Related papers: Fitch Graph Completion
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
This article deals with homomorphisms of oriented graphs with respect to push equivalence. Here homomorphisms refer to arc preserving vertex mappings, and push equivalence refers to the equivalence class of orientations of a graph $G$ those…
The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…
Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs…
The competition graph of a doubly partial order is known to be an interval graph. The CCE graph and the niche graph of a doubly partial order are also known to be interval graphs if the graphs do not contain a cycle of length four and three…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
Real-world graphs generally have only one kind of tendency in their connections. These connections are either homophily-prone or heterophily-prone. While graphs with homophily-prone edges tend to connect nodes with the same class (i.e.,…
Heterogeneous graph neural networks (HGNNs) have attracted increasing research interest in recent three years. Most existing HGNNs fall into two classes. One class is meta-path-based HGNNs which either require domain knowledge to handcraft…
Graph Neural Networks (GNNs) have been highly successful for the node classification task. GNNs typically assume graphs are homophilic, i.e. neighboring nodes are likely to belong to the same class. However, a number of real-world graphs…
A biclique is a maximal induced complete bipartite subgraph of a graph. We investigate the intersection structure of edge-sets of bicliques in a graph. Specifically, we study the associated edge-biclique hypergraph whose hyperedges are…
For a fixed graph H with t vertices, an H-factor of a graph G with n vertices, where t divides n, is a collection of vertex disjoint (not necessarily induced) copies of H in G covering all vertices of G. We prove that for a fixed tree T on…
Hypergraphs are generalisation of graphs in which a hyperedge can connect any number of vertices. It can describe n-ary relationships and high-order information among entities compared to conventional graphs. In this paper, we study the…
We introduce a new oriented evolving graph model inspired by biological networks. A node is added at each time step and is connected to the rest of the graph by random oriented edges emerging from older nodes. This leads to a statistical…
Graph neural networks (GNNs) have become powerful tools for processing graph-based information in various domains. A desirable property of GNNs is transferability, where a trained network can swap in information from a different graph…
In this paper we investigate the extremal relationship between two well-studied graph parameters: the order of the largest homogeneous set in a graph $G$ and the maximal number of distinct degrees appearing in an induced subgraph of $G$,…
Traditional classification tasks learn to assign samples to given classes based solely on sample features. This paradigm is evolving to include other sources of information, such as known relations between samples. Here we show that, even…
Given a graph, we associate each edge with the transposition which exchanges the endvertices. Fixing a linear order on the edge set, we obtain a permutation of the vertices. D\'enes proved that the permutation is a full cyclic permutation…
Horizontal gene transfer (HGT) is an important process in bacterial evolution. Current phylogeny-based approaches to capture it cannot however appropriately account for the fact that HGT can occur between bacteria living in different…