Related papers: Efficient Parameterized Pattern Matching in Sublin…
The research on indexing repetitive string collections has focused on the same search problems used for regular string collections, though they can make little sense in this scenario. For example, the basic pattern matching query "list all…
The parameterized model-checking problem for a class of first-order sentences (queries) asks to decide whether a given sentence from the class holds true in a given relational structure (database); the parameter is the length of the…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
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…
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…
Karpinski and Nekrich (2008) introduced the problem of parameterized range majority, which asks us to preprocess a string of length $n$ such that, given the endpoints of a range, one can quickly find all the distinct elements whose relative…
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…
We present the first worst-case linear time algorithm that directly computes the parameterized suffix and LCP arrays for constant sized alphabets. Previous algorithms either required quadratic time or the parameterized suffix tree to be…
Parameterized local search combines classic local search heuristics with the paradigm of parameterized algorithmics. While most local search algorithms aim to improve given solutions by performing one single operation on a given solution,…
In this work, we consider pattern matching variants in small space, that is, in the read-only setting, where we want to bound the space usage on top of storing the strings. Our main contribution is a space-time trade-off for the Internal…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
The Permutation Pattern Matching problem, asking whether a pattern permutation $\pi$ is contained in a permutation $\tau$, is known to be NP-complete. In this paper we present two polynomial time algorithms for special cases. The first…
Given a log and a specification, timed pattern matching aims at exhibiting for which start and end dates a specification holds on that log. For example, "a given action is always followed by another action before a given deadline". This…
Pattern matching is one of the fundamental problems in Computer Science. Both the classic version of the problem as well as the more sophisticated version where wildcards can also appear in the input can be solved in almost linear time…
String matching is the problem of finding all the substrings of a text which match a given pattern. It is one of the most investigated problems in computer science, mainly due to its very diverse applications in several fields. Recently,…
A degenerate string is a sequence of sets of characters. A generalized degenerate (GD) string extends this notion to the sequence of sets of strings, where strings of the same set are of equal length. Finding an exact match for a pattern…
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…
In the Interval Completion problem we are given a graph G and an integer k, and the task is to turn G using at most k edge additions into an interval graph, i.e., a graph admitting an intersection model of intervals on a line. Motivated by…