Related papers: Five Equivalent Representations of a Phylogenetic …
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
In this paper, we introduce a specific type of Euclidean tree called LED (Leaