Related papers: Separating Sets of Strings by Finding Matching Pat…
The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…
Computing the {\em matching statistics} of a string $P[1..m]$ with respect to a text $T[1..n]$ is a fundamental problem which has application to genome sequence comparison. In this paper, we study the problem of computing the matching…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
A parameterized string (p-string) is a string over an alphabet $(\Sigma_{s} \cup \Sigma_{p})$, where $\Sigma_{s}$ and $\Sigma_{p}$ are disjoint alphabets for static symbols (s-symbols) and for parameter symbols (p-symbols), respectively.…
The generalized function matching (GFM) problem has been intensively studied starting with [Ehrenfeucht and Rozenberg, 1979]. Given a pattern p and a text t, the goal is to find a mapping from the letters of p to non-empty substrings of t,…
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…
The NP-hard Metric Dimension problem is to decide for a given graph G and a positive integer k whether there is a vertex subset of size at most k that separates all vertex pairs in G. Herein, a vertex v separates a pair {u,w} if the…
Microarrays are research tools used in gene discovery as well as disease and cancer diagnostics. Two prominent but challenging problems related to microarrays are the Border Minimization Problem (BMP) and the Border Minimization Problem…
Asking which sets are fixed-parameter tractable for a given parameterization constitutes much of the current research in parameterized complexity theory. This approach faces some of the core difficulties in complexity theory. By focussing…
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…
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…
Zimin words are very special finite words which are closely related to the pattern-avoidability problem. This problem consists in testing if an instance of a given pattern with variables occurs in almost all words over any finite alphabet.…
We study computational complexity of the class of distance-constrained graph labeling problems from the fixed parameter tractability point of view. The parameters studied are neighborhood diversity and clique width. We rephrase the distance…
Many problems in Computer Science can be abstracted to the following question: given a set of objects and rules respectively, which new objects can be produced? In the paper, we consider a succinct version of the question: given a set of…
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…
We initiate a program of parameterized proof complexity that aims to provide evidence that FPT is different from W[1]. A similar program already exists for the classes W[2] and W[SAT]. We contrast these programs and prove upper and lower…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
We study the "set parameterized matching" problem, a generalization of the classical parameterized matching problem introduced by Baker. In set parameterized matching, both the pattern and text are sequences where each position contains a…
String complexity is defined as the cardinality of a set of all distinct words (factors) of a given string. For two strings, we introduce the joint string complexity as the cardinality of a set of words that are common to both strings.…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…