Hybrid Genetic Algorithm for DNA Sequencing with Errors

In the paper, a new hybrid genetic algorithm solving the DNA sequencing problem with negative and positive errors is presented. The algorithm has as its input a set of oligonucleotides coming from a hybridization experiment. The aim is to reconstruct an original DNA sequence of a known length on the basis of this set. No additional information about the oligonucleotides nor about the errors is assumed. Despite that, the algorithm returns for computationally hard instances surprisingly good results, of a very high similarity to original sequences.     

Sequencing by hybridization: an enhanced crossover operator for a hybrid genetic algorithm

This paper presents a genetic algorithm for an important computational biology problem. The problem appears in the computational part of a new proposal for DNA sequencing denominated sequencing by hybridization. The general usage of this method for real sequencing purposes depends mainly on the development of good algorithmic procedures for solving its computational phase. The proposed genetic algorithm is a modified version of a previously proposed hybrid genetic algorithm for the same problem. It is compared with two well suited meta-heuristic approaches reported in the literature: the hybrid genetic algorithm, which is the origin of our proposed variant, and a tabu-scatter search algorithm. Experimental results carried out on real DNA data show the advantages of using the proposed algorithm. Furthermore, statistical tests confirm the superiority of the proposed variant over the state-of-the-art heuristics.     

An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors

Positional DNA sequencing by hybridization (PSBH) is a recently proposed enhancement of DNA sequencing by hybridization (SBH, potentially a powerful alternative to the DNA sequencing by gel electrophoresis). It has been discussed in many papers and applied to large scale sequencing by hybridization. However, the computational part of PSBH reconstruction is a difficult problem, especially for the occurrence of hybridization errors. So far the problem has not been solved well. Taking PSBH as a combinatorial optimization problem, a novel reconstruction approach to PSBH is presented in this paper. The proposed approach accepts both the negative and positive errors and can greatly reduce ambiguities in the reconstruction of PSBH. The computational experiment shows that our algorithm works satisfactorily and correctly on the test data, especially for the positive errors and k-tuple repetitions.     

Pattern Based Vocabulary Building for Effectively Sequencing Mixed-Model Assembly Lines

In this paper, the problem of sequencing mixed-model assembly lines in case of fixed rate launching and closed stations is considered. The problem consists of finding an intermixed sequence of different models of a basic product, which are jointly produced on an assembly line, such that customer demands are fulfilled and total work overload is minimized. For solving this problem an informed tabu search procedure with a pattern based vocabulary building strategy is developed. Computational tests demonstrate that considerable improvements are obtained by comparison to methods which do not incorporate such an approach.     

Heuristic Techniques for Single Line Train Scheduling

Optimising a train schedule on a single line track is known to be NP-Hard with respect to the number of conflicts in the schedule. This makes it difficult to determine optimum solutions to real life problems in reasonable time and raises the need for good heuristic techniques. The heuristics applied and compared in this paper are a local search heuristic with an improved neighbourhood structure, genetic algorithms, tabu search and two hybrid algorithms. When no time constraints are enforced on solution time, the genetic and hybrid algorithms were within five percent of the optimal solution for at least ninety percent of the test problems.     

第三方库存-路线问题的模型及混合遗传算法设计

根据第三方库存-路线问题的特点,以车辆租赁费用和运行费用之和为目标函数,不限制客户每次的配送量小于车辆容量,建立了满载运输和非满载运输混合的整数规划模型.针对第三方库存-路线问题的复杂性,本文设计嵌入禁忌搜索的遗传算法来同时决策库存和路线问题.首先对配送间隔进行编码,然后用禁忌搜索法计算每天需要配送的车辆路线问题.最后与其下界值进行比较,结果表明该算法是一个有效的算法,不但第三方能取得较低的运营总成本和较高的车辆利用率,而且也能为客户节约库存空间.     

允许长度估计误差的SBH最优重构问题及其算法

本文讨论了允许长度估计误差和杂交错误的更实际SBH(Sequencing by Hybridization)最优重构问题.通过对SBH谱集中k-tuple之间的相关信息的分析和最优重构性质的讨论,我们得到若干非最优解的删除法则和最优解的判定法则,并获得了一个能够极大地减少最优解重构随意性的动态规划计算方法.由此,我们给出了该SBH问题的一个新重构算法.该算法既允许SBH谱集含有一般杂交实验中可能出现的探针错配所产生的正错误,也允许目标DNA序列长度有估计误差,所以本文的算法具有更一般的适应性和实用性.模拟计算结果表明我们的算法也是十分有效的(即使在谱集有多达100%的正错误情况).     

