Learning the dominance in diploid genetic algorithms for changing optimization problems

Using diploid representation with dominance scheme is one of the approaches developed for genetic algorithms to address dynamic optimization problems. This paper proposes an adaptive dominance mechanism for diploid genetic algorithms in dynamic environments. In this scheme, the genotype to phenotype mapping in each gene locus is controlled by a dominance probability, which is learnt adaptively during the searching progress. The proposed dominance scheme isexperimentally compared to two other schemes for diploid genetic algorithms. Experimental results validate the efficiency of the dominance learning scheme

Dominance learning in diploid genetic algorithms for dynamic optimization problems

Copyright @ 2006 YangThis paper proposes an adaptive dominance mechanism for diploidy genetic algorithms in dynamic environments. In this scheme, the genotype to phenotype mapping in each gene locus is controlled by a dominance probability, which is learned adaptively during the searching progress and hence is adapted to the dynamic environment. Using a series of dynamic test problems, the proposed dominance scheme is compared to two other dominance schemes for diploidy genetic algorithms. The experimental results validate the efficiency of the proposed dominance learning scheme

Exploring Task Mappings on Heterogeneous MPSoCs using a Bias-Elitist Genetic Algorithm

Exploration of task mappings plays a crucial role in achieving high performance in heterogeneous multi-processor system-on-chip (MPSoC) platforms. The problem of optimally mapping a set of tasks onto a set of given heterogeneous processors for maximal throughput has been known, in general, to be NP-complete. The problem is further exacerbated when multiple applications (i.e., bigger task sets) and the communication between tasks are also considered. Previous research has shown that Genetic Algorithms (GA) typically are a good choice to solve this problem when the solution space is relatively small. However, when the size of the problem space increases, classic genetic algorithms still suffer from the problem of long evolution times. To address this problem, this paper proposes a novel bias-elitist genetic algorithm that is guided by domain-specific heuristics to speed up the evolution process. Experimental results reveal that our proposed algorithm is able to handle large scale task mapping problems and produces high-quality mapping solutions in only a short time period.Comment: 9 pages, 11 figures, uses algorithm2e.st

Fuzzy C-Mean And Genetic Algorithms Based Scheduling For Independent Jobs In Computational Grid

The concept of Grid computing is becoming the most important research area in the high performance computing. Under this concept, the jobs scheduling in Grid computing has more complicated problems to discover a diversity of available resources, select the appropriate applications and map to suitable resources. However, the major problem is the optimal job scheduling, which Grid nodes need to allocate the appropriate resources for each job. In this paper, we combine Fuzzy C-Mean and Genetic Algorithms which are popular algorithms, the Grid can be used for scheduling. Our model presents the method of the jobs classifications based mainly on Fuzzy C-Mean algorithm and mapping the jobs to the appropriate resources based mainly on Genetic algorithm. In the experiments, we used the workload historical information and put it into our simulator. We get the better result when compared to the traditional algorithms for scheduling policies. Finally, the paper also discusses approach of the jobs classifications and the optimization engine in Grid scheduling

From Regular Expression Matching to Parsing

Given a regular expression $R$ and a string $Q$, the regular expression parsing problem is to determine if $Q$ matches $R$ and if so, determine how it matches, e.g., by a mapping of the characters of $Q$ to the characters in $R$. Regular expression parsing makes finding matches of a regular expression even more useful by allowing us to directly extract subpatterns of the match, e.g., for extracting IP-addresses from internet traffic analysis or extracting subparts of genomes from genetic data bases. We present a new general techniques for efficiently converting a large class of algorithms that determine if a string $Q$ matches regular expression $R$ into algorithms that can construct a corresponding mapping. As a consequence, we obtain the first efficient linear space solutions for regular expression parsing

Distributed gene clinical decision support system based on cloud computing

Background: The clinical decision support system can effectively break the limitations of doctors’ knowledge and reduce the possibility of misdiagnosis to enhance health care. The traditional genetic data storage and analysis methods based on stand-alone environment are hard to meet the computational requirements with the rapid genetic data growth for the limited scalability. Methods: In this paper, we propose a distributed gene clinical decision support system, which is named GCDSS. And a prototype is implemented based on cloud computing technology. At the same time, we present CloudBWA which is a novel distributed read mapping algorithm leveraging batch processing strategy to map reads on Apache Spark. Results: Experiments show that the distributed gene clinical decision support system GCDSS and the distributed read mapping algorithm CloudBWA have outstanding performance and excellent scalability. Compared with state-of-the-art distributed algorithms, CloudBWA achieves up to 2.63 times speedup over SparkBWA. Compared with stand-alone algorithms, CloudBWA with 16 cores achieves up to 11.59 times speedup over BWA-MEM with 1 core. Conclusions: GCDSS is a distributed gene clinical decision support system based on cloud computing techniques. In particular, we incorporated a distributed genetic data analysis pipeline framework in the proposed GCDSS system. To boost the data processing of GCDSS, we propose CloudBWA, which is a novel distributed read mapping algorithm to leverage batch processing technique in mapping stage using Apache Spark platform. Keywords: Clinical decision support system, Cloud computing, Spark, Alluxio, Genetic data analysis, Read mappin

USE OF HIDDEN MARKOV MODELS FOR QTL MAPPING

An important aspect of the QTL mapping problem is the treatment of missing genotype data. If complete genotype data were available, QTL mapping would reduce to the problem of model selection in linear regression. However, in the consideration of loci in the intervals between the available genetic markers, genotype data is inherently missing. Even at the typed genetic markers, genotype data is seldom complete, as a result of failures in the genotyping assays or for the sake of economy (for example, in the case of selective genotyping, where only individuals with extreme phenotypes are genotyped). We discuss the use of algorithms developed for hidden Markov models (HMMs) to deal with the missing genotype data problem

Genetic Algorithms Applied To The (\u27p\u27)-median Problem

This thesis is concerned with the application of genetic algorithms to solve the p-median problem. The problem finds a specified number of locations that are the most accessible among a fixed set of locations. Genetic algorithms are an adaptive search method based on models of mathematical population genetics. Basically, the algorithms simulate the evolution of a population in an environment, where selective pressure during evolution forces the population to improve. Modification to fit a particular environment is in a sense optimization. The extended analogy has the environment as the objective function of the p-median, the population as a set of solutions, and the optimal solution as creation after evolution.;This study describes the extant methodologies for solving the problem, and concludes that because they are either limited by computation time, or to small problems, methods with reliability and/or speed are needed.;The quantitative developments in population genetics are described together with the theory of natural selection. Artificial adaptive systems have used natural systems to confirm their models. Natural selection, or reproduction in proportion to measured performance, has been equated to optimization. The mechanisms of genetic algorithms are described as a stochastic process, where knowledge about the entire population is obtained through patterned sampling.;The implementation of a genetic algorithm to solve the p-median first requires a representation that is suitable for the genetic operators that simulate the reproduction of genetic material by recombining and mutation the existing material. A representation for this problem was designed and its operability proved in two algorithms. The two algorithms used in testing are given and the parameters adjusted during experimentation are reviewed.;The genetic algorithms required significant fine tuning and the invention of a new mutation operator for the p-median. Three methods of calculation the probability of selection were tested. Scaling of the objective functions prior to selection was a substantially superior method.;Several factors are thought to be responsible for the less than robust performance of the algorithm: The selective pressures may have been incorrectly specified via the probabilities of selection, and the mapping of solutions in the representation was prone to epistasis that was exacerbated by genetic drift and resulted in suboptimal solution. (Abstract shortened with permission of author.