Related papers: Shared ancestry graphs and symbolic arboreal maps

Orchards are a biologically relevant class of phylogenetic networks as they can describe treelike evolutionary histories augmented with horizontal transfer events. Moreover, the class has attractive mathematical characterizations that can…

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…

In Francis and Steel (2015), it was shown that there exists non-trivial networks on $4$ leaves upon which the distance metric affords a metric on a tree which is not the base tree of the network. In this paper we extend this result in two…

A tree $T$ on $2^n$ vertices is called set-sequential if the elements in $V(T)\cup E(T)$ can be labeled with distinct nonzero $(n+1)$-dimensional $01$-vectors such that the vector labeling each edge is the component-wise sum modulo $2$ of…

We prove that every oriented tree on $n$ vertices with bounded maximum degree appears as a spanning subdigraph of every directed graph on $n$ vertices with minimum semidegree at least $n/2+o(n)$. This can be seen as a directed graph…

The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…

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…

It is well known that the spectral radius of a tree whose maximum degree is D cannot exceed 2sqrt{D-1}. Similar upper bound holds for arbitrary planar graphs, whose spectral radius cannot exceed sqrt{8D}+10, and more generally, for all…

Recent investigations in computational biology have focused on a family of 2-colored digraphs, called 2-colored best match graphs, which naturally arise from rooted phylogenetic trees. Actually the defining properties of such graphs are…

We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…

An acyclic digraph in which every vertex has indegree at most $i$ and outdegree at most $j$ is called an $(i,j)$ digraph for some positive integers $i$ and $j$. The phylogeny graph of a digraph $D$ has $V(D)$ as the vertex set and an edge…

In 1998, B\"{o}cker and Dress gave a 1-to-1 correspondence between symbolically dated rooted trees and symbolic ultrametrics. We consider the corresponding problem for unrooted trees. More precisely, given a tree $T$ with leaf set $X$ and a…

Graph symmetries intervene in diverse applications, from enumeration, to graph structure compression, to the discovery of graph dynamics (e.g., node arrival order inference). Whereas Erd\H{o}s-R\'enyi graphs are typically asymmetric, real…

We exhibit the joint symmetric distribution of the following two parameters on the set of unlabeled, simple, connected graphs with $n$ vertices. The first parameter is the maximal number of leaves attached to a vertex. The second parameter…

We introduce the concept of a \textbf{neuro-symbolic pair} -- neural and symbolic approaches that are linked through a common knowledge representation. Next, we present \textbf{taxonomic networks}, a type of discrimination network in which…

Many data sets, crucial for today's applications, consist essentially of enormous networks, containing millions or even billions of elements. Having the possibility of visualizing such networks is of paramount importance. We propose an…

We define two families of determinantal random spanning subgraphs of a finite connected graph, one supported by acyclic spanning subgraphs (spanning forests) with fixed number of connected components, the other by connected spanning…

An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…

The betweenness structure of a finite metric space $M = (X, d)$ is a pair $\mathcal{B}(M) = (X,\beta_M)$ where $\beta_M$ is the so-called betweenness relation of $M$ that consists of point triplets $(x, y, z)$ such that $d(x, z) = d(x, y) +…

We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…