Minimal Suffix and Rotation of a Substring in Optimal Time

For a text given in advance, the substring minimal suffix queries ask to determine the lexicographically minimal non-empty suffix of a substring specified by the location of its occurrence in the text. We develop a data structure answering such queries optimally: in constant time after linear-time preprocessing. This improves upon the results of Babenko et al. (CPM 2014), whose trade-off solution is characterized by $\Theta(n\log n)$ product of these time complexities. Next, we extend our queries to support concatenations of $O(1)$ substrings, for which the construction and query time is preserved. We apply these generalized queries to compute lexicographically minimal and maximal rotations of a given substring in constant time after linear-time preprocessing. Our data structures mainly rely on properties of Lyndon words and Lyndon factorizations. We combine them with further algorithmic and combinatorial tools, such as fusion trees and the notion of order isomorphism of strings

Lyndon Factorization of Grammar Compressed Texts Revisited

We revisit the problem of computing the Lyndon factorization of a string w of length N which is given as a straight line program (SLP) of size n. For this problem, we show a new algorithm which runs in O(P(n, N) + Q(n, N)n log log N) time and O(n log N + S(n, N)) space where P(n, N), S(n,N), Q(n,N) are respectively the pre-processing time, space, and query time of a data structure for longest common extensions (LCE) on SLPs. Our algorithm improves the algorithm proposed by I et al. (TCS \u2717), and can be more efficient than the O(N)-time solution by Duval (J. Algorithms \u2783) when w is highly compressible

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

Optimal construction of compressed indexes for highly repetitive texts

We propose algorithms that, given the input string of length n over integer alphabet of size σ, construct the Burrows–Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in O(n/ logσ n + r polylog n) time and working space, where r is the number of runs in the BWT of the input. These are the essential components of many compressed indexes such as compressed suffix tree, FM-index, and grammar and LZ77-based indexes, but also find numerous applications in sequence analysis and data compression. The value of r is a common measure of repetitiveness that is significantly smaller than n if the string is highly repetitive. Since just accessing every symbol of the string requires Ω(n/ logσ n) time, the presented algorithms are time and space optimal for inputs satisfying the assumption n/r ∈ Ω(polylog n) on the repetitiveness. For such inputs our result improves upon the currently fastest general algorithms of Belazzougui (STOC 2014) and Munro et al. (SODA 2017) which run in O(n) time and use O(n/ logσ n) working space. We also show how to use our techniques to obtain optimal solutions on highly repetitive data for other fundamental string processing problems such as: Lyndon factorization, construction of run-length compressed suffix arrays, and some classical “textbook” problems such as computing the longest substring occurring at least some fixed number of times. Copyright © 2019 by SIAMPeer reviewe

Compressibility-Aware Quantum Algorithms on Strings

Sublinear time quantum algorithms have been established for many fundamental problems on strings. This work demonstrates that new, faster quantum algorithms can be designed when the string is highly compressible. We focus on two popular and theoretically significant compression algorithms -- the Lempel-Ziv77 algorithm (LZ77) and the Run-length-encoded Burrows-Wheeler Transform (RL-BWT), and obtain the results below. We first provide a quantum algorithm running in $\tilde{O}(\sqrt{zn})$ time for finding the LZ77 factorization of an input string $T[1..n]$ with $z$ factors. Combined with multiple existing results, this yields an $\tilde{O}(\sqrt{rn})$ time quantum algorithm for finding the RL-BWT encoding with $r$ BWT runs. Note that $r = \tilde{\Theta}(z)$. We complement these results with lower bounds proving that our algorithms are optimal (up to polylog factors). Next, we study the problem of compressed indexing, where we provide a $\tilde{O}(\sqrt{rn})$ time quantum algorithm for constructing a recently designed $\tilde{O}(r)$ space structure with equivalent capabilities as the suffix tree. This data structure is then applied to numerous problems to obtain sublinear time quantum algorithms when the input is highly compressible. For example, we show that the longest common substring of two strings of total length $n$ can be computed in $\tilde{O}(\sqrt{zn})$ time, where $z$ is the number of factors in the LZ77 factorization of their concatenation. This beats the best known $\tilde{O}(n^\frac{2}{3})$ time quantum algorithm when $z$ is sufficiently small

Rank, select and access in grammar-compressed strings

Given a string $S$ of length $N$ on a fixed alphabet of $\sigma$ symbols, a grammar compressor produces a context-free grammar $G$ of size $n$ that generates $S$ and only $S$. In this paper we describe data structures to support the following operations on a grammar-compressed string: \mbox{rank}_c(S,i) (return the number of occurrences of symbol $c$ before position $i$ in $S$); \mbox{select}_c(S,i) (return the position of the $i$th occurrence of $c$ in $S$); and \mbox{access}(S,i,j) (return substring $S[i,j]$). For rank and select we describe data structures of size $O(n\sigma\log N)$ bits that support the two operations in $O(\log N)$ time. We propose another structure that uses $O(n\sigma\log (N/n)(\log N)^{1+\epsilon})$ bits and that supports the two queries in $O(\log N/\log\log N)$, where $\epsilon>0$ is an arbitrary constant. To our knowledge, we are the first to study the asymptotic complexity of rank and select in the grammar-compressed setting, and we provide a hardness result showing that significantly improving the bounds we achieve would imply a major breakthrough on a hard graph-theoretical problem. Our main result for access is a method that requires $O(n\log N)$ bits of space and $O(\log N+m/\log_\sigma N)$ time to extract $m=j-i+1$ consecutive symbols from $S$. Alternatively, we can achieve $O(\log N/\log\log N+m/\log_\sigma N)$ query time using $O(n\log (N/n)(\log N)^{1+\epsilon})$ bits of space. This matches a lower bound stated by Verbin and Yu for strings where $N$ is polynomially related to $n$.Comment: 16 page