Related papers: Cut-Down de Bruijn Sequences
We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…
Cutwidth of a digraph is a width measure introduced by Chudnovsky, Fradkin, and Seymour [4] in connection with development of a structural theory for tournaments, or more generally, for semi-complete digraphs. In this paper we provide an…
A superpermutation is a sequence that contains every permutation of $n$ distinct symbols as a contiguous substring. For instance, a valid example for three symbols is a sequence that contains all six permutations. This paper introduces a…
We solve an open problem related to an optimal encoding of a straight line program (SLP), a canonical form of grammar compression deriving a single string deterministically. We show that an information-theoretic lower bound for representing…
Sequences with a low correlation have very important applications in communications, cryptography, and compressed sensing. In the literature, many efforts have been made to construct good sequences with various lengths where binary…
de Bruijn sequences of order $\ell$, i.e., sequences that contain each $\ell$-tuple as a window exactly once, have found many diverse applications in information theory and most recently in DNA storage. This family of binary sequences has…
We consider the (exact, minimum) $k$-cut problem: given a graph and an integer $k$, delete a minimum-weight set of edges so that the remaining graph has at least $k$ connected components. This problem is a natural generalization of the…
We study the Laplacian of the undirected De Bruijn graph over an alphabet $A$ of order $k$. While the eigenvalues of this Laplacian were found in 1998 by Delorme and Tillich [1], an explicit description of its eigenvectors has remained…
We present an algorithm computing the longest periodic subsequence of a string of length $n$ in $O(n^7)$ time with $O(n^4)$ words of space. We obtain improvements when restricting the exponents or extending the search allowing the reported…
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…
Matrix multiplication is a fundamental task in almost all computational fields, including machine learning and optimization, computer graphics, signal processing, and graph algorithms (static and dynamic). Twin-width is a natural complexity…
We propose a general greedy algorithm for binary de Bruijn sequences, called Generalized Prefer-Opposite (GPO) Algorithm, and its modifications. By identifying specific feedback functions and initial states, we demonstrate that most…
Given a string $T$ of length $n$, a substring $u = T[i..j]$ of $T$ is called a shortest unique substring (SUS) for an interval $[s,t]$ if (a) $u$ occurs exactly once in $T$, (b) $u$ contains the interval $[s,t]$ (i.e. $i \leq s \leq t \leq…
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…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
The circular dictionary matching problem is an extension of the classical dictionary matching problem where every string in the dictionary is interpreted as a circular string: after reading the last character of a string, we can move back…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…
Unbreakable decomposition, introduced by Cygan et al. (SICOMP'19) and Cygan et al. (TALG'20), has proven to be one of the most powerful tools for parameterized graph cut problems in recent years. Unfortunately, all known constructions…
Suppose an oracle knows a string $S$ that is unknown to us and that we want to determine. The oracle can answer queries of the form "Is $s$ a substring of $S$?". In 1995, Skiena and Sundaram showed that, in the worst case, any algorithm…
In the paper, the Levenshtein's sequence reconstruction problem is considered in the case where at most $t$ substitution errors occur in each of the $N$ channels and the decoder outputs a list of length $\mathcal{L}$. Moreover, it is…