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In the Shortest Common Superstring problem (SCS), one needs to find the shortest superstring for a set of strings. While SCS is NP-hard and MAX-SNP-hard, the Greedy Algorithm "choose two strings with the largest overlap; merge them; repeat"…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
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,…
A subset of Q^n is called semilinear (or piecewise linear) if it is Boolean combination of linear half-spaces. We study the computational complexity of the constraint satisfaction problem (CSP) over the rationals when all the constraints…
This paper shows that a simple algorithm produces the {\em all-prefixes-LCSs-graph} in $O(mn)$ time for two input sequences of size $m$ and $n$. Given any prefix $p$ of the first input sequence and any prefix $q$ of the second input…
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…
A technique using a systolic array structure is proposed for solving the common approximate substring (CAS) problem. This approach extends the technique introduced in earlier work from the computation of the edit-distance between two…
Non-parametric entropy estimation on sequential data is a fundamental tool in signal processing, capturing information flow within or between processes to measure predictability, redundancy, or similarity. Methods based on longest common…
This paper addresses the Variable Gapped Longest Common Subsequence (VGLCS) problem, a generalization of the classical LCS problem involving flexible gap constraints between consecutive solutions' characters. The problem arises in molecular…
Sublinear time quantum algorithms have been established for many fundamental problems on strings. This work demonstrates that new, faster quantum algorithms can be designed when the string is highly compressible. We focus on two popular and…
This paper presents our solution for optimization task of the 3rd ACM-China IPCC. By the complexity analysis, we identified three time-consuming subroutines of original algorithm: marking edges, computing pseudo inverse and sorting edges.…
The closest string problem is an NP-hard problem, whose task is to find a string that minimizes maximum Hamming distance to a given set of strings. This can be reduced to an integer program (IP). However, to date, there exists no known…
This work presents an algorithmic scheme for solving the infinite-time constrained linear quadratic regulation problem. We employ an accelerated version of a popular proximal gradient scheme, commonly known as the Forward-Backward Splitting…
In this paper, a robust sequential quadratic programming method for constrained optimization is generalized to problem with an {expectation} objective function {and} deterministic equality and inequality constraints. A stochastic line…
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…
Finding the common structural features of two molecules is a fundamental task in cheminformatics. Most drugs are small molecules, which can naturally be interpreted as graphs. Hence, the task is formalized as maximum common subgraph…
Lately, there is a growing interest in dynamic string matching problems. Specifically, the dynamic Longest Common Factor problem has been researched and some interesting results has been reached. In this paper we examine another classic…
We investigate the use of linear programming tools for solving semidefinite programming relaxations of quadratically constrained quadratic problems. Classes of valid linear inequalities are presented, including sparse PSD cuts, and…
String constraint solving refers to solving combinatorial problems involving constraints over string variables. String solving approaches have become popular over the last years given the massive use of strings in different application…
We consider the general problem of the Longest Common Subsequence (LCS) on weighted sequences. Weighted sequences are an extension of classical strings, where in each position every letter of the alphabet may occur with some probability.…