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Given two strings of length $n$ over alphabet $\Sigma$, and an upper bound $k$ on their edit distance, the algorithm of Myers (Algorithmica'86) and Landau and Vishkin (JCSS'88) computes the unweighted string edit distance in…
Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…
A Dyck sequence is a sequence of opening and closing parentheses (of various types) that is balanced. The Dyck edit distance of a given sequence of parentheses $S$ is the smallest number of edit operations (insertions, deletions, and…
We study the online variant of the language distance problem for two classical formal languages, the language of palindromes and the language of squares, and for the two most fundamental distances, the Hamming distance and the edit…
The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet $\Sigma$. It is defined as the minimum number of node edits (insertions, deletions, and relabelings) required to…
In this paper, we present and study the \emph{Hamming distance oracle problem}. In this problem, the task is to preprocess two strings $S$ and $T$ of lengths $n$ and $m$, respectively, to obtain a data-structure that is able to answer…
In the $k$-mismatch problem we are given a pattern of length $n$ and a text and must find all locations where the Hamming distance between the pattern and the text is at most $k$. A series of recent breakthroughs have resulted in an…
In the Interval Completion problem we are given a graph G and an integer k, and the task is to turn G using at most k edge additions into an interval graph, i.e., a graph admitting an intersection model of intervals on a line. Motivated by…
Edit distance is a measure of similarity of two strings based on the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. The edit distance can be computed exactly using a…
Distance geometry explores the properties of distance spaces that can be exactly represented as the pairwise Euclidean distances between points in $\mathbb{R}^d$ ($d \geq 1$), or equivalently, distance spaces that can be isometrically…
The longest common substring with $k$-mismatches problem is to find, given two strings $S_1$ and $S_2$, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance between $A_1$ and $A_2$ is $\le k$. We introduce a…
The recently introduced longest common substring with $k$-mismatches ($k$-LCF) problem is to find, given two sequences $S_1$ and $S_2$ of length $n$ each, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance…
We study edit distance computation with preprocessing: the preprocessing algorithm acts on each string separately, and then the query algorithm takes as input the two preprocessed strings. This model is inspired by scenarios where we would…
We consider the streaming complexity of a fundamental task in approximate pattern matching: the $k$-mismatch problem. It asks to compute Hamming distances between a pattern of length $n$ and all length-$n$ substrings of a text for which the…
We consider approximate circular pattern matching (CPM, in short) under the Hamming and edit distance, in which we are given a length-$n$ text $T$, a length-$m$ pattern $P$, and a threshold $k>0$, and we are to report all starting positions…
The decades-old Pattern Matching with Edits problem, given a length-$n$ string $T$ (the text), a length-$m$ string $P$ (the pattern), and a positive integer $k$ (the threshold), asks to list all fragments of $T$ that are at edit distance at…
The problem of finding \emph{distance} between \emph{pattern} of length $m$ and \emph{text} of length $n$ is a typical way of generalizing pattern matching to incorporate dissimilarity score. For both Hamming and $L_1$ distances only a…
The edit distance between two rooted ordered trees with $n$ nodes labeled from an alphabet~$\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling…
The Dyck language, which consists of well-balanced sequences of parentheses, is one of the most fundamental context-free languages. The Dyck edit distance quantifies the number of edits (character insertions, deletions, and substitutions)…
The (unweighted) tree edit distance problem for $n$ node trees asks to compute a measure of dissimilarity between two rooted trees with node labels. The current best algorithm from more than a decade ago runs in $O(n ^ 3)$ time [Demaine,…