Related papers: Linear-size CDAWG: new repetition-aware indexing a…
The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression…
Various grammar compression algorithms have been proposed in the last decade. A grammar compression is a restricted CFG deriving the string deterministically. An efficient grammar compression develops a smaller CFG by finding duplicated…
We present a highly parallelizable text compression algorithm that scales efficiently to terabyte-sized datasets. Our method builds on locally consistent grammars, a lightweight form of compression, combined with simple recompression…
We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $\sigma$, our algorithm uses…
Pattern matching is the most central task for text indices. Most recent indices leverage compression techniques to make pattern matching feasible for massive but highly-compressible datasets. Within this kind of indices, we propose a new…
A string $w$ is said to be a minimal absent word (MAW) for a string $S$ if $w$ does not occur in $S$ and any proper substring of $w$ occurs in $S$. We focus on non-trivial MAWs which are of length at least 2. Finding such non-trivial MAWs…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
We introduce a new class of straight-line programs (SLPs), named the Lyndon SLP, inspired by the Lyndon trees (Barcelo, 1990). Based on this SLP, we propose a self-index data structure of $O(g)$ words of space that can be built from a…
In this paper we present a simple linear-time algorithm constructing a context-free grammar of size O(g log(N/g)) for the input string, where N is the size of the input string and g the size of the optimal grammar generating this string.…
We introduce the first grammar-compressed representation of a sequence that supports searches in time that depends only logarithmically on the size of the grammar. Given a text $T[1..u]$ that is represented by a (context-free) grammar of…
Two recent lower bounds on the compressibility of repetitive sequences, $\delta \le \gamma$, have received much attention. It has been shown that a length-$n$ string $S$ over an alphabet of size $\sigma$ can be represented within the…
The circular dictionary matching problem is an extension of the classical dictionary matching problem where every string in the dictionary is interpreted as a circular string: after reading the last character of a string, we can move back…
We present a new on-line algorithm for computing the Lempel-Ziv factorization of a string that runs in $O(N\log N)$ time and uses only $O(N\log\sigma)$ bits of working space, where $N$ is the length of the string and $\sigma$ is the size of…
We present a new graph compressor that works by recursively detecting repeated substructures and representing them through grammar rules. We show that for a large number of graphs the compressor obtains smaller representations than other…
In this paper, we propose a new \emph{dynamic compressed index} of $O(w)$ space for a dynamic text $T$, where $w = O(\min(z \log N \log^*M, N))$ is the size of the signature encoding of $T$, $z$ is the size of the Lempel-Ziv77 (LZ77)…
Re-Pair is an effective grammar-based compression scheme achieving strong compression rates in practice. Let $n$, $\sigma$, and $d$ be the text length, alphabet size, and dictionary size of the final grammar, respectively. In their original…
Re-Pair is an efficient grammar compressor that operates by recursively replacing high-frequency character pairs with new grammar symbols. The most space-efficient linear-time algorithm computing Re-Pair uses $(1+\epsilon)n+\sqrt n$ words…
In this paper, we present the following results: (1) We propose a new \emph{dynamic compressed index} of $O(w)$ space, that supports searching for a pattern $P$ in the current text in $O(|P| f(M,w) + \log w \log |P| \log^* M (\log N + \log…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
Indexing highly repetitive texts - such as genomic databases, software repositories and versioned text collections - has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts…