Skip to main content

A\(^*\)-Based Compilation of Relaxed Decision Diagrams for the Longest Common Subsequence Problem

  • Conference paper
  • First Online:
Integration of Constraint Programming, Artificial Intelligence, and Operations Research (CPAIOR 2021)

Abstract

We consider the longest common subsequence (LCS) problem and propose a new method for obtaining tight upper bounds on the solution length. Our method relies on the compilation of a relaxed multi-valued decision diagram (MDD) in a special way that is based on the principles of A\(^*\) search. An extensive experimental evaluation on several standard LCS benchmark instance sets shows that the novel construction algorithm clearly outperforms a traditional top-down construction (TDC) of MDDs. We are able to obtain stronger and at the same time more compact relaxed MDDs than TDC and this in shorter time. For several groups of benchmark instances new best known upper bounds are obtained. In comparison to existing simple upper bound procedures, the obtained bounds are on average 14.8% better.

This project is partially funded by the Doctoral Program “Vienna Graduate School on Computational Optimization”, Austrian Science Foundation (FWF) Project No. W1260-N35.

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 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

References

  1. Andersen, H.R., Hadzic, T., Hooker, J.N., Tiedemann, P.: A constraint store based on multivalued decision diagrams. In: Bessière, C. (ed.) CP 2007. LNCS, vol. 4741, pp. 118–132. Springer, Heidelberg (2007). https://doi.org/10.1007/978-3-540-74970-7_11

    Chapter  Google Scholar 

  2. Beal, R., Afrin, T., Farheen, A., Adjeroh, D.: A new algorithm for “the LCS problem” with application in compressing genome resequencing data. BMC Genom. 17(4), 544 (2016). https://doi.org/10.1186/s12864-016-2793-0

    Article  Google Scholar 

  3. Bergman, D., Cire, A.A., van Hoeve, W.J., Hooker, J.N.: Discrete optimization with decision diagrams. INFORMS J. Comput. 28(1), 47–66 (2016)

    Article  MathSciNet  Google Scholar 

  4. Bergman, D., Cire, A.A., von Hoeve, W.J., Hooker, J.N.: Optimization bounds from binary decision diagrams. INFORMS J. Comput. 26(2), 253–268 (2014)

    Article  MathSciNet  Google Scholar 

  5. Bergman, D., Cire, A.A., van Hoeve, W.J., Hooker, J.N.: Decision Diagrams for Optimization. Artificial Intelligence: Foundations, Theory, and Algorithms. Springer, Heidelberg (2016). https://doi.org/10.1007/978-3-319-42849-9

    Book  MATH  Google Scholar 

  6. Bergman, D., Cire, A.A., van Hoeve, W.-J., Yunes, T.: BDD-based heuristics for binary optimization. J. Heuristics 20(2), 211–234 (2014). https://doi.org/10.1007/s10732-014-9238-1

    Article  Google Scholar 

  7. Blum, C., Blesa, M.J.: Probabilistic beam search for the longest common subsequence problem. In: Stützle, T., Birattari, M., Hoos, H.H. (eds.) SLS 2007. LNCS, vol. 4638, pp. 150–161. Springer, Heidelberg (2007). https://doi.org/10.1007/978-3-540-74446-7_11

    Chapter  Google Scholar 

  8. Blum, C., Blesa, M.J., López-Ibáñez, M.: Beam search for the longest common subsequence problem. Comput. Oper. Res. 36(12), 3178–3186 (2009)

    Article  MathSciNet  Google Scholar 

  9. Blum, C., et al.: Solving longest common subsequence problems via a transformation to the maximum clique problem. Comput. Oper. Res. 125, 105089 (2021). https://doi.org/10.1016/j.cor.2020.105089

    Article  MathSciNet  MATH  Google Scholar 

  10. Blum, C., Festa, P.: Longest common subsequence problems. In: Metaheuristics for String Problems in Bioinformatics, chap. 3, pp. 45–60. Wiley (2016)

    Google Scholar 

  11. Bonizzoni, P., Della Vedova, G., Mauri, G.: Experimenting an approximation algorithm for the LCS. Discret. Appl. Math. 110(1), 13–24 (2001)

    Article  MathSciNet  Google Scholar 

  12. Brisk, P., Kaplan, A., Sarrafzadeh, M.: Area-efficient instruction set synthesis for reconfigurable system-on-chip designs. In: Proceedings of DAC 2004 - the 41st Annual Design Automation Conference, pp. 395–400. IEEE Press (2004)

    Google Scholar 

  13. Chan, H.T., Yang, C.B., Peng, Y.H.: The generalized definitions of the two-dimensional largest common substructure problems. In: Proceedings of the 33rd Workshop on Combinatorial Mathematics and Computation Theory, pp. 1–12. National Taiwan University (2016)

    Google Scholar 

  14. Cire, A.A., van Hoeve, W.J.: Multivalued decision diagrams for sequencing problems. Oper. Res. 61(6), 1411–1428 (2013)

    Article  MathSciNet  Google Scholar 

  15. Djukanovic, M., Raidl, G.R., Blum, C.: A beam search for the longest common subsequence problem guided by a novel approximate expected length calculation. In: Nicosia, G., Pardalos, P., Umeton, R., Giuffrida, G., Sciacca, V. (eds.) LOD 2019. LNCS, vol. 11943, pp. 154–167. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-37599-7_14

    Chapter  Google Scholar 

  16. Djukanovic, M., Raidl, G.R., Blum, C.: Finding longest common subsequences: new anytime A* search results. Appl. Soft Comput. 95, 106499 (2020). https://doi.org/10.1016/j.asoc.2020.106499

    Article  Google Scholar 

  17. Easton, T., Singireddy, A.: A large neighborhood search heuristic for the longest common subsequence problem. J. Heuristics 14(3), 271–283 (2008). https://doi.org/10.1007/s10732-007-9038-y

    Article  MATH  Google Scholar 

  18. Fraser, C.B.: Subsequences and supersequences of strings. Ph.D. thesis, University of Glasgow, UK (1995)

    Google Scholar 

  19. Gusfield, D.: Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge (1997)

    Book  Google Scholar 

  20. Hart, P., Nilsson, N., Raphael, B.: A formal basis for the heuristic determination of minimum cost paths. IEEE Trans. Syst. Sci. Cybern. 4(2), 100–107 (1968)

    Article  Google Scholar 

  21. Horn, M., Maschler, J., Raidl, G.R., Rönnberg, E.: A*-based construction of decision diagrams for a prize-collecting scheduling problem. Comput. Oper. Res. 126, 105125 (2021). https://doi.org/10.1016/j.cor.2020.105125

    Article  MathSciNet  MATH  Google Scholar 

  22. Huang, K., Yang, C., Tseng, K.: Fast algorithms for finding the common subsequences of multiple sequences. In: Proceedings of the IEEE International Computer Symposium, pp. 1006–1011. IEEE Press (2004)

    Google Scholar 

  23. Jiang, T., Lin, G., Ma, B., Zhang, K.: A general edit distance between RNA structures. J. Comput. Biol. 9(2), 371–388 (2002)

    Article  Google Scholar 

  24. Kinable, J., Cire, A.A., van Hoeve, W.J.: Hybrid optimization methods for time-dependent sequencing problems. Eur. J. Oper. Res. 259(3), 887–897 (2017)

    Article  MathSciNet  Google Scholar 

  25. Kruskal, J.B.: An overview of sequence comparison: time warps, string edits, and macromolecules. SIAM Rev. 25(2), 201–237 (1983)

    Article  MathSciNet  Google Scholar 

  26. Li, Y., Wang, Y., Zhang, Z., Wang, Y., Ma, D., Huang, J.: A novel fast and memory efficient parallel mlcs algorithm for long and large-scale sequences alignments. In: 2016 IEEE 32nd International Conference on Data Engineering (ICDE), pp. 1170–1181. IEEE Press (2016)

    Google Scholar 

  27. Maier, D.: The complexity of some problems on subsequences and supersequences. J. ACM 25(2), 322–336 (1978)

    Article  MathSciNet  Google Scholar 

  28. Peng, Z., Wang, Y.: A novel efficient graph model for the multiple longest common subsequences (MLCS) problem. Front. Genet. 8, 104 (2017)

    Article  Google Scholar 

  29. Shyu, S.J., Tsai, C.Y.: Finding the longest common subsequence for multiple biological sequences by ant colony optimization. Comput. Oper. Res. 36(1), 73–91 (2009)

    Article  MathSciNet  Google Scholar 

  30. Smith, T., Waterman, M.: Identification of common molecular subsequences. J. Mol. Biol. 147(1), 195–197 (1981)

    Article  Google Scholar 

  31. Wang, Q., Korkin, D., Shang, Y.: A fast multiple longest common subsequence (MLCS) algorithm. IEEE Trans. Knowl. Data Eng. 23(3), 321–334 (2011)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Matthias Horn .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Horn, M., Raidl, G.R. (2021). A\(^*\)-Based Compilation of Relaxed Decision Diagrams for the Longest Common Subsequence Problem. In: Stuckey, P.J. (eds) Integration of Constraint Programming, Artificial Intelligence, and Operations Research. CPAIOR 2021. Lecture Notes in Computer Science(), vol 12735. Springer, Cham. https://doi.org/10.1007/978-3-030-78230-6_5

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-78230-6_5

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-78229-0

  • Online ISBN: 978-3-030-78230-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics