Related papers: Approximating Edit Distance in the Fully Dynamic M…
The algorithmic tasks of computing the Hamming distance between a given pattern of length $m$ and each location in a text of length $n$ is one of the most fundamental algorithmic tasks in string algorithms. Unfortunately, there is evidence…
We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…
We provide improved upper bounds for the simultaneous sketching complexity of edit distance. Consider two parties, Alice with input $x\in\Sigma^n$ and Bob with input $y\in\Sigma^n$, that share public randomness and are given a promise that…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
This study aims to publish a novel similarity metric to increase the speed of comparison operations. Also the new metric is suitable for distance-based operations among strings. Most of the simple calculation methods, such as string length…
The Dynamic Time Warping (DTW) distance is a popular similarity measure for polygonal curves (i.e., sequences of points). It finds many theoretical and practical applications, especially for temporal data, and is known to be a robust,…
String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…
We revisit a fundamental problem in string matching: given a pattern of length m and a text of length n, both over an alphabet of size $\sigma$, compute the Hamming distance between the pattern and the text at every location. Several…
We give an $\tilde O(n^2)$ time algorithm for computing the exact Dynamic Time Warping distance between two strings whose run-length encoding is of size at most $n$. This matches (up to log factors) the known (conditional) lower bound, and…
The trace reconstruction problem studies the number of noisy samples needed to recover an unknown string $\boldsymbol{x}\in\{0,1\}^n$ with high probability, where the samples are independently obtained by passing $\boldsymbol{x}$ through a…
Although several self-indexes for highly repetitive text collections exist, developing an index and search algorithm with editing operations remains a challenge. Edit distance with moves (EDM) is a string-to-string distance measure that…
In this paper we define a novel edit distance for merge trees, which we argue to be suitable for a good range of applications. Relying also on some technical results contained in other works, we investigate its stability properties, which…
Kondo et al. (DS 2014) proposed methods for computing distances between unordered rooted trees by transforming an instance of the distance computing problem into an instance of the integer programming problem. They showed that the tree edit…
The substring edit error is the operation of replacing a substring $u$ of $x$ with another string $v$, where the lengths of $u$ and $v$ are bounded by a given constant $k$. It encompasses localized insertions, deletions, and substitutions…
We present Optimal Completion Distillation (OCD), a training procedure for optimizing sequence to sequence models based on edit distance. OCD is efficient, has no hyper-parameters of its own, and does not require pretraining or joint…
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…
We consider the problem of preprocessing two strings $S$ and $T$, of lengths $m$ and $n$, respectively, in order to be able to efficiently answer the following queries: Given positions $i,j$ in $S$ and positions $a,b$ in $T$, return the…
We propose an algorithm for approximative dictionary lookup, where altered strings are matched against reference forms. The algorithm makes use of a divergence function between strings -- broadly belonging to the family of edit distances;…
The tree edit distance (TED) 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 valid operations consisting of insertions, deletions…