Related papers: Arboreal Ultrametrics
Models of growing networks are a central topic in network science. In these models, vertices are usually labeled by their arrival time, distinguishing even those node pairs whose structural roles are identical. In contrast, unlabeled…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
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…
Phylogeny is the study of the relations between biological entities. From it, the need to compare tree-like graphs has risen and several metrics were established and researched, but since there is no definitive way to compare them, its…
A classic problem in unsupervised learning and data analysis is to find simpler and easy-to-visualize representations of the data that preserve its essential properties. A widely-used method to preserve the underlying hierarchical structure…
We consider three different schemes for signal routing on a tree. The vertices of the tree represent transceivers that can transmit and receive signals, and are equipped with i.i.d. weights representing the strength of the transceivers. The…
The problem of comparing trees representing the evolutionary histories of cancerous tumors has turned out to be crucial, since there is a variety of different methods which typically infer multiple possible trees. A departure from the…
Motivation: While the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well-known that numerous other coexisting processes (e.g. horizontal gene…
Different types of two- and three-dimensional representations of a finite metric space are studied that focus on the accurate representation of the linear order among the distances rather than their actual values. Lower and upper bounds for…
We consider sequences of finite weighted random graphs that converge locally to unimodular i.i.d. weighted random trees. When the weights are atomless, we prove that the matchings of maximal weight converge locally to a matching on the…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
We develop a geometric framework to study the structure and function of complex networks. We assume that hyperbolic geometry underlies these networks, and we show that with this assumption, heterogeneous degree distributions and strong…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
Metrics in Grassmannians, or distances between subspaces of same dimension, have many uses, and extending them to the Total Grassmannian of subspaces of different dimensions is an important problem, as usual extensions lack good properties…
To improve our understanding of connected systems, different tools derived from statistics, signal processing, information theory and statistical physics have been developed in the last decade. Here, we will focus on the graph comparison…
We study the properties of several proximity measures for the vertices of weighted multigraphs and multidigraphs. Unlike the classical distance for the vertices of connected graphs, these proximity measures are applicable to weighted…
We extend known results on chordal graphs and distance-hereditary graphs to much larger graph classes by using only a common metric property of these graphs. Specifically, a graph is called $\alpha_i$-metric ($i\in \mathcal{N}$) if it…
We study the problem of fitting an ultrametric distance to a dissimilarity graph in the context of hierarchical cluster analysis. Standard hierarchical clustering methods are specified procedurally, rather than in terms of the cost function…
We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…