Related papers: Subsequences With Gap Constraints: Complexity Boun…
We consider the Consensus Patterns problem, where, given a set of input strings, one is asked to extract a long-enough pattern which appears (with some errors) in all strings. We prove that this problem is W[1]-hard when parameterized by…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the given pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation…
Regular expressions with backreferences (regex, for short), as supported by most modern libraries for regular expression matching, have an NP-complete matching problem. We define a complexity parameter of regex, called active variable…
A {\em subsequence} of a word $w$ is a word $u$ that can be obtained by deleting some letters from $w$ while maintaining the relative order of the remaining letters, e.g., $\mathtt{lala}$ is a subsequence of $\mathtt{alfalfa}$. A word, over…
The {\em shortest common superstring} and the {\em shortest common supersequence} are two well studied problems having a wide range of applications. In this paper we consider both problems with resource constraints, denoted as the…
Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…
The constrained synchronization problem (CSP) asks for a synchronizing word of a given input automaton contained in a regular set of constraints. It could be viewed as a special case of synchronization of a discrete event system under…
Constraint Satisfaction Problems (CSP) constitute a convenient way to capture many combinatorial problems. The general CSP is known to be NP-complete, but its complexity depends on a template, usually a set of relations, upon which they are…
In a constraint satisfaction problem (CSP) the goal is to find an assignment of a given set of variables subject to specified constraints. A global cardinality constraint is an additional requirement that prescribes how many variables must…
A graph G is well-covered if all its maximal independent sets are of the same cardinality. Assume that a weight function w is defined on its vertices. Then G is w-well-covered if all maximal independent sets are of the same weight. For…
Let \Gamma be a structure with a finite relational signature and a first-order definition in (R;*,+) with parameters from R, that is, a relational structure over the real numbers where all relations are semi-algebraic sets. In this article,…
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…
The subset sum problem is one of the simplest and most fundamental NP-hard problems in combinatorial optimization. We consider two extensions of this problem: The subset sum problem with digraph constraint (SSG) and subset sum problem with…
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…
We consider compound geometric approximation for a nonnegative, integer-valued random variable $W$. The bound we give is straightforward but relies on having a lower bound on the failure rate of $W$. Applications are presented to M/G/1…
An absent factor of a string $w$ is a string $u$ which does not occur as a contiguous substring (a.k.a. factor) inside $w$. We extend this well-studied notion and define absent subsequences: a string $u$ is an absent subsequence of a string…
Finding paths in graphs is a fundamental graph-theoretic task. In this work, we we are concerned with finding a path with some constraints on its length and the number of vertices neighboring the path, that is, being outside of and incident…
Problems related to finding induced subgraphs satisfying given properties form one of the most studied areas within graph algorithms. Such problems have given rise to breakthrough results and led to development of new techniques both within…
A weakly consecutive sequence (WCS) is a permutation $\sigma$ of $\{1, \ldots, k\}$ such that if an integer $d$ divides $\sigma(i)$, then $d$ also divides $\sigma(i \pm d)$ insofar as these are defined. The structure of weakly consecutive…
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…