A hybrid algorithm for k-medoid clustering of large data sets

In this paper, we propose a novel local search heuristic and then hybridize it with a genetic algorithm for k-medoid clustering of large data sets, which is an NP-hard optimization problem. The local search heuristic selects k-medoids from the data set and tries to efficiently minimize the total dissimilarity within each cluster. In order to deal with the local optimality, the local search heuristic is hybridized with a genetic algorithm and then the Hybrid K-medoid Algorithm (HKA) is proposed. Our experiments show that, compared with previous genetic algorithm based k-medoid clustering approaches - GCA and RAR/sub w/GA, HKA can provide better clustering solutions and do so more efficiently. Experiments use two gene expression data sets, which may involve large noise components

Hard and soft clustering of categorical time series based on two novel distances with an application to biological sequences

Financiado para publicación en acceso aberto: Universidade da Coruña/CISUG.[Abstract]: Two novel distances between categorical time series are introduced. Both of them measure discrepancies between extracted features describing the underlying serial dependence patterns. One distance is based on well-known association measures, namely Cramer's v and Cohen's κ. The other one relies on the so-called binarization of a categorical process, which indicates the presence of each category by means of a canonical vector. Binarization is used to construct a set of innovative association measures which allow to identify different types of serial dependence. The metrics are used to perform crisp and fuzzy clustering of nominal series. The proposed approaches are able to group together series generated from similar stochastic processes, achieve accurate results with series coming from a broad range of models and are computationally efficient. Extensive simulation studies show that both hard and soft clustering algorithms outperform several alternative procedures proposed in the literature. Two applications involving biological sequences from different species highlight the usefulness of the introduced techniques.Xunta de Galicia; ED431G 2019/01Xunta de Galicia; ED431C-2020-14The research of Ángel López-Oriona and José A. Vilar has been supported by the Ministerio de Economía y Competitividad (MINECO) grants MTM2017-82724-R and PID2020-113578RB-100, the Xunta de Galicia (Grupos de Referencia Competitiva ED431C-2020-14), and the Centro de Investigación del Sistema Universitario de Galicia “CITIC” grant ED431G 2019/01; all of them through the European Regional Development Fund (ERDF). This work has received funding for open access charge by Universidade da Coruña/CISUG. The author Ángel López-Oriona is very grateful to researcher Maite Freire for her lessons about DNA theory

An analytics-based heuristic decomposition of a bilevel multiple-follower cutting stock problem

This paper presents a new class of multiple-follower bilevel problems and a heuristic approach to solving them. In this new class of problems, the followers may be nonlinear, do not share constraints or variables, and are at most weakly constrained. This allows the leader variables to be partitioned among the followers. We show that current approaches for solving multiple-follower problems are unsuitable for our new class of problems and instead we propose a novel analytics-based heuristic decomposition approach. This approach uses Monte Carlo simulation and k-medoids clustering to reduce the bilevel problem to a single level, which can then be solved using integer programming techniques. The examples presented show that our approach produces better solutions and scales up better than the other approaches in the literature. Furthermore, for large problems, we combine our approach with the use of self-organising maps in place of k-medoids clustering, which significantly reduces the clustering times. Finally, we apply our approach to a real-life cutting stock problem. Here a forest harvesting problem is reformulated as a multiple-follower bilevel problem and solved using our approachThis publication has emanated from research conducted with the financial support of Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/228

A Comprehensive Empirical Investigation on Failure Clustering in Parallel Debugging

The clustering technique has attracted a lot of attention as a promising strategy for parallel debugging in multi-fault scenarios, this heuristic approach (i.e., failure indexing or fault isolation) enables developers to perform multiple debugging tasks simultaneously through dividing failed test cases into several disjoint groups. When using statement ranking representation to model failures for better clustering, several factors influence clustering effectiveness, including the risk evaluation formula (REF), the number of faults (NOF), the fault type (FT), and the number of successful test cases paired with one individual failed test case (NSP1F). In this paper, we present the first comprehensive empirical study of how these four factors influence clustering effectiveness. We conduct extensive controlled experiments on 1060 faulty versions of 228 simulated faults and 141 real faults, and the results reveal that: 1) GP19 is highly competitive across all REFs, 2) clustering effectiveness decreases as NOF increases, 3) higher clustering effectiveness is easier to achieve when a program contains only predicate faults, and 4) clustering effectiveness remains when the scale of NSP1F is reduced to 20%

