Accelerating high-dimensional clustering with lossless data reduction

Bioinformatics
Bahjat F QaqishKatie J Clowers

Abstract

For cluster analysis, high-dimensional data are associated with instability, decreased classification accuracy and high-computational burden. The latter challenge can be eliminated as a serious concern. For applications where dimension reduction techniques are not implemented, we propose a temporary transformation which accelerates computations with no loss of information. The algorithm can be applied for any statistical procedure depending only on Euclidean distances and can be implemented sequentially to enable analyses of data that would otherwise exceed memory limitations. The method is easily implemented in common statistical software as a standard pre-processing step. The benefit of our algorithm grows with the dimensionality of the problem and the complexity of the analysis. Consequently, our simple algorithm not only decreases the computation time for routine analyses, it opens the door to performing calculations that may have otherwise been too burdensome to attempt. R, Matlab and SAS/IML code for implementing lossless data reduction is freely available in the Appendix. obrienj@hms.harvard.edu.

References

Oct 9, 2001·Bioinformatics·K Y Yeung, W L Ruzzo
Aug 20, 2002·Genome Biology·Sandrine Dudoit, Jane Fridlyand
Jan 21, 2006·The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences·J Christopher Corton, Holly M Brown-Borg
Aug 3, 2006·Bioinformatics·Anbupalam ThalamuthuGeorge C Tseng
Mar 11, 2008·Nature Biotechnology·Markus Ringnér
Apr 9, 2008·BMC Bioinformatics·Jengnan TzengWen-Hsiung Li
Apr 30, 2010·Bioinformatics·Matthew D Wilkerson, D Neil Hayes
Sep 25, 2012·Nature·UNKNOWN Cancer Genome Atlas Network

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