Multidimensional partitioning and bi-partitioning: analysis and application to gene expression data sets

Abstract

Eigenvectors and, more generally, singular vectors, have proved to be useful tools for data mining and dimension reduction. Spectral clustering and reordering algorithms have been designed and implemented in many disciplines, and they can be motivated from several different standpoints. Here we give a general, unified derivation from an applied linear algebra perspective. We use a variational approach that has the benefit of (a) naturally introducing an appropriate scaling, (b) allowing for a solution in any desired dimension, and (c) dealing with both the clustering and bi-clustering issues in the same framework. The motivation and analysis is then backed up with examples involving two large data sets from modern, high-throughput, experimental cell biology. Here, the objects of interest are genes and tissue samples, and the experimental data represents gene activity. We show that looking beyond the dominant, or Fiedler, direction reveals important information.

Keywords:

• Data mining dimension reduction
• Graph Laplacian
• Microarray
• Singular value decomposition
• Tumour classification

Acknowledgements

This work was supported by EPSRC grant GR/S62383/01.