An investigation of K-means clustering to high and multi-dimensional biological data

• Published in: Kybernetes Vol. 42; no. 4; pp. 614 - 627
• Main Authors: Baridam, Barileé B., Montaz Ali, M.
• Format: Journal Article
• Language: English
• Published: London Emerald Group Publishing Limited 01.01.2013
• Subjects: Algorithms; Amino acids; Biological; Clustering; Clusters; Deoxyribonucleic acid; DNA; Genomics; Hydrogen bonds; Preprocessing; Studies; Tasks; Cluster analysis; Silhouette validity index; Dimensionality; Categorical data; Data management; Clustering; Bioinformatics; Programming and algorithm theory; Computational intelligence
• ISSN: 0368-492X; 1758-7883
• DOI: 10.1108/K-02-2013-0028

Purpose - The K-means clustering algorithm has been intensely researched owing to its simplicity of implementation and usefulness in the clustering task. However, there have also been criticisms on its performance, in particular, for demanding the value of K before the actual clustering task. It is evident from previous researches that providing the number of clusters a priori does not in any way assist in the production of good quality clusters. The authors' investigations in this paper also confirm this finding. The purpose of this paper is to investigate further, the usefulness of the K-means clustering in the clustering of high and multi-dimensional data by applying it to biological sequence data.Design methodology approach - The authors suggest a scheme which maps the high dimensional data into low dimensions, then show that the K-means algorithm with pre-processor produces good quality, compact and well-separated clusters of the biological data mapped in low dimensions. For the purpose of clustering, a character-to-numeric conversion was conducted to transform the nucleic amino acids symbols to numeric values.Findings - A preprocessing technique has been suggested.Originality value - Conceptually this is a new paper with new results.