Biomedical subjects

Stephen Swift

Publications and source records attributed to Stephen Swift.

4 recordsLinked to original sources

PubMed2005

A Weighted Sum Validity Function for clustering with a Hybrid Niching Genetic Algorithm.

Clustering is inherently a difficult problem, both with respect to the construction of adequate objective functions as well as to the optimization of the objective functions. In this paper, we suggest an objective function called the Weighted Sum Validity Function (WSVF), which is a weighted sum of the several normalized cluster validity functions. Further, we propose a Hybrid Niching Genetic Algorithm (HNGA), which can be used for the optimization of the WSVF to automatically evolve the proper number of clusters as well as appropriate partitioning of the data set. Within the HNGA, a niching method is developed to preserve both the diversity of the population with respect to the number of clusters encoded in the individuals and the diversity of the subpopulation with the same number of clusters during the search. In addition, we hybridize the niching method with the k-means algorithm. In the experiments, we show the effectiveness of both the HNGA and the WSVF. In comparison with other related genetic clustering algorithms, the HNGA can consistently and efficiently converge to the best known optimum corresponding to the given data in concurrence with the convergence result. The WSVF is found generally able to improve the confidence of clustering solutions and achieve more accurate and robust results.

Algorithms↗

PubMed2005

RGFGA: an efficient representation and crossover for grouping genetic algorithms.

There is substantial research into genetic algorithms that are used to group large numbers of objects into mutually exclusive subsets based upon some fitness function. However, nearly all methods involve degeneracy to some degree. We introduce a new representation for grouping genetic algorithms, the restricted growth function genetic algorithm, that effectively removes all degeneracy, resulting in a more efficient search. A new crossover operator is also described that exploits a measure of similarity between chromosomes in a population. Using several synthetic datasets, we compare the performance of our representation and crossover with another well known state-of-the-art GA method, a strawman optimisation method and a well-established statistical clustering algorithm, with encouraging results.

Algorithms↗

PubMed2004

Consensus clustering and functional interpretation of gene-expression data.

Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus clustering, which provides such an advantage. When coupled with a statistically based gene functional analysis, our method allowed the identification of novel genes regulated by NFkappaB and the unfolded protein response in certain B-cell lymphomas.

Cluster Analysis↗

PubMed2002

Predicting glaucomatous visual field deterioration through short multivariate time series modelling.

In bio-medical domains there are many applications involving the modelling of multivariate time series (MTS) data. One area that has been largely overlooked so far is the particular type of time series where the dataset consists of a large number of variables but with a small number of observations. In this paper, we describe the development of a novel computational method based on genetic algorithms that bypasses the size restrictions of traditional statistical MTS methods, makes no distribution assumptions, and also locates the order and associated parameters as a whole step. We apply this method to the prediction and modelling of glaucomatous visual field deterioration.

Algorithms↗