Fuzzy-Rough Supervised Attribute Clustering Algorithm and Classification of Microarray Data

• Published in: IEEE transactions on systems, man and cybernetics. Part B, Cybernetics Vol. 41; no. 1; pp. 222 - 233
• Main Author: Maji, Pradipta
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.02.2011
• Subjects: Accuracy; Algorithms; Arthritis; Artificial Intelligence; Attribute clustering; Bayes Theorem; Cancer; Categories; Classification; Classification algorithms; Cluster Analysis; Clustering; Clustering algorithms; Clustering methods; Computational Biology - methods; Cybernetics; Databases, Genetic; Female; Fuzzy Logic; Gene expression; gene selection; Genes; Humans; Male; microarray analysis; Neoplasms; Oligonucleotide Array Sequence Analysis; Redundancy; rough sets; Similarity; Support vector machine classification; Support vector machines; Tasks
• ISSN: 1083-4419; 1941-0492; 1941-0492
• DOI: 10.1109/TSMCB.2010.2050684

One of the major tasks with gene expression data is to find groups of coregulated genes whose collective expression is strongly associated with sample categories. In this regard, a new clustering algorithm, termed as fuzzy-rough supervised attribute clustering (FRSAC), is proposed to find such groups of genes. The proposed algorithm is based on the theory of fuzzy-rough sets, which directly incorporates the information of sample categories into the gene clustering process. A new quantitative measure is introduced based on fuzzy-rough sets that incorporates the information of sample categories to measure the similarity among genes. The proposed algorithm is based on measuring the similarity between genes using the new quantitative measure, whereby redundancy among the genes is removed. The clusters are refined incrementally based on sample categories. The effectiveness of the proposed FRSAC algorithm, along with a comparison with existing supervised and unsupervised gene selection and clustering algorithms, is demonstrated on six cancer and two arthritis data sets based on the class separability index and predictive accuracy of the naive Bayes' classifier, the K-nearest neighbor rule, and the support vector machine.