Detecting Pattern Efficiently with Don’t Cares | SpringerLink
Skip to main content
Springer Nature Link
Log in

Detecting Pattern Efficiently with Don’t Cares

  • Conference paper
  • First Online:
Proceedings of the 21st EANN (Engineering Applications of Neural Networks) 2020 Conference (EANN 2020)

Part of the book series: Proceedings of the International Neural Networks Society ((INNS,volume 2))

  • 1104 Accesses

Abstract

In this paper, we introduce our efficient simple method which can locate all occurrences of pattern P of k subpatterns with “don’t cares” of length m in text S of length n. Our algorithm employs advanced data structure and the Kangaroo method, which can be applied to selected suffixes of the suffix tree of S to answer subsequent queries in O(k) time using a predefined computational method to find all occurrences of pattern P with “don’t cares” in text S in a fast and effective manner.

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

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
¥17,985 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
JPY 3498
Price includes VAT (Japan)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
JPY 22879
Price includes VAT (Japan)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
JPY 28599
Price includes VAT (Japan)
  • 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

Similar content being viewed by others

References

  1. Aho, A.V., Corasick, M.J.: Efficient string matching: an aid to bibliographic search. Commun. ACM 18(6), 333–340 (1975)

    Article  MathSciNet  Google Scholar 

  2. Alamro, H., Badkobeh, G., Belazzougui, D., Iliopoulos, C.S., Puglisi, S.J.: Computing the antiperiod (s) of a string. In: 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik (2019)

    Google Scholar 

  3. Alstrup, S., Husfeldt, T., Rauhe, T.: Marked ancestor problems. In: Proceedings 39th Annual Symposium on Foundations of Computer Science (Cat. no. 98CB36280), pp. 534–543. IEEE (1998)

    Google Scholar 

  4. Amir, A., Lewenstein, M., Porat, E.: Faster algorithms for string matching with k mismatches. J. Algorithms 50(2), 257–275 (2004)

    Article  MathSciNet  Google Scholar 

  5. Bille, P., Gørtz, I.L., Vildhøj, H.W., Vind, S.: String indexing for patterns with wildcards. Theory Comput. Syst. 55(1), 41–60 (2014)

    Article  MathSciNet  Google Scholar 

  6. Boyer, R.S., Moore, J.S.: A fast string searching algorithm. Commun. ACM 20(10), 762–772 (1977). https://doi.org/10.1145/359842.359859

    Article  MATH  Google Scholar 

  7. Chen, G., Wu, X., Zhu, X., Arslan, A.N., He, Y.: Efficient string matching with wildcards and length constraints. Knowl. Inf. Syst. 10(4), 399–419 (2006)

    Article  Google Scholar 

  8. Clifford, R., Efremenko, K., Porat, E., Rothschild, A.: Pattern matching with don’t cares and few errors. J. Comput. Syst. Sci. 76(2), 115–124 (2010)

    Article  MathSciNet  Google Scholar 

  9. Clifford, R., Porat, E.: A filtering algorithm for k-mismatch with don’t cares. In: International Symposium on String Processing and Information Retrieval, pp. 130–136. Springer (2007)

    Google Scholar 

  10. Cole, R., Gottlieb, L.A., Lewenstein, M.: Dictionary matching and indexing with errors and don’t cares. In: Proceedings of the Thirty-Sixth Annual ACM Symposium on Theory of Computing, pp. 91–100 (2004)

    Google Scholar 

  11. Cole, R., Hariharan, R.: Approximate string matching: a simpler faster algorithm. SIAM J. Comput. 31(6), 1761–1782 (2002)

    Article  MathSciNet  Google Scholar 

  12. Cole, R., Hariharan, R.: Verifying candidate matches in sparse and wildcard matching. In: Proceedings of the Thirty-Fourth Annual ACM Symposium on Theory of Computing, pp. 592–601 (2002)

    Google Scholar 

  13. Commentz-Walter, B.: A string matching algorithm fast on the average. In: International Colloquium on Automata, Languages, and Programming, pp. 118–132. Springer (1979)

    Google Scholar 

  14. Crochemore, M., Hancart, C.: Pattern matching in strings. In: Mikhail, J.A. (ed.) Algorithms and Theory of Computation Handbook, pp. 11.1–11.28. CRC Press (1998). https://hal-upec-upem.archives-ouvertes.fr/hal-00620790

    Google Scholar 

  15. Crochemore, M., Hancart, C., Lecroq, T.: Algorithms on Strings. Cambridge University Press, Cambridge (2007)

    Book  Google Scholar 

  16. Crochemore, M., Perrin, D.: Pattern matching in strings. In: Image Analysis and Processing II, pp. 67–79. Springer (1988)

    Google Scholar 

  17. Farach, M.: Optimal suffix tree construction with large alphabets. In: Proceedings 38th Annual Symposium on Foundations of Computer Science, pp. 137–143. IEEE (1997)

    Google Scholar 

  18. Fischer, J., Huson, D.H.: New common ancestor problems in trees and directed acyclic graphs. Inf. Process. Lett. 110(8–9), 331–335 (2010)

    Article  MathSciNet  Google Scholar 

  19. Fischer, M.J., Paterson, M.S.: String-matching and other products. Tech. rep. Massachusetts Institute of Technology, Cambridge Project MAC (1974)

