Issue No. 04 - April (2013 vol. 24)

ISSN: 1045-9219

pp: 724-733

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TPDS.2012.149

C. E. R. Alves , Univ. Sao Judas Tadeu, Sao Paulo, Brazil

E. N. Caceres , Fac. de Comput., Univ. Fed. do Mato Grosso do Sul, Campo Grande, Brazil

Siang Wun Song , Univ. of Sao Paulo, Sao Paulo, Brazil

ABSTRACT

Given a sequence A of real numbers, we wish to find a list of all nonoverlapping contiguous subsequences of A that are maximal. A maximal subsequence M of A has the property that no proper subsequence of M has a greater sum of values. Furthermore, M may not be contained properly within any subsequence of A with this property. This problem has several applications in Computational Biology and can be solved sequentially in linear time. We present a BSP/CGM algorithm that solves this problem using p processors in O(|A|=p) time and O(|A|=p) space per processor. The algorithm uses a constant number of communication rounds of size at most O(|A|=p). Thus, the algorithm achieves linear speedup and is highly scalable. To our knowledge, there are no previous known parallel BSP/CGM algorithms to solve this problem.

INDEX TERMS

Parallel algorithms, Algorithm design and analysis, Program processors, Computational modeling, Materials, Amino acids, Multiprocessor interconnection, communication rounds, All maximal subsequences problem, maximum subsequence problem, parallel algorithm, coarse-grained multicomputer

CITATION

Siang Wun Song, E. N. Caceres and C. E. Alves, "Finding All Maximal Contiguous Subsequences of a Sequence of Numbers in O(1) Communication Rounds," in

*IEEE Transactions on Parallel & Distributed Systems*, vol. 24, no. , pp. 724-733, 2013.

doi:10.1109/TPDS.2012.149

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