Related papers: Solving the Minimum Common String Partition Proble…
This study develops an algorithm to solve a variation of the Shortest Common Superstring (SCS) problem. There are two modifications to the base SCS problem. First, one string in the set S is allowed to have up to K mistakes, defined as not…
Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time…
We consider the classical minimum and maximum cut problems: find a partition of vertices of a graph into two disjoint subsets that minimize or maximize the sum of the weights of edges with endpoints in different subsets. It is known that if…
In this paper we focus on finding high quality solutions for the problem of maximum partitioning of graphs with supply and demand (MPGSD). There is a growing interest for the MPGSD due to its close connection to problems appearing in the…
Our research deals with the optimization version of the set partition problem, where the objective is to minimize the absolute difference between the sums of the two disjoint partitions. Although this problem is known to be NP-hard and…
The minimum conductance problem is an NP-hard graph partitioning problem. Apart from the search for bottlenecks in complex networks, the problem is very closely related to the popular area of network community detection. In this paper, we…
We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…
We propose a zero-order optimization method for sequential min-max problems based on two populations of interacting particles. The systems are coupled so that one population aims to solve the inner maximization problem, while the other aims…
The paper presents an exponential pheromone deposition approach to improve the performance of classical Ant System algorithm which employs uniform deposition rule. A simplified analysis using differential equations is carried out to study…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
Set partitioning is a key component of many algorithms in machine learning, signal processing, and communications. In general, the problem of finding a partition that minimizes a given impurity (loss function) is NP-hard. As such, there…
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 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…
String matching is the problem of finding all the substrings of a text which match a given pattern. It is one of the most investigated problems in computer science, mainly due to its very diverse applications in several fields. Recently,…
We study the problem of computing similarity joins under edit distance on a set of strings. Edit similarity joins is a fundamental problem in databases, data mining and bioinformatics. It finds important applications in data cleaning and…
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 study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…
In this work, a graph partitioning problem in a fixed number of connected components is considered. Given an undirected graph with costs on the edges, the problem consists of partitioning the set of nodes into a fixed number of subsets with…
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…
We study the {\em maximum duo-preservation string mapping} ({\sc Max-Duo}) problem, which is the complement of the well studied {\em minimum common string partition} ({\sc MCSP}) problem. Both problems have applications in many fields…