Related papers: Computing nearest neighbour interchange distances …
Geodesic distance, sometimes called shortest path length, has proven useful in a great variety of applications, such as information retrieval on networks including treelike networked models. Here, our goal is to analytically determine the…
Searching in partially ordered structures has been considered in the context of information retrieval and efficient tree-like indexes, as well as in hierarchy based knowledge representation. In this paper we focus on tree-like partial…
We study the problem of finding small trees. Classical network design problems are considered with the additional constraint that only a specified number $k$ of nodes are required to be connected in the solution. A prototypical example is…
We study the NP-hard Shortest Path Most Vital Edges problem arising in the context of analyzing network robustness. For an undirected graph with positive integer edge lengths and two designated vertices $s$ and $t$, the goal is to delete as…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Considering a graph with unknown weights, can we find the shortest path for a pair of nodes if we know the minimal Steiner trees associated with some subset of nodes? That is, with respect to a fixed latent decision-making system (e.g., a…
We start with a review of the pervasiveness of the nearest neighbor search problem and techniques used to solve it along with some experimental results. In the second chapter, we show reductions between two different classes of geo- metric…
The concept of Reload cost in a graph refers to the cost that occurs while traversing a vertex via two of its incident edges. This cost is uniquely determined by the colors of the two edges. This concept has various applications in…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
Base polytopes of polymatroids, also known as generalized permutohedra, are polytopes whose edges are parallel to a vector of the form $\mathbf{e}_i - \mathbf{e}_j$. We consider the following computational problem: Given two vertices of a…
In 2007, Eickmeyer et al. showed that the tree topologies outputted by the Neighbor-Joining (NJ) algorithm and the balanced minimum evolution (BME) method for phylogenetic reconstruction are each determined by a polyhedral subdivision of…
The general communication tree embedding problem is the problem of mapping a set of communicating terminals, represented by a graph G, into the set of vertices of some physical network represented by a tree T. In the case where the vertices…
We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…
The minimum degree spanning tree (MDST) problem requires the construction of a spanning tree $T$ for graph $G=(V,E)$ with $n$ vertices, such that the maximum degree $d$ of $T$ is the smallest among all spanning trees of $G$. In this paper,…
We study the problem of decomposing (clustering) a tree with respect to costs attributed to pairs of nodes, so as to minimize the sum of costs for those pairs of nodes that are in the same component (cluster). For the general case and for…
Neighborhood finders and nearest neighbor queries are fundamental parts of sampling based motion planning algorithms. Using different distance metrics or otherwise changing the definition of a neighborhood produces different algorithms with…
We consider the multiple traveling salesman problem on a weighted tree. In this problem there are $m$ salesmen located at the root initially. Each of them will visit a subset of vertices and return to the root. The goal is to assign a tour…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…