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A Metric Index for Approximate String Matching

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LATIN 2002: Theoretical Informatics (LATIN 2002)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2286))

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Abstract

We present a radically new indexing approach for approximate string matching. The scheme uses the metric properties of the edit distance and can be applied to any other metric between strings. We build a metric space where the sites are the nodes of the suffix tree of the text, and the approximate query is seen as a proximity query on that metric space. This permits us finding the R occurrences of a pattern of length m in a text of length n in average time O(mlog2 n+m 2+R), using O(n log n) space and O(n log2 n) index construction time. This complexity improves by far over all other previous methods. We also show a simpler scheme needing O(n) space.

Supported by CYTED VII.19 RIBIDI project (both authors), CONACyT grant 36911 (first author), and Fondecyt grant 1-000929 (second author).

On leave of absence at Universidad de Chile.

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References

  1. A. Apostolico. The myriad virtues of subword trees. In Combinatorial Algorithms on Words, NATO ISI Series, pages 85–96. Springer-Verlag, 1985.

    Google Scholar 

  2. A. Apostolico and Z. Galil. Combinatorial Algorithms on Words. Springer-Verlag, New York, 1985.

    Book  Google Scholar 

  3. R. Baeza-Yates and G. Navarro. Block-addressing indices for approximate text retrieval. In Proc. ACM CIKM’97, pages 1–8, 1997.

    Google Scholar 

  4. R. Baeza-Yates and G. Navarro. Fast approximate string matching in a dictionary. In Proc. SPIRE’98, pages 14–22. IEEE Computer Press, 1998.

    Google Scholar 

  5. R. Baeza-Yates and G. Navarro. A practical q-gram index for text retrieval allowing errors. CLEI Electronic Journal, 1(2), 1998. http://www.clei.cl.

  6. R. Baeza-Yates and G. Navarro. A hybrid indexing method for approximate string matching. J. of Discrete Algorithms (JDA), 1(1):205–239, 2000. Special issue on Matching Patterns.

    MathSciNet  Google Scholar 

  7. N. Beckmann, H. Kriegel, R. Schneider, and B. Seeger. The R*-tree: an efficient and robust access method for points and rectangles. In Proc. ACM SIGMOD’90, pages 322–331, 1990.

    Article  Google Scholar 

  8. E. Bugnion, T. Roos, F. Shi, P. Widmayer, and F. Widmer. Approximate multiple string matching using spatial indexes. In Proc. 1st South American Workshop on String Processing (WSP’93), pages 43–54, 1993.

    Google Scholar 

  9. E. Chávez and G. Navarro. An effective clustering algorithm to index high dimensional metric spaces. In Proc. SPIRE’2000, pages 75–86. IEEE CS Press, 2000.

    Google Scholar 

  10. E. Chávez, G. Navarro, R. Baeza-Yates, and J. Marroquín. Searching in metric spaces. ACM Comp. Surv., 2001. To appear.

    Google Scholar 

  11. A. Cobbs. Fast approximate matching using suffix trees. In Proc. CPM’95, pages 41–54, 1995. LNCS 937.

    Google Scholar 

  12. M. Crochemore. Transducers and repetitions. Theor. Comp. Sci., 45:63–86, 1986.

    Article  MathSciNet  Google Scholar 

  13. C. Faloutsos and I. Kamel. Beyond uniformity and independence: analysis of Rtrees using the concept of fractal dimension. In Proc. ACM PODS’94, pages 4–13, 1994.

    Google Scholar 

  14. V. Gaede and O. Günther. Multidimensional access methods. ACM Comp. Surv., 30(2):170–231, 1998.

    Article  Google Scholar 

  15. G. Gonnet. A tutorial introduction to Computational Biochemistry using Darwin. Technical report, Informatik E.T.H., Zuerich, Switzerland, 1992.

    Google Scholar 

  16. A. Guttman. R-trees: a dynamic index structure for spatial searching. In Proc. ACM SIGMOD’84, pages 47–57, 1984.

    Google Scholar 

  17. P. Jokinen and E. Ukkonen. Two algorithms for approximate string matching in static texts. In Proc. MFCS’91, volume 16, pages 240–248, 1991.

