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In the Determinant Maximization problem, given an $n\times n$ positive semi-definite matrix $\bf{A}$ in $\mathbb{Q}^{n\times n}$ and an integer $k$, we are required to find a $k\times k$ principal submatrix of $\bf{A}$ having the maximum…
We consider the Consensus Patterns problem, where, given a set of input strings, one is asked to extract a long-enough pattern which appears (with some errors) in all strings. We prove that this problem is W[1]-hard when parameterized by…
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…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
In this paper we consider two problems concerning string factorisation. Specifically given a string $w$ and an integer $k$ find a factorisation of $w$ where each factor has length bounded by $k$ and has the minimum (the FmD problem) or the…
Consensus problems for strings and sequences appear in numerous application contexts, ranging from bioinformatics over data mining to machine learning. Closing some gaps in the literature, we show that several fundamental problems in this…
The minimum unsatisfiability version of a constraint satisfaction problem (MinCSP) asks for an assignment where the number of unsatisfied constraints is minimum possible, or equivalently, asks for a minimum-size set of constraints whose…
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one…
Parameterized complexity enables the practical solution of generally intractable NP-hard problems when certain parameters are small, making it particularly useful in real-world applications. The study of string problems in this framework…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
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…
The cyclability of a graph is the maximum integer $k$ for which every $k$ vertices lie on a cycle. The algorithmic version of the problem, given a graph $G$ and a non-negative integer $k,$ decide whether the cyclability of $G$ is at least…
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…
In this paper, we define the reoptimization variant of the closest substring problem (CSP) under sequence addition. We show that, even with the additional information we have about the problem instance, the problem of finding a closest…
This paper studies the unification problem with associative, commutative, and associative-commutative functions mainly from a viewpoint of the parameterized complexity on the number of variables. It is shown that both associative and…
A matching is a set of edges in a graph with no common endpoint. A matching M is called acyclic if the induced subgraph on the endpoints of the edges in M is acyclic. Given a graph G and an integer k, Acyclic Matching Problem seeks for an…
We study the parameterized complexity of the following fundamental geometric problems with respect to the dimension $d$: i) Given $n$ points in $\Rd$, compute their minimum enclosing cylinder. ii) Given two $n$-point sets in $\Rd$, decide…
In the Closest String problem one is given a family $\mathcal S$ of equal-length strings over some fixed alphabet, and the task is to find a string $y$ that minimizes the maximum Hamming distance between $y$ and a string from $\mathcal S$.…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
In this paper, we prove that it is W[2]-hard to approximate k-SetCover within any constant ratio. Our proof is built upon the recently developed threshold graph composition technique. We propose a strong notion of threshold graphs and use a…