Related papers: Gapped String Indexing in Subquadratic Space and S…
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…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
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 revisit various string indexing problems with range reporting features, namely, position-restricted substring searching, indexing substrings with gaps, and indexing substrings with intervals. We obtain the following main results.…
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
We consider the problem of indexing a string $t$ of length $n$ to report the occurrences of a query pattern $p$ containing $m$ characters and $j$ wildcards. Let $occ$ be the number of occurrences of $p$ in $t$, and $\sigma$ the size of the…
A classic data structure problem is to preprocess a string T of length $n$ so that, given a query $q$, we can quickly find all substrings of T with Hamming distance at most $k$ from the query string. Variants of this problem have seen…
We study the non-overlapping indexing problem: Given a text T, preprocess it so that you can answer queries of the form: given a pattern P, report the maximal set of non-overlapping occurrences of P in T. A generalization of this problem is…
The classic string indexing problem is to preprocess a string $S$ into a compact data structure that supports efficient subsequent pattern matching queries, that is, given a pattern string $P$, report all occurrences of $P$ within $S$. In…
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…
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…
Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…
Bille and G{\o}rtz (2011) recently introduced the problem of substring range counting, for which we are asked to store compactly a string $S$ of $n$ characters with integer labels in ([0, u]), such that later, given an interval ([a, b]) and…
Given a string $S$, the \emph{compressed indexing problem} is to preprocess $S$ into a compressed representation that supports fast \emph{substring queries}. The goal is to use little space relative to the compressed size of $S$ while…
The Binary Jumbled String Matching problem is defined as: Given a string $s$ over $\{a,b\}$ of length $n$ and a query $(x,y)$, with $x,y$ non-negative integers, decide whether $s$ has a substring $t$ with exactly $x$ $a$'s and $y$ $b$'s.…
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…
A Random Access query to a string $T\in [0..\sigma)^n$ asks for the character $T[i]$ at a given position $i\in [0..n)$. In $O(n\log\sigma)$ bits of space, this fundamental task admits constant-time queries. While this is optimal in the…
Suppose that we are given a string $s$ of length $n$ over an alphabet $\{0,1,\ldots,n^{O(1)}\}$ and $\delta$ is the string complexity of $s$, a known compression measure. We describe an index on $s$ with $O(\delta\log\frac{n}{\delta})$…