相关论文: All that Glisters is not Galled

The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…

Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…

When a founder cell and its progeny divide with incomplete cytokinesis, a network forms in which each intercellular bridge corresponds to a past mitotic event. Networks built in this manner are required for gamete production in many…

Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…

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,…

Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa. They generalize phylogenetic trees since for example, unlike trees, they permit lineages to combine. Recently, there has been…

In this paper we enumerate and give bijections for the following four sets of vertices among rooted ordered trees of a fixed size: (i) first-children of degree $k$ at level $\ell$, (ii) non-first-children of degree $k$ at level $\ell-1$,…

Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the Network Multispecies Coalescent Model, individual gene trees arising from a network can have any topology, but…

Tree-child networks are an important class of phylogenetic network used to model reticulate evolutionary processes. These networks have attracted increasing attention from researchers with interests in both combinatorics and algorithms. A…

A graph is called set-sequential if its vertices can be labeled with distinct nonzero vectors in $\mathbb{F}_2^n$ such that when each edge is labeled with the sum$\pmod{2}$ of its vertices, every nonzero vector in $\mathbb{F}_2^n$ is the…

An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…

Models of growing networks are a central topic in network science. In these models, vertices are usually labeled by their arrival time, distinguishing even those node pairs whose structural roles are identical. In contrast, unlabeled…

The trophic levels of nodes in directed networks can reveal their functional properties. Moreover, the trophic coherence of a network, defined in terms of trophic levels, is related to properties such as cycle structure, stability and…

The Yule model and the coalescent model are two neutral stochastic models for generating trees in phylogenetics and population genetics, respectively. Although these models are quite different, they lead to identical distributions…

Group convolutional layers with respect to some group $G$ are modeled by convolutions or cross-correlations with a filter, and they provide the fundamental building block for group convolutional neural networks. For entirely unconstrained…

Let $T$ be a tree on $n$ vertices. We can regard the edges of $T$ as transpositions of the vertex set; their product (in any order) is a cyclic permutation. All possible cyclic permutations arise (each exactly once) if and only if the tree…

The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…

Using the theory of Properly Embedded Graphs developed in an earlier work we define an involutory duality on the set labeled non-crossing trees that lifts the obvious duality in the set of unlabeled non-crossing trees. The set of…

Staged tree models are a discrete generalization of Bayesian networks. We show that these form curved exponential families and derive their natural parameters, sufficient statistic, and cumulant-generating function as functions of their…

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…