Related papers: Generalized Fitch Graphs: Edge-labeled Graphs that…
Homophily is a graph property describing the tendency of edges to connect similar nodes; the opposite is called heterophily. It is often believed that heterophilous graphs are challenging for standard message-passing graph neural networks…
Tree representations of (sets of) symmetric binary relations, or equivalently edge-colored undirected graphs, are of central interest, e.g.\ in phylogenomics. In this context symbolic ultrametrics play a crucial role. Symbolic ultrametrics…
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…
A family of graphs $\mathcal{F}$ is hereditary if $\mathcal{F}$ is closed under isomorphism and taking induced subgraphs. The speed of $\mathcal{F}$ is the sequence $\{|\mathcal{F}^n|\}_{n \in \mathbb{N}}$, where $\mathcal{F}^n$ denotes the…
Graphs drawn in the plane are ubiquitous, arising from data sets through a variety of methods ranging from GIS analysis to image classification to shape analysis. A fundamental problem in this type of data is comparison: given a set of such…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
We study homomorphism problems of signed graphs from a computational point of view. A signed graph $(G,\Sigma)$ is a graph $G$ where each edge is given a sign, positive or negative; $\Sigma\subseteq E(G)$ denotes the set of negative edges.…
Much information about a graph can be obtained by studying its spanning trees. On the other hand, a graph can be regarded as a 1-dimensional cell complex, raising the question of developing a theory of trees in higher dimension. As observed…
Let $S$ be a set of transpositions generating the symmetric group $S_n$. The transposition graph of $S$ is defined to be the graph with vertex set $\{1,\ldots,n\}$, and with vertices $i$ and $j$ being adjacent in $T(S)$ whenever $(i,j) \in…
In this paper we study graphs which admit acyclic orientations that contain a pair of arc-disjoint out-branching and in-branching (such an orientation is called good) and we focus on edge-minimal such graphs. A 2T-graph is a graph whose…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
Graphs derived from groups are a widely studied class of graphs, motivated by their highly symmetric structure. In particular, G-graphs offer an easy and interesting alternative construction of semi-symmetric graphs. After recalling the…
A median graph is a connected graph, such that for any three vertices $u,v,w$ there is exactly one vertex $x$ that lies simultaneously on a shortest $(u,v)$-path, a shortest $(v,w)$-path and a shortest $(w,u)$-path. Examples of median…
A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…
Let $G$ be a graph and $A$ be its adjacency matrix. A graph $G$ is invertible if its adjacency matrix $A$ is invertible and the inverse of $G$ is a weighted graph with adjacency matrix $A^{-1}$. A signed graph $(G,\sigma)$ is a weighted…
A $k$-edge-colored graph is a finite, simple graph with edges labeled by numbers $1,\ldots,k$. A function from the vertex set of one $k$-edge-colored graph to another is a homomorphism if the endpoints of any edge are mapped to two…
Given a graph $G$ rooted at a vertex $r$ and weight functions, $\gamma, \tau: E(G) \rightarrow \mathbb{R}$, the generalized cable-trench problem (CTP) is to find a single spanning tree that simultaneously minimizes the sum of the total edge…
We provide a general mathematical framework based on the theory of graphical models to study admixture graphs. Admixture graphs are used to describe the ancestral relationships between past and present populations, allowing for population…
The center, median and the security center are three central parts defined for any connected graph whereas the characteristic set, subtree core and core vertices are three central parts defined for trees only. We extend the concept of the…