Related papers: Alphabet-Dependent String Searching with Wexponent…
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 weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
We propose new succinct representations of ordinal trees, which have been studied extensively. It is known that any $n$-node static tree can be represented in $2n + o(n)$ bits and a number of operations on the tree can be supported in…
Given a dynamic set $K$ of $k$ strings of total length $n$ whose characters are drawn from an alphabet of size $\sigma$, a keyword dictionary is a data structure built on $K$ that provides locate, prefix search, and update operations on…
We present two algorithms for dynamically maintaining a spanning forest of a graph undergoing edge insertions and deletions. Our algorithms guarantee {\em worst-case update time} and work against an adaptive adversary, meaning that an edge…
We give two fully dynamic algorithms that maintain a $(1+\varepsilon)$-approximation of the weight $M$ of a minimum spanning forest (MSF) of an $n$-node graph $G$ with edges weights in $[1,W]$, for any $\varepsilon>0$. (1) Our deterministic…
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…
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…
In this work, we study the limits of compressed data structures, i.e., structures that support various queries on an input text $T\in\Sigma^n$ using space proportional to the size of $T$ in compressed form. Nearly all fundamental queries…
The problem of Text Indexing is a fundamental algorithmic problem in which one wishes to preprocess a text in order to quickly locate pattern queries within the text. In the ever evolving world of dynamic and on-line data, there is also a…
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…
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…
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…
We show how to determine whether a given pattern p of length m occurs in a given text t of length n in ${\tilde O}(\sqrt{n}+\sqrt{m})$\footnote{${\tilde O}$ allows for logarithmic factors in m and $n/m$} time, with inverse polynomial…
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 revisit the fundamental problem of dictionary look-up with mismatches. Given a set (dictionary) of $d$ strings of length $m$ and an integer $k$, we must preprocess it into a data structure to answer the following queries: Given a query…
We introduce a compressed suffix array representation that, on a text $T$ of length $n$ over an alphabet of size $\sigma$, can be built in $O(n)$ deterministic time, within $O(n\log\sigma)$ bits of working space, and counts the number of…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
We consider a range of simply stated dynamic data structure problems on strings. An update changes one symbol in the input and a query asks us to compute some function of the pattern of length $m$ and a substring of a longer text. We give…
We study the problem of supporting queries on a string $S$ of length $n$ within a space bounded by the size $\gamma$ of a string attractor for $S$. Recent works showed that random access on $S$ can be supported in optimal…