Abstract
We present the use of KICA to perform clustering of gene expression data. Comparison experiments between KICA and two other methods, PCA and ICA, are performed. Three clustering algorithms, including weighted graph partitioning, k-means and agglomerative hierarchical clustering, and two similarity measures, including Euclidean and Pearson correlation, are also evaluated. The results indicate that KICA is an efficient feature extraction approach for gene expression data clustering. Our empirical study showed that clustering with the components instead of the original variables does improve cluster quality. In particular, the first few components by KICA capture most of the cluster structure. We also showed that clustering with components has different impact on different algorithms and different similarity metrics. Overall, we would recommend KICA before clustering gene expression data.
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Jin, X., Xu, A., Bie, R., Guo, P. (2006). Kernel Independent Component Analysis for Gene Expression Data Clustering. In: Rosca, J., Erdogmus, D., Príncipe, J.C., Haykin, S. (eds) Independent Component Analysis and Blind Signal Separation. ICA 2006. Lecture Notes in Computer Science, vol 3889. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11679363_57
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DOI: https://doi.org/10.1007/11679363_57
Publisher Name: Springer, Berlin, Heidelberg
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