Properties and algorithms of the (n, k)-star graphs

The (n, k)-star interconnection network was proposed in 1995 as an attractive alternative to the n-star topology in parallel computation. The (n, k )-star has significant advantages over the n-star which itself was proposed as an attractive alternative to the popular hypercube. The major advantage of the (n, k )-star network is its scalability, which makes it more flexible than the n-star as an interconnection network. In this thesis, we will focus on finding graph theoretical properties of the (n, k )-star as well as developing parallel algorithms that run on this network. The basic topological properties of the (n, k )-star are first studied. These are useful since they can be used to develop efficient algorithms on this network. We then study the (n, k )-star network from algorithmic point of view. Specifically, we will investigate both fundamental and application algorithms for basic communication, prefix computation, and sorting, etc. A literature review of the state-of-the-art in relation to the (n, k )-star network as well as some open problems in this area are also provided.

Properties and algorithms of the (n, k)-arrangement graphs

The (n, k)-arrangement interconnection topology was first introduced in 1992. The (n, k )-arrangement graph is a class of generalized star graphs. Compared with the well known n-star, the (n, k )-arrangement graph is more flexible in degree and diameter. However, there are few algorithms designed for the (n, k)-arrangement graph up to present. In this thesis, we will focus on finding graph theoretical properties of the (n, k)- arrangement graph and developing parallel algorithms that run on this network. The topological properties of the arrangement graph are first studied. They include the cyclic properties. We then study the problems of communication: broadcasting and routing. Embedding problems are also studied later on. These are very useful to develop efficient algorithms on this network. We then study the (n, k )-arrangement network from the algorithmic point of view. Specifically, we will investigate both fundamental and application algorithms such as prefix sums computation, sorting, merging and basic geometry computation: finding convex hull on the (n, k )-arrangement graph. A literature review of the state-of-the-art in relation to the (n, k)-arrangement network is also provided, as well as some open problems in this area.

Properties and Algorithms of the KCube Graphs

The KCube interconnection topology was rst introduced in 2010. The KCube graph is a compound graph of a Kautz digraph and hypercubes. Compared with the at- tractive Kautz digraph and well known hypercube graph, the KCube graph could accommodate as many nodes as possible for a given indegree (and outdegree) and the diameter of interconnection networks. However, there are few algorithms designed for the KCube graph. In this thesis, we will concentrate on nding graph theoretical properties of the KCube graph and designing parallel algorithms that run on this network. We will explore several topological properties, such as bipartiteness, Hamiltonianicity, and symmetry property. These properties for the KCube graph are very useful to develop efficient algorithms on this network. We will then study the KCube network from the algorithmic point of view, and will give an improved routing algorithm. In addition, we will present two optimal broadcasting algorithms. They are fundamental algorithms to many applications. A literature review of the state of the art network designs in relation to the KCube network as well as some open problems in this field will also be given.

Decoding algorithms using side-effect machines

Bioinformatics applies computers to problems in molecular biology. Previous research has not addressed edit metric decoders. Decoders for quaternary edit metric codes are finding use in bioinformatics problems with applications to DNA. By using side effect machines we hope to be able to provide efficient decoding algorithms for this open problem. Two ideas for decoding algorithms are presented and examined. Both decoders use Side Effect Machines(SEMs) which are generalizations of finite state automata. Single Classifier Machines(SCMs) use a single side effect machine to classify all words within a code. Locking Side Effect Machines(LSEMs) use multiple side effect machines to create a tree structure of subclassification. The goal is to examine these techniques and provide new decoders for existing codes. Presented are ideas for best practices for the creation of these two types of new edit metric decoders.

