Related papers: Representing distance-hereditary graphs with multi…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
Distance-hereditary graphs are known to be the graphs that are totally decomposable for the split decomposition. We characterise distance-hereditary graphs whose complement is also distance-hereditary by their split decomposition and by…
Quasi-trees generalize trees in that the unique "path" between two nodes may be infinite and have any countable order type. They are used to define the rank-width of a countable graph in such a way that it is equal to the least upper-bound…
Bayesian networks are a widely-used class of probabilistic graphical models capable of representing symmetric conditional independence between variables of interest using the topology of the underlying graph. For categorical variables, they…
Given any complex directed network, a set of acyclic subgraphs - the hierarchical backbone of the network - can be extracted that will provide valuable information about its hierarchical structure. The current paper presents how the…
We present a concept called the branch-depth of a connectivity function, that generalizes the tree-depth of graphs. Then we prove two theorems showing that this concept aligns closely with the notions of tree-depth and shrub-depth of graphs…
Random graphs are more and more used for modeling real world networks such as evolutionary networks of proteins. For this purpose we look at two different models and analyze how properties like connectedness and degree distributions are…
A rooted acyclic digraph N with labelled leaves displays a tree T when there exists a way to select a unique parent of each hybrid vertex resulting in the tree T. Let Tr(N) denote the set of all trees displayed by the network N. In general,…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
For a labeled tree on the vertex set $\set{1,2,\ldots,n}$, the local direction of each edge $(i\,j)$ is from $i$ to $j$ if $i<j$. For a rooted tree, there is also a natural global direction of edges towards the root. The number of edges…
It is known that many networks modeling real-life complex systems are small-word (large local clustering and small diameter) and scale-free (power law of the degree distribution), and very often they are also hierarchical. Although most of…
In this paper, we revisit the split decomposition of graphs and give new combinatorial and algorithmic results for the class of totally decomposable graphs, also known as the distance hereditary graphs, and for two non-trivial subclasses,…
We give a short and direct proof of a remarkable identity that arises in the enumeration of labeled trees with respect to their indegree sequence, where all edges are oriented from the vertex with lower label towards the vertex with higher…
To any directed graph we associate an algebra with edges of the graph as generators and with relations defined by all pairs of directed paths with the same origin and terminus. Such algebras are related to factorizations of polynomials over…
Rooted tree maps assign to an element of the Connes-Kreimer Hopf algebra of rooted trees a linear map on the noncommutative polynomial algebra in two letters. Evaluated at any admissible word these maps induce linear relations between…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
In this short note we provide a proof of boundedness of solutions for a network system composed of heterogeneous nonlinear autonomous systems interconnected over a directed graph. The sole assumptions imposed are that the systems are…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
Our previous paper shows that the (vertex) spanning tree degree enumerator polynomial of a connected graph $G$ is a real stable polynomial (id est is non-zero if all variables have positive imaginary parts) if and only if $G$ is…
The modular decomposition of a symmetric map $\delta\colon X\times X \to \Upsilon$ (or, equivalently, a set of symmetric binary relations, a 2-structure, or an edge-colored undirected graph) is a natural construction to capture key features…