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Random Access to Grammar-Compressed Strings and Trees

Random access to grammar-compressed strings and trees
Authors: Philip Bille; Gad M. Landau; Rajeev Raman; Kunihiko Sadakane; Srinivasa Rao Satti; Oren Weimann;

Random Access to Grammar-Compressed Strings and Trees

Abstract

Summary: Grammar-based compression, where one replaces a long string by a small context-free grammar that generates the string, is a simple and powerful paradigm that captures (sometimes with slight reduction in efficiency) many of the popular compression schemes, including the Lempel-Ziv family, run-length encoding, byte-pair encoding, Sequitur, and Re-Pair. In this paper, we present a novel grammar representation that allows efficient random access to any character or substring without decompressing the string. Let \(S\) be a string of length \(N\) compressed into a context-free grammar \(\mathcal{S}\) of size \(n\). We present two representations of \(\mathcal{S}\) achieving \(O(\log N)\) random access time, and either \(O(n\cdot\alpha_k(n))\) construction time and space on the pointer machine model, or \(O(n)\) construction time and space on the RAM. Here, \(\alpha_k(n)\) is the inverse of the \(k\)th row of Ackermann's function. Our representations also efficiently support decompression of any substring in \(S\): we can decompress any substring of length \(m\) in the same complexity as a single random access query and additional \(O(m)\) time. Combining these results with fast algorithms for uncompressed approximate string matching leads to several efficient algorithms for approximate string matching on grammar-compressed strings without decompression. For instance, we can find all approximate occurrences of a pattern \(P\) with at most \(k\) errors in time \(O(n(\min\{|P|k,k^4+|P|\}+\log N)+\mathrm{occ})\), where \(\mathrm{occ}\) is the number of occurrences of \(P\) in \(S\). Finally, we generalize our results to navigation and other operations on grammar-compressed ordered trees. All of the above bounds significantly improve the currently best known results. To achieve these bounds, we introduce several new techniques and data structures of independent interest, including a predecessor data structure, two ``biased'' weighted ancestor data structures, and a compact representation of heavy paths in grammars.

Countries
Denmark, United Kingdom
Keywords

approximate string matching, Data structures, straight-line program, Grammars and rewriting systems, 005, tree compression, grammar-based compression, Coding and information theory (compaction, compression, models of communication, encoding schemes, etc.) (aspects in computer science), Algorithms on strings

  • BIP!
    Impact byBIP!
    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    75
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Top 10%
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
75
Top 10%
Top 10%
Top 10%
Green
bronze