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An O(N^2) Algorithm for Discovering Optimal Boolean Pattern Pairs
October-December 2004 (vol. 1 no. 4)
pp. 159-170
ASCII Text
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Hideo Bannai, Heikki Hyyr?, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano, "An O(N^2) Algorithm for Discovering Optimal Boolean Pattern Pairs," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, no. 4, pp. 159-170, October-December, 2004.
 
 
BibTex
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@article{ 10.1109/TCBB.2004.36,
author = {Hideo Bannai and Heikki Hyyr? and Ayumi Shinohara and Masayuki Takeda and Kenta Nakai and Satoru Miyano},
title = {An O(N^2) Algorithm for Discovering Optimal Boolean Pattern Pairs},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {1},
number = {4},
issn = {1545-5963},
year = {2004},
pages = {159-170},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2004.36},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - An O(N^2) Algorithm for Discovering Optimal Boolean Pattern Pairs
IS - 4
SN - 1545-5963
SP159
EP170
EPD - 159-170
A1 - Hideo Bannai,
A1 - Heikki Hyyr?,
A1 - Ayumi Shinohara,
A1 - Masayuki Takeda,
A1 - Kenta Nakai,
A1 - Satoru Miyano,
PY - 2004
KW - Pattern discovery
KW - Boolean patterns
KW - suffix tree
KW - suffix array.
VL - 1
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 

Abstract—We consider the problem of finding the optimal combination of string patterns, which characterizes a given set of strings that have a numeric attribute value assigned to each string. Pattern combinations are scored based on the correlation between their occurrences in the strings and the numeric attribute values. The aim is to find the combination of patterns which is best with respect to an appropriate scoring function. We present an O(N^2) time algorithm for finding the optimal pair of substring patterns combined with Boolean functions, where N is the total length of the sequences. The algorithm looks for all possible Boolean combinations of the patterns, e.g., patterns of the form p \land \lnot q, which indicates that the pattern pair is considered to occur in a given string s, if p occurs in s, AND q does NOT occur in s. An efficient implementation using suffix arrays is presented, and we further show that the algorithm can be adapted to find the best k{\hbox{-}}{\rm pattern} Boolean combination in O(N^k) time. The algorithm is applied to mRNA sequence data sets of moderate size combined with their turnover rates for the purpose of finding regulatory elements that cooperate, complement, or compete with each other in enhancing and/or silencing mRNA decay.

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Index Terms:
Pattern discovery, Boolean patterns, suffix tree, suffix array.
Citation:
Hideo Bannai, Heikki Hyyr?, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano, "An O(N^2) Algorithm for Discovering Optimal Boolean Pattern Pairs," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, no. 4, pp. 159-170, Oct.-Dec. 2004, doi:10.1109/TCBB.2004.36
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