Related papers: Consensus Patterns parameterized by input string l…
The usefulness of parameterized algorithmics has often depended on what Niedermeier has called, "the art of problem parameterization". In this paper we introduce and explore a novel but general form of parameterization: the number of…
Regular expression patterns are a key feature of document processing languages like Perl and XDuce. It is in this context that the first and longest match policies have been proposed to disambiguate the pattern matching process. We formally…
Strings form a fundamental data type in computer systems. String searching has been extensively studied since the inception of computer science. Increasingly many applications have to deal with imprecise strings or strings with fuzzy…
In the Shortest Superstring problem we are given a set of strings $S=\{s_1, \ldots, s_n\}$ and integer $\ell$ and the question is to decide whether there is a superstring $s$ of length at most $\ell$ containing all strings of $S$ as…
In phylogenetics, the consensus problem consists in summarizing a set of phylogenetic trees that all classify the same set of species into a single tree. Several definitions of consensus exist in the literature; in this paper we focus on…
Frequent pattern mining is widely used to find ``important'' or ``interesting'' patterns in data. While it is not easy to mathematically define such patterns, maximal frequent patterns are promising candidates, as frequency is a natural…
The dichotomy conjecture for the parameterized embedding problem states that the problem of deciding whether a given graph $G$ from some class $K$ of "pattern graphs" can be embedded into a given graph $H$ (that is, is isomorphic to a…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
In this paper, we propose a new indexing structure for parameterized strings which we call PLSTs, by generalizing linear-size suffix tries for ordinary strings. Two parameterized strings are said to match if there is a bijection on the…
In this paper we consider several variants of the pattern matching problem. In particular, we investigate the following problems: 1) Pattern matching with k mismatches; 2) Approximate counting of mismatches; and 3) Pattern matching with…
The avoidability, or unavoidability of patterns in words over finite alphabets has been studied extensively. A word (pattern) over a finite set is said to be unavoidable if, for all but finitely many words, there exists a morphism mapping…
In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of…
A resolving set $S$ of a graph $G$ is a subset of its vertices such that no two vertices of $G$ have the same distance vector to $S$. The Metric Dimension problem asks for a resolving set of minimum size, and in its decision form, a…
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…
A decision problem is called parameterized if its input is a pair of strings. One of these strings is referred to as a parameter. The problem: given a propositional logic program P and a non-negative integer k, decide whether P has a stable…
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
Patterns are words with terminals and variables. The language of a pattern is the set of words obtained by uniformly substituting all variables with words that contain only terminals. In their original definition, patterns only allow for…
We address the problem of counting the number of strings in a collection where a given pattern appears, which has applications in information retrieval and data mining. Existing solutions are in a theoretical stage. We implement these…
We consider the problem of packing fixed-length patterns into a permutation, and develop a connection between the number of large patterns and the number of bonds in a permutation. Improving upon a result of Kaplansky and Wolfowitz, we…
Given a text and a pattern over two types of symbols called constants and variables, the parameterized pattern matching problem is to find all occurrences of substrings of the text that the pattern matches by substituting a variable in the…