Related papers: The Exact Closest String Problem as a Constraint S…

Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…

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…

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…

We build on a recently proposed method for explaining solutions of constraint satisfaction problems. An explanation here is a sequence of simple inference steps, where the simplicity of an inference step is measured by the number and types…

We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…

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 constraint programming framework, state-of-the-art static and dynamic decomposition techniques are hard to apply to problems with complete initial constraint graphs. For such problems, we propose a hybrid approach of these techniques…

Exactly solving first-order constraints (i.e., first-order formulas over a certain predefined structure) can be a very hard, or even undecidable problem. In continuous structures like the real numbers it is promising to compute approximate…

Designing a search heuristic for constraint programming that is reliable across problem domains has been an important research topic in recent years. This paper concentrates on one family of candidates: counting-based search. Such…

Regular expressions are a classical concept in formal language theory. Regular expressions in programming languages (RegEx) such as JavaScript, feature non-standard semantics of operators (e.g. greedy/lazy Kleene star), as well as…

We propose an algorithm for solving bound-constrained mathematical programs with complementarity constraints on the variables. Each iteration of the algorithm involves solving a linear program with complementarity constraints in order to…

We initiate a study of the streaming complexity of constraint satisfaction problems (CSPs) when the constraints arrive in a random order. We show that there exists a CSP, namely $\textsf{Max-DICUT}$, for which random ordering makes a…

This paper is an attempt to remedy the problem of slow convergence for first-order numerical algorithms by proposing an adaptive conditioning heuristic. First, we propose a parallelizable numerical algorithm that is capable of solving…

In the Shortest Superstring problem, we are given a set of strings and we are asking for a common superstring, which has the minimum number of characters. The Shortest Superstring problem is NP-hard and several constant-factor approximation…

We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…

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…

Constraint satisfaction problems have been studied in numerous fields with practical and theoretical interests. In recent years, major breakthroughs have been made in a study of counting constraint satisfaction problems (or #CSPs). In…

We introduce a novel definition of approximate palindromes in strings, and provide an algorithm to find all maximal approximate palindromes in a string with up to $k$ errors. Our definition is based on the usual edit operations of…

Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…

Cutting and packing problems are present in many, at first glance unconnected, areas, therefore it's beneficial to have a good understanding of their underlying structure, to select proper techniques for finding solutions. Cutting and…