Related papers: Polynomial-Time Solutions for Longest Common Subse…
The {\em longest common subsequence (LCS)} problem is a classic and well-studied problem in computer science. LCS is a central problem in stringology and finds broad applications in text compression, error-detecting codes and biological…
We study the design of fixed-parameter algorithms for problems already known to be solvable in polynomial time. The main motivation is to get more efficient algorithms for problems with unattractive polynomial running times. Here, we focus…
Color-constrained subgraph problems are those where we are given an edge-colored (directed or undirected) graph and the task is to find a specific type of subgraph, like a spanning tree, an arborescence, a single-source shortest path tree,…
Parallel real-time systems (e.g., autonomous driving systems) often contain functionalities with complex dependencies and execution uncertainties, leading to significant timing variability which can be represented as a probabilistic…
We study reconfiguration problems for cliques in a graph, which determine whether there exists a sequence of cliques that transforms a given clique into another one in a step-by-step fashion. As one step of a transformation, we consider…
Counting and uniform sampling of directed acyclic graphs (DAGs) from a Markov equivalence class are fundamental tasks in graphical causal analysis. In this paper, we show that these tasks can be performed in polynomial time, solving a…
We consider the longest common subsequence (LCS) problem with the restriction that the common subsequence is required to consist of at least $k$ length substrings. First, we show an $O(mn)$ time algorithm for the problem which gives a…
In this work, we consider a variant of the classical Longest Common Subsequence problem called Doubly-Constrained Longest Common Subsequence (DC-LCS). Given two strings s1 and s2 over an alphabet A, a set C_s of strings, and a function Co…
In this paper, we provide polynomial-time algorithms for different extensions of the matching counting problem, namely maximal matchings, path matchings (linear forest) and paths, on graph classes of bounded clique-width. For maximal…
We consider hypergraph network design problems where the goal is to construct a hypergraph that satisfies certain connectivity requirements. For graph network design problems where the goal is to construct a graph that satisfies certain…
In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
Many complex questions in biology, physics, and mathematics can be mapped to the graph isomorphism problem and the closely related graph automorphism problem. In particular, these problems appear in the context of network visualization,…
The independent set on a graph $G=(V,E)$ is a subset of $V$ such that no two vertices in the subset have an edge between them. The MIS problem on $G$ seeks to identify an independent set with maximum cardinality, i.e. maximum independent…
In this paper, we investigate the computational complexity of subgraph reconfiguration problems in directed graphs. More specifically, we focus on the problem of reconfiguring arborescences in a digraph, where an arborescence is a directed…
Counting and sampling directed acyclic graphs from a Markov equivalence class are fundamental tasks in graphical causal analysis. In this paper we show that these tasks can be performed in polynomial time, solving a long-standing open…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
In this paper, we show that given a weighted, directed planar graph $G$, and any $\epsilon >0$, there exists a polynomial time and $O(n^{\frac{1}{2}+\epsilon})$ space algorithm that computes the shortest path between two fixed vertices in…
In this paper, we consider a generalized longest common subsequence problem, the string-excluding constrained LCS problem. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a constraint string $P$ of length $r$, the…
The longest common subsequence (LCS) is a fundamental problem in string processing which has numerous algorithmic studies, extensions, and applications. A sequence $u_1, \ldots, u_f$ of $f$ strings s said to be an ($f$-)segmentation of a…