相关论文: Shared ancestry graphs and symbolic arboreal maps

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…

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…

A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines…

An acyclic digraph each vertex of which has indegree at most $i$ and outdegree at most $j$ is called an $(i, j)$ digraph for some positive integers $i$ and $j$. Lee {\it et al.} (2017) studied the phylogeny graphs of $(2, 2)$ digraphs and…

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…

Three-way dissimilarities are a generalization of (two-way) dissimilarities which can be used to indicate the lack of homogeneity or resemblance between any three objects. Such maps have applications in cluster analysis, and have been used…

Arboreal networks are multi-rooted phylogenetic networks whose underlying graph is a tree. We give an encoding of stack-free arboreal networks in terms of triplets and the novel concept of a duet. This yields a polynomial time algorithm to…

Jones conjectures the arboreal representation of a degree two rational map will have finite index in the full automorphism group of a binary rooted tree except under certain conditions. We prove a version of Jones' Conjecture for quadratic…

Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…

Binary relations derived from labeled rooted trees play an import role in mathematical biology as formal models of evolutionary relationships. The (symmetrized) Fitch relation formalizes xenology as the pairs of genes separated by at least…

Packing graphs is a combinatorial problem where several given graphs are being mapped into a common host graph such that every edge is used at most once. In the planar tree packing problem we are given two trees T1 and T2 on n vertices and…

Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…

Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…

It is known from the algebraic graph theory that if $L$ is the Laplacian matrix of some tree $G$ with a vertex degree sequence $\mathbf{d}=(d_1, ..., d_n)^\top$ and $D$ is its distance matrix, then…

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…

Consider a graph $G$ where each vertex is visibly labelled as a member of a distinct class, but also has a hidden binary state: wild or tame. Edges with end points in the same class are called agreement edges. Premise: an edge connecting…

Subgraph matching is a fundamental building block for graph-based applications and is challenging due to its high-order combinatorial nature. Existing studies usually tackle it by combinatorial optimization or learning-based methods.…

We propose a novel subgraph image representation for classification of network fragments with the targets being their parent networks. The graph image representation is based on 2D image embeddings of adjacency matrices. We use this image…

Bispanning graphs are undirected graphs with an edge set that can be decomposed into two disjoint spanning trees. The operation of symmetrically swapping two edges between the trees, such that the result is a different pair of disjoint…

Hefner [K. A. S. Hefner, K. F. Jones, S. -R. Kim, R. J. Lundgren and F. S. Roberts: $(i,j)$ competition graphs, Discrete Applied Mathematics, 32, (1991) 241-262] characterized acyclic digraphs each vertex of which has inderee and outdegree…