Related papers: A Fixed-Parameter Algorithm for Minimum Common Str…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
In the classical combinatorial (adaptive) group testing problem, one is given two integers \(d\) and \(n\), where \(0\le d\le n\), and a population of \(n\) items, exactly \(d\) of which are known to be defective. The question is to devise…
In this paper we investigate the parameterized complexity of the Maximum-Duo Preservation String Mapping Problem, the complementary of the Minimum Common String Partition Problem. We show that this problem is fixed-parameter tractable when…
String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…
The Closest String Problem is an NP-complete problem which appears more commonly in bioinformatics and coding theory. Less surprisingly, classical approaches have been pursued with two prominent algorithms being the genetic algorithm and…
NP-hard problems such as the maximum clique or minimum vertex cover problems, two of Karp's 21 NP-hard problems, have several applications in computational chemistry, biochemistry and computer network security. Adiabatic quantum annealers…
The graph partitioning problem is a well-known NP-hard problem. In this paper, we formulate a 0-1 quadratic integer programming model for the graph partitioning problem with vertex weight constraints and fixed vertex constraints, and…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…
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…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
What is the minimal information that a robot must retain to achieve its task? To design economical robots, the literature dealing with reduction of combinatorial filters approaches this problem algorithmically. As lossless state compression…
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
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…
Partitioning algorithms play a key role in many scientific and engineering disciplines. A partitioning algorithm divides a set into a number of disjoint subsets or partitions. Often, the quality of the resulted partitions is measured by the…
Finding the smallest $d$-chain with a specific $(d-1)$-boundary in a simplicial complex is known as the \textsc{Minimum Bounded Chain} (MBC$_d$) problem. The MBC$_d$ problem is NP-hard for all $d\geq 2$. In this paper, we prove that it is…
This paper presents how to perform minimax optimal classification, regression, and density estimation based on fixed-$k$ nearest neighbor (NN) searches. We consider a distributed learning scenario, in which a massive dataset is split into…
We study distributed algorithms for string matching problem in presence of wildcard characters. Given a string T (a text), we look for all occurrences of another string P (a pattern) as a substring of string T . Each wildcard character in…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
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…