Related papers: Iterative Rounding for the Closest String Problem
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…
We study the fundamental problem of finding the best string to represent a given set, in the form of the Closest String problem: Given a set $X \subseteq \Sigma^d$ of $n$ strings, find the string $x^*$ minimizing the radius of the smallest…
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…
Many consensus string problems are based on Hamming distance. We replace Hamming distance by the more flexible (e.g., easily coping with different input string lengths) dynamic time warping distance, best known from applications in time…
In this paper we study the fine-grained complexity of finding exact and approximate solutions to problems in P. Our main contribution is showing reductions from exact to approximate solution for a host of such problems. As one (notable)…
We report (to our knowledge) the first evaluation of Constraint Satisfaction as a computational framework for solving closest string problems. We show that careful consideration of symbol occurrences can provide search heuristics that…
We consider the problem of finding a minimum common partition of two strings (MCSP). The problem has its application in genome comparison. MCSP problem is proved to be NP-hard. In this paper, we develop an Integer Programming (IP)…
In this paper we consider the $p$-Norm Hamming Centroid problem which asks to determine whether some given binary strings have a centroid with a bound on the $p$-norm of its Hamming distances to the strings. Specifically, given a set of…
Given real numbers whose sum is an integer, we study the problem of finding integers which match these real numbers as closely as possible, in the sense of L^p norm, while preserving the sum. We describe the structure of solutions for this…
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…
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…
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…
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…
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 $\mathcal S$.…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…
The Integer Programming Problem (IP) for a polytope P \subseteq R^n is to find an integer point in P or decide that P is integer free. We give an algorithm for an approximate version of this problem, which correctly decides whether P…
The Sparse Approximation problem asks to find a solution $x$ such that $||y - Hx|| < \alpha$, for a given norm $||\cdot||$, minimizing the size of the support $||x||_0 := \#\{j \ |\ x_j \neq 0 \}$. We present valid inequalities for Mixed…
Considering matrices with missing entries, we study NP-hard matrix completion problems where the resulting completed matrix shall have limited (local) radius. In the pure radius version, this means that the goal is to fill in the entries…
In this paper, we consider the network slicing problem which attempts to map multiple customized virtual network requests (also called services) to a common shared network infrastructure and allocate network resources to meet diverse…
In the minimum common string partition (MCSP) problem two related input strings are given. "Related" refers to the property that both strings consist of the same set of letters appearing the same number of times in each of the two strings.…