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We consider the rooted prize-collecting walks (PCW) problem, wherein we seek a collection $C$ of rooted walks having minimum prize-collecting cost, which is the (total cost of walks in $C$) + (total node-reward of nodes not visited by any…
Reducing the running time of graph algorithms is vital for tackling real-world problems such as shortest paths and matching in large-scale graphs, where path information plays a crucial role. To address this critical challenge, this paper…
We present a new $4$-approximation algorithm for the Combinatorial Motion Planning problem which runs in $\mathcal{O}(n^2\alpha(n^2,n))$ time, where $\alpha$ is the functional inverse of the Ackermann function, and a fully distributed…
Given an undirected graph $G=(V,E)$ with positive edge lengths and two vertices $s$ and $t$, the next-to-shortest path problem is to find an $st$-path which length is minimum amongst all $st$-paths strictly longer than the shortest path…
We present two new and efficient algorithms for computing all-pairs shortest paths. The algorithms operate on directed graphs with real (possibly negative) weights. They make use of directed path consistency along a vertex ordering d. Both…
Given a directed graph $G$ on $n$ vertices with a special vertex $s$, the directed minimum degree spanning tree problem requires computing a incoming spanning tree rooted at $s$ whose maximum tree in-degree is the smallest among all such…
We propose a novel heuristic quantum algorithm for the Minimum Vertex Cover (MVC) problem based on continuous-time quantum walks (CTQWs). In this framework, the coherent propagation of a quantum walker over a graph encodes its structural…
The Stacker Crane Problem (SCP) is a variant of the Traveling Salesman Problem. In SCP, pairs of pickup and delivery points are designated on a graph, and a crane must visit these points to move objects from each pickup location to its…
This paper proposes a local search algorithm for a specific combinatorial optimisation problem in graph theory: the Hamiltonian Completion Problem (HCP) on undirected graphs. In this problem, the objective is to add as few edges as possible…
Motivation: Working with a large number of genomes simultaneously is of great interest in genetic population and comparative genomics research. Bubbles discovery in multi-genomes coloured de bruijn graph for de novo genome assembly is a…
A well-studied continuous model of graphs considers each edge as a continuous unit-length interval of points. In the problem $\delta$-Tour defined within this model, the objective to find a shortest tour that comes within a distance of…
Background Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig…
The random order graph streaming model has received significant attention recently, with problems such as matching size estimation, component counting, and the evaluation of bounded degree constant query testable properties shown to admit…
Efficient planning and sequence selection are central to intelligence, yet current approaches remain largely incompatible with biological computation. Classical graph algorithms like Dijkstra's or A* require global state and biologically…
Motivations Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large data sets or…
De novo DNA sequence assembly is based on finding paths in overlap graphs, which is a NP-hard problem. We developed a quantum algorithm for de novo assembly based on quantum walks in graphs. The overlap graph is partitioned repeatedly to…
Given a graph $G$, the longest path problem asks to compute a simple path of $G$ with the largest number of vertices. This problem is the most natural optimization version of the well known and well studied Hamiltonian path problem, and…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
The Clique Interdiction Problem (CIP) aims to minimize the size of the largest clique in a given graph by removing a given number of vertices. The CIP models a special Stackelberg game and has important applications in fields such as…
Similarity search over a bipartite graph aims to retrieve from the graph the nodes that are similar to each other, which finds applications in various fields such as online advertising, recommender systems etc. Existing similarity measures…