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。     

求解多重序列比对问题的蚁群算法*

多重序列比对是生物信息学特别是生物序列分析中一个重要的基本操作。提出求解多重序列比对问题的蚁群算法,利用人工蚂蚁逐个选择各个序列中的字符进行配对。在算法中,蚂蚁根据信息素、字符匹配得分以及位置偏差等信息决定选择各序列中字符的概率,通过信息素的更新与调节相结合的策略较为有效地解决了局部收敛的问题,加强了算法寻求全局最优解的能力。另外在该算法的基础上,提出了基于分治策略的多序列比对蚁群求解算法,不但减少了原算法的计算时间,而且显著改善了算法所求得的解的质量。     

遗传混合算法路径规划研究

遗传算法和蚁群算法被广泛应用于路径规划,但遗传算法收敛速度慢,蚁群算法易陷入局部最优,在求解旅行商问题上都有一定的缺陷。本文采用遗传与蚁群混合算法,充分利用遗传算法的快速全局搜索能力和蚁群算法的智能性,用蚁群算法迭代每只蚂蚁走过的路径序列作为遗传算法的初始种群,克服随机选择的盲目性,从而提高算法的性能。仿真计算结果表明,该算法可以找到最优解或近似最优解,并提高了求解效率。     

蚁群算法与遗传算法对TSP的一种融合

蚁群算法是通过信息素的累积和更新收敛于最优路径上,求解速度慢,而遗传算法具有快速随机的局部搜索能力。为此本文将遗传算法和蚁群算法相融合,给出一种改进的算法并用于TSP问题的求解。在问题求解中,用蚁群算法迭代每只蚂蚁走过的路径序列作为遗传算法的初始种群,克服随机选择的盲目性,从而提高算法的性能。模拟结果显示该算法是有效的和可行的。     

基于混合蚁群遗传算法的Agent联盟求解

针对混合蚁群遗传算法容易融合时机过早或过晚、种群进化经历的代数过多、效率低等问题,首先改进了蚁群算法,并将改进的蚁群算法和遗传算法结合,应用于Agent联盟求解.提出了基于混合蚁群遗传算法的Agent联盟求解算法(Hybrid Ant Colony and Genetic Algorithm,HAGA),算法的核心是动态寻找两个算法的衔接点,在该点左侧使用遗传算法,右侧使用蚁群算法.与其他传统算法的实验比较,证明了该算法在求解联盟的最优解的时问和精度上都有较高的效果.把HAGA应用于RoboCup 2D龙队客户端程序中,使用比赛分析工具软件SoccerDoctor对比赛结果进行了统计分析,结果显示龙队在诸多技术参数方面均占有明显优势.     

基于蚁群-遗传融合框架的仓储群机器人任务分配

将智能仓储中的自主移动群机器人订单任务分配,建模成群机器人协同调度的多目标优化问题,将成员机器人完成拣货任务的路径代价和时间代价作为优化目标.设计了蚁群-遗传算法融合框架并在其中求解.该框架中,蚁群算法作为副算法,用于初始种群优化;遗传算法改进后作为主算法.具体地,在遗传算法轮盘赌选择算子后引入精英保留策略,并在遗传操作中加入逆转算子.针对不同数量的订单任务,使用不同规模的群机器人系统进行了任务分配仿真实验.结果表明,在本文所提的融合框架中求解,较分别使用蚁群算法或遗传算法单独求解,性能上具有明显优势,能够发挥蚁群算法鲁棒性好和遗传算法全局搜索能力强的特点,提高智能仓储系统的整体运行效率.     

一种求解函数优化的混合蚁群算法*

将遗传算法与蚁群算法中的协同模型进行有机结合,在蚁群算法中引入交叉、变异、选择算子来改进基本蚁群算法,克服了蚁群算法不太适合求解连续空间优化问题的缺陷。通过测试函数表明该方法具有较好的收敛速度和稳定性,求解结果好于遗传算法。     

基于遗传算法与星比对的多序列比对混合算法

多序列比对(MSA)是一个典型的NP完全问题，星比对是一种有效的多序列比对算法。文章针对MSA问题提出了将遗传算法与星比对算法结合在一起的混合算法，该算法充分发挥了遗传算法和星比对算法的优越性，可提高求解MSA问题的计算精度和计算速度，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。实验表明，该算法是有效的。     

一种求解TSP问题的蚁群遗传混合算法

提出了一种蚁群算法与遗传算法相混合的算法。将遗传算法加入到蚁群算法的每一次迭代的过程中,利用遗传算法全局快速收敛的特点,来加快蚁群算法的收敛速度。并且遗传算法中的变异机制,帮助提高了蚁群算法取不到局部最优解的能力。不仅阐述了新算法的原理,而且以TSP问题的求解为例进行了相关的实验,实验结果表明新算法即蚁群遗传混合算法(ACGA)在求解时间和求解质量上都取得了很好的效果。     

多序列比对问题的粒子群优化算法求解

文章提出了一新的算法,利用粒子群优化算法求解多序列比对的问题,这是粒子群优化算法在生物信息学方面的一个新的应用。文章从粒子群算法的原理和多序列比对问题模型入手,来提出怎样改造粒子群优化算法使其可以解决多序列比对问题,最后给出利用粒子群优化算法求解多序列比对的算法,及其测试结果。     

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.     

