We present a technique for clustering categorical data by generating many dissimilarity matrices and averaging over them. We begin by demonstrating our technique on low dimensional categorical data and comparing it to several other techniques that have been proposed. Then we give conditions under which our method should yield good results in general. Our method extends to high dimensional categorical data of equal lengths by ensembling over many choices of explanatory variables. In this context we compare our method with two other methods. Finally, we extend our method to high dimensional categorical data vectors of unequal length by using alignment techniques to equalize the lengths. We give examples to show that our method continues to provide good results, in particular, better in the context of genome sequences than clusterings suggested by phylogenetic trees.
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