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Cilibrasi, Rudi ; Vitany, Paul M. B.

A New Quartet Tree Heuristic for Hierarchical Clustering

06061.VitanyiPaulB.Paper.598.pdf (0.2 MB)


We present a new quartet heuristic for hierarchical clustering from a given distance matrix. We determine a dendrogram (ternary tree) by a new quartet method and a fast heuristic to implement it. We do not assume that there is a true ternary tree that generated the distances and which we with to recover as closeley as possible. Our aim is to model the distance matrix as faithfully as possible by the dendrogram. Our algorithm is essentially randomized hill-climbing, using parallellized Genetic Programming, where undirected trees evolve in a random walk driven by a prescribed fitness function. Our method is capable of handling up to 60--80 objects in a matter of hours, while no existing quartet heuristic can directly compute a quartet tree of more than about 20--30 objects without running for years. The method is implemented and available as public software at We present applications in many areas like music, literature, bird-flu (H5N1) virus clustering, and automatic meaning discovery using Google.

BibTeX - Entry

  author =	{Rudi Cilibrasi and Paul M. B. Vitany},
  title =	{A New Quartet Tree Heuristic for Hierarchical Clustering},
  booktitle =	{Theory of Evolutionary Algorithms},
  year =	{2006},
  editor =	{Dirk V. Arnold and Thomas Jansen and Michael D. Vose and Jonathan E. Rowe},
  number =	{06061},
  series =	{Dagstuhl Seminar Proceedings},
  ISSN =	{1862-4405},
  publisher =	{Internationales Begegnungs- und Forschungszentrum f{\"u}r Informatik (IBFI), Schloss Dagstuhl, Germany},
  address =	{Dagstuhl, Germany},
  URL =		{},
  annote =	{Keywords: Genetic programming, hierarchical clustering, quartet tree method}

Keywords: Genetic programming, hierarchical clustering, quartet tree method
Seminar: 06061 - Theory of Evolutionary Algorithms
Issue Date: 2006
Date of publication: 07.07.2006

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