CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2008 vol.5 Issue No.03 - July-September

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Issue No.03 - July-September (2008 vol.5)

pp: 368-384

George Lee , Rutgers University, Piscataway

Carlos Rodriguez , University of Puerto Rico, Mayagez

Anant Madabhushi , Rutgers University, Piscataway

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.36

ABSTRACT

The recent explosion in procurement and availability of high-dimensional gene- and protein-expression profile datasets for cancer diagnostics has necessitated the development of sophisticated machine learning tools with which to analyze them. A major limitation in the ability to accurate classify these high-dimensional datasets stems from the 'curse of dimensionality', occurring in situations where the number of genes or peptides significantly exceeds the total number of patient samples. Previous attempts at dealing with this issue have mostly centered on the use of a dimensionality reduction (DR) scheme, Principal Component Analysis (PCA), to obtain a low-dimensional projection of the high-dimensional data. However, linear PCA and other linear DR methods, which rely on Euclidean distances to estimate object similarity, do not account for the inherent underlying nonlinear structure associated with most biomedical data. The motivation behind this work is to identify the appropriate DR methods for analysis of high-dimensional gene- and protein-expression studies. Towards this end, we empirically and rigorously compare three nonlinear (Isomap, Locally Linear Embedding, Laplacian Eigenmaps) and three linear DR schemes (PCA, Linear Discriminant Analysis, Multidimensional Scaling) with the intent of determining a reduced subspace representation in which the individual object classes are more easily discriminable.

INDEX TERMS

Bioinformatics (genome or protein) databases, Clustering, classification, and association rules, Data and knowledge visualization, Data mining, Feature extraction or construction

CITATION

George Lee, Carlos Rodriguez, Anant Madabhushi, "Investigating the Efficacy of Nonlinear Dimensionality Reduction Schemes in Classifying Gene and Protein Expression Studies",

*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, vol.5, no. 3, pp. 368-384, July-September 2008, doi:10.1109/TCBB.2008.36REFERENCES