A probabilistic simulator for population dynamics of quasispecies

We constructed a probabilistic simulator that allows all the events in population dynamics such as death, birth, mutation, and suppression/stimulation to be described by probabilistic rules. The simulator also facilitates a lattice used for expressing distribution and diversity (number of distinct strains) of quasispecies. The simulator is used to investigate the diversity threshold in HIV and T-cell interaction. This work was presented in part at the 13th International Symposium on Artificial Life and Robotics, Oita, Japan, January 31–February 2, 2008     

Seepage safety monitoring model for an earth rock dam under influence of high-impact typhoons based on particle swarm optimization algorithm

Extreme hydrological events induced by typhoons in reservoir areas have presented severe challenges to the safe operation of hydraulic structures. Based on analysis of the seepage characteristics of an earth rock dam, a novel seepage safety monitoring model was constructed in this study. The nonlinear influence processes of the antecedent reservoir water level and rainfall were assumed to follow normal distributions. The particle swarm optimization (PSO) algorithm was used to optimize the model parameters so as to raise the fitting accuracy. In addition, a mutation factor was introduced to simulate the sudden increase in the piezometric level induced by short-duration heavy rainfall and the possible historical extreme reservoir water level during a typhoon. In order to verify the efficacy of this model, the earth rock dam of the Siminghu Reservoir was used as an example. The piezometric level at the SW1-2 measuring point during Typhoon Fitow in 2013 was fitted with the present model, and a corresponding theoretical expression was established. Comparison of fitting results of the piezometric level obtained from the present statistical model and traditional statistical model with monitored values during the typhoon shows that the present model has a higher fitting accuracy and can simulate the uprush feature of the seepage pressure during the typhoon perfectly.     

A new Probe Guided Mutation operator and its application for solving the cardinality constrained portfolio optimization problem

This paper revisits the classical Polynomial Mutation (PLM) operator and proposes a new probe guided version of the PLM operator designed to be used in conjunction with Multiobjective Evolutionary Algorithms (MOEAs). The proposed Probe Guided Mutation (PGM) operator is validated by using data sets from six different stock markets. The performance of the proposed PGM operator is assessed in comparison with the one of the classical PLM with the assistance of the Non-dominated Sorting Genetic Algorithm II (NSGAII) and the Strength Pareto Evolutionary Algorithm 2 (SPEA2). The evaluation of the performance is based on three performance metrics, namely Hypervolume, Spread and Epsilon indicator. The experimental results reveal that the proposed PGM operator outperforms with confidence the performance of the classical PLM operator for all performance metrics when applied to the solution of the cardinality constrained portfolio optimization problem (CCPOP). We also calculate the True Efficient Frontier (TEF) of the CCPOP by formulating the CCPOP as a Mixed Integer Quadratic Program (MIQP) and we compare the relevant results with the approximate efficient frontiers that are generated by the proposed PGM operator. The results confirm that the PGM operator generates near optimal solutions that lie very close or in certain cases overlap with the TEF.     

A QM/MM study of the catalytic mechanism of aspartate ammonia lyase

Aspartate ammonia lyase (Asp) is one of three types of ammonia lyases specific for aspartate or its derivatives as substrates, which catalyzes the reversible reaction of l-aspartate to yield fumarate and ammonia. In this paper, the catalytic mechanism of Asp has been studied by using combined quantum-mechanical/molecular-mechanical (QM/MM) approach. The calculation results indicate that the overall reaction only contains two elementary steps. The first step is the abstraction of C_β proton of l-aspartate by Ser318, which is calculated to be rate limiting. The second step is the cleavage of C_αN bond of l-aspartate to form fumarate and ammonia. Ser318 functions as the catalytic base, whereas His188 is a dispensable residue, but its protonation state can influence the active site structure and the existing form of leaving amino group, thereby influences the activity of the enzyme, which can well explain the pH dependence of enzymatic activity. Mutation of His188 to Ala only changes the active site structure and slightly elongates the distance of C_β proton of substrate with Ser318, causing the enzyme to remain significant but reduced activity.     

克服恋食行为的PSO算法改进研究

基本粒子群优化算法(PSO)存在易陷入局部极值的缺点.为此,研究鸟群迁徙觅食中的行为习惯,以加强PSO的鸟群社会模型和对鸟群行为的模拟.在所提出的改进算法中,历史飞行速度在实际觅食中不作为判断因子,只有发生位置重复时粒子才发生变异或摄动,以此增强粒子群优化算法跳出局部最优解的能力.实验结果表明,新算法的全局搜索能力有了显著提高.     