    Google Scholar 

  20. Galil, Z., Giancarlo, R.: Improved string matching with k mismatches. ACM SIGACT News 17(4), 52–54 (1986)

    Article  Google Scholar 

  21. Gusfield, D.: Algorithms on stings, trees, and sequences: computer science and computational biology. ACM SIGACT News 28(4), 41–60 (1997)

    Article  Google Scholar 

  22. Iliopoulos, C.S., Rahman, M.S.: Pattern matching algorithms with don’t cares. In: Proceedings of 33rd SOFSEM, pp. 116–126 (2007)

    Google Scholar 

  23. Indyk, P.: Faster algorithms for string matching problems: matching the convolution bound. In: Proceedings 39th Annual Symposium on Foundations of Computer Science (Cat. no. 98CB36280), pp. 166–173. IEEE (1998)

    Google Scholar 

  24. Kalai, A.T.: Efficient pattern-matching with don’t cares. In: SODA 2002 Proceedings of the Thirteenth Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 655–656. ACM Press (January 2002). https://www.microsoft.com/en-us/research/publication/efficient-pattern-matching-dont-cares/

  25. Karp, R.M., Rabin, M.O.: Efficient randomized pattern-matching algorithms. IBM J. Res. Dev. 31(2), 249–260 (1987)

    Article  MathSciNet  Google Scholar 

  26. Knuth, D.E., Morris Jr., J.H., Pratt, V.R.: Fast pattern matching in strings. SIAM J. Comput. 6(2), 323–350 (1977)

    Article  MathSciNet  Google Scholar 

  27. Lam, T.W., Sung, W.K., Tam, S.L., Yiu, S.M.: Space efficient indexes for string matching with don’t cares. In: International Symposium on Algorithms and Computation, pp. 846–857. Springer (2007)

    Google Scholar 

  28. Landau, G.M., Vishkin, U.: Fast parallel and serial approximate string matching. J. Algorithms 10(2), 157–169 (1989)

    Article  MathSciNet  Google Scholar 

  29. Liu, N., Xie, F., Wu, X.: Multi-pattern matching with variable-length wildcards using suffix tree. Pattern Anal. Appl. 21(4), 1151–1165 (2018)

    Article  MathSciNet  Google Scholar 

  30. Nicolae, M., Rajasekaran, S.: On pattern matching with k mismatches and few don’t cares. Inf. Process. Lett. 118, 78–82 (2017)

    Article  MathSciNet  Google Scholar 

  31. Pinter, R.Y.: Efficient string matching with don’t-care patterns. In: Combinatorial Algorithms on Words, pp. 11–29. Springer (1985)

    Google Scholar 

  32. Rahman, M.S., Iliopoulos, C.S., Lee, I., Mohamed, M., Smyth, W.F.: Finding patterns with variable length gaps or don’t cares. In: International Computing and Combinatorics Conference, pp. 146–155. Springer (2006)

    Google Scholar 

  33. Sahinalp, S.C., Vishkin, U.: Efficient approximate and dynamic matching of patterns using a labeling paradigm. In: Proceedings of 37th Conference on Foundations of Computer Science, pp. 320–328. IEEE (1996)

    Google Scholar 

  34. Sung, W.K.: Algorithms in Bioinformatics: A Practical Introduction. CRC Press, Boca Raton (2009)

    Book  Google Scholar 

  35. Ukkonen, E.: On-line construction of suffix trees. Algorithmica 14(3), 249–260 (1995)

    Article  MathSciNet  Google Scholar 

  36. Wu, S., Manber, U., et al.: A fast algorithm for multi-pattern searching. University of Arizona, Department of Computer Science (1994)

    Google Scholar 

  37. Ziviani, N., Baeza-Yates, R.: String processing and information retrieval. In: 14th International Symposium, SPIRE 2007 Santiago, Chile, October 29–31, 2007 Proceedings, vol. 4726. Springer (2007)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Informatics, King’s College London, London, UK

    Hayam Alamro & Costas Iliopoulos

  2. Department of Information Systems, Princess Nourah Bint Abdulrahman University, Riyadh, Kingdom of Saudi Arabia

    Hayam Alamro

Authors
  1. Hayam Alamro
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Costas Iliopoulos
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hayam Alamro .

Editor information

Editors and Affiliations

  1. School of Engineering, Department of Civil Engineering, Democritus University of Thrace, Xanthi, Greece

    Lazaros Iliadis

  2. Lancaster University, Lancaster, UK

    Plamen Parvanov Angelov

  3. School of Computing and Digital Technologies, Teesside University, Middlesbrough, UK

    Chrisina Jayne

  4. University of the West of England, Bristol, UK

    Elias Pimenidis

Rights and permissions

Reprints and permissions

Copyright information

© 2020 The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Alamro, H., Iliopoulos, C. (2020). Detecting Pattern Efficiently with Don’t Cares. In: Iliadis, L., Angelov, P., Jayne, C., Pimenidis, E. (eds) Proceedings of the 21st EANN (Engineering Applications of Neural Networks) 2020 Conference. EANN 2020. Proceedings of the International Neural Networks Society, vol 2. Springer, Cham. https://doi.org/10.1007/978-3-030-48791-1_35

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-48791-1_35

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-48790-4

  • Online ISBN: 978-3-030-48791-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation