一种基于蚁群算法的生物序列并行比对方法

生物序列比对是生物信息领域的重要课题,比对结果的合理性和正确性关系到基于比对结果研究的正确性。在保证正确性的前提下利用并行计算充分挖掘计算潜力对提高比对效率有重要意义。针对双序列的全局比对问题,提出了基于蚁群算法的双序列比对并行化方案。对耗时最多的搜索比对路径和信息素更新两个步骤给出了基于共享内存模型的并行化方法。"天河二号"上OpenMP实验结果表明,8线程并行情况下,加速比可达5.03,且序列越长性能越高。     

蚁群优化算法在求解随机组合优化问题中的应用综述*

不确定条件下的优化问题更贴近真实世界环境,因而日益受到广泛关注。综述了蚁群优化在求解一组不确定条件下的组合优化问题,即随机组合优化问题方面的应用。首先介绍了不确定条件下组合优化问题的概念分类模型,给出了随机组合优化问题的一般定义;然后指出了其与求解传统确定性组合优化问题的不同之处,即目标函数的计算存在不确定性,并详细论述了目前解决方法的进展;最后分析了该领域值得重点关注的几个研究方向,并对其未来发展进行了展望。     

A software model to prototype ant colony optimization algorithms

The study of multi-agent systems usually begins by implementing a base-algorithm, which is changed as required by the aim of the research. In this context, carrying out different algorithms, which have already been established, is not a trivial task as it requires implementing these algorithms. This paper presents a software model that allows one to prototype variations of the Ant Colony Optimization metaheuristic. This model can be used to avoid implementations in duplicity, allowing, with less effort, the generation of different algorithms to be used on the same problem. Results shown that, specially for more elaborated algorithms, the adoption of the proposed software model reduce significantly the coding effort required.     

一类自适应蚁群算法及其收敛性分析

为了克服蚁群算法易陷入局部最小点的缺点,同时提高算法的收敛速度,提出一类自适应蚁群算法.该算法利用自适应改变信息激素的挥发系数改善传统蚁群算法的全局搜索能力和收敛速度.通过马尔科夫过程对算法的全局收敛性进行分析,得出该类蚁群算法全局收敛性条件.并构造出该类算法的一种信息激素更新策略,证明了这种算法全局收敛性.利用提出的算法对典型的TSP问题进行仿真研究,结果表明比典型蚁群算法在收敛速度和解的性能上都有较大改善.     

利用蚁群优化算法的粗糙集属性约简方法

随着高维数据的扩散,特征选择成为学习过程中不可或缺的一项任务。属性约简是特征选择的重要方法,为了寻找有效的属性约简方法,将粗糙集与蚁群算法相结合,提出了利用蚁群优化算法的粗糙集属性约简方法。首先从信息素的更新开始,限制其信息素值的上、下限范围,然后根据寻址方式改进候选解的构造方案。实验表明,该方法具有一定的优越性。     

A novel ant colony optimization algorithm for large-distorted fingerprint matching

Large distortion may be introduced by non-orthogonal finger pressure and 3D–2D mapping during the process of fingerprint capturing. Furthermore, large variations in resolution and geometric distortion may exist among the fingerprint images acquired from different types of sensors. This distortion greatly challenges the traditional minutiae-based fingerprint matching algorithms. In this paper, we propose a novel ant colony optimization algorithm to establish minutiae correspondences in large-distorted fingerprints. First, minutiae similarity is measured by local features, and an assignment graph is constructed by local search. Then, the minutiae correspondences are established by a pseudo-greedy rule and local propagation, and the pheromone matrix is updated by the local and global update rules. Finally, the minutiae correspondences that maximize the matching score are selected as the matching result. To compensate resolution difference of fingerprint images captured from disparate sensors, a common resolution method is adopted. The proposed method is tested on FVC2004 DB1 and a FINGERPASS cross-matching database established by our lab. The experimental results demonstrate that the proposed algorithm can effectively improve the performance of large-distorted fingerprint matching, especially for those fingerprint images acquired from different modes of acquisition.     

Solving the feeder bus network design problem by genetic algorithms and ant colony optimization

This paper proposes the design and analysis of two metaheuristics, genetic algorithms and ant colony optimization, for solving the feeder bus network design problem. A study of how these proposed heuristics perform is carried out on several randomly generated test problems to evaluate their computational efficiency and the quality of solutions obtained by them. The results are also compared to those published in the literature. Computational experiments have shown that both heuristics are comparable to the state-of-the-art algorithms such as simulated annealing and tabu search.     