    Google Scholar 

  18. I. Kamel and C. Faloutsos. On packing R-trees. In Proc. ACM CIKM’93, pages 490–499, 1993.

    Google Scholar 

  19. V. Levenshtein. Binary codes capable of correcting spurious insertions and deletions of ones. Problems of Information Transmission, 1:8–17, 1965.

    MATH  Google Scholar 

  20. U. Manber and E. Myers. Suffix arrays: a new method for on-line string searches. SIAM J. on Computing, pages 935–948, 1993.

    Article  MathSciNet  Google Scholar 

  21. U. Manber and S. Wu. glimpse: A tool to search through entire file systems. In Proc. USENIX Technical Conference, pages 23–32, Winter 1994.

    Google Scholar 

  22. E. McCreight. A space-economical suffix tree construction algorithm. J. of the ACM, 23(2):262–272, 1976.

    Article  MathSciNet  Google Scholar 

  23. D. Morrison. PATRICIA-practical algorithm to retrieve information coded in alphanumeric. J. of the ACM, 15(4):514–534, 1968.

    Article  Google Scholar 

  24. E. Myers. A sublinear algorithm for approximate keyword searching. Algorithmica, 12(4/5):345–374, Oct/Nov 1994.

    Article  MathSciNet  Google Scholar 

  25. G. Navarro. A guided tour to approximate string matching. ACM Comp. Surv., 33(1):31–88, 2001.

    Article  Google Scholar 

  26. B. Pagel, H. Six, H. Toben, and P. Widmayer. Towards an analysis of range queries. In Proc. ACM PODS’93, pages 241–221, 1993.

    Google Scholar 

  27. D. Papadias, Y. Theodoridis, and E. Stefanakis. Multidimensional range queries with spatial relations. Geographical Systems, 4(4):343–365, 1997.

    Google Scholar 

  28. J. Robinson. The K-D-B-tree: a search structure for large multidimensional dynamic indexes. In Proc. ACM PODS’81, pages 10–18, 1981.

    Google Scholar 

  29. R. Sedgewick and P. Flajolet. Analysis of Algorithms. Addison-Wesley, 1996.

    Google Scholar 

  30. F. Shi. Fast approximate string matching with q-blocks sequences. In Proc. WSP’96, pages 257–271. Carleton University Press, 1996.

    Google Scholar 

  31. E. Sutinen and J. Tarhio. Filtration with q-samples in approximate string matching. In Proc. CPM’96, LNCS 1075, pages 50–61, 1996.

    Google Scholar 

  32. W. Szpankowski. Probabilistic analysis of generalized suffix trees. In Proc. CPM’92, LNCS 644, pages 1–14, 1992.

    Google Scholar 

  33. Y. Thedoridis and T. Sellis. A model for the prediction of R-tree performance. In Proc. ACM PODS’96, pages 161–171, 1996.

    Google Scholar 

  34. E. Ukkonen. Approximate string matching over suffix trees. In Proc. CPM’93, pages 228–242, 1993.

    Google Scholar 

  35. E. Ukkonen. Constructing suffix trees on-line in linear time. Algorithmica, 14(3):249–260, 1995.

    Article  MathSciNet  Google Scholar 

  36. D. White and R. Jain. Algorithms and strategies for similarity retrieval. Technical Report VCL-96-101, Visual Comp. Lab., Univ. of California, July 1996.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Escuela de Ciencias Físico-Matemáticas, Universidad Michoacana, Edificio “B”, Ciudad Universitaria, 58000, Morelia, Mich, Mexico

    Edgar Chávez

  2. Depto. de Ciencias de la Computación, Universidad de Chile, Blanco Encalada, 2120, Santiago, Chile

    Gonzalo Navarro

Authors
  1. Edgar Chávez
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  2. Gonzalo Navarro
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Editor information

Editors and Affiliations

  1. Compaq Cambridge Research Laboratory, One Cambridge Center, 02142-1612, Cambridge, MA, USA

    Sergio Rajsbaum

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© 2002 Springer-Verlag Berlin Heidelberg

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Chávez, E., Navarro, G. (2002). A Metric Index for Approximate String Matching. In: Rajsbaum, S. (eds) LATIN 2002: Theoretical Informatics. LATIN 2002. Lecture Notes in Computer Science, vol 2286. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45995-2_20

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  • DOI: https://doi.org/10.1007/3-540-45995-2_20

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-43400-9

  • Online ISBN: 978-3-540-45995-8

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