Related papers: Parameterized Complexity of Superstring Problems
A polynomial Turing kernel for some parameterized problem $P$ is a polynomial-time algorithm that solves $P$ using queries to an oracle of $P$ whose sizes are upper-bounded by some polynomial in the parameter. Here the term "polynomial"…
A kernelization algorithm for a computational problem is a procedure which compresses an instance into an equivalent instance whose size is bounded with respect to a complexity parameter. For the Boolean satisfiability problem (SAT), and…
A kernelization for a parameterized decision problem $\mathcal{Q}$ is a polynomial-time preprocessing algorithm that reduces any parameterized instance $(x,k)$ into an instance $(x',k')$ whose size is bounded by a function of $k$ alone and…
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…
We show that if DTIME[2^O(n)] is not included in DSPACE[2^o(n)], then, for every set B in PSPACE/poly, all strings x in B of length n can be represented by a string compressed(x) of length at most log(|B^{=n}|)+O(log n), such that a…
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…
In the NP-hard Edge Dominating Set problem (EDS) we are given a graph $G=(V,E)$ and an integer $k$, and need to determine whether there is a set $F\subseteq E$ of at most $k$ edges that are incident with all (other) edges of $G$. It is…
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…
Integer linear programs (ILPs) are a widely applied framework for dealing with combinatorial problems that arise in practice. It is known, e.g., by the success of CPLEX, that preprocessing and simplification can greatly speed up the process…
The normalized substring complexity $\delta$ of a string is defined as $\max_k \{c[k]/k\}$, where $c[k]$ is the number of \textit{distinct} substrings of length $k$. This simply defined measure has recently attracted attention due to its…
Let $\Sigma$ be an alphabet. For two strings $X$, $Y$, and a constrained string $P$ over the alphabet $\Sigma$, the constrained longest common subsequence and substring problem for two strings $X$ and $Y$ with respect to $P$ is to find a…
Kernelization is an important tool in parameterized algorithmics. Given an input instance accompanied by a parameter, the goal is to compute in polynomial time an equivalent instance of the same problem such that the size of the reduced…
In the longest common substring problem, we are given two strings of length $n$ and must find a substring of maximal length that occurs in both strings. It is well known that the problem can be solved in linear time, but the solution is not…
The propositional planning problem is a notoriously difficult computational problem. Downey et al. (1999) initiated the parameterized analysis of planning (with plan length as the parameter) and B\"ackstr\"om et al. (2012) picked up this…
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…
For a string $S$, a palindromic substring $S[i..j]$ is said to be a \emph{shortest unique palindromic substring} ($\mathit{SUPS}$) for an interval $[s, t]$ in $S$, if $S[i..j]$ occurs exactly once in $S$, the interval $[i, j]$ contains $[s,…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
Given two strings $S$ and $P$, the Episode Matching problem is to find the shortest substring of $S$ that contains $P$ as a subsequence. The best known upper bound for this problem is $\tilde O(nm)$ by Das et al. (1997) , where $n,m$ are…
Kernelization---a mathematical key concept for provably effective polynomial-time preprocessing of NP-hard problems---plays a central role in parameterized complexity and has triggered an extensive line of research. This is in part due to a…
We investigate the question whether Subset Sum can be solved by a polynomial-time algorithm with access to a certificate of length poly(k) where k is the maximal number of bits in an input number. In other words, can it be solved using only…