Pattern discovery in colored strings

DOI10.1145/3429280MaRDI QIDQ5102044zbMATH OpenOpenAlexFDO

Authors Zsuzsanna Lipták, Simon J. Puglisi, Massimiliano Rossi

Publication date 6 September 2022

Published in ACM Journal of Experimental Algorithmics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2004.04858

zbMATH Keywords

efficient algorithmpattern miningproperty testingsuffix tree

Mathematics Subject Classification ID

Algorithms on strings (68W32)

Abstract: In this paper, we consider the problem of identifying patterns of interest in colored strings. A colored string is a string where each position is assigned one of a finite set of colors. Our task is to find substrings of the colored string that always occur followed by the same color at the same distance. The problem is motivated by applications in embedded systems verification, in particular, assertion mining. The goal there is to automatically find properties of the embedded system from the analysis of its simulation traces. We show that, in our setting, the number of patterns of interest is upper-bounded by $mathcalO(n^2)$, where $n$ is the length of the string. We introduce a baseline algorithm, running in $mathcalO(n^2)$ time, which identifies all patterns of interest satisfying certain minimality conditions, for all colors in the string. For the case where one is interested in patterns related to one color only, we also provide a second algorithm which runs in $mathcalO(n^{2}logn)$ time in the worst case but is faster than the baseline algorithm in practice. Both solutions use suffix trees, and the second algorithm also uses an appropriately defined priority queue, which allows us to reduce the number of computations. We performed an experimental evaluation of the proposed approaches over both synthetic and real-world datasets, and found that the second algorithm outperforms the first algorithm on all simulated data, while on the real-world data, the performance varies between a slight slowdown (on half of the datasets) and a speedup by a factor of up to 11.

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Cites work

• Algorithms on Strings, Trees and Sequences
• Pattern discovery in colored strings
• Space-efficient preprocessing schemes for range minimum queries on static arrays

Cited in

(3)

• Finding Gale strings
• Counting Colours in Compressed Strings
• Pattern discovery in colored strings

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