一种新的调节交叉和变异概率的自适应算法

提出一种新的基于模糊控制策略的交叉和变异概率自适应调节算法.该算法以相邻两代群体之间平均适应度函数和标准差的差值作为输入,以交叉和变异概率的变化量作为输出.并提出了与输入相对应的自适应归一化算子以及新的基于启发式知识的模糊规则,用于交叉和变异概率的调节.对3种不同测试函数的数值仿真研究表明,与其他2种自适应模糊控制算法相比,该调节算法可使遗传算法具有更快的搜索速度和更高的搜索质量.     

On guiding the augmentation of an automated test suite via mutation analysis

Mutation testing has traditionally been used as a defect injection technique to assess the effectiveness of a test suite as represented by a “mutation score.” Recently, mutation testing tools have become more efficient, and industrial usage of mutation analysis is experiencing growth. Mutation analysis entails adding or modifying test cases until the test suite is sufficient to detect as many mutants as possible and the mutation score is satisfactory. The augmented test suite resulting from mutation analysis may reveal latent faults and provides a stronger test suite to detect future errors which might be injected. Software engineers often look for guidance on how to augment their test suite using information provided by line and/or branch coverage tools. As the use of mutation analysis grows, software engineers will want to know how the emerging technique compares with and/or complements coverage analysis for guiding the augmentation of an automated test suite. Additionally, software engineers can benefit from an enhanced understanding of efficient mutation analysis techniques. To address these needs for additional information about mutation analysis, we conducted an empirical study of the use of mutation analysis on two open source projects. Our results indicate that a focused effort on increasing mutation score leads to a corresponding increase in line and branch coverage to the point that line coverage, branch coverage and mutation score reach a maximum but leave some types of code structures uncovered. Mutation analysis guides the creation of additional “common programmer error” tests beyond those written to increase line and branch coverage. We also found that 74% of our chosen set of mutation operators is useful, on average, for producing new tests. The remaining 26% of mutation operators did not produce new test cases because their mutants were immediately detected by the initial test suite, indirectly detected by test suites we added to detect other mutants, or were not able to be detected by any test.

MC/DC Test Data Generation Algorithm Based on Whale Genetic Algorithm

The automatic generation of test data is a key step in realizing automated testing. Most automated testing tools for unit testing only provide test case execution drivers and cannot generate test data that meets coverage requirements. This paper presents an improved Whale Genetic Algorithm for generating test data required for unit testing MC/DC coverage. The proposed algorithm introduces an elite retention strategy to avoid the genetic algorithm from falling into iterative degradation. At the same time, the mutation threshold of the whale algorithm is introduced to balance the global exploration and local search capabilities of the genetic algorithm. The threshold is dynamically adjusted according to the diversity and evolution stage of current population, which positively guides the evolution of the population. Finally, an improved crossover strategy is proposed to accelerate the convergence of the algorithm. The improved whale genetic algorithm is compared with genetic algorithm, whale algorithm and particle swarm algorithm on two benchmark programs. The results show that the proposed algorithm is faster for test data generation than comparison methods and can provide better coverage with fewer evaluations, and has great advantages in generating test data.     

Web服务器集群的负载均衡中遗传算子的设计

应用遗传算法进行作业调度已被越来越多的学者关注。在Web服务器集群环境中,对于客户端的Web请求分配问题,采用常规的遗传算法进行负载均衡并不总是有效的,好的遗传算子对算法收敛性及收敛到最优解非常重要。基于集群环境中Web请求分配的特点,设计了有针对性的遗传算子,即改进的内外结合交叉算子和主动变异算子。模拟实验结果与分析表明这些算子对Web集群的请求分配是有效的。     

基于两阶段领导的多目标粒子群优化算法

提出一种基于两阶段领导的多目标粒子群算法(P-AMOPSO).该算法包含4个改进策略:基于强支配排序与拥挤距离排序相结合的构造外部集策略,基于两阶段的领导粒子选择策略,基于高斯分布及均匀分布相结合的变异策略,基于邻域认知的个体极值更新策略.通过几个典型的多目标测试函数对P-AMOPSO算法的性能进行测试,并与多目标优化算法进行对比.结果表明,P-AMOPSO算法具有较好的搜索性能.