The use of explicit algorithms and episodic context to teach subtraction to students with learning problems in mathematics /

This research attempted to address the question of the role of explicit algorithms and episodic contexts in the acquisition of computational procedures for regrouping in subtraction. Three groups of students having difficulty learning to subtract with regrouping were taught procedures for doing so through either an explicit algorithm, an episodic content or an examples approach. It was hypothesized that the use of an explicit algorithm represented in a flow chart format would facilitate the acquisition and retention of specific procedural steps relative to the other two conditions. On the other hand, the use of paragraph stories to create episodic content was expected to facilitate the retrieval of algorithms, particularly in a mixed presentation format. The subjects were tested on similar, near, and far transfer questions over a four-day period. Near and far transfer algorithms were also introduced on Day Two. The results suggested that both explicit and episodic context facilitate performance on questions requiring subtraction with regrouping. However, the differential effects of these two approaches on near and far transfer questions were not as easy to identify. Explicit algorithms may facilitate the acquisition of specific procedural steps while at the same time inhibiting the application of such steps to transfer questions. Similarly, the value of episodic context in cuing the retrieval of an algorithm may be limited by the ability of a subject to identify and classify a new question as an exemplar of a particular episodically deflned problem type or category. The implications of these findings in relation to the procedures employed in the teaching of Mathematics to students with learning problems are discussed in detail.

Properties and algorithms of the hyper-star graph and its related graphs

The hyper-star interconnection network was proposed in 2002 to overcome the drawbacks of the hypercube and its variations concerning the network cost, which is defined by the product of the degree and the diameter. Some properties of the graph such as connectivity, symmetry properties, embedding properties have been studied by other researchers, routing and broadcasting algorithms have also been designed. This thesis studies the hyper-star graph from both the topological and algorithmic point of view. For the topological properties, we try to establish relationships between hyper-star graphs with other known graphs. We also give a formal equation for the surface area of the graph. Another topological property we are interested in is the Hamiltonicity problem of this graph. For the algorithms, we design an all-port broadcasting algorithm and a single-port neighbourhood broadcasting algorithm for the regular form of the hyper-star graphs. These algorithms are both optimal time-wise. Furthermore, we prove that the folded hyper-star, a variation of the hyper-star, to be maixmally fault-tolerant.

Quadtree representation and compression of spatial data

Spatial data representation and compression has become a focus issue in computer graphics and image processing applications. Quadtrees, as one of hierarchical data structures, basing on the principle of recursive decomposition of space, always offer a compact and efficient representation of an image. For a given image, the choice of quadtree root node plays an important role in its quadtree representation and final data compression. The goal of this thesis is to present a heuristic algorithm for finding a root node of a region quadtree, which is able to reduce the number of leaf nodes when compared with the standard quadtree decomposition. The empirical results indicate that, this proposed algorithm has quadtree representation and data compression improvement when in comparison with the traditional method.

Using genetic algorithms for the single allocation hub location problem

Hub location problem is an NP-hard problem that frequently arises in the design of transportation and distribution systems, postal delivery networks, and airline passenger flow. This work focuses on the Single Allocation Hub Location Problem (SAHLP). Genetic Algorithms (GAs) for the capacitated and uncapacitated variants of the SAHLP based on new chromosome representations and crossover operators are explored. The GAs is tested on two well-known sets of real-world problems with up to 200 nodes. The obtained results are very promising. For most of the test problems the GA obtains improved or best-known solutions and the computational time remains low. The proposed GAs can easily be extended to other variants of location problems arising in network design planning in transportation systems.

Comparison of classification ability of hyperball algorithms to neural network and k-nearest neighbour algorithms

The main focus of this thesis is to evaluate and compare Hyperbalilearning algorithm (HBL) to other learning algorithms. In this work HBL is compared to feed forward artificial neural networks using back propagation learning, K-nearest neighbor and 103 algorithms. In order to evaluate the similarity of these algorithms, we carried out three experiments using nine benchmark data sets from UCI machine learning repository. The first experiment compares HBL to other algorithms when sample size of dataset is changing. The second experiment compares HBL to other algorithms when dimensionality of data changes. The last experiment compares HBL to other algorithms according to the level of agreement to data target values. Our observations in general showed, considering classification accuracy as a measure, HBL is performing as good as most ANn variants. Additionally, we also deduced that HBL.:s classification accuracy outperforms 103's and K-nearest neighbour's for the selected data sets.

