Skip to main content

Split-Order Distance for Clustering and Classification Hierarchies

  • Conference paper
Scientific and Statistical Database Management (SSDBM 2009)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 5566))

Abstract

Clustering and classification hierarchies are organizational structures of a set of objects. Multiple hierarchies may be derived over the same set of objects, which makes distance computation between hierarchies an important task. In this paper, we model the classification and clustering hierarchies as rooted, leaf-labeled, unordered trees. We propose a novel distance metric Split-Order distance to evaluate the organizational structure difference between two hierarchies over the same set of leaf objects. Split-Order distance reflects the order in which subsets of the tree leaves are differentiated from each other and can be used to explain the relationships between the leaf objects. We also propose an efficient algorithm for computing Split-Order distance between two trees in O(n 2 d 4) time, where n is the number of leaves, and d is the maximum number of children of any node. Our experiments on both real and synthetic data demonstrate the efficiency and effectiveness of our algorithm.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Allen, B.L., Steel, M.: Subtree transfer operations and their induced metrics on evolutionary trees. Annals of Combinatorics 5, 1–13 (2001)

    Article  MathSciNet  MATH  Google Scholar 

  2. Amir, A., Keselman, D.: Maximum agreement subtree in a set of evolutionary trees: metrics and efficient algorithms. Proc. of the SIAM Journal on Computing 26(6), 1656–1669 (1997)

    Article  MathSciNet  MATH  Google Scholar 

  3. Bille, P.: A survey on tree edit distance and related problems. Theoretical Computer Science, 217–239 (2005)

    Google Scholar 

  4. Demaine, E.D., Mozes, S., Rossman, B., Weimann, O.: An Optimal Decomposition Algorithm for Tree Edit Distance. In: Arge, L., Cachin, C., Jurdziński, T., Tarlecki, A. (eds.) ICALP 2007. LNCS, vol. 4596, pp. 146–157. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  5. Eastabrook, G.F., McMorris, F.R., Meacham, C.A.: Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Syst. Zool (1985)

    Google Scholar 

  6. Felsenstein, J.: Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27, 401–410 (1978)

    Article  Google Scholar 

  7. Iyer, V.R., Eisen, M.B., Ross, D.T., Schuler, G., Moore, T., Lee, J.C., Trent, J.M., Staudt, L.M., Hudson Jr., J., Boguski, M.S., Lashkari, D., Shalon, D., Botstein, D., Brown, P.O.: Transcriptional program in the response of human fibroblasts to serum. Science 283, 83–87 (1996)

    Article  Google Scholar 

  8. Jiang, D., Pei, J., Zhang, A.: DHC: a density-based hierarchical clustering method for time series gene expression data. In: Proc. of the The Third Symposium on Bioinformatics and Bioengineering, pp. 393–400 (2003)

    Google Scholar 

  9. Karypis, G.: CLUTO - A Clustering Toolkit. Tech Report, Dept. of Computer Science, University of Minnesota (2002)

    Google Scholar 

  10. Klein, P.N.: Computing the edit-distance between unrooted ordered trees. In: Bilardi, G., Pietracaprina, A., Italiano, G.F., Pucci, G. (eds.) ESA 1998. LNCS, vol. 1461, p. 91. Springer, Heidelberg (1998)

    Google Scholar 

  11. Lu, S.Y.: A tree-to-tree distance and its application to cluster analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI) (1979)

    Google Scholar 

  12. Robinson, D.F., Foulds, L.R.: Comparison of weighted labeled trees. Combinatorial mathematics VI, 119–126 (1979)

    MATH  Google Scholar 

  13. Robinson, D.F., Foulds, L.: Comparison of phylogenetic trees. Math. Biosci. 53(1-2), 131–147 (1981)

    Article  MathSciNet  MATH  Google Scholar 

  14. Saitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. The Mol. Biol. Evol. 4(4), 406–425 (1987)

    Google Scholar 

  15. Shasha, D., Wang, J.T.L., Zhang, S.: Unordered Tree Mining with Applications to Phylogeny. In: Proc. IEEE International Conference on Data Engineering (ICDE 2004) (2004)

    Google Scholar 

  16. Sneath, P.H.A., Sokal, R.R.: Numerical Taxonomy, pp. 230–234. WH Freeman and Company, New York (1973)

    MATH  Google Scholar 

  17. Touzet, H.: Tree edit distance with gaps. Information Processing Letters 85(3), 123–129 (2003)

    Article  MathSciNet  MATH  Google Scholar 

  18. Wang, J.T., Zhang, K., Jeong, K., Shasha, D.: A system for approximate tree matching. IEEE Transactions on Knowledge and Data Engineering 6(4), 559–571 (1994)

    Article  Google Scholar 

  19. Eastabrook, G.F., McMorris, F.R., Meacham, C.A.: TreeRank: A similarity measure for nearest neighbor searching in phylogenetic databases. In: Proc. of the 15th International Conference on Scientific and Statistical Database Management (1985)

    Google Scholar 

  20. Waterman, M.S., Smith, T.F.: On the similarity of dendrograms. Journal of Theoretical Biology 73, 789–800 (1978)

    Article  MathSciNet  Google Scholar 

  21. Zhang, K., Shasha, D.: Simple fast algorithms for the editing distance between trees and related problems. SIAM Journal of Computing (1989)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Zhang, Q., Liu, E.Y., Sarkar, A., Wang, W. (2009). Split-Order Distance for Clustering and Classification Hierarchies. In: Winslett, M. (eds) Scientific and Statistical Database Management. SSDBM 2009. Lecture Notes in Computer Science, vol 5566. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02279-1_37

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-02279-1_37

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02278-4

  • Online ISBN: 978-3-642-02279-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics