Related papers: Unified Compression-Based Acceleration of Edit-Dis…

In the $k$-Edit Circular Pattern Matching ($k$-Edit CPM) problem, we are given a length-$n$ text $T$, a length-$m$ pattern $P$, and a positive integer threshold $k$, and we are to report all starting positions of the substrings of $T$ that…

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…

In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…

We study the problem of approximating edit distance in sublinear time. This is formalized as the $(k,k^c)$-Gap Edit Distance problem, where the input is a pair of strings $X,Y$ and parameters $k,c>1$, and the goal is to return YES if…

We study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…

Grammar compression is a general compression framework in which a string $T$ of length $N$ is represented as a context-free grammar of size $n$ whose language contains only $T$. In this paper, we focus on studying the limitations of…

We propose the neural string edit distance model for string-pair matching and string transduction based on learnable string edit distance. We modify the original expectation-maximization learned edit distance algorithm into a differentiable…

The tree edit distance problem is a natural generalization of the classic string edit distance problem. Given two ordered, edge-labeled trees $T_1$ and $T_2$, the edit distance between $T_1$ and $T_2$ is defined as the minimum total cost of…

Many consensus string problems are based on Hamming distance. We replace Hamming distance by the more flexible (e.g., easily coping with different input string lengths) dynamic time warping distance, best known from applications in time…

Edit Distance is a classic family of dynamic programming problems, among which Time Warp Edit Distance refines the problem with the notion of a metric and temporal elasticity. A novel Improved Time Warp Edit Distance algorithm that is both…

Let $W$ be a string of length $n$ over an alphabet $\Sigma$, $k$ be a positive integer, and $\mathcal{S}$ be a set of length-$k$ substrings of $W$. The ETFS problem asks us to construct a string $X_{\mathrm{ED}}$ such that: (i) no string of…

The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…

The text-to-pattern Hamming distances problem asks to compute the Hamming distances between a given pattern of length $m$ and all length-$m$ substrings of a given text of length $n\ge m$. We focus on the $k$-mismatch version of the problem,…

The problem of computing the edit-distance between a string and a finite automaton arises in a variety of applications in computational biology, text processing, and speech recognition. This paper presents linear-space algorithms for…

We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…

For any $T \geq 1$, there are constants $R=R(T) \geq 1$ and $\zeta=\zeta(T)>0$ and a randomized algorithm that takes as input an integer $n$ and two strings $x,y$ of length at most $n$, and runs in time $O(n^{1+\frac{1}{T}})$ and outputs an…

The longest common substring problem consists in finding a longest string that appears as a (contiguous) substring of two input strings. We consider the dynamic variant of this problem, in which we are to maintain two dynamic strings $S$…

We introduce fast-decodable indexing schemes for edit distance which can be used to speed up edit distance computations to near-linear time if one of the strings is indexed by an indexing string $I$. In particular, for every length $n$ and…

String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…

We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…