Related papers: Subsequences With Gap Constraints: Complexity Boun…
For two strings u, v over some alphabet A, we investigate the problem of embedding u into w as a subsequence under the presence of generalised gap constraints. A generalised gap constraint is a triple (i, j, C_{i, j}), where 1 <= i < j <=…
We consider the longest common subsequence problem in the context of subsequences with gap constraints. In particular, following Day et al. 2022, we consider the setting when the distance (i. e., the gap) between two consecutive symbols of…
In this paper, we consider a variant of the classical algorithmic problem of checking whether a given word $v$ is a subsequence of another word $w$. More precisely, we consider the problem of deciding, given a number $p$ (defining a…
In this paper, we study a series of algorithmic problems related to the subsequences occurring in the strings of a given language, under the assumption that this language is succinctly represented by a grammar generating it, or an automaton…
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…
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…
It is well-known that checking whether a given string $w$ matches a given regular expression $r$ can be done in quadratic time $O(|w|\cdot |r|)$ and that this cannot be improved to a truly subquadratic running time of $O((|w|\cdot…
We show that Closest Substring, one of the most important problems in the field of biological sequence analysis, is W[1]-hard when parameterized by the number k of input strings (and remains so, even over a binary alphabet). This problem is…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…
String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…
We address the satisfiability problem for string constraints that combine relational constraints represented by transducers, word equations, and string length constraints. This problem is undecidable in general. Therefore, we propose a new…
An instance of Max CSP is a finite collection of constraints on a set of variables, and the goal is to assign values to the variables that maximises the number of satisfied constraints. Max CSP captures many well-known problems (such as Max…
Frequent sequence mining methods often make use of constraints to control which subsequences should be mined. A variety of such subsequence constraints has been studied in the literature, including length, gap, span, regular-expression, and…
A value of a CSP instance is typically defined as a fraction of constraints that can be simultaneously met. We propose an alternative definition of a value of an instance and show that, for purely combinatorial reasons, a value of an…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…
Several popular language models represent local contexts in an input text $x$ as bags of words. Such representations are naturally encoded by a sequence graph whose vertices are the distinct words occurring in $x$, with edges representing…
A wide range of problems can be modelled as constraint satisfaction problems (CSPs), that is, a set of constraints that must be satisfied simultaneously. Constraints can either be represented extensionally, by explicitly listing allowed…
We study parameterized Constraint Satisfaction Problem for infinite constraint languages. The parameters that we study are weight of the satisfying assignment, number of constraints, maximum number of occurrences of a variable in the…
We consider the general problem of the Longest Common Subsequence (LCS) on weighted sequences. Weighted sequences are an extension of classical strings, where in each position every letter of the alphabet may occur with some probability.…