Related papers: Faster Pattern Matching under Edit Distance
The regular expression matching problem asks whether a given regular expression of length $m$ matches a given string of length $n$. As is well known, the problem can be solved in $O(nm)$ time using Thompson's algorithm. Moreover, recent…
We study the approximability of two related problems on graphs with $n$ nodes and $m$ edges: $n$-Pairs Shortest Paths ($n$-PSP), where the goal is to find a shortest path between $O(n)$ prespecified pairs, and All Node Shortest Cycles…
The Permutation Pattern Matching problem asks, given two permutations $\sigma$ on $n$ elements and $\pi$, whether $\sigma$ admits a subsequence with the same relative order as $\pi$ (or, in the counting version, how many such subsequences…
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…
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
The $k$-mappability problem has two integers parameters $m$ and $k$. For every subword of size $m$ in a text $S$, we wish to report the number of indices in $S$ in which the word occurs with at most $k$ mismatches. The problem was lately…
We give new sublinear and parallel algorithms for the extensively studied problem of approximating n-variable r-CSPs (constraint satisfaction problems with constraints of arity r up to an additive error. The running time of our algorithms…
We consider the problem of counting the copies of a length-$k$ pattern $\sigma$ in a sequence $f \colon [n] \to \mathbb{R}$, where a copy is a subset of indices $i_1 < \ldots < i_k \in [n]$ such that $f(i_j) < f(i_\ell)$ if and only if…
The edit distance between two strings is defined as the smallest number of insertions, deletions, and substitutions that need to be made to transform one of the strings to another one. Approximating edit distance in subquadratic time is…
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…
Given a context free language $\mathcal{L(G)}$ over alphabet $\Sigma$ and a string $s \in \Sigma^*$, {\em the language edit distance} problem seeks the minimum number of edits (insertions, deletions and substitutions) required to convert…
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…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…
Edit distance is a fundamental measure of distance between strings and has been widely studied in computer science. While the problem of estimating edit distance has been studied extensively, the equally important question of actually…
Given a set $\Pi$ of permutation patterns of length at most $k$, we present an algorithm for building $S_{\le n}(\Pi)$, the set of permutations of length at most $n$ avoiding the patterns in $\Pi$, in time $O(|S_{\le n - 1}(\Pi)| \cdot k +…
The convolution between a text string $S$ of length $N$ and a pattern string $P$ of length $m$ can be computed in $O(N \log m)$ time by FFT. It is known that various types of approximate string matching problems are reducible to…
The {\em maximum cardinality} and {\em maximum weight matching} problems can be solved in time $\tilde{O}(m\sqrt{n})$, a bound that has resisted improvement despite decades of research. (Here $m$ and $n$ are the number of edges and…
In this paper, a fully compressed pattern matching problem is studied. The compression is represented by straight-line programs (SLPs), i.e. a context-free grammars generating exactly one string; the term fully means that both the pattern…
We present an $\tilde O(m+n^{1.5})$-time randomized algorithm for maximum cardinality bipartite matching and related problems (e.g. transshipment, negative-weight shortest paths, and optimal transport) on $m$-edge, $n$-node graphs. For…
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 $S$…