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The notion of tree entropy was introduced by the author as a normalized limit of the number of spanning trees in finite graphs, but is defined on random infinite rooted graphs. We give some new expressions for tree entropy; one uses…
A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution of species that have undergone reticulate evolution, there…
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…
Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…
We present recent advances in harmonic analysis on infinite graphs. Our approach combines combinatorial tools with new results from the theory of unbounded Hermitian operators in Hilbert space, geometry, boundary constructions, and spectral…
We prove asymptotic normality for the number of fringe subtrees isomorphic to any given tree in uniformly random trees with given vertex degrees. As applications, we also prove corresponding results for random labelled trees with given…
Inspired by a concept in comparative genomics, we investigate properties of randomly chosen members of G_1(m,n,t), the set of bipartite graphs with $m$ left vertices, n right vertices, t edges, and each vertex of degree at least one. We…
Past studies on the local limit of maximal weight matchings in edge-weighted large random graphs rely fundamentally on the assumption that the weights are atomless, which ensures that the maximal weight matching is unique. This excludes de…
Motivated by limits of critical inhomogeneous random graphs, we construct a family of sequences of measured metric spaces that we call continuous multiplicative graphs, that are expected to be the universal limit of graphs related to the…
Let $F=\{H_1,...,H_k\}$ be a family of graphs. A graph $G$ with $m$ edges is called {\em totally $F$-decomposable} if for {\em every} linear combination of the form $\alpha_1 e(H_1) + ... + \alpha_k e(H_k) = m$ where each $\alpha_i$ is a…
Consider a rooted $N$-ary tree. To every vertex of this tree, we attach an i.i.d. continuous random variable. A vertex is called accessible if along its ancestral line, the attached random variables are increasing. We keep accessible…
Real-world networks evolve over time via additions or removals of vertices and edges. In current network evolution models, vertex degree varies or grows arbitrarily. A recently introduced degree-preserving network growth (DPG) family of…
In this paper, we investigate the problem of generating the spanning trees of a graph $G$ up to the automorphisms or "symmetries" of $G$. After introducing and surveying this problem for general input graphs, we present algorithms that…
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…
We study various classes of random processes defined on the regular tree $T_d$ that are invariant under the automorphism group of $T_d$. Most important ones are factor of i.i.d. processes (randomized local algorithms), branching Markov…
We introduce a dynamical network model which unifies a number of network families which are individually known to exhibit $q$-exponential degree distributions. The present model dynamics incorporates static (non-growing) self-organizing…
In a recent paper, Caron and Fox suggest a probabilistic model for sparse graphs which are exchangeable when associating each vertex with a time parameter in $\mathbb{R}_+$. Here we show that by generalizing the classical definition of…
We study the structure of genealogical trees associated with explosive Crump-Mode-Jagers branching processes (stopped at the explosion time), proving criteria for the associated tree to contain a node of infinite degree (a star) or an…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees.…
Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…