Related papers: Rollercoasters with Plateaus
A factor $u$ of a word $w$ is a cover of $w$ if every position in $w$ lies within some occurrence of $u$ in $w$. A word $w$ covered by $u$ thus generalizes the idea of a repetition, that is, a word composed of exact concatenations of $u$.…
Following (Kolpakov et al., 2013; Gawrychowski and Manea, 2015), we continue the study of {\em $\alpha$-gapped repeats} in strings, defined as factors $uvu$ with $|uv|\leq \alpha |u|$. Our main result is the $O(\alpha n)$ bound on the…
We consider the problem of maintaining a collection of strings while efficiently supporting splits and concatenations on them, as well as comparing two substrings, and computing the longest common prefix between two suffixes. This problem…
We revisit the fundamental problem of dictionary look-up with mismatches. Given a set (dictionary) of $d$ strings of length $m$ and an integer $k$, we must preprocess it into a data structure to answer the following queries: Given a query…
The longest square subsequence (LSS) problem consists of computing a longest subsequence of a given string $S$ that is a square, i.e., a longest subsequence of form $XX$ appearing in $S$. It is known that an LSS of a string $S$ of length…
The subword complexity of a finite word $w$ of length $N$ is a function which associates to each $n\le N$ the number of all distinct subwords of $w$ having the length $n$. We define the \emph{maximal complexity} C(w) as the maximum of the…
The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…
A \emph{palindrome} is a word that reads the same forwards and backwards. A \emph{block palindrome factorization} (or \emph{BP-factorization}) is a factorization of a word into blocks that becomes palindrome if each identical block is…
A gapped repeat is a factor of the form $uvu$ where $u$ and $v$ are nonempty words. The period of the gapped repeat is defined as $|u|+|v|$. The gapped repeat is maximal if it cannot be extended to the left or to the right by at least one…
Given a word $w$, what is the maximum possible number of appearances of $w$ reading contiguously along any of the directions in $\{-1, 0, 1\}^d \setminus \{\mathbf{0}\}$ in a large $d$-dimensional grid (as in a word search)? Patchell and…
To gain a better theoretical understanding of how evolutionary algorithms (EAs) cope with plateaus of constant fitness, we propose the $n$-dimensional Plateau$_k$ function as natural benchmark and analyze how different variants of the $(1 +…
A graph is called $k$-representable if there exists a word $w$ over the nodes of the graph, each node occurring exactly $k$ times, such that there is an edge between two nodes $x,y$ if and only after removing all letters distinct from…
The numbers we study in this paper are of the form $B_{n, p}(k)$, which is the number of binary words of length $n$ that contain the word $p$ (as a subsequence) exactly $k$ times. Our motivation comes from the analogous study of pattern…
Let $N(n,r,k)$ denote the number of binary words of length $n$ that begin with $0$ and contain exactly $k$ runs (i.e., maximal subwords of identical consecutive symbols) of length $r$. We show that the generating function for the sequence…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
We study a class of finite state machines, called \defi{$w$-matching machines}, which yield to simulate the behavior of pattern matching algorithms while searching for a pattern $w$. They can be used to compute the asymptotic speed, i.e.…
Graph spanners are sparse subgraphs that faithfully preserve the distances in the original graph up to small stretch. Spanner have been studied extensively as they have a wide range of applications ranging from distance oracles, labeling…
In this paper we present algorithms for several string problems in the Congested Clique model. In the Congested Clique model, $n$ nodes (computers) are used to solve some problem. The input to the problem is distributed among the nodes, and…
An {\it Omnibus Sequence} of length $n$ is one that has each possible "message" of length $k$ embedded in it as a subsequence. We study various properties of Omnibus Sequences in this paper, making connections, whenever possible, to the…
Given a string $w$, another string $v$ is said to be a subsequence of $w$ if $v$ can be obtained from $w$ by removing some of its letters; on the other hand, $v$ is called an absent subsequence of $w$ if $v$ is not a subsequence of $w$. The…