Related papers: Representing distance-hereditary graphs with multi…
In Chapter 1 we fully characterise pairs of finite graphs which form a gap in the full homomorphism order. This leads to a simple proof of the existence of generalised duality pairs. We also discuss how such results can be carried to…
Geometric graphs appear in many real-world data sets, such as road networks, sensor networks, and molecules. We investigate the notion of distance between embedded graphs and present a metric to measure the distance between two geometric…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
This paper outlines a method to determine whether two label-regular directed trees, are isomorphic and when they are almost isomorphic. The approach involves reinterpreting label-regular directed trees as universal covers of rooted graphs.…
Treewidth is a parameter that emerged from the study of minor closed classes of graphs (i.e. classes closed under vertex and edge deletion, and edge contraction). It in some sense describes the global structure of a graph. Roughly, a graph…
Phylogenetic networks are used to study evolutionary relationships between species in biology. Such networks are often categorized into classes by their topological features, which stem from both biological and computational motivations. We…
Daily internet communication relies heavily on tree-structured graphs, embodied by popular data formats such as XML and JSON. However, many recent generative (probabilistic) models utilize neural networks to learn a probability distribution…
Many real-world networks are intrinsically directed. Such networks include activation of genes, hyperlinks on the internet, and the network of followers on Twitter among many others. The challenge, however, is to create a network model that…
This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…
Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…
In this paper, we consider the problem of reconstructing a directed graph using path queries. In this query model of learning, a graph is hidden from the learner, and the learner can access information about it with path queries. For a…
This paper studies the structure of graphs with given tree-width and excluding a fixed complete bipartite subgraph, which generalises the bounded degree setting. We give a new structural description of such graphs in terms of so-called…
We study the bounded regions in a generic slice of the hyperplane arrangement in $\mathbb{R}^n$ consisting of the hyperplanes defined by $x_i$ and $x_i+x_j$. The bounded regions are in bijection with several classes of combinatorial…
Network-based modeling of complex systems and data using the language of graphs has become an essential topic across a range of different disciplines. Arguably, this graph-based perspective derives its success from the relative simplicity…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing such networks is via a distance-based approach, where one is…
A transversal in a rooted tree is any set of nodes that meets every path from the root to a leaf. We let c(T,k) denote the number of transversals of size k in a rooted tree T. We define a partial order on the set of all rooted trees with n…
The distribution of distances in the star graph $ST_n$, ($1<n\in\Z$), is established, and subsequently a threaded binary tree is obtained that realizes an orientation of $ST_n$ whose levels are given by the distances to the identity…
Compound graphs are networks in which vertices can be grouped into larger subsets, with these subsets capable of further grouping, resulting in a nesting that can be many levels deep. In several applications, including biological workflows,…