Improving Short DNA Sequence Alignment with Parallel Computing

Variations in different types of genomes have been found to be responsible for a large degree of physical diversity such as appearance and susceptibility to disease. Identification of genomic variations is difficult and can be facilitated through computational analysis of DNA sequences. Newly available technologies are able to sequence billions of DNA base pairs relatively quickly. These sequences can be used to identify variations within their specific genome but must be mapped to a reference sequence first. In order to align these sequences to a reference sequence, we require mapping algorithms that make use of approximate string matching and string indexing methods. To date, few mapping algorithms have been tailored to handle the massive amounts of output generated by newly available sequencing technologies. In otrder to handle this large amount of data, we modified the popular mapping software BWA to run in parallel using OpenMPI. Parallel BWA matches the efficiency of multithreaded BWA functions while providing efficient parallelism for BWA functions that do not currently support multithreading. Parallel BWA shows significant wall time speedup in comparison to multithreaded BWA on high-performance computing clusters, and will thus facilitate the analysis of genome sequencing data.

Heuristics for the Critical Node Detection Problem in Large Complex Networks

Complex networks have recently attracted a significant amount of research attention due to their ability to model real world phenomena. One important problem often encountered is to limit diffusive processes spread over the network, for example mitigating pandemic disease or computer virus spread. A number of problem formulations have been proposed that aim to solve such problems based on desired network characteristics, such as maintaining the largest network component after node removal. The recently formulated critical node detection problem aims to remove a small subset of vertices from the network such that the residual network has minimum pairwise connectivity. Unfortunately, the problem is NP-hard and also the number of constraints is cubic in number of vertices, making very large scale problems impossible to solve with traditional mathematical programming techniques. Even many approximation algorithm strategies such as dynamic programming, evolutionary algorithms, etc. all are unusable for networks that contain thousands to millions of vertices. A computationally efficient and simple approach is required in such circumstances, but none currently exist. In this thesis, such an algorithm is proposed. The methodology is based on a depth-first search traversal of the network, and a specially designed ranking function that considers information local to each vertex. Due to the variety of network structures, a number of characteristics must be taken into consideration and combined into a single rank that measures the utility of removing each vertex. Since removing a vertex in sequential fashion impacts the network structure, an efficient post-processing algorithm is also proposed to quickly re-rank vertices. Experiments on a range of common complex network models with varying number of vertices are considered, in addition to real world networks. The proposed algorithm, DFSH, is shown to be highly competitive and often outperforms existing strategies such as Google PageRank for minimizing pairwise connectivity.

Multi-Objective Genetic Algorithms for the Single Allocation Hub Location Problem

Hub Location Problems play vital economic roles in transportation and telecommunication networks where goods or people must be efficiently transferred from an origin to a destination point whilst direct origin-destination links are impractical. This work investigates the single allocation hub location problem, and proposes a genetic algorithm (GA) approach for it. The effectiveness of using a single-objective criterion measure for the problem is first explored. Next, a multi-objective GA employing various fitness evaluation strategies such as Pareto ranking, sum of ranks, and weighted sum strategies is presented. The effectiveness of the multi-objective GA is shown by comparison with an Integer Programming strategy, the only other multi-objective approach found in the literature for this problem. Lastly, two new crossover operators are proposed and an empirical study is done using small to large problem instances of the Civil Aeronautics Board (CAB) and Australian Post (AP) data sets.

Characterizing Dynamic Optimization Benchmarks for the Comparison of Multi-Modal Tracking Algorithms

Population-based metaheuristics, such as particle swarm optimization (PSO), have been employed to solve many real-world optimization problems. Although it is of- ten sufficient to find a single solution to these problems, there does exist those cases where identifying multiple, diverse solutions can be beneficial or even required. Some of these problems are further complicated by a change in their objective function over time. This type of optimization is referred to as dynamic, multi-modal optimization. Algorithms which exploit multiple optima in a search space are identified as niching algorithms. Although numerous dynamic, niching algorithms have been developed, their performance is often measured solely on their ability to find a single, global optimum. Furthermore, the comparisons often use synthetic benchmarks whose landscape characteristics are generally limited and unknown. This thesis provides a landscape analysis of the dynamic benchmark functions commonly developed for multi-modal optimization. The benchmark analysis results reveal that the mechanisms responsible for dynamism in the current dynamic bench- marks do not significantly affect landscape features, thus suggesting a lack of representation for problems whose landscape features vary over time. This analysis is used in a comparison of current niching algorithms to identify the effects that specific landscape features have on niching performance. Two performance metrics are proposed to measure both the scalability and accuracy of the niching algorithms. The algorithm comparison results demonstrate the algorithms best suited for a variety of dynamic environments. This comparison also examines each of the algorithms in terms of their niching behaviours and analyzing the range and trade-off between scalability and accuracy when tuning the algorithms respective parameters. These results contribute to the understanding of current niching techniques as well as the problem features that ultimately dictate their success.

