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Bioinformatics Vol. 17 no. 90001 2001
Pages S22-S29
© 2001 Oxford University Press

Fast optimal leaf ordering for hierarchical clustering

Ziv Bar-Joseph 1, David K. Gifford 1,2 and Tommi S. Jaakkola 2

1 Laboratory for Computer Science, MIT, 545 Technology Square, Cambridge, MA, 02139, USA
2 Artificial Intelligence Laboratory, MIT, 545 Technology Square, Cambridge, MA, 02139, USA

Received on February 5, 2001 ; revised on March 26, 2001 ; accepted on March 26, 2001

We present the first practical algorithm for the optimal linear leaf ordering of trees that are generated by hierarchical clustering. Hierarchical clustering has been extensively used to analyze gene expression data, and we show how optimal leaf ordering can reveal biological structure that is not observed with an existing heuristic ordering method. For a tree with n leaves, there are 2n-1 linear orderings consistent with the structure of the tree. Our optimal leaf ordering algorithm runs in time O(n4), and we present further improvements that make the running time of our algorithm practical.

Contact: {zivbj,gifford}@mit.edu; tommi{at}ai.mit.edu


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