Heuristic solution approaches for the cumulative capacitated vehicle routing problem

Cumulative capacitated vehicle routing problem (CCVRP) is an extension of the well-known capacitated vehicle routing problem, where the objective is minimization of sum of the arrival times at nodes instead of minimizing the total tour cost. This type of routing problem arises when a priority is given to customer needs or dispatching vital goods supply after a natural disaster. This paper focuses on comparing the performances of neighbourhood and population-based approaches for the new problem CCVRP. Genetic algorithm (GA), an evolutionary algorithm using particle swarm optimization mechanism with GA operators, and tabu search (TS) are compared in terms of required CPU time and obtained objective values. In addition, a nearest neighbourhood-based initial solution technique is also proposed within the paper. To the best of authors’ knowledge, this paper constitutes a base for comparisons along with GA, and TS for further possible publications on the new problem CCVRP.     

多无线WMN中干扰最小化信道分配算法研究

为了提高无线迈适网的通信容量,网络中的每个路由节点均配备有多个无线网卡,并提供多个可用的无线信道.如何将这些信道合理地分配到网络的各个通信链路上,使得整个网络的干扰最小是一个至关重要问题.分析了基于禁忌搜索的信道分配算法,并针对该算法存在的问题,提出了初步的改进算法.     

A Combined Evolutionary Search and Multilevel Optimisation Approach to Graph-Partitioning

The graph-partitioning problem is to divide a graph into several pieces so that the number of vertices in each piece is the same within some defined tolerance and the number of cut edges is minimised. Important applications of the problem arise, for example, in parallel processing where data sets need to be distributed across the memory of a parallel machine. Very effective heuristic algorithms have been developed for this problem which run in real-time, but it is not known how good the partitions are since the problem is, in general, NP-complete. This paper reports an evolutionary search algorithm for finding benchmark partitions. A distinctive feature is the use of a multilevel heuristic algorithm to provide an effective crossover. The technique is tested on several example graphs and it is demonstrated that our method can achieve extremely high quality partitions significantly better than those found by the state-of-the-art graph-partitioning packages.     

A Beam Search approach for the optimization version of the Car Sequencing Problem

The Car Sequencing Problem (CSP) is a feasibility problem that has attracted the attention of the Constraint Programming community for a number of years now. In this paper, a new version (opt-CSP) that extends the original problem is defined, converting this into an optimization problem in which the goal is to satisfy the typical hard constraints. This paper presents a solution procedure for opt-CSP using Beam Search. Computational results are presented using public instances that verify the goodness of the procedure and demonstrate its excellent performance in obtaining feasible solutions for the majority of instances while satisfying the new constraints.     

An Evolutionary Approach to Spatial Fuzzy c-Means Clustering

Fuzzy c-means clustering algorithm (FCM) can provide a non-parametric and unsupervised approach to the cluster analysis of data. Several efforts of fuzzy clustering have been undertaken by Bezdek and other researchers. Earlier studies in this field have reported problems due to the setting of optimum initial condition, cluster validity measure, and high computational load. More recently, the fuzzy clustering has benefited of a synergistic approach with Genetic Algorithms (GA) that play the role of an useful optimization technique that helps to better tolerate some classical drawbacks, such as sensitivity to initialization, noise and outliers, and susceptibility to local minima. We propose a genetic-level clustering methodology able to cluster objects represented by R ^p spaces. The unsupervised cluster algorithm, called SFCM (Spatial Fuzzy c-Means), is based on a fuzzy clustering c-means method that searches the best fuzzy partition of the universe assuming that the evaluation of each object with respect to some features is unknown, but knowing that it belongs to circular regions of R ² space. Next we present a Java implementation of the algorithm, which provides a complete and efficient visual interaction for the setting of the parameters involved into the system. To demonstrate the applications of SFCM, we discuss a case study where it is shown the generality of our model by treating a simple 3-way data fuzzy clustering as example of a multicriteria optimization problem.     

带有资源转移时间的RCPSP资源流模型及算法

本文在传统资源受限项目调度问题(resource-constrained project scheduling problem, RCPSP)中引入资源转移时间,为有效获得问题的最优解,采用资源流编码方式表示可行解,建立了带有资源转移时间的RCPSP资源流优化模型,目标为最小化项目工期。根据问题特征设计了改进的资源流重构邻域算子,分别设计了改进的禁忌搜索算法和贪心随机自适应禁忌搜索算法求解模型。数据实验结果表明,相较于现有文献中的方法,所提两种算法均可针对更多的项目实例求得最优解,并且得到最优解的时间更短,求解效率更高。此外,分析了算法在求解具有不同特征的项目实例时的性能,所得结果为项目经理结合项目特征评价算法适用性提供了指导。     

Complete Local Search with Memory

Neighborhood search heuristics like local search and its variants are some of the most popular approaches to solve discrete optimization problems of moderate to large size. Apart from tabu search, most of these heuristics are memoryless. In this paper we introduce a new neighborhood search heuristic that makes effective use of memory structures in a way that is different from that in common implementations of tabu search. We report computational experiments with this heuristic on the traveling salesperson problem and the subset sum problem.     

