Location via proxy:   [ UP ]  
[Report a bug]   [Manage cookies]                
Skip to main content

Run-Length Encoded Nondeterministic KMP and Suffix Automata

  • Conference paper
  • First Online:
Implementation and Application of Automata (CIAA 2015)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9223))

Included in the following conference series:

  • 494 Accesses

Abstract

We present a novel bit-parallel representation, based on the run-length encoding, of the nondeterministic KMP and suffix automata for a string P with at least two distinct symbols. Our encoding requires \(O((\sigma + m)\lceil \rho / w\rceil )\) space and allows one to simulate the automata on a string in time \(O(\lceil \rho / w\rceil )\) per transition, where \(\sigma \) is the alphabet size, m is the length of P, \(\rho \) is the length of the run-length encoding of P and w is the machine word size in bits. The input string can be given in either unencoded or run-length encoded form. Finally, we present practical variants of the Shift-And and BNDM algorithms based on this encoding.

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

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /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
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 EPUB and 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

Institutional subscriptions

Similar content being viewed by others

References

  1. Amir, A., Landau, G.M., Vishkin, U.: Efficient pattern matching with scaling. J. Algorithms 13(1), 2–32 (1992)

    Article  MATH  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.: Faster approximate string matching. Algorithmica 23(2), 127–158 (1999)

    Article  MathSciNet  MATH  Google Scholar 

  4. Bagnall, A.J., Ratanamahatana, C.A., Keogh, E.J., Lonardi, S., Janacek, G.J.: A bit level representation for time series data mining with shape based similarity. Data Min. Knowl. Discov. 13(1), 11–40 (2006)

    Article  MathSciNet  Google Scholar 

  5. Cantone, D., Faro, S., Giaquinta, E.: A compact representation of nondeterministic (suffix) automata for the bit-parallel approach. Inf. Comput. 213, 3–12 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  6. Crochemore, M., Rytter, W.: Text Algorithms. Oxford University Press, New York (1994)

    MATH  Google Scholar 

  7. Durian, B., Holub, J., Peltola, H., Tarhio, J.: Improving practical exact string matching. Inf. Process. Lett. 110(4), 148–152 (2010)

    Article  MathSciNet  MATH  Google Scholar 

  8. Ďurian, B., Peltola, H., Salmela, L., Tarhio, J.: Bit-parallel search algorithms for long patterns. In: Festa, P. (ed.) SEA 2010. LNCS, vol. 6049, pp. 129–140. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  9. Fredriksson, K., Giaquinta, E.: On a compact encoding of the swap automaton. Inf. Process. Lett. 114(7), 392–396 (2014)

    Article  MathSciNet  MATH  Google Scholar 

  10. Fredriksson, K., Grabowski, S.: Average-optimal string matching. J. Discrete Algorithms 7(4), 579–594 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  11. Hyyrö, H.: Improving the bit-parallel NFA of Baeza-Yates and Navarro for approximate string matching. Inf. Process. Lett. 108(5), 313–319 (2008)

    Article  Google Scholar 

  12. Hyyrö, H., Navarro, G.: Bit-parallel witnesses and their applications to approximate string matching. Algorithmica 41(3), 203–231 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  13. Knuth, D.E.: The Art of Computer Programming, Volume I: Fundamental Algorithms, 2nd edn. Addison-Wesley, Boston (1973)

    Google Scholar 

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

    Article  MathSciNet  MATH  Google Scholar 

  15. Navarro, G., Raffinot, M.: Fast and flexible string matching by combining bit-parallelism and suffix automata. ACM J. Exp. Algorithmics 5, 4 (2000)

    Article  MathSciNet  Google Scholar 

  16. Navarro, G., Raffinot, M.: Flexible Pattern Matching in Strings - Practical on-Line Search Algorithms for Texts and Biological Sequences. Cambridge University Press, Cambridge (2002)

    MATH  Google Scholar 

  17. Peltola, H., Tarhio, J.: Alternative algorithms for bit-parallel string matching. In: Nascimento, M.A., de Moura, E.S., Oliveira, A.L. (eds.) SPIRE 2003. LNCS, vol. 2857, pp. 80–93. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

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

    Article  Google Scholar 

Download references

Acknowledgments

The author thanks Jorma Tarhio, Djamal Belazzougui and the anonymous reviewers for helpful comments.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Emanuele Giaquinta .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer International Publishing Switzerland

About this paper

Cite this paper

Giaquinta, E. (2015). Run-Length Encoded Nondeterministic KMP and Suffix Automata. In: Drewes, F. (eds) Implementation and Application of Automata. CIAA 2015. Lecture Notes in Computer Science(), vol 9223. Springer, Cham. https://doi.org/10.1007/978-3-319-22360-5_9

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-22360-5_9

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-22359-9

  • Online ISBN: 978-3-319-22360-5

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics