NDLI: Compressed Property Suffix Trees

Content Provider	IEEE Xplore Digital Library
Author	Wing-Kai Hon Patil, M. Shah, R. Thankachan, S.V.
Copyright Year	2011
Abstract	Property matching is a biologically motivated problem where the task is to find those occurrences of an online pattern $P$ in a string text $T$ (of size $n$), such that the matched part in $T$ satisfies some conceptual property. The property of a string is a set $\pi$ of (possibly overlapping) intervals $\{(s_1, f_1), (s_2, f_2), \ldots\}$ corresponding to the part of $T$, and an occurrence of a pattern $P$ at $T[i..(i+\|P\|-1)]$ is a valid output under the property $\pi$ only if $T[i..(i+\|P\|-1)]$ is completely contained in some interval $(s_j,f_j) \in \pi$. Algorithmically this problem can be solved in time linear to the size of text. Amir et al. (2008) introduced the indexing version of this problem, where they preprocess the text in $O(n\log\sigma+n\log\log n)$ time and maintain an $O(n\log n)$ bits index, named \emph{Property Suffix Tree} (PST), where $\sigma$ denotes the alphabet size. PST can perform property matching in optimal $O(\|P\|\log\sigma+ occ_{\pi}$) time, where $occ_{\pi}$ is the number of occurrences of $P$ in $T$ which satisfies the property. Later, Iliopoulos and Rahman (2008) proposed an alternative index which can be constructed in linear time. Recently Kopelowitz (2010) considered the dynamic version of this problem where intervals can be added or deleted. However, all these indexes requires space of $O(n\log n)$ bits, which can be much more than the size of the text ($n\log\sigma $ bits). In this paper, we propose the first index for property matching which takes space close to the entropy compressed space requirement of the text. Our compressed index takes $\|CSA\|+n(2+\epsilon+o(1))$ bits space and can perform query answering in $O(t(\|P\|)+\frac{1}{\epsilon}occ_{\pi} t_{SA})$ time, where $\|CSA\|$ is the size of compressed suffix array (CSA), $t(\|P\|)$ and $t_{SA}$ are the time for searching a pattern of length $\|P\|$ and the time for computing the suffix array value using CSA, respectively, and $\epsilon$ is a constant. We also introduce a dynamic index, taking $\|CSA\|+ n(2+\epsilon+o(1))+O(\|\pi\|\log n)$ bits of space, which can perform query answering in $O(t(\|P\|)+ \frac{1}{\epsilon}occ_{\pi} (\log n/\log\log n +t_{SA})\log n)$ time and can update (insert or delete) an interval $(s,f)$ in $O((f-s+1)(\log n+\log\|\pi\|+t_{SA}))$ time.
Starting Page	123
Ending Page	132
File Size	228608
Page Count	10
File Format	PDF
ISBN	9781612842790
ISSN	10680314
DOI	10.1109/DCC.2011.19
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-03-29
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Arrays Pattern matching Bioinformatics Genomics Indexing Suffix Tree Compressed Indexes Property Matching Pattern Matching
Content Type	Text
Resource Type	Article
Subject	Computer Networks and Communications

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