Clustering of Cancer Tissues Using Diffusion Maps and Fuzzy ART with Gene Expression Data

Rui Xu, Missouri University of Science and Technology
Steven Damelin
Donald C. Wunsch, Missouri University of Science and Technology

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Early detection of a tumor's site of origin is particularly important for cancer diagnosis and treatment. The employment of gene expression profiles for different cancer types or subtypes has already shown significant advantages over traditional cancer classification methods. Here, we apply a neural network clustering theory, Fuzzy ART, to generate the division of cancer samples, which is useful in investigating unknown cancer types or subtypes. On the other hand, we use diffusion maps, which interpret the eigenfunctions of Markov matrices as a system of coordinates on the original data set in order to obtain efficient representation of data geometric descriptions, for dimensionality reduction. The curse of dimensionality is a major problem in cancer type recognition-oriented gene expression data analysis due to the overwhelming number of measures of gene expression levels versus the small number of samples. Experimental results on the small round blue-cell tumor (SRBCT) data set, compared with other widely used clustering algorithms, demonstrate the effectiveness of our proposed method in addressing multidimensional gene expression data.