Related papers: A framework for cost-constrained genome rearrangem…
In an edge-colored graph, a traversal cost occurs at a vertex along a path when consecutive edges with different colors are traversed. The value of the traversal cost depends only on the colors of the traversed edges. This concept leads to…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
In Two-Sets Cut-Uncut, we are given an undirected graph $G=(V,E)$ and two terminal sets $S$ and $T$. The task is to find a minimum cut $C$ in $G$ (if there is any) separating $S$ from $T$ under the following ``uncut'' condition. In the…
The reload cost refers to the cost that occurs along a path on an edge-colored graph when it traverses an internal vertex between two edges of different colors. Galbiati et al.[1] introduced the Minimum Reload Cost Cycle Cover problem,…
We study a number of multi-route cut problems: given a graph G=(V,E) and connectivity thresholds k_(u,v) on pairs of nodes, the goal is to find a minimum cost set of edges or vertices the removal of which reduces the connectivity between…
One of the fundamental and most-studied algorithmic problems in distributed computing on networks is graph coloring, both in bounded-degree and in general graphs. Recently, the study of this problem has been extended in two directions.…
The minimum cost multicut problem is the NP-hard/APX-hard combinatorial optimization problem of partitioning a real-valued edge-weighted graph such as to minimize the total cost of the partition. While graph convolutional neural networks…
In this work we consider the problem of finding the minimum-weight loop cover of an undirected graph. This combinatorial optimization problem is called 2-matching and can be seen as a relaxation of the traveling salesman problem since one…
Consider the following problem: given a graph with edge costs and a subset Q of vertices, find a minimum-cost subgraph in which there are two edge-disjoint paths connecting every pair of vertices in Q. The problem is a failure-resilient…
We investigate the minimum cost of a wide class of combinatorial optimization problems over random bipartite geometric graphs in $\mathbb{R}^d$ where the edge cost between two points is given by a $p$-th power of their Euclidean distance.…
The Single Cut or Join (SCJ) operation on genomes, generalizing chromosome evolution by fusions and fissions, is the computationally simplest known model of genome rearrangement. While most genome rearrangement problems are already hard…
Establishing a distance between genomes is a significant problem in computational genomics, because its solution can be used to establish evolutionary relationships including phylogeny. The "double cut and join" (DCJ) model of chromosomal…
We analyze models of genome evolution based on both restricted and unrestricted double-cut-and-join (DCJ) operations. We compare the number of operations along the evolutionary trajectory to the DCJ distance of the genome from its ancestor…
We study an extension of the classical graph cut problem, wherein we replace the modular (sum of edge weights) cost function by a submodular set function defined over graph edges. Special cases of this problem have appeared in different…
For a connected graph G=(V,E), a subset U of V is called a disconnected cut if U disconnects the graph and the subgraph induced by U is disconnected as well. We show that the problem to test whether a graph has a disconnected cut is…
In this work, we explore heuristics for the Adjacency Graph Packing problem, which can be applied to the Double Cut and Join (DCJ) Distance Problem. The DCJ is a rearrangement operation and the distance problem considering it is a well…
The graph partitioning problem is a well-known NP-hard problem. In this paper, we formulate a 0-1 quadratic integer programming model for the graph partitioning problem with vertex weight constraints and fixed vertex constraints, and…
Given a connected undirected graph $\bar{G}$ on $n$ vertices, and non-negative edge costs $c$, the 2ECM problem is that of finding a $2$-edge~connected spanning multisubgraph of $\bar{G}$ of minimum cost. The natural linear program (LP) for…
This paper provides a short and transparent solution for the covering cost of white-grey trees which play a crucial role in the algorithm of Bergeron {\it et al.}\ to compute the rearrangement distance between two multichromosomal genomes…