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Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…
In this paper, we study the induced homological sequence and the induced merge tree of a discrete Morse function on a tree. A discrete Morse function on a tree gives rise to a sequence of Betti numbers that keep track of the number of…
In mathematical phylogenetics, the time-consistent galled trees provide a simple class of rooted binary network structures that can be used to represent a variety of different biological phenomena. We study the enumerative combinatorics of…
This work studies the statistical implications of using features comprised of general linear combinations of covariates to partition the data in randomized decision tree and forest regression algorithms. Using random tessellation theory in…
A quasiconformal tree $T$ is a (compact) metric tree that is doubling and of bounded turning. We call $T$ trivalent if every branch point of $T$ has exactly three branches. If the set of branch points is uniformly relatively separated and…
This paper demonstrates that every ultrametric space is homeomorphic to a clade space of a pruned tree, i.e., a subspace of a tree's canopy. Furthermore, it characterizes several topological properties of ultrametrizable spaces through the…
We investigate the interrelations between labeled trees and ultrametric spaces generated by these trees. The labeled trees, which generate complete ultrametrics, totally bounded ultrametrics, and discrete ones, are characterized up to…
We study random trees which are invariant in law under the operation of contracting each edge independently with probability $p\in(0,1)$. We show that all such trees can be constructed through Poissonian sampling from a certain class of…
In order to study convergences of looptrees, we construct continuum trees and looptrees from real-valued c\`adl\`ag functions without negative jumps called excursions. We then provide a toolbox to manipulate the two resulting codings of…
We study tree-to-tree transformations that can be defined in first-order logic or monadic second-order logic. We prove a decomposition theorem, which shows that every transformation can be obtained from prime transformations, such as…
In this paper we investigate the use of the concept of tree dimension in Horn clause analysis and verification. The dimension of a tree is a measure of its non-linearity - for example a list of any length has dimension zero while a complete…
We present a construction, called the limit of a tree system of spaces (or, less formally, a tree of spaces). The construction is designed to produce compact metric spaces that resemble fractals, out of more regular spaces, such as closed…
The goal of this work is to decompose random populations with a genealogy in subfamilies of a given degree of kinship and to obtain a notion of infinitely divisible genealogies. We model the genealogical structure of a population by…
We describe those complete linearly ordered topological spaces $X$ which are homogeneous (=CHLOTS). That is, $X$ is order isomorphic with any nonempty open interval in $X$. Using countable tail-like ordinals as indices, we build towers of…
Certain families of combinatorial objects admit recursive descriptions in terms of generating trees: each node of the tree corresponds to an object, and the branch leading to the node encodes the choices made in the construction of the…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
The time-ordered multilayer integrals have long been cited as major challenges in the analytical study of cosmological correlators and wavefunction coefficients. The recently proposed family tree decomposition technique solved these time…
The monadic second-order theory of trees allows quantification over elements and over arbitrary subsets. We classify the class of trees with respect to the question: does a tree T have a definable choice function (by a monadic formula with…
This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…
We study the enumeration problem for different kind of tree parking functions introduced recently, called tree parking functions, tree parking distributions, prime tree parking functions, and prime tree parking distributions, for rooted…