Finger Search in Grammar-Compressed Strings

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 many popular compression schemes. Given a grammar, the random access problem is to compactly represent the grammar while supporting random access, that is, given a position in the original uncompressed string report the character at that position. In this paper we study the random access problem with the finger search property, that is, the time for a random access query should depend on the distance between a specified index $f$, called the \emph{finger}, and the query index $i$. We consider both a static variant, where we first place a finger and subsequently access indices near the finger efficiently, and a dynamic variant where also moving the finger such that the time depends on the distance moved is supported. Let $n$ be the size the grammar, and let $N$ be the size of the string. For the static variant we give a linear space representation that supports placing the finger in $O(\log N)$ time and subsequently accessing in $O(\log D)$ time, where $D$ is the distance between the finger and the accessed index. For the dynamic variant we give a linear space representation that supports placing the finger in $O(\log N)$ time and accessing and moving the finger in $O(\log D + \log \log N)$ time. Compared to the best linear space solution to random access, we improve a $O(\log N)$ query bound to $O(\log D)$ for the static variant and to $O(\log D + \log \log N)$ for the dynamic variant, while maintaining linear space. As an application of our results we obtain an improved solution to the longest common extension problem in grammar compressed strings. To obtain our results, we introduce several new techniques of independent interest, including a novel van Emde Boas style decomposition of grammars

Fully dynamic data structure for LCE queries in compressed space

A Longest Common Extension (LCE) query on a text $T$ of length $N$ asks for the length of the longest common prefix of suffixes starting at given two positions. We show that the signature encoding $\mathcal{G}$ of size $w = O(\min(z \log N \log^* M, N))$ [Mehlhorn et al., Algorithmica 17(2):183-198, 1997] of $T$, which can be seen as a compressed representation of $T$, has a capability to support LCE queries in $O(\log N + \log \ell \log^* M)$ time, where $\ell$ is the answer to the query, $z$ is the size of the Lempel-Ziv77 (LZ77) factorization of $T$, and $M \geq 4N$ is an integer that can be handled in constant time under word RAM model. In compressed space, this is the fastest deterministic LCE data structure in many cases. Moreover, $\mathcal{G}$ can be enhanced to support efficient update operations: After processing $\mathcal{G}$ in $O(w f_{\mathcal{A}})$ time, we can insert/delete any (sub)string of length $y$ into/from an arbitrary position of $T$ in $O((y+ \log N\log^* M) f_{\mathcal{A}})$ time, where $f_{\mathcal{A}} = O(\min \{ \frac{\log\log M \log\log w}{\log\log\log M}, \sqrt{\frac{\log w}{\log\log w}} \})$. This yields the first fully dynamic LCE data structure. We also present efficient construction algorithms from various types of inputs: We can construct $\mathcal{G}$ in $O(N f_{\mathcal{A}})$ time from uncompressed string $T$; in $O(n \log\log n \log N \log^* M)$ time from grammar-compressed string $T$ represented by a straight-line program of size $n$; and in $O(z f_{\mathcal{A}} \log N \log^* M)$ time from LZ77-compressed string $T$ with $z$ factors. On top of the above contributions, we show several applications of our data structures which improve previous best known results on grammar-compressed string processing.Comment: arXiv admin note: text overlap with arXiv:1504.0695

A Space-Optimal Grammar Compression

A grammar compression is a context-free grammar (CFG) deriving a single string deterministically. For an input string of length N over an alphabet of size sigma, the smallest CFG is O(log N)-approximable in the offline setting and O(log N log^* N)-approximable in the online setting. In addition, an information-theoretic lower bound for representing a CFG in Chomsky normal form of n variables is log (n!/n^sigma) + n + o(n) bits. Although there is an online grammar compression algorithm that directly computes the succinct encoding of its output CFG with O(log N log^* N) approximation guarantee, the problem of optimizing its working space has remained open. We propose a fully-online algorithm that requires the fewest bits of working space asymptotically equal to the lower bound in O(N log log n) compression time. In addition we propose several techniques to boost grammar compression and show their efficiency by computational experiments

Longest Common Extensions with Recompression

Given two positions i and j in a string T of length N, a longest common extension (LCE) query asks for the length of the longest common prefix between suffixes beginning at i and j. A compressed LCE data structure stores T in a compressed form while supporting fast LCE queries. In this article we show that the recompression technique is a powerful tool for compressed LCE data structures. We present a new compressed LCE data structure of size O(z lg (N/z)) that supports LCE queries in O(lg N) time, where z is the size of Lempel-Ziv 77 factorization without self-reference of T. Given T as an uncompressed form, we show how to build our data structure in O(N) time and space. Given T as a grammar compressed form, i.e., a straight-line program of size n generating T, we show how to build our data structure in O(n lg (N/n)) time and O(n + z lg (N/z)) space. Our algorithms are deterministic and always return correct answers