Related papers: Approximating longest common substring with $k$ mi…
Let $S$ be a string of length $n$. In this paper we introduce the notion of \emph{string attractor}: a subset of the string's positions $[1,n]$ such that every distinct substring of $S$ has an occurrence crossing one of the attractor's…
The problem of finding longest common subsequence (LCS) is one of the fundamental problems in computer science, which finds application in fields such as computational biology, text processing, information retrieval, data compression etc.…
The largest common embeddable subtree problem asks for the largest possible tree embeddable into two input trees and generalizes the classical maximum common subtree problem. Several variants of the problem in labeled and unlabeled rooted…
The equidistant subsequence pattern matching problem is considered. Given a pattern string $P$ and a text string $T$, we say that $P$ is an \emph{equidistant subsequence} of $T$ if $P$ is a subsequence of the text such that consecutive…
We consider the problem of updating the information about multiple longest common sub-sequences. This kind of sub-sequences is used to highlight information that is shared across several information sequences, therefore it is extensively…
Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…
This paper performs the analysis necessary to bound the running time of known, efficient algorithms for generating all longest common subsequences. That is, we bound the running time as a function of input size for algorithms with time…
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…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
Given a finite metric space $(X\cup Y, \mathbf{d})$ the $k$-median problem is to find a set of $k$ centers $C\subseteq Y$ that minimizes $\sum_{p\in X} \min_{c\in C} \mathbf{d}(p,c)$. In general metrics, the best polynomial time algorithm…
Many problems in bioinformatics are about finding strings that approximately represent a collection of given strings. We look at more general problems where some input strings can be classified as outliers. The Close to Most Strings problem…
Abelian string matching problems are becoming an object of considerable interest in last years. Very recently, Alatabbi et al. \cite{AILR2015} presented the first solution for the longest common Abelian factor problem for a pair of strings,…
It is shown that the length of the algorithmic minimal sufficient statistic of a binary string x, either in a representation of a finite set, computable semimeasure, or a computable function, has a length larger than the computational depth…
The classic exact pattern matching problem, given two strings -- a pattern $P$ of length $m$ and a text $T$ of length $n$ -- asks whether $P$ occurs as a substring of $T$. A property tester for the problem needs to distinguish (with high…
The determination of the maximal length of maximum distance separable (MDS) codes arising from elliptic curves is a central problem in coding theory. For an elliptic curve $E$ over $\mathbb{F}_q$, let $\operatorname{MEC}(k,q)$ denote the…
We study the following natural variation on the classical universality problem: given a language $L(M)$ represented by $M$ (e.g., a DFA/RE/NFA/PDA), does there exist an integer $\ell \geq 0$ such that $\Sigma^\ell \subseteq L(M)$? In the…
We study the fundamental problem of finding the best string to represent a given set, in the form of the Closest String problem: Given a set $X \subseteq \Sigma^d$ of $n$ strings, find the string $x^*$ minimizing the radius of the smallest…
Given a redundant dictionary $\Phi$, represented by an $M \times N$ matrix ($\Phi \in \mathbb{R}^{M \times N}$) and a target signal $y \in \mathbb{R}^M$, the \emph{sparse approximation problem} asks to find an approximate representation of…
In this paper, we consider a generalized longest common subsequence problem, in which a constraining sequence of length $s$ must be included as a substring and the other constraining sequence of length $t$ must be excluded as a subsequence…