A modified distance method for multicriteria optimization, using genetic algorithms

The common application areas of Genetic Algorithms (GAs) have been to single criterion difficult optimization problems. The GA selection mechanism is often dependent upon a single valued scalar objective funtion. In this paper, we present results of a modified distance method. The distance method was proposed earlier by us, for solving multiple criteria problems with GAs. The Pareto set estimation method, which is fundamental to multicriteria analysis, is used to perform the multicriteria optimization using GAs. First, the Pareto set is found out from the population of the initial generation of the GA. The fitness of a new solution, is calculated by a distance measure with reference to the Pareto set of the previous runs. We calculate the distances of a solution from all the Pareto solutions found since the previous run, but the minimum of these distances is taken under consideration while evaluating the fitness of the solution. Thus the GA tries to maximize the distance of future Pareto solutions from present Pareto solutions in the positive Pareto space of the given problem. Here we modify distance method, by using an improved algorithm to assign and make use of the latent potential of the Pareto solutions which are found during the runs. Two detailed numerical examples and computer generated results are also presented.     

融合遗传和蚁群算法并行求解最短公共超串

依据各级缓存容量,将CPU主存中种群个体和蚂蚁个体数据划分存储到一级、二级和三级缓存中,以减少并行计算过程中数据在各级存储之间的传输开销,在CPU与GPU之间采取异步传送和不完全传送数据、GPU多个内核函数异步执行多个流的方法,设置GPU block线程数量为16的倍数、GPU共享存储器划分大小为32倍的bank,使用GPU常量存储器存储交叉概率、变异概率等需频繁访问的只读参数,将输入串矩阵和重叠部分长度矩阵只读大数据结构绑定到GPU纹理存储器,设计实现了一种多核CPU和GPU协同求解最短公共超串问题的计算、存储和通信高效的并行算法。求解多种规模的最短公共超串问题的实验结果表明,多核CPU与GPU协同并行算法比串行算法快70倍以上。     

蚁群算法中信息素增量和扩散模型的研究

文章提出一种新的基于信息素增量和扩散模型的蚁群算法。首先,基于能量守恒与转换定律对信息素的增量模型进行修正,以体现蚂蚁在不同路径上行走时所产生的信息量差异;其次,以蚂蚁经过的路径(直线段)作为信息素扩散浓度场的信源,改善了信息素扩散模型,强化了蚂蚁间的协作和交流。大量TSP(Traveling Salesman Problem)问题的实验表明:该算法不仅能获得更好的解,而且能加快算法的收敛速度。     

改进的蚁群遗传优化算法及其应用

针对当前移动机器人的一些路径规划算法存在的局限性,提出了一种基于改进蚁群优化和遗传优化的融合算法。利用改进的信息素更新技术和路径节点选择技术使算法尽快找到优化路径,来形成融合算法的初始种群,机器人每前进一步,蚂蚁就对局部路径重新搜索,并处理随机出现的障碍物;然后利用遗传算法(GA)对种群个体进行全局优化,从而能使机器人沿一条全局优化的路径到达终点。仿真结果表明了该融合算法的可行性和有效性。     

基于蚁群遗传算法的氨基酸序列比对方法

蚁群遗传算法是在蚁群算法的基础上用遗传算法对其参数进行优化而产生的一种改进算法。把蚁群遗传算法应用于生物信息学中的氨基酸序列比对上,从而提出了一种新颖的蚁群遗传序列比对算法,实验结果表明这种新颖的序列比对算法是非常有效的。     

Genetic algorithm with ant colony optimization (GA-ACO) for multiple sequence alignment

Multiple sequence alignment, known as NP-complete problem, is among the most important and challenging tasks in computational biology. For multiple sequence alignment, it is difficult to solve this type of problems directly and always results in exponential complexity. In this paper, we present a novel algorithm of genetic algorithm with ant colony optimization for multiple sequence alignment. The proposed GA-ACO algorithm is to enhance the performance of genetic algorithm (GA) by incorporating local search, ant colony optimization (ACO), for multiple sequence alignment. In the proposed GA-ACO algorithm, genetic algorithm is conducted to provide the diversity of alignments. Thereafter, ant colony optimization is performed to move out of local optima. From simulation results, it is shown that the proposed GA-ACO algorithm has superior performance when compared to other existing algorithms.     

