Related papers: Reciprocal Best Match Graphs
Geometric graphs appear in many real-world data sets, such as road networks, sensor networks, and molecules. We investigate the notion of distance between embedded graphs and present a metric to measure the distance between two geometric…
2-colored quasi best match graphs (2-qBMGs) are directed graphs that arose in phylogenetics. Investigations of 2-qBMGs have mostly focused on computational issues. However, 2-qBMGs also have relevant properties for structural graph theory;…
An $r$-matching in a graph $G$ is a collection of edges in $G$ such that the distance between any two edges is at least $r$. A $2$-matching is also called an induced matching. In this paper, we estimate the maximum number of $r$-matchings…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…
The Random Geometric Graph (RGG) is a random graph model for network data with an underlying spatial representation. Geometry endows RGGs with a rich dependence structure and often leads to desirable properties of real-world networks such…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies…
In this paper, we study orthogonal colourings of random geometric graphs. Two colourings of a graph are orthogonal if they have the property that when two vertices receive the same colour in one colouring, then those vertices receive…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
Random forests are considered one of the best out-of-the-box classification and regression algorithms due to their high level of predictive performance with relatively little tuning. Pairwise proximities can be computed from a trained…
In this paper we consider Contact graphs of Paths on a Grid (CPG graphs), i.e. graphs for which there exists a family of interiorly disjoint paths on a grid in one-to-one correspondence with their vertex set such that two vertices are…
Merge trees, a type of topological descriptor, serve to identify and summarize the topological characteristics associated with scalar fields. They present a great potential for the analysis and visualization of time-varying data. First,…
The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…
In the Properly Colored Spanning Tree problem, we are given an edge-colored undirected graph and the goal is to find a properly colored spanning tree, i.e., a spanning tree in which any two adjacent edges have distinct colors. The problem…
Graphs drawn in the plane are ubiquitous, arising from data sets through a variety of methods ranging from GIS analysis to image classification to shape analysis. A fundamental problem in this type of data is comparison: given a set of such…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
Genetic algorithms have played an important role in engineering optimization. Traditional GAs treat each gene separately. However, biophysical studies of gene regulatory networks revealed direct associations between different genes. It…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…