Skip to main content
SpringerLink
Log in
Book cover

International Symposium on String Processing and Information Retrieval

SPIRE 2005: String Processing and Information Retrieval pp 246–255Cite as

Faster Generation of Super Condensed Neighbourhoods Using Finite Automata

  • Conference paper

  • 1500 Accesses

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3772))

Abstract

We present a new algorithm for generating super condensed neighbourhoods. Super condensed neighbourhoods have recently been presented as the minimal set of words that represent a pattern neighbourhood. These sets play an important role in the generation phase of hybrid algorithms for indexed approximate string matching. An existing algorithm for this purpose is based on a dynamic programming approach, implemented using bit-parallelism. In this work we present a bit-parallel algorithm based on automata which is faster, conceptually much simpler and uses less memory than the existing method.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
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

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Baeza-Yates, R.A.: Text-retrieval: Theory and practice. In: van Leeuwen, J. (ed.) IFIP Congress (1). IFIP Transactions, vol. A-12, pp. 465–476. North-Holland, Amsterdam (1992)

    Google Scholar 

  2. Baeza-Yates, R.A., Gonnet, G.H.: A new approach to text searching. Commun. ACM 35(10), 74–82 (1992)

    Article  Google Scholar 

  3. Baeza-Yates, R.A., Navarro, G.: A faster algorithm for approximate string matching. In: Hirschberg, D.S., Meyers, G. (eds.) CPM 1996. LNCS, vol. 1075, pp. 1–23. Springer, Heidelberg (1996)

    Google Scholar 

  4. Baeza-Yates, R.A., Navarro, G.: Faster approximate string matching. Algorithmica 23(2), 127–158 (1999)

    Article  MATH  MathSciNet  Google Scholar 

  5. Cobbs, A.L.: Fast approximate matching using suffix trees. In: Galil, Z., Ukkonen, E. (eds.) CPM 1995. LNCS, vol. 937, pp. 41–54. Springer, Heidelberg (1995)

    Google Scholar 

  6. Hyyrö, H., Navarro, G.: A practical index for genome searching. In: Nascimento, M.A., de Moura, E.S., Oliveira, A.L. (eds.) SPIRE 2003. LNCS, vol. 2857, pp. 341–349. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  7. Hyyrö, H.: Practical Methods for Approximate String Matching. PhD thesis, Faculty of Information of the University of Tampere (2003)

    Google Scholar 

  8. Hyyrö, H.: An improvement and an extension on the hybrid index for approximate string matching. In: Apostolico, A., Melucci, M. (eds.) SPIRE 2004. LNCS, vol. 3246, pp. 208–209. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  9. Myers, E.: A sublinear algorithm for approximate keyword matching. Algorithmica (12), 345–374 (1994)

    Google Scholar 

  10. Myers, G.: A fast bit-vector algorithm for approximate string matching based on dynamic programming. In: Farach-Colton, M. (ed.) CPM 1998. LNCS, vol. 1448, pp. 1–13. Springer, Heidelberg (1998)

    Chapter  Google Scholar 

  11. Navarro, G.: A guided tour to approximate string matching. ACM Computing Surveys 33(1), 31–88 (2001)

    Article  Google Scholar 

  12. Navarro, G., Baeza-Yates, R.: A hybrid indexing method for approximate string matching. Journal of Discrete Algorithms 1(1), 205–239 (2000)

    MathSciNet  Google Scholar 

  13. Navarro, G., Baeza-Yates, R., Sutinen, E., Tarhio, J.: Indexing methods for approximate string matching. IEEE Data Engineering Bulletin 24(4), 19–27 (2001)

    Google Scholar 

  14. Russo, L.M.S., Oliveira, A.L.: An efficient algorithm for generating super condensed neighborhoods. In: Apostolico, A., Crochemore, M., Park, K. (eds.) CPM 2005. LNCS, vol. 3537, pp. 104–115. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  15. Ukkonen, E.: Finding approximate patterns in strings. Journal of Algorithms, 132–137 (1985)

    Google Scholar 

  16. Ukkonen, E.: Approximate string-matching over suffix trees. In: Apostolico, A., Crochemore, M., Galil, Z., Manber, U. (eds.) CPM 1993. LNCS, vol. 684, pp. 228–242. Springer, Heidelberg (1993)

    Chapter  Google Scholar 

  17. Wu, S., Manber, U.: Fast text searching allowing errors. Commun. ACM 35(10), 83–91 (1992)

    Article  Google Scholar 

  18. File 20ng-train-all-terms, from http://www.gia.ist.utl.pt/~acardoso/datasets

Download references

Author information

Authors and Affiliations

  1. IST / INESC-ID, R. Alves Redol 9, 1000, LISBOA, Portugal

    Luís M. S. Russo & Arlindo L. Oliveira

Authors
  1. Luís M. S. Russo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Arlindo L. Oliveira
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. University of Toronto,  

    Mariano Consens

  2. Dept. of Computer Science, University of Chile,  

    Gonzalo Navarro

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Russo, L.M.S., Oliveira, A.L. (2005). Faster Generation of Super Condensed Neighbourhoods Using Finite Automata. In: Consens, M., Navarro, G. (eds) String Processing and Information Retrieval. SPIRE 2005. Lecture Notes in Computer Science, vol 3772. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11575832_28

Download citation

  • DOI: https://doi.org/10.1007/11575832_28

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-29740-6

  • Online ISBN: 978-3-540-32241-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation