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Finding All Minimal Maximum Subsequences in Parallel

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Future Data and Security Engineering (FDSE 2019)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 11814))

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Abstract

A maximum contiguous subsequence of a real-valued sequence is a contiguous subsequence with the maximum cumulative sum. A minimal maximum contiguous subsequence is a minimal contiguous subsequence among all maximum ones of the sequence. We have previously designed and implemented a domain-decomposed parallel algorithm on cluster systems with Message Passing Interface that finds all successive minimal maximum subsequences of a random sample sequence from a normal distribution with negative mean. The parallel cluster algorithm employs the theory of random walk to derive an approximate probabilistic length upper bound for overlapping subsequences in an appropriate probabilistic setting, which is incorporated in the algorithm to facilitate the concurrent computation of all minimal maximum subsequences in hosting processors. We present in this article: (1) a generalization of the parallel cluster algorithm with improvements for input of arbitrary real-valued sequence, and (2) an empirical study of the speedup and efficiency achieved by the parallel algorithm with synthetic normally-distributed random sequences.

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References

  1. Akl, S.G., Guenther, G.R.: Applications of broadcasting with selective reduction to the maximal sum subsegment problem. Int. J. High Speed Comput. 3(2), 107–119 (1991)

    Article  Google Scholar 

  2. Altschul, S.F.: Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol. 219(3), 555–565 (1991)

    Article  Google Scholar 

  3. Alves, C.E.R., Cáceres, E.N., Song, S.W.: Finding all maximal contiguous subsequences of a sequence of numbers in \(O(1)\) communication rounds. IEEE Trans. Parallel Distrib. Syst. 24(3), 724–733 (2013)

    Article  Google Scholar 

  4. Bernholt, T., Hofmeister, T.: An algorithm for a generalized maximum subsequence problem. In: Correa, J.R., Hevia, A., Kiwi, M. (eds.) LATIN 2006. LNCS, vol. 3887, pp. 178–189. Springer, Heidelberg (2006). https://doi.org/10.1007/11682462_20

    Chapter  Google Scholar 

  5. Brendel, V., Bucher, P., Nourbakhsh, I.R., Blaisdell, B.E., Karlin, S.: Methods and algorithms for statistical analysis of protein sequences. Proc. Nat. Acad. Sc. U.S.A. 89(6), 2002–2006 (1992)

    Article  Google Scholar 

  6. Dai, H.-K., Su, H.-C.: A parallel algorithm for finding all successive minimal maximum subsequences. In: Correa, J.R., Hevia, A., Kiwi, M. (eds.) LATIN 2006. LNCS, vol. 3887, pp. 337–348. Springer, Heidelberg (2006). https://doi.org/10.1007/11682462_33

    Chapter  Google Scholar 

  7. Dai, H.K., Wang, Z.: A parallel algorithm for finding all minimal maximum subsequences via random walk. In: Dediu, A.-H., Formenti, E., Martín-Vide, C., Truthe, B. (eds.) LATA 2015. LNCS, vol. 8977, pp. 133–144. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-15579-1_10

    Chapter  Google Scholar 

  8. Dembo, A., Karlin, S.: Strong limit theorems of empirical functionals for large exceedances of partial sums of I.I.D. variables. Ann. Probab. 19(4), 1737–1755 (1991)

    Article  MathSciNet  Google Scholar 

  9. Feller, W.: An Introduction to Probability Theory and Its Applications. Wiley Series in Probability and Mathematical Statistics, 2nd Edn., vol. 2. Wiley, New York (1971)

    Google Scholar 

  10. He, X., Huang, C.-H.: Communication efficient BSP algorithm for all nearest smaller values problem. J. Parallel Distrib. Comput. 61(10), 1425–1438 (2001)

    Article  Google Scholar 

  11. JáJá, J.: An Introduction to Parallel Algorithms. Addison-Wesley, Boston (1992)

    MATH  Google Scholar 

  12. Karlin, S., Altschul, S.F.: Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Nat. Acad. Sci. U.S.A. 87(6), 2264–2268 (1990)

    Article  Google Scholar 

  13. Karlin, S., Altschul, S.F.: Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Nat. Acad. Sci. U.S.A. 90(12), 5873–5877 (1993)

    Article  Google Scholar 

  14. Karlin, S., Brendel, V.: Chance and statistical significance in protein and DNA sequence analysis. Science 257(5066), 39–49 (1992)

    Article  Google Scholar 

  15. Karlin, S., Dembo, A.: Limit distributions of maximal segmental score among Markov-dependent partial sums. Adv. Appl. Probab. 24, 113–140 (1992)

    Article  MathSciNet  Google Scholar 

  16. Karlin, S., Dembo, A., Kawabata, T.: Statistical composition of high-scoring segments from molecular sequences. Ann. Stat. 18(2), 571–581 (1990)

    Article  MathSciNet  Google Scholar 

  17. Lin, T.-C., Lee, D.T.: Randomized algorithm for the sum selection problem. Theoret. Comput. Sci. 377(1–3), 151–156 (2007)

    Article  MathSciNet  Google Scholar 

  18. Ruzzo, W.L., Tompa, M.: A linear time algorithm for finding all maximal scoring subsequences. In: Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, pp. 234–241. International Society for Computational Biology (1999)

    Google Scholar 

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Dai, H.K. (2019). Finding All Minimal Maximum Subsequences in Parallel. In: Dang, T., Küng, J., Takizawa, M., Bui, S. (eds) Future Data and Security Engineering. FDSE 2019. Lecture Notes in Computer Science(), vol 11814. Springer, Cham. https://doi.org/10.1007/978-3-030-35653-8_12

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  • DOI: https://doi.org/10.1007/978-3-030-35653-8_12

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-35652-1

  • Online ISBN: 978-3-030-35653-8

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