On the approximation of protein threading

In this paper, we study the protein threading problem, which was proposed for predicting a folded 3D protein structure from an amino acid sequence. Since this problem was already proved to be NP-hard, we study polynomial time approximation algorithms. We show several hardness results for the approximation, which includes a MAX SNP-hardness result. We also show approximation algorithms for a special case and a general case, where a graph representing interactions between amino acid residues is restricted to be planar in a special case. For this special case, we obtain a constant approximation ratio.     

多处理机环境下线程模型性能评测与分析

在线程环境设计中存在三种结构不同的线程模型:多对一、一对一和多对多,一直以来,线程模型的特性分析仍然主要位于感性层面,缺乏完整的测试数据验证。FreeBSD5提供了基于三种线程模型的线程环境,为评测不同线程环境的性能提供了条件。论文以FreeBSD5下的测试结果为基础,结合Linux下一对一模型线程库NPTL的测试结果,分析了三种模型的不同特点,指出一对一模型和多对多模型均具有良好的性能,同时,基于SchedulerActivations的多对多模型也有很大的发展空间。     

An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing

To fully utilize all available information in protein structure prediction, including both backbone and side-chain structures, we present a novel algorithm for solving a generalized threading problem. In this problem, we consider simultaneously backbone threading and side-chain packing during the process of a protein structure prediction. For a given query protein sequence and a template structure, our goal is to find a threading alignment between the query sequence and the template structure, along with a rotamer assignment for each side-chain of the query protein, which optimizes an energy function that combines a backbone threading energy and a side-chain packing energy. This highly computationally challenging problem is solved through first formulating this problem as a graph-based optimization problem. Various graph-theoretic techniques are employed to achieve the computational efficiency to make our algorithm practically useful, which takes advantage of a number of special properties of the graph representing this generalized threading problem. The overall framework of our algorithm is a dynamic programming algorithm implemented on an optimal tree decomposition of the graph representation of our problem. By using various additional heuristic techniques such as the dead-end elimination, we have demonstrated that our algorithm can solve a generalized threading problem within practically acceptable amount of time and space, the first of its kind.     

量子遗传算法研究

量子遗传算法是在遗传算法中引入量子计算的概念,是20世纪90年代新兴的研究领域。介绍了遗传算法(GA)和量子算法(QC)的特点,以及量子遗传算法(QGA)的基本理论与方法。并在Matlab下编程对量子遗传算法与传统遗传算法的效率进行比较。     

基于事务性执行的投机并行多线程软件模拟

基于事务性执行的投机并行多线程是一种适合未来多核微处理器架构的新型并行程序设计和编译技术.但在此基础上的并行程序执行过程更为复杂,程序执行过程的模拟成为关键问题之一.本文提出利用二进制代码级动态插桩技术对投机并行多线程程序进行功能性模拟,设计并实现了完整的软件平台,可精确地模拟和监控并行程序的线程级投机执行过程,检测访存冲突,从而实现投机并行多线程的语义.该软件平台同时可以作为进一步研究投机多线程并行程序真实执行过程的基础,并有效支持投机并行多线程编译器的设计和分析.     

Genetic doping algorithm (GenD): theory and applications

Abstract: This paper describes an evolutionary algorithm, GenD, conceived by Buscema in 1998 at the Centro Ricerche di Scienze della Comunicazione – Semeion in Rome, where it is still successfully used and has been further developed. Unlike classic genetic algorithms, the GenD system maintains an inner instability during evolution, presenting a continuous evolution of the evolution and a natural increase in biodiversity during the progress of the algorithm. The theory which leads to defining the GenD system is outlined. Specific characteristics of GenD, such as the definition of a species‐health aware evolutionary law, the use of genetic operators and the adoption of a structured organization of individuals (tribes), are described. In order to measure GenD capabilities, we investigated also different problems, such as that known as the travelling sales person problem, which belongs to the class of full NP problems.     

遗传算法在Snake模型中的应用

文章针对Snake模型应用于图像边缘检测时对于噪音过于敏感的不足,提出了一种改进的方法。利用遗传算法的全局优化特性改进Snake模型局部优化的缺点,并取得了较好的效果。     

遗传算法的改进与应用

遗传算法是一种借鉴生物界自然选择和自然遗传机制的随机搜索算法,它与传统的算法不同。大多数古典的优化算法是基于一个单一的度量函数(评估函数)的梯度或较高次统计,以产生一个确定性的试验解序列;遗传算法不依赖于梯度信息,而是通过模拟自然进化过程来搜索最优解。该文针对传统遗传算法的缺陷,提出了一些新的改进思路,即从搜索技术和遗传算子等的角度来改进遗传算法。     

Hybrid Genetic Algorithms for a Rostering Problem

Hybrid Genetic Algorithms are described for a large-size real-life rostering problem (railway workers' job scheduling and roster optimization). The new algorithm uses an order-based representation which encodes as a chromosome the list of job units to schedule. First, a greedy algorithm is considered, which uses a randomly generated job units list, and satisfies only the constraints pertaining to the workers' job contract. Then, a genetic algorithm optimizes the global roster, minimizing its length and achieving some desired homogenizations. Finally, a second genetic algorithm (GA) is used to find the best parameter values for the first genetic algorithm. Thus, this work investigates the use of a GA together with a greedy algorithm and of a second GA to optimize the parameter values of the first GA. The results of significant tests on real data are reported. They compare favourably with the known results on Rostering Problems, both in terms of execution time and solution accuracy. This work considers a practical Rostering Problem concerning the Railway workers' rosters optimization. The size of the input data is very challenging: about 1000 duties (i.e. job-units called ‘links’) based on a large-size city location; 125 days to consider for roster optimization (summer rostering); the goal is to optimize the structure of the working-turn for any worker, and to minimize the global cost of the rosters. It should be emphasised that this is a very large problem: we will use GAs to solve the problem within an execution time in the order of a few minutes on a common workstation.     

Genetic neuro-nester

In this paper, the integration of artificial neural networks and genetic algorithms is explored for solving uncured composite stock cutting problem, which is an NP-complete problem. The input patterns can be either rectangular or irregular, and the proposed approach can accommodate any orientation and size restrictions. A genetic algorithm is used to generate sequences of the input patterns to be allocated. The scrap percentage of each allocation is used as an evaluation criterion. The allocation algorithm uses the sliding method integrated with an artificial neural network, based on the adaptive resonance theory (ART1) paradigm, to allocate the patterns according to the sequence generated by the genetic algorithm. The results obtained by this approach give packing densities on the order of 80–95%.     

从头预测蛋白质骨架的一种并行蚁群方法及其在CASP8/9中的应用

从低同源关系的氨基酸序列预测蛋白质的三维结构被称为从头预测,它是计算生物学领域中的挑战之一.蛋白质骨架预测是从头预测的必要先导步骤.本文应用一种基于共享信息素的并行蚁群优化算法,在现有能量函数指导下,通过不同能量项之间的定性互补,构建具有最低能量的蛋白质骨架结构,并通过聚类选择构象候选集合中具有最低自由能的构象.在CASP8/9所公布的从头建模目标上应用了该方法,CASP8的13个从头建模目标中,模型1中有2个目标的预测结果超过CASP8中最好的结果,7个位列前10名;CASP9的29个从头建模目标中,候选集中的最佳结果中有20个进入Server组的前10名,模型1中有11个进入前10名.本文的结果说明融合多个不同的能量函数指导并行搜索,可以更好地模拟天然蛋白质的折叠行为.同时,在本算法载体上实现了不同种类搜索策略的融合并行,对于用非确定性算法解决类似的优化问题来说也是一种新颖的方法.     

基于遗传算法的入侵检测技术的研究

在简要介绍入侵检测和遗传算法的基础上,给出了基于异常检测的训练算法模型。详细介绍了遗传算法的构造过程,包括染色体的构造以及选择、交叉、变异等操作,并予以简单实现。算法提高了入侵检测的效率,并能检测部分未知攻击。     

遗传算法在乘务员排班系统中的应用

在排班系统中,一种公平、合理的排班方法对于调动工作人员的工作积极性、提高工作效率都具有重要的意义。阐述了乘务员排班系统基本情况,并建立了排班系统的排班通用算法模型和任务均衡算法模型,通过遗传算法对排班模型进行优化实现。基于航空公司实际数据证明算法是合理的,也是有效的。     

Exact Schema Theory for Genetic Programming and Variable-Length Genetic Algorithms with One-Point Crossover

A few schema theorems for genetic programming (GP) have been proposed in the literature in the last few years. Since they consider schema survival and disruption only, they can only provide a lower bound for the expected value of the number of instances of a given schema at the next generation rather than an exact value. This paper presents theoretical results for GP with one-point crossover which overcome this problem. First, we give an exact formulation for the expected number of instances of a schema at the next generation in terms of microscopic quantities. Due to this formulation we are then able to provide an improved version of an earlier GP schema theorem in which some (but not all) schema creation events are accounted for. Then, we extend this result to obtain an exact formulation in terms of macroscopic quantities which makes all the mechanisms of schema creation explicit. This theorem allows the exact formulation of the notion of effective fitness in GP and opens the way to future work on GP convergence, population sizing, operator biases, and bloat, to mention only some of the possibilities.     

遗传算法的改进

简要介绍了一般遗传算法的基本原理，由此提出了一个新的改进算法，它导向以适应度比较高的模式为祖先的染色体“家族”方向。文中给出了两个典型求最大值的例子，从结果中看，改进后的遗传算法大大提高了算法的速度，精度也有所提高。     

An Empirical Study of Multipopulation Genetic Programming

This paper presents an experimental study of distributed multipopulation genetic programming. Using three well-known benchmark problems and one real-life problem, we discuss the role of the parameters that characterize the evolutionary process of standard panmictic and parallel genetic programming. We find that distributing individuals between subpopulations offers in all cases studied here an advantage both in terms of the quality of solutions and of the computational effort spent, when compared to single populations. We also study the influence of communication patterns such as the communication topology, the number of individuals exchanged and the frequency of exchange on the evolutionary process. We empirically show that the topology does not have a marked influence on the results for the test cases studied here, while the frequency and number of individuals exchanged are related and there exists a suitable range for those parameters which is consistently similar for all the problems studied.     

Overview of Information Security Using Genetic Algorithm and Chaos

ABSTRACT

Security, integrity, nonrepudiation, confidentiality, and authentication services are the most important factors in information security. Genetic algorithms (GAs) are a class of optimization algorithms. Many problems can be solved using genetic algorithms through modeling a simplified version of genetic processes. The application of a genetic algorithm to the field of cryptology is unique. Few works exist on this topic. In this article, an attempt has been made to give an overview of genetic algorithm-based cryptography and to propose a new approach to GA with pseudorandom sequence to encrypt data stream. The feature of such an approach includes high data security and high feasibility for easy integration with commercial multimedia transmission applications. The experimental results of the proposed technique confirm that high throughput rate needed for real time data protection is achieved.     

基于遗传算法的八数码问题的设计及实现

介绍了遗传算法（GA）在八数码问题中的应用。首先介绍了八数码问题及遗传算法的相关知识,分析了求解八数码问题的传统解决方案;然后给出了八数码问题的遗传算法模型,并对此模型进行了算法的设计,即确定编码的表示、选择算子、交叉算子、变异算子及适应度函数;最后把此算法运用到基于八数码问题的拼图游戏求解过程的动态演示上。文中对此算法进行了多角度试验,试验表明采用遗传算法解决八数码问题是有效的、稳定的,具有较高的搜索效率。     

混沌在遗传算法中的应用

通过对由差分方程生成的混沌序列的分析,利用混沌序列内在的伪随机性,将混沌引入到遗传算法的初始种群的生成、交叉算子、变异算子中,由此得到了混沌遗传优化算法。该算法在克服基本遗传算法中的早熟收敛方面显示了有效性,对大多数检测函数的检测结果表明,算法令人满意。