriate parameters for maximizing the performance of NSGA-II. The algorithm provided the optimum reaction conditions (reaction temperature, reaction time, amount of catalyst, and amount of co-catalyst), which maximize the reaction conversion and minimize the difference between the obtained viscometric molecular weight and the desired molecular weight. The algorithm has proven to be able to find the entire non-dominated Pareto front and to quickly evolve optimal solutions as an acceptable compromise between objectives competing with each other. The use of the neural network makes it also suitable to the multi-objective optimization of processes for which the amount of knowledge is limited.     

生物序列比对算法的实现与集成

为了使不同的比对算法产生的结果能够方便地横向比较进而评价最佳的比对模式,深入地研究了序列比对领域最经典和最常用的比对算法,其中包括经典的动态规划、半经验式的BLAST和FASTA、启发式的CLUSTALW以及相似组方法等,并对各种方法加以程序化的实现,研制成功了集成化的序列比对平台,为科研人员提供了有效的序列比对及其评价工具。