Related papers: Arboreal Ultrametrics
We study the properties of ultrametric matrices aiming to design methods for fast ultrametric matrix-vector multiplication. We show how to encode such a matrix as a tree structure in quadratic time and demonstrate how to use the resulting…
Following a review of metric, ultrametric and generalized ultrametric, we review their application in data analysis. We show how they allow us to explore both geometry and topology of information, starting with measured data. Some themes…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
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…
In a recent paper on 'Estimating Species Trees from Unrooted Gene Trees' Liu and Yu observe that the distance matrix on the underlying taxon set, which is built up from expected internode distances on gene trees under the multispecies…
This is a survey article on trees, with a modest number of proofs to give a flavor of the way these topologies can be efficiently handled. Trees are defined in set-theorist fashion as partially ordered sets in which the elements below each…
The root is an important organ of a plant since it is responsible for water and nutrient uptake. Analyzing and modelling variabilities in the geometry and topology of roots can help in assessing the plant's health, understanding its growth…
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the…
This paper presents methods to compare high order networks, defined as weighted complete hypergraphs collecting relationship functions between elements of tuples. They can be considered as generalizations of conventional networks where only…
The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…
Rooted, weighted continuum random trees are used to describe limits of sequences of random discrete trees. Formally, they are random quadruples $(\mathcal{T},d,r,p)$, where $(\mathcal{T},d)$ is a tree-like metric space, $r\in\mathcal{T}$ is…
In this paper, we investigate adaptive nonlinear regression and introduce tree based piecewise linear regression algorithms that are highly efficient and provide significantly improved performance with guaranteed upper bounds in an…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
A quasiconformal tree is a doubling (compact) metric tree in which the diameter of each arc is comparable to the distance of its endpoints. We show that for each integer $n\geq 2$, the class of all quasiconformal trees with uniform branch…
The concepts of orthology, paralogy, and xenology play a key role in molecular evolution. Orthology and paralogy distinguish whether a pair of genes originated by speciation or duplication. The corresponding binary relations on a set of…
Abstractly, tropical hyperelliptic curves are metric graphs that admit a two-to-one harmonic morphism to a tree. They also appear as embedded tropical curves in the plane arising from triangulations of polygons with all interior lattice…
Distances are pervasive in machine learning. They serve as similarity measures, loss functions, and learning targets; it is said that a good distance measure solves a task. When defining distances, the triangle inequality has proven to be a…
We introduce a general framework for analyzing data modeled as parameterized families of networks. Building on a Gromov-Wasserstein variant of optimal transport, we define a family of parameterized Gromov-Wasserstein distances for comparing…