Related papers: An Efficient Generalized Shift-Rule for the Prefer…

The reduction of the fragment assembly problem to (variations of) the classical Eulerian trail problem [Pevzner et al., PNAS 2001] has led to remarkable progress in genome assembly. This reduction employs the notion of de Bruijn graph…

Let be the following strategy to construct a walk in a labeled digraph: at each vertex, we follow the unvisited arc of minimum label. In this work we study for which languages, applying the previous strategy over the corresponding de Bruijn…

We study the influence of a graph parameter called modular-width on the time complexity for optimally solving well-known polynomial problems such as Maximum Matching, Triangle Counting, and Maximum $s$-$t$ Vertex-Capacitated Flow. The…

In this paper we study those generic intervals in the Bruhat order of the symmetric group that are isomorphic to the principal order ideal of a permutation w, and consider when the minimum and maximum elements of those intervals are related…

In the recent research of data mining, frequent structures in a sequence of graphs have been studied intensively, and one of the main concern is changing structures along a sequence of graphs that can capture dynamic properties of data. On…

Universal cycles are generalizations of de Bruijn cycles and Gray codes that were introduced originally by Chung, Diaconis, and Graham in 1990. They have been developed by many authors since, for various combinatorial objects such as…

Given a string $T$ on an alphabet of size $\sigma$, we describe a bidirectional Burrows-Wheeler index that takes $O(|T|\log{\sigma})$ bits of space, and that supports the addition \emph{and removal} of one character, on the left or right…

This paper considers a sequence of random variables generated according to a common distribution. The distribution might undergo periods of transient changes at an unknown set of time instants, referred to as change-points. The objective is…

To each one-dimensional subshift $X$, we may associate a winning shift $W(X)$ which arises from a combinatorial game played on the language of $X$. Previously it has been studied what properties of $X$ does $W(X)$ inherit. For example, $X$…

Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…

A factorization $f_1, \ldots, f_m$ of a string $w$ of length $n$ is called a repetition factorization of $w$ if $f_i$ is a repetition, i.e., $f_i$ is a form of $x^kx'$, where $x$ is a non-empty string, $x'$ is a (possibly-empty) proper…

Given a permutation sigma of the integers {-n,-n+1,...,n} we consider the Markov chain X_{sigma}, which jumps from k to sigma (k\pm 1) equally likely if k\neq -n,n. We prove that the expected hitting time of {-n,n} starting from any point…

Transformers have achieved state-of-the-art performance in numerous tasks. In this paper, we propose a continuous-time formulation of transformers. Specifically, we consider a dynamical system whose governing equation is parametrized by…

The random access problem for compressed strings is to build a data structure that efficiently supports accessing the character in position $i$ of a string given in compressed form. Given a grammar of size $n$ compressing a string of size…

Let $\sigma$ be a permutation of $\{0,\ldots,n\}$. We consider the Markov chain $X$ which jumps from $k\neq 0,n$ to $\sigma(k+1)$ or $\sigma(k-1)$, equally likely. When $X$ is at 0 it jumps to either $\sigma(0)$ or $\sigma(1)$ equally…

In the Proper Interval Completion problem we are given a graph G and an integer k, and the task is to turn G using at most k edge additions into a proper interval graph, i.e., a graph admitting an intersection model of equal-length…

The de Bruijn torus (or grid) problem looks to find an $n$-by-$m$ binary matrix in which every possible $j$-by-$k$ submatrix appears exactly once. The existence and construction of these binary matrices was determined in the 70's, with…

We improve the best known upper bound on the length of the shortest reset words of synchronizing automata. The new bound is slightly better than $114 n^3 / 685 + O(n^2)$. The \v{C}ern\'y conjecture states that $(n-1)^2$ is an upper bound.…

Universal Cycles, or U-cycles, as originally defined by de Bruijn, are an efficient method to exhibit a large class of combinatorial objects in a compressed fashion, and with no repeats. de Bruijn's theorem states that U-cycles for $n$…

Given a word $w$ and a Parikh vector $\mathcal{P}$, an abelian run of period $\mathcal{P}$ in $w$ is a maximal occurrence of a substring of $w$ having abelian period $\mathcal{P}$. We give an algorithm that finds all the abelian runs of…