Feature Selection and Classification Using Age Layered Population Structure Genetic Programming

The curse of dimensionality is a major problem in the fields of machine learning, data mining and knowledge discovery. Exhaustive search for the most optimal subset of relevant features from a high dimensional dataset is NP hard. Sub–optimal population based stochastic algorithms such as GP and GA are good choices for searching through large search spaces, and are usually more feasible than exhaustive and deterministic search algorithms. On the other hand, population based stochastic algorithms often suffer from premature convergence on mediocre sub–optimal solutions. The Age Layered Population Structure (ALPS) is a novel metaheuristic for overcoming the problem of premature convergence in evolutionary algorithms, and for improving search in the fitness landscape. The ALPS paradigm uses an age–measure to control breeding and competition between individuals in the population. This thesis uses a modification of the ALPS GP strategy called Feature Selection ALPS (FSALPS) for feature subset selection and classification of varied supervised learning tasks. FSALPS uses a novel frequency count system to rank features in the GP population based on evolved feature frequencies. The ranked features are translated into probabilities, which are used to control evolutionary processes such as terminal–symbol selection for the construction of GP trees/sub-trees. The FSALPS metaheuristic continuously refines the feature subset selection process whiles simultaneously evolving efficient classifiers through a non–converging evolutionary process that favors selection of features with high discrimination of class labels. We investigated and compared the performance of canonical GP, ALPS and FSALPS on high–dimensional benchmark classification datasets, including a hyperspectral image. Using Tukey’s HSD ANOVA test at a 95% confidence interval, ALPS and FSALPS dominated canonical GP in evolving smaller but efficient trees with less bloat expressions. FSALPS significantly outperformed canonical GP and ALPS and some reported feature selection strategies in related literature on dimensionality reduction.

Feature Selection and Classification Using Age Layered Population Structure Genetic Programming

The curse of dimensionality is a major problem in the fields of machine learning, data mining and knowledge discovery. Exhaustive search for the most optimal subset of relevant features from a high dimensional dataset is NP hard. Sub–optimal population based stochastic algorithms such as GP and GA are good choices for searching through large search spaces, and are usually more feasible than exhaustive and determinis- tic search algorithms. On the other hand, population based stochastic algorithms often suffer from premature convergence on mediocre sub–optimal solutions. The Age Layered Population Structure (ALPS) is a novel meta–heuristic for overcoming the problem of premature convergence in evolutionary algorithms, and for improving search in the fitness landscape. The ALPS paradigm uses an age–measure to control breeding and competition between individuals in the population. This thesis uses a modification of the ALPS GP strategy called Feature Selection ALPS (FSALPS) for feature subset selection and classification of varied supervised learning tasks. FSALPS uses a novel frequency count system to rank features in the GP population based on evolved feature frequencies. The ranked features are translated into probabilities, which are used to control evolutionary processes such as terminal–symbol selection for the construction of GP trees/sub-trees. The FSALPS meta–heuristic continuously refines the feature subset selection process whiles simultaneously evolving efficient classifiers through a non–converging evolutionary process that favors selection of features with high discrimination of class labels. We investigated and compared the performance of canonical GP, ALPS and FSALPS on high–dimensional benchmark classification datasets, including a hyperspectral image. Using Tukey’s HSD ANOVA test at a 95% confidence interval, ALPS and FSALPS dominated canonical GP in evolving smaller but efficient trees with less bloat expressions. FSALPS significantly outperformed canonical GP and ALPS and some reported feature selection strategies in related literature on dimensionality reduction.