A Metaheuristic to Solve a Location-Routing Problem with Non-Linear Costs

The paper deals with a location-routing problem with non-linear cost functions. To the best of our knowledge, a mixed integer linear programming formulation for the addressed problem is proposed here for the first time. Since the problem is NP-hard exact algorithms are able to solve only particular cases, thus to solve more general versions heuristics are needed. The algorithm proposed in this paper is a combination of a p-median approach to find an initial feasible solution and a metaheuristic to improve the solution. It is a hybrid metaheuristic merging Variable Neighborhood Search (VNS) and Tabu Search (TS) principles and exploiting the synergies between the two. Computational results and conclusions close the paper.     

货物装卸中的一个排序问题

本文考虑货物装卸管理中船主和港口之间的下述相互制约关系：有n条船在时刻零同时抵达同一码头装卸货物,因而也希望在同一时刻守成装卸货物。如某船的货物不能如期装卸守而延误了该船的离港,船主会向港方索取赔偿,反之如货物提前装卸完而使该船河提前投入运输,则船主会向港方付取奖金,加上正常装卸费用,从港方来说要适当考虑n条船的一个装卸顺序,使总费用减少,对这一NP-困难的排序问题,文中给出了几个多项式可解的特殊情形,一般情况下的一个快速下界估计方法以及相应的分支定界算法。     

Parallelization of a Two-Phase Metaheuristic for Routing Problems with Time Windows

This paper describes the parallelization of a two-phase metaheuristic for the vehicle routing problem with time windows and a central depot (VRPTW). The underlying objective function combines the minimization of the number of vehicles in the first search phase of the metaheuristic with the minimization of the total travel distance in the second search phase. The parallelization of the metaheuristic follows a type 3 parallelization strategy (cf. Crainic and Toulouse (2001). In F. Glover and G. Kochenberger (eds.). State-of-the-Art Handbook in Metaheuristics. Norwell, MA: Kluwer Academic Publishers), i.e. several concurrent searches of the solution space are carried out with a differently configured metaheuristic. The concurrently executed processes cooperate through the exchange of solutions. The parallelized two-phase metaheuristic was subjected to a comparative test on the basis of 358 problems from the literature with sizes varying from 100 to 1000 customers. The derived results seem to justify the proposed parallelization concept.     

Metaheuristics for High School Timetabling

In this paper we present the results of an investigation of the possibilities offered by three well-known metaheuristic algorithms to solve the timetable problem, a multi-constrained, NP-hard, combinatorial optimization problem with real-world applications. First, we present our model of the problem, including the definition of a hierarchical structure for the objective function, and of the neighborhood search operators which we apply to matrices representing timetables. Then we report about the outcomes of the utilization of the implemented systems to the specific case of the generation of a school timetable. We compare the results obtained by simu lated annealing, tabu search and two versions, with and without local search, of the genetic algorithm. Our results show that GA with local search and tabu search based on temporary problem relaxations both outperform simulated annealing and handmade timetables.     

一种改进的禁忌搜索算法及其在连续全局优化中的应用

禁忌搜索算法是一种元启发式的全局优化算法,是局部搜索算法的一种推广,已被成功地应用于许多组合优化问题中。本文针对有界闭区域上的连续函数全局优化问题,提出了一种改进的禁忌搜索算法,并进行了理论分析和数值实验。数值实验表明,对于连续函数全局优化问题的求解该算法是可行有效的,并且结构简单,迭代次数较少,是一种较好的全局启发式优化算法。     

Schemata, Distributions and Graphical Models in Evolutionary Optimization

In this paper the optimization of additively decomposed discrete functions is investigated. For these functions genetic algorithms have exhibited a poor performance. First the schema theory of genetic algorithms is reformulated in probability theory terms. A schema defines the structure of a marginal distribution. Then the conceptual algorithm BEDA is introduced. BEDA uses a Boltzmann distribution to generate search points. From BEDA a new algorithm, FDA, is derived. FDA uses a factorization of the distribution. The factorization captures the structure of the given function. The factorization problem is closely connected to the theory of conditional independence graphs. For the test functions considered, the performance of FDA—in number of generations till convergence—is similar to that of a genetic algorithm for the OneMax function. This result is theoretically explained.