Related papers: Optimal Time Random Access to Grammar-Compressed S…
In the last decades, the necessity to process massive amounts of textual data fueled the development of compressed text indexes: data structures efficiently answering queries on a given text while occupying space proportional to the…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…
The representation of a dynamic ordered set of $n$ integer keys drawn from a universe of size $m$ is a fundamental data structuring problem. Many solutions to this problem achieve optimal time but take polynomial space, therefore preserving…
Suppose an oracle knows a string $S$ that is unknown to us and that we want to determine. The oracle can answer queries of the form "Is $s$ a substring of $S$?". In 1995, Skiena and Sundaram showed that, in the worst case, any algorithm…
Given a string $T$ of length $n$ over an alphabet $\Sigma\subset \{1,2,\ldots,n^{O(1)}\}$ of size $\sigma$, we are to preprocess $T$ so that given a range $[i,j]$, we can return a representation of a shortest string over $\Sigma$ that is…
A well-known fact in the field of lossless text compression is that high-order entropy is a weak model when the input contains long repetitions. Motivated by this, decades of research have generated myriads of so-called dictionary…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
Let $\D = $$ \{d_1,d_2,...d_D\}$ be a given set of $D$ string documents of total length $n$, our task is to index $\D$, such that the $k$ most relevant documents for an online query pattern $P$ of length $p$ can be retrieved efficiently. We…
In this paper we describe compressed indexes that support pattern matching queries for strings with wildcards. For a constant size alphabet our data structure uses $O(n\log^{\varepsilon}n)$ bits for any $\varepsilon>0$ and reports all…
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…
We consider the problem of storing a dynamic string $S$ over an alphabet $\Sigma=\{\,1,\ldots,\sigma\,\}$ in compressed form. Our representation supports insertions and deletions of symbols and answers three fundamental queries:…
We study the fundamental problem of finding the best string to represent a given set, in the form of the Closest String problem: Given a set $X \subseteq \Sigma^d$ of $n$ strings, find the string $x^*$ minimizing the radius of the smallest…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
A key principle in string processing is local consistency: using short contexts to handle matching fragments of a string consistently. String synchronizing sets [Kempa, Kociumaka; STOC 2019] are an influential instantiation of this…
Given a string $T$ of length $N$, the goal of grammar compression is to construct a small context-free grammar generating only $T$. Among existing grammar compression methods, RePair (recursive paring) [Larsson and Moffat, 1999] is notable…
In this paper we are interested in indexing texts for substring matching queries with one edit error. That is, given a text $T$ of $n$ characters over an alphabet of size $\sigma$, we are asked to build a data structure that answers the…
In the context of the compressed sensing problem, we propose a new ensemble of sparse random matrices which allow one (i) to acquire and compress a {\rho}0-sparse signal of length N in a time linear in N and (ii) to perfectly recover the…
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…
We consider the problem of decompressing the Lempel--Ziv 77 representation of a string $S$ of length $n$ using a working space as close as possible to the size $z$ of the input. The folklore solution for the problem runs in $O(n)$ time but…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In this paper we consider the basic variant where the pattern is…