Related papers: On Tree Representations of Relations and Graphs: S…
Over the past decade, we witness an increasing amount of interest in the design of exact exponential-time and parameterized algorithms for problems in Graph Drawing. Unfortunately, we still lack knowledge of general methods to develop such…
A graph covering projection, also referred to as a locally bijective homomorphism, is a mapping between the vertices and edges of two graphs that preserves incidences and is a local bijection. This concept originates in topological graph…
Geometric trees are characterized by their tree-structured layout and spatially constrained nodes and edges, which significantly impacts their topological attributes. This inherent hierarchical structure plays a crucial role in domains such…
The concepts of orthology, paralogy, and xenology play a key role in molecular evolution. Orthology and paralogy distinguish whether a pair of genes originated by speciation or duplication. The corresponding binary relations on a set of…
The challenge of answering graph queries over incomplete knowledge graphs is gaining significant attention in the machine learning community. Neuro-symbolic models have emerged as a promising approach, combining good performance with high…
Ultametrics are an important class of distances used in applications such as phylogenetics, clustering and classification theory. Ultrametrics are essentially distances that can be represented by an edge-weighted rooted tree so that all of…
2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
Topological drawings are representations of graphs in the plane, where vertices are represented by points, and edges by simple curves connecting the points. A drawing is simple if two edges intersect at most in a single point, either at a…
The aim of this chapter is to provide an adequate graph theoretic framework for the description of periodic bifurcations which have recently been discovered in descendant trees of finite p-groups. The graph theoretic concepts of rooted…
In this paper we fix 7 types of undirected graphs: paths, paths with prescribed endvertices, circuits, forests, spanning trees, (not necessarily spanning) trees and cuts. Given an undirected graph $G=(V,E)$ and two "object types"…
In the Properly Colored Spanning Tree problem, we are given an edge-colored undirected graph and the goal is to find a spanning tree in which any two adjacent edges have distinct colors. Since finding such a tree is NP-hard in general,…
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…
Binary relations derived from labeled rooted trees play an import role in mathematical biology as formal models of evolutionary relationships. The (symmetrized) Fitch relation formalizes xenology as the pairs of genes separated by at least…
For a fixed "pattern" graph $G$, the $\textit{colored $G$-subgraph isomorphism problem}$ (denoted $\mathrm{SUB}(G)$) asks, given an $n$-vertex graph $H$ and a coloring $V(H) \to V(G)$, whether $H$ contains a properly colored copy of $G$.…
Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
The graph is one of the most widely used mathematical structures in engineering and science because of its representational power and inherent ability to demonstrate the relationship between objects. The objective of this work is to…
Cographs are graphs in which no four vertices induce a simple connected path $P_4$. Cograph editing is to find for a given graph $G = (V,E)$ a set of at most $k$ edge additions and deletions that transform $G$ into a cograph. This…