Multi-objective evolutionary algorithms for data clustering

In this work we investigate the use of Multi-Objective metaheuristics for the data-mining task of clustering. We �first investigate methods of evaluating the quality of clustering solutions, we then propose a new Multi-Objective clustering algorithm driven by multiple measures of cluster quality and then perform investigations into the performance of different Multi-Objective clustering algorithms. In the context of clustering, a robust measure for evaluating clustering solutions is an important component of an algorithm. These Cluster Quality Measures (CQMs) should rely solely on the structure of the clustering solution. A robust CQM should have three properties: it should be able to reward a \good" clustering solution; it should decrease in value monotonically as the solution quality deteriorates and, it should be able to evaluate clustering solutions with varying numbers of clusters. We review existing CQMs and present an experimental evaluation of their robustness. We find that measures based on connectivity are more robust than other measures for cluster evaluation. We then introduce a new Multi-Objective Clustering algorithm (MOCA). The use of Multi-Objective optimisation in clustering is desirable because it permits the incorporation of multiple measures of cluster quality. Since the definition of what constitutes a good clustering is far from clear, it is beneficial to develop algorithms that allow for multiple CQMs to be accommodated. The selection of the clustering quality measures to use as objectives for MOCA is informed by our previous work with internal evaluation measures. We explain the implementation details and perform experimental work to establish its worth. We compare MOCA with k-means and find some promising results. We�find that MOCA can generate a pool of clustering solutions that is more likely to contain the optimal clustering solution than the pool of solutions generated by k-means. We also perform an investigation into the performance of different implementations of MOEA algorithms for clustering. We�find that representations of clustering based around centroids and medoids produce more desirable clustering solutions and Pareto fronts. We also �find that mutation operators that greatly disrupt the clustering solutions lead to better exploration of the Pareto front whereas mutation operators that modify the clustering solutions in a more moderate way lead to higher quality clustering solutions. We then perform more specific investigations into the performance of mutation operators focussing on operators that promote clustering solution quality, exploration of the Pareto front and a hybrid combination. We use a number of techniques to assess the performance of the mutation operators as the algorithms execute. We confirm that a disruptive mutation operator leads to better exploration of the Pareto front and mutation operators that modify the clustering solutions lead to the discovery of higher quality clustering solutions. We find that our implementation of a hybrid mutation operator does not lead to a good improvement with respect to the other mutation operators but does show promise for future work

Model-based clustering of array CGH data

Motivation: Analysis of array comparative genomic hybridization (aCGH) data for recurrent DNA copy number alterations from a cohort of patients can yield distinct sets of molecular signatures or profiles. This can be due to the presence of heterogeneous cancer subtypes within a supposedly homogeneous population

Multiobjective Particle Swarm Optimization Based on PAM and Uniform Design

In MOPSO (multiobjective particle swarm optimization), to maintain or increase the diversity of the swarm and help an algorithm to jump out of the local optimal solution, PAM (Partitioning Around Medoid) clustering algorithm and uniform design are respectively introduced to maintain the diversity of Pareto optimal solutions and the uniformity of the selected Pareto optimal solutions. In this paper, a novel algorithm, the multiobjective particle swarm optimization based on PAM and uniform design, is proposed. The differences between the proposed algorithm and the others lie in that PAM and uniform design are firstly introduced to MOPSO. The experimental results performing on several test problems illustrate that the proposed algorithm is efficient

Ensemble clustering via heuristic optimisation

This thesis was submitted for the degree of Doctor of Philosophy and was awarded by Brunel UniversityTraditional clustering algorithms have different criteria and biases, and there is no single algorithm that can be the best solution for a wide range of data sets. This problem often presents a significant obstacle to analysts in revealing meaningful information buried among the huge amount of data. Ensemble Clustering has been proposed as a way to avoid the biases and improve the accuracy of clustering. The difficulty in developing Ensemble Clustering methods is to combine external information (provided by input clusterings) with internal information (i.e. characteristics of given data) effectively to improve the accuracy of clustering. The work presented in this thesis focuses on enhancing the clustering accuracy of Ensemble Clustering by employing heuristic optimisation techniques to achieve a robust combination of relevant information during the consensus clustering stage. Two novel heuristic optimisation-based Ensemble Clustering methods, Multi-Optimisation Consensus Clustering (MOCC) and K-Ants Consensus Clustering (KACC), are developed and introduced in this thesis. These methods utilise two heuristic optimisation algorithms (Simulated Annealing and Ant Colony Optimisation) for their Ensemble Clustering frameworks, and have been proved to outperform other methods in the area. The extensive experimental results, together with a detailed analysis, will be presented in this thesis