Related papers: Representing distance-hereditary graphs with multi…
Many standard graph classes are known to be characterized by means of layouts (a permutation of its vertices) excluding some patterns. Important such graph classes are among others: proper interval graphs, interval graphs, chordal graphs,…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
Unigraphs are graphs identifiable up to isomorphism from their degree sequences. Given a class $\mathcal{A}$ of graphs, we define the class of $\mathcal{A}$-unigraphs to be graphs identifiable from degree sequence and membership in…
A graph is a $k$-leaf power of a tree $T$ if its vertices are leaves of $T$ and two vertices are adjacent in $T$ if and only if their distance in $T$ is at most $k$. Then $T$ is a $k$-leaf root of $G$. This notion was introduced by…
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…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
Graphs and complex networks can be successively separated into connected components associated to respective seed nodes, therefore establishing a respective hierarchical organization. In the present work, we study the properties of the…
Exchangeable random graphs serve as an important probabilistic framework for the statistical analysis of network data. In this work we develop an alternative parameterization for a large class of exchangeable random graphs, where the nodes…
A path graph is the intersection graph of paths in a tree. A directed path graph is the intersection graph of paths in a directed tree. Even if path graphs and directed path graphs are characterized very similarly, their recognition…
In this paper, we propose a new type of graph, denoted as "embedded-graph", and its theory, which employs a distributed representation to describe the relations on the graph edges. Embedded-graphs can express linguistic and complicated…
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any…
As a generalization of the Edmonds arborescence packing theorem, Kamiyama--Katoh--Takizawa (2009) gave a good characterization of directed graphs that contain arc-disjoint arborescences spanning the set of vertices reachable from each root.…
Traditional random graph models of networks generate networks that are locally tree-like, meaning that all local neighborhoods take the form of trees. In this respect such models are highly unrealistic, most real networks having strongly…
Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set $X$ of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization, that cannot be captured by trees. A variety of…
The distance matrix of a connected graph is the symmetric matrix with columns and rows indexed by the vertices and entries that are the pairwise distances between the corresponding vertices. We give a construction for graphs which differ in…
Based on the Connes--Kreimer Hopf algebra of rooted trees, the rooted tree maps are defined as linear maps on noncommutative polynomial algebra in two indeterminates. It is known that they induce a large class of linear relations for…
We prove that a hereditary graph class $\mathcal{G}$ defined by finitely many excluded induced subgraphs has bounded tree-$\alpha$ if and only if it is "$(\mathrm{tw},\omega)$-bounded" (that is, for all $t\in \mathbb N$, the class of all…
We show that for every graph $H$, there is a hereditary weakly sparse graph class $\mathcal C_H$ of unbounded treewidth such that the $H$-free (i.e., excluding $H$ as an induced subgraph) graphs of $\mathcal C_H$ have bounded treewidth.…
Gurski and Wanke showed that a graph class C has bounded tree-width if and only if its associated class of directed line graphs has bounded clique-width. Inevitably -- asking whether this relationship lifts to directed graphs -- we…
Since Darwin, species trees have been used as a simplified description of the relationships which summarize the complicated network $N$ of reality. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are…