Related papers: Compressed Indexing with Signature Grammars
We describe the first self-indexes able to count and locate pattern occurrences in optimal time within a space bounded by the size of the most popular dictionary compressors. To achieve this result we combine several recent findings,…
The random access problem for compressed strings is to build a data structure that efficiently supports accessing the character in position $i$ of a string given in compressed form. Given a grammar of size $n$ compressing a string of size…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
We consider document listing on string collections, that is, finding in which strings a given pattern appears. In particular, we focus on repetitive collections: a collection of size $N$ over alphabet $[1,\sigma]$ is composed of $D$ copies…
We consider the $Parameterized$ $Pattern$ $Matching$ problem, where a pattern $P$ matches some location in a text $\mathsf{T}$ iff there is a one-to-one correspondence between the alphabet symbols of the pattern to those of the text. More…
Countless variants of the Lempel-Ziv compression are widely used in many real-life applications. This paper is concerned with a natural modification of the classical pattern matching problem inspired by the popularity of such compression…
The Karp-Rabin fingerprint of a string is a type of hash value that due to its strong properties has been used in many string algorithms. In this paper we show how to construct a data structure for a string $S$ of size $N$ compressed by a…
Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…
Given a pattern $P$ and a text $T$, both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of $P$ occurs in $T$. The indexed version of this problem, i.e., preprocessing a…
In this paper we describe a data structure that supports pattern matching queries on a dynamically arriving text over an alphabet ofconstant size. Each new symbol can be prepended to $T$ in O(1) worst-case time. At any moment, we can report…
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…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
We consider a natural generalization of the classical pattern matching problem: given compressed representations of a pattern p[1..M] and a text t[1..N] of sizes m and n, respectively, does p occur in t? We develop an optimal linear time…
In Gapped String Indexing, the goal is to compactly represent a string $S$ of length $n$ such that for any query consisting of two strings $P_1$ and $P_2$, called patterns, and an integer interval $[\alpha, \beta]$, called gap range, we can…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
Practical data structures for the edit-sensitive parsing (ESP) are proposed. Given a string S, its ESP tree is equivalent to a context-free grammar G generating just S, which is represented by a DAG. Using the succinct data structures for…
Given a string $S$ over an alphabet $\Sigma$, the 'string indexing problem' is to preprocess $S$ to subsequently support efficient pattern matching queries, i.e., given a pattern string $P$ report all the occurrences of $P$ in $S$. In this…
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…
A compressed self-index stores a string in compressed form while supporting locate queries without decompression. For highly repetitive strings (arising in web crawls, versioned documents, and genomic collections), static self-indexes can…