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Issue No.06 - November/December (2011 vol.8)
pp: 1522-1534
Jung Hun Oh , University of Texas at Arlington, Arlington, TX
Jean Gao , The University of Texas at Arlington, Arlington, TX
ABSTRACT
The classification of serum samples based on mass spectrometry (MS) has been increasingly used for monitoring disease progression and for diagnosing early disease. However, the classification task in mass spectrometry data is extremely challenging due to the very huge size of peaks (features) on mass spectra. Linear discriminant analysis (LDA) has been widely used for dimension reduction and feature extraction in many applications. However, the conversional LDA suffers from the singularity problem when dealing with high-dimensional features. Another critical limitation is its linearity property which results in failing in classification problems over nonlinearly clustered data sets. To overcome such problems, we develop a new fast kernel discriminant analysis (FKDA) that is pretty fast in the calculation of optimal discriminant vectors. FKDA is applied to the classification of liver cancer mass spectrometry data that consist of three categories: hepatocellular carcinoma, cirrhosis, and healthy that was originally analyzed by Ressom et al. [CHECK END OF SENTENCE]. We demonstrate the superiority and effectiveness of FKDA when compared to other classification techniques.
INDEX TERMS
FKDA, LDA, hepatocellular carcinoma, cirrhosis, classification, singularity.
CITATION
Jung Hun Oh, Jean Gao, "Fast Kernel Discriminant Analysis for Classification of Liver Cancer Mass Spectra", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, no. 6, pp. 1522-1534, November/December 2011, doi:10.1109/TCBB.2010.42
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