A New Quartet Tree Heuristic for Hierarchical Clustering

Authors Rudi Cilibrasi, Paul M. B. Vitany

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Rudi Cilibrasi
Paul M. B. Vitany

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Rudi Cilibrasi and Paul M. B. Vitany. A New Quartet Tree Heuristic for Hierarchical Clustering. In Theory of Evolutionary Algorithms. Dagstuhl Seminar Proceedings, Volume 6061, pp. 1-13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)


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 www.complearn.org. We present applications in many areas like music, literature, bird-flu (H5N1) virus clustering, and automatic meaning discovery using Google.
  • Genetic programming
  • hierarchical clustering
  • quartet tree method


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