Related papers: Faster two-dimensional pattern matching with $k$ m…
Given strings $P$ of length $m$ and $T$ of length $n$ over an alphabet of size $\sigma$, the string matching with $k$-mismatches problem is to find the positions of all the substrings in $T$ that are at Hamming distance at most $k$ from…
Matching is a method of the design of experiments. If we had an even number of patients and wanted to form pairs of patients such that their ages, for example, in each pair be as close as possible, we would use nonbipartite matching. Not…
In this paper we study lower bounds for the fundamental problem of text indexing with mismatches and differences. In this problem we are given a long string of length $n$, the "text", and the task is to preprocess it into a data structure…
In this work, we consider pattern matching variants in small space, that is, in the read-only setting, where we want to bound the space usage on top of storing the strings. Our main contribution is a space-time trade-off for the Internal…
Given a pattern $P$ and a text $T$, both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of $P$ occurs in $T$. The indexed version of this problem, i.e., preprocessing a…
In this paper we define a new problem, motivated by computational biology, $LCSk$ aiming at finding the maximal number of $k$ length $substrings$, matching in both input strings while preserving their order of appearance. The traditional…
Longest Common Substring (LCS) is an important text processing problem, which has recently been investigated in the quantum query model. The decisional version of this problem, LCS with threshold $d$, asks whether two length-$n$ input…
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,…
In the problem of the longest common substring with $k$ mismatches we are given two strings $X, Y$ and must find the maximal length $\ell$ such that there is a length-$\ell$ substring of $X$ and a length-$\ell$ substring of $Y$ that differ…
More than 120 algorithms have been developed for exact string matching within the last 40 years. We show by experiments that the \naive{} algorithm exploiting SIMD instructions of modern CPUs (with symbols compared in a special order) is…
Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…
Edit distance similarity search, also called approximate pattern matching, is a fundamental problem with widespread database applications. The goal of the problem is to preprocess $n$ strings of length $d$, to quickly answer queries $q$ of…
We revisit the exact shortest unique substring (SUS) finding problem, and propose its approximate version where mismatches are allowed, due to its applications in subfields such as computational biology. We design a generic in-place…
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…
Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…
A sample of n generic points in the xy-plane defines a permutation that relates their ranks along the two axes. Every subset of k points similarly defines a pattern, which occurs in that permutation. The number of occurrences of small…
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…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
The problem of dictionary matching is a classical problem in string matching: given a set S of d strings of total length n characters over an (not necessarily constant) alphabet of size sigma, build a data structure so that we can match in…
The 2-LCPS problem, first introduced by Chowdhury et al. [Fundam. Inform., 129(4):329-340, 2014], asks one to compute (the length of) a longest palindromic common subsequence between two given strings $A$ and $B$. We show that the 2-LCPS…