渐进方法结合蚁群算法求解多序列比对问题

在所有多重序列比对算法中,渐进比对方法由于简单的算法和高效的计算在生物信息学中得到了广泛的应用。但是渐进方法最大的缺点是在早期阶段形成的错误不能在后期的计算中纠正过来。针对这个问题,我们设计了ProAnt比对算法,即渐进方法和蚁群算法相结合来求解多重序列比对问题。首先,对输入的多个序列进行预处理,用蚁群算法和概率一致性更新计算出所有字符对在最终比对中出现的概率,称为“后验概率”,计算后验概率是为了预防早期错误的发生。然后我们将后验概率作为字符对之间的匹配得分,用渐进方法得到最终的比对结果。用BAliBASE数据库对算法进行测试,实验结果显示,该算法能够在保持合理的运算时间的前提下显著改善渐进比对方法的正确性。     

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。     

A novel method for alignment of two nucleic acid sequences using ant colony optimization and genetic algorithms

We describe a new method for pairwise nucleic acid sequence alignment that can also be used for pattern searching and tandem repeat searching within a nucleic acid sequence. The method is broadly a hybrid algorithm employing ant colony optimization (ACO) and the simple genetic algorithm. The method first employs ACO to obtain a set of alignments, which are then further processed by an elitist genetic algorithm, which employs primitive selection and a novel multipoint crossover-mutation operator to generate accurate alignments. The resulting alignments show a fair amount of accuracy for smaller and medium size sequences. Furthermore, this algorithm can be used rather quickly and efficiently for aligning shorter sequences and also for pattern searching in both nucleic acid and amino acid sequences. Furthermore, it can be used as an effective local alignment method or as a global alignment tool. On improvement of accuracy, this method can be extended for use towards multiple sequence alignment.     

Ant-Tree: an ant colony optimization approach to the generalized minimum spanning tree problem

The ant colony optimization is a meta-heuristic inspired by knowledge sharing amongst ants using pheromone, which serves as a kind of collective memory. Since the past few years, there have been several successful applications of this new approach for finding approximate solutions for computationally difficult problems in reasonable times. In this paper, we study the generalized minimum spanning tree problem that involves the design of a minimum weight connected network spanning at least one node out of every disjoint subset of the nodes in a graph. This problem has a wealth of pertinence to a wide range of applications in different areas. As the problem is known as computationally challenging, we adopt the ant colony optimization strategy and present a new solution method, called Ant-Tree, to develop approximate solutions. As an initial attempt, our study aims to provide an investigation of the ant colony optimization approach for coping with tree optimization problems. Through computational experiments, we compare the performances of our approach and the method available in the literature. Numerical results indicate that the proposed method is effective in producing quality approximate solutions.     

A new ant colony algorithm for makespan minimization in permutation flow shops

The problem of scheduling in permutation flow shop with the objective of minimizing the maximum completion time, or makespan, is considered. A new ant colony optimization algorithm is developed for solving the problem. A novel mechanism is employed in initializing the pheromone trails based on an initial sequence. Moreover, the pheromone trail intensities are limited between lower and upper bounds which change dynamically. When a complete sequence of jobs is constructed by an artificial ant, a local search is performed to improve the performance quality of the solution. The proposed ant colony algorithm is applied to Taillard’s benchmark problems. Computational experiments suggest that the algorithm yields better results than well-known ant colony optimization algorithms available in the literature.     

On the Invariance of Ant Colony Optimization

Ant colony optimization (ACO) is a promising metaheuristic and a great amount of research has been devoted to its empirical and theoretical analysis. Recently, with the introduction of the hypercube framework, Blum and Dorigo have explicitly raised the issue of the invariance of ACO algorithms to transformation of units. They state (Blum and Dorigo, 2004) that the performance of ACO depends on the scale of the problem instance under analysis. In this paper, we show that the ACO internal state - commonly referred to as the pheromone - indeed depends on the scale of the problem at hand. Nonetheless, we formally prove that this does not affect the sequence of solutions produced by the three most widely adopted algorithms belonging to the ACO family: ant system, MAX-MIN ant system, and ant colony system. For these algorithms, the sequence of solutions does not depend on the scale of the problem instance under analysis. Moreover, we introduce three new ACO algorithms, the internal state of which is independent of the scale of the problem instance considered. These algorithms are obtained as minor variations of ant system, MAX-MIN ant system, and ant colony system. We formally show that these algorithms are functionally equivalent to their original counterparts. That is, for any given instance, these algorithms produce the same sequence of solutions as the original ones.     

基于蚁群算法的通信线路最佳抢修路径问题的研究

通信线路最佳抢修路径问题,其实质就是交通路网中的最优路径问题。该文在研究蚁群算法的原理和基本模型的基础上,提出用一种改进的蚁群算法来解决最优路径问题。实验表明,该方法能在较短时间内发现最优解,对研究通信线路最佳抢修路径问题具有较大的实际意义。