Fast Average-Case Pattern Matching on Weighted Sequences

DOI10.1142/S0129054118430062MaRDI QIDQ5384623zbMATH OpenWikidataFDO

Authors Carl Barton, Chang Liu, Solon P. Pissis

Publication date 24 June 2019

Published in International Journal of Foundations of Computer Science (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1512.01085

zbMATH Keywords

online algorithmspattern matchinguncertain sequencesweighted strings

Mathematics Subject Classification ID

Online algorithms; streaming algorithms (68W27) Algorithms on strings (68W32)

Abstract: A weighted string over an alphabet of size $sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences, naturally arise in many contexts. In this article, we study the problem of weighted string matching with a special focus on average-case analysis. Given a weighted pattern string $x$ of length $m$, a text string $y$ of length $n>m$, and a cumulative weight threshold $1/z$, defined as the minimal probability of occurrence of factors in a weighted string, we present an algorithm requiring average-case search time $o(n)$ for pattern matching for weight ratio $fraczm<minfrac1logz,fraclogsigmalogz(logm+loglogsigma)$. For a pattern string $x$ of length $m$, a weighted text string $y$ of length $n>m$, and a cumulative weight threshold $1/z$, we present an algorithm requiring average-case search time $o(sigman)$ for the same weight ratio. The importance of these results lies on the fact that these algorithms work in average-case sublinear search time in the size of the text, and in linear preprocessing time and space in the size of the pattern, for these ratios.

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Cites work

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• scientific article; zbMATH DE number 6792413 (Why is no real title available?)
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• Weighted LCS

Cited in

(16)

• Algorithmic complexity of protein identification: Combinatorics of weighted strings
• Crochemore's partitioning on weighted strings and applications
• On-line weighted pattern matching
• Pattern matching and consensus problems on weighted sequences and profiles
• Indexing weighted sequences: neat and efficient
• Experimental results in pattern matching on weighted sequences
• Linear-time computation of prefix table for weighted strings
• Self-overlapping Occurrences and Knuth-Morris-Pratt Algorithm for Weighted Matching
• Pattern matching and consensus problems on weighted sequences and profiles
• Approximate Matching in Weighted Sequences
• Combinatorial Pattern Matching
• scientific article; zbMATH DE number 6792413 (Why is no real title available?)
• Computational and Information Science
• Property Suffix Array with Applications in Indexing Weighted Sequences
• Finding submasses in weighted strings with fast Fourier transform
• Property matching and weighted matching

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