Related papers: Tree-metrizable HGT networks
Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…
SpectralNet is a graph clustering method that uses neural network to find an embedding that separates the data. So far it was only used with $k$-nn graphs, which are usually constructed using a distance metric (e.g., Euclidean distance).…
Phylogenetic trees in genetics and biology in general are all binary. We make an attempt to answer one fundamental question: Is such binary branching from the coarsest to the finest scales sustained by data? We convert this question into an…
Horizontal gene transfer is an important contributor to evolution. According to Walter M.\ Fitch, two genes are xenologs if they are separated by at least one HGT. More formally, the directed Fitch graph has a set of genes is its vertices,…
The metric dimension has been introduced independently by Harary, Melter and Slater in 1975 to identify vertices of a graph G using its distances to a subset of vertices of G. A resolving set X of a graph G is a subset of vertices such…
In this work, we adapt a method based on multiple hypothesis tracking (MHT) that has been shown to give state-of-the-art vessel segmentation results in interactive settings, for the purpose of extracting trees. Regularly spaced tubular…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
The evolution of aligned DNA sequence sites is generally modeled by a Markov process operating along the edges of a phylogenetic tree. It is well known that the probability distribution on the site patterns at the tips of the tree…
Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of the…
Inference of evolutionary trees and rates from biological sequences is commonly performed using continuous-time Markov models of character change. The Markov process evolves along an unknown tree while observations arise only from the tips…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
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…
We propose Graph Tree Networks (GTNets), a deep graph learning architecture with a new general message passing scheme that originates from the tree representation of graphs. In the tree representation, messages propagate upward from the…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
Gromov-Hausdorff (GH) distance is a natural way to measure the distortion between two metric spaces. However, there has been only limited algorithmic development to compute or approximate this distance. We focus on computing the…
A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing such networks is via a distance-based approach, where one is…