火力优化分配问题的小生境遗传蚂蚁算法

火力分配问题是NP难题,经典的求解算法存在指数级的时间复杂度。文中提出一种小生境遗传算法与蚁群优化算法相结合的小生境遗传蚂蚁算法,并针对具体问题提出蚂蚁搜索的禁忌规则。对该算法进行了实验,并将实验结果与其他算法进行比较分析,分析结果表明：新算法无论是在优化性能还是在时间性能都取得了非常好的效果。文中算法对其他的NP问题同样适用。     

基于蚁群算法的PID控制参数优化

蚁群算法是近几年优化领域中新出现的一种仿生进化算法,该算法采用的分布式并行计算机制特别适用于组合优化问题（COP）的求解。在简要介绍蚁群算法的基础上,针对PID控制参数整定问题提出了一种基于蚁群算法的PID参数优化策略,并给出了该算法的具体实现步骤。仿真试验结果表明同传统的Ziegler-Nichols（ZN）法、遗传算法优化整定的结果进行比较,系统单位阶跃响应的超调量σ分别减少了51.5％和22％和调整时间ts分别减少了61.4％和67.5％,动态和稳态性能进一步改善,进而验证了该方法的可行性和有效性。     

A hybrid ant colony optimization for continuous domains

Research on optimization in continuous domains gains much of focus in swarm computation recently. A hybrid ant colony optimization approach which combines with the continuous population-based incremental learning and the differential evolution for continuous domains is proposed in this paper. It utilizes the ant population distribution and combines the continuous population-based incremental learning to dynamically generate the Gaussian probability density functions during evolution. To alleviate the less diversity problem in traditional population-based ant colony algorithms, differential evolution is employed to calculate Gaussian mean values for the next generation in the proposed method. Experimental results on a large set of test functions show that the new approach is promising and performs better than most of the state-of-the-art ACO algorithms do in continuous domains.     

A robust ant colony optimization for continuous functions

Ant colony optimization (ACO) for continuous functions has been widely applied in recent years in different areas of expert and intelligent systems, such as steganography in medical systems, modelling signal strength distribution in communication systems, and water resources management systems. For these problems that have been addressed previously, the optimal solutions were known a priori and contained in the pre-specified initial domains. However, for practical problems in expert and intelligent systems, the optimal solutions are often not known beforehand. In this paper, we propose a robust ant colony optimization for continuous functions (RACO), which is robust to domains of variables. RACO applies self-adaptive approaches in terms of domain adjustment, pheromone increment, domain division, and ant size without any major conceptual change to ACO's framework. These new characteristics make the search of ants not limited to the given initial domain, but extended to a completely different domain. In the case of initial domains without the optimal solution, RACO can still obtain the correct result no matter how the initial domains vary. In the case of initial domains with the optimal solution, we also show that RACO is a competitive algorithm. With the assistance of RACO, there is no need to estimate proper initial domains for practical continuous optimization problems in expert and intelligent systems.     

改进的求解TSP问题文化蚁群优化方法

在文化算法基础上提出了一种改进的用于求解TSP问题的蚁群优化算法。改进算法采用新的双层进化机制对文化算法的种群空间与信念空间进行了重新设计,用最大最小蚁群系统（MMAS）构建种群空间,在信念空间中对当前最优解进行改进的3-OPT交叉变换操作,由于采用了这种双层进化机制,种群空间获得了更高的进化效率。通过仿真实验结果表明,改进算法比传统的蚁群算法（ACO）、文化蚁群算法（CACS）效果更好,收敛速度更快,精确度更高。     

一种基于蚁群算法的呼叫中心人力需求计算方法

针对呼叫中心人力需求优化这一离散约束问题,基于Dantzig提出的集合覆盖模型,建立了单技能呼叫中心的人力需求计算线性规划模型,并提出一种基于改进蚁群算法的求解方法.在该方法中,对算法的信息素更新规则进行了修改,并基于MATLAB编程针对实例进行仿真分析.选取统计学指标将算法的仿真结果与遗传算法进行对比,结果表明:基于蚁群算法的方法计算复杂度可行;能够节约人力,且话务员匹配度可满足实际运营需求;为智能算法在呼叫中心人力需求计算问题上的应用研究提供了一种新的解决思路.