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It has been shown that the parallel Lattice Linear Predicate (LLP) algorithm solves many combinatorial optimization problems such as the shortest path problem, the stable marriage problem and the market clearing price problem. In this…
Consider two independent random strings having same length and taking values uniformly in a common finite alphabet. We study the order of the variance of the length of the longest common subsequences (LCS) of these strings when long blocks,…
We propose a methodology at the nexus of operations research and machine learning (ML) leveraging generic approximators available from ML to accelerate the solution of mixed-integer linear two-stage stochastic programs. We aim at solving…
The Shortest Common Supersequence problem (SCS for short) consists in finding a shortest common supersequence of a finite set of words on a fixed alphabet Sigma. It is well-known that its decision version denoted [SR8] in [Garey and…
Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the…
Longest Common Substring (LCS) is an important text processing problem, which has recently been investigated in the quantum query model. The decisional version of this problem, LCS with threshold $d$, asks whether two length-$n$ input…
We propose efficient algorithms for enumerating maximal common subsequences (MCSs) of two strings. Efficiency of the algorithms are estimated by the preprocessing-time, space, and delay-time complexities. One algorithm prepares a…
This paper reformulates the problem of finding a longest common increasing subsequence of the two given input sequences in a very succinct way. An extremely simple linear space algorithm based on the new formula can find a longest common…
The Longest Common Increasing Subsequence problem (LCIS) is a natural variant of the celebrated Longest Common Subsequence (LCS) problem. For LCIS, as well as for LCS, there is an $O(n^2)$-time algorithm and a SETH-based conditional lower…
Given a sequence $S$ of length $n$, a letter-duplicated subsequence is a subsequence of $S$ in the form of $x_1^{d_1}x_2^{d_2}\cdots x_k^{d_k}$ with $x_i\in\Sigma$, $x_j\neq x_{j+1}$ and $d_i\geq 2$ for all $i$ in $[k]$ and $j$ in $[k-1]$.…
In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$…
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…
Suppose we want to seek the longest common subsequences (LCSs) of two strings as informative patterns that explain the relationship between the strings. The dynamic programming algorithm gives us a table from which all LCSs can be extracted…
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…
The Maximum Common Subgraph (MCS) problem plays a crucial role across various domains, bridging theoretical exploration and practical applications in fields like bioinformatics and social network analysis. Despite its wide applicability,…
Let $A$ and $B$ be two number sequences of length $n$ and $m$, respectively, where $m\le n$. Given a positive number $\delta$, a common almost increasing sequence $s_1\ldots s_k$ is a common subsequence for both $A$ and $B$ such that for…
Given $m$ documents of total length $n$, we consider the problem of finding a longest string common to at least $d \geq 2$ of the documents. This problem is known as the \emph{longest common substring (LCS) problem} and has a classic $O(n)$…
The integration of Large Language Models (LLMs) into optimization has created a powerful synergy, opening exciting research opportunities. This paper investigates how LLMs can enhance existing optimization algorithms. Using their…
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)…
This paper studies the Graph-Connected Clique-Partitioning Problem (GCCP), a clustering optimization model in which units are characterized by both individual and relational data. This problem, introduced by Benati et al. (2017) under the…