Related papers: Separating Sets of Strings by Finding Matching Pat…
The most fundamental problem considered in algorithms for text processing is pattern matching: given a pattern $p$ of length $m$ and a text $t$ of length $n$, does $p$ occur in $t$? Multiple versions of this basic question have been…
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…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Symmetry breaking for graphs and other combinatorial objects is notoriously hard. On the one hand, complete symmetry breaks are exponential in size. On the other hand, current, state-of-the-art, partial symmetry breaks are often considered…
There are two methods for counting the number of occurrences of a string in another large string. One is to count the number of places where the string is found. The other is to determine how many pieces of string can be extracted without…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
The exact matching problem is a constrained variant of the maximum matching problem: given a graph with each edge having a weight $0$ or $1$ and an integer $k$, the goal is to find a perfect matching of weight exactly $k$. Mulmuley,…
Permutation Pattern Matching (or PPM) is a decision problem whose input is a pair of permutations $\pi$ and $\tau$, represented as sequences of integers, and the task is to determine whether $\tau$ contains a subsequence order-isomorphic to…
The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…
Parameterized analysis provides powerful mechanisms for obtaining fine-grained insights into different types of algorithms. In this work, we combine this field with evolutionary algorithms and provide parameterized complexity analysis of…
In this short note we present a comprehensive bibliography for the online exact string matching problem. The problem consists in finding all occurrences of a given pattern in a text. It is an extensively studied problem in computer science,…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
Patterns provide a concise, syntactic way of describing a set of strings, but their expressive power comes at a price: a number of fundamental decision problems concerning (erasing) pattern languages, such as the membership problem and…
Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks. To find bigger networks, one can attempt to combine small…
Many graph problems were first shown to be fixed-parameter tractable using the results of Robertson and Seymour on graph minors. We show that the combination of finite, computable, obstruction sets and efficient order tests is not just one…
Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…
The problem of matching a query string to a directed graph, whose vertices are labeled by strings, has application in different fields, from data mining to computational biology. Several variants of the problem have been considered,…
We argue that parameterized complexity is a useful tool with which to study global constraints. In particular, we show that many global constraints which are intractable to propagate completely have natural parameters which make them…
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…
Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…