Related papers: A Short Note on Undirected Fitch Graphs
Coloured graphical models are Gaussian statistical models determined by an undirected coloured graph. These models can be described by linear spaces of symmetric matrices. We outline a relationship between the symmetries of the graph and…
The classical Dehn--Sommerville relations assert that the $h$-vector of an Eulerian simplicial complex is symmetric. We establish three generalizations of the Dehn--Sommerville relations: one for the $h$-vectors of pure simplicial…
We enumerate graph homomorphisms to quasi-complete graphs, i.e., graphs obtained from complete graphs by removing one edge. The source graphs are complete graphs, quasi-complete graphs, cycles, paths, wheels and broken wheels. These…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
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…
Exploiting symmetries and invariance in data is a powerful, yet not fully exploited, way to achieve better generalisation with more efficiency. In this paper, we introduce two graph network architectures that are equivariant to several…
We provide precise asymptotic estimates for the number of general phylogenetic networks by using analytic combinatorial methods. Recently, this approach is studied by Fuchs, Gittenberger, and the author himself (Australasian Journal of…
The article starts with some introductory material about resolution graphs of normal surface singularities (definitions, topological/homological properties, etc). We then discuss the case when the normal surface singularity is an N-fold…
We give some properties of skew spectrum of a graph, especially, we answer negatively a problem concerning the skew characteristic polynomial and matching polynomial in [M. Cavers et al., Skew-adjacency matrices of graphs, Linear Algebra…
In this paper, we propose a new type of graph, denoted as "embedded-graph", and its theory, which employs a distributed representation to describe the relations on the graph edges. Embedded-graphs can express linguistic and complicated…
Symmetric independence relations are often studied using graphical representations. Ancestral graphs or acyclic directed mixed graphs with $m$-separation provide classes of symmetric graphical independence models that are closed under…
We consider families of coded systems that contain the Dyck shifts and that are closed under topological conjugacy. We introduce a notion of hyposynchronization of subshifts. We introduce a notion of restricted complexity of…
In this paper, we extend the ideas of graph pebbling to oriented graphs and find a classification for all graphs with fully traversable pebbling assignments that are isomorphic to their assignment graph. We then give some cases in which a…
It is well known that a graph $G$ has a symmetric spectrum if and only if it is bipartite, a signed graph $\Gamma=(G,\sigma)$ has a symmetric spectrum if $G$ is bipartite. However, there exists a spectrally symmetric signed graph…
Graph invariants provide a powerful analytical tool for investigation of abstract structures of graphs. They, combined in convenient relations, carry global and general information about a graph and its various substructures such as cycle…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
We introduce a new model of indeterminacy in graphs: instead of specifying all the edges of the graph, the input contains all triples of vertices that form a connected subgraph. In general, different (labelled) graphs may have the same set…
It is shown that if an infinite synchronized system has a flip, then it has infinitely many non-conjugate flips, and that the result cannot be extended to the class of coded systems.
We prove that a fractional perfect matching in a non-bipartite graph can be written, in polynomial time, as a convex combination of perfect matchings. This extends the Birkhoff-von Neumann Theorem from bipartite to non-bipartite graphs. The…
Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set $X$ of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization, that cannot be captured by trees. A variety of…