Journal Article10.1137/090779759
Space-Efficient Preprocessing Schemes for Range Minimum Queries on Static Arrays
Johannes Fischer,Volker Heun +1 more
311
TL;DR: This work builds a data structure that allows us to answer efficiently subsequent on-line queries of the form “what is the position of a minimum element in the subarray ranging from $i to $j$?”
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Abstract: Given a static array of $n$ totally ordered objects, the range minimum query problem is to build a data structure that allows us to answer efficiently subsequent on-line queries of the form “what is the position of a minimum element in the subarray ranging from $i$ to $j$?”. We focus on two settings, where (1) the input array is available at query time, and (2) the input array is available only at construction time. In setting (1), we show new data structures (a) of size $\frac{2n}{c(n)}-\Theta\bigl(\frac{n\lg\lg n}{c(n)\lg n}\bigr)$ bits and query time $O(c(n))$ for any positive integer function $c(n)\in O\bigl(n^\varepsilon\bigr)$ for an arbitrary constant $0<\varepsilon<1$, or (b) with $O(nH_k)+o(n)$ bits and $O(1)$ query time, where $H_k$ denotes the empirical entropy of $k$th order of the input array. In setting (2), we give a data structure of size $2n+o(n)$ bits and query time $O(1)$. All data structures can be constructed in linear time and almost in-place.
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Citations
Succinct de bruijn graphs
Alexander Bowe,Taku Onodera,Kunihiko Sadakane,Tetsuo Shibuya +3 more
- 10 Sep 2012
TL;DR: A new succinct de Bruijn graph representation of k-mers in a DNA sequence of length N has m edges, which can be represented in 4m+o(m) bits much smaller than existing ones.
Fully Functional Suffix Trees and Optimal Text Searching in BWT-Runs Bounded Space
TL;DR: This article shows how to extend the Run-Length FM-index so that it can locate the occ occurrences efficiently (in O(occ log log n) time) within O(r) space, and outperforms the space-competitive alternatives by 1--2 orders of magnitude in time.
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•Proceedings Article
Optimal-time text indexing in BWT-runs bounded space
Travis Gagie,Gonzalo Navarro,Nicola Prezza +2 more
- 07 Jan 2018
TL;DR: In this paper, the Run-Length FM-index was extended to O(r log n/r) space, where r is the number of runs in their Burrows-Wheeler Transform (BWT).
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•Journal Article
Theoretical and practical improvements on the RMQ-problem, with applications to LCA and LCE
Johannes Fischer,Volker Heun +1 more
TL;DR: In this paper, the authors present a linear preprocessing time and constant query time algorithm for the range minimum query problem without making use of any dynamic data structure, which consumes less than half of the space that is needed by the method by Berkman and Vishkin.
116
Variable-Order de Bruijn Graphs
Christina Boucher,Alex Bowe,Travis Gagie,Simon J. Puglisi,Kunihiko Sadakane +4 more
- 07 Apr 2015
TL;DR: The experiments show the augmenting of a succinct de Bruijn graph representation by Bowe et al. to support new operations that let us change order on the fly only modestly increases space usage, construction time, and navigation time compared to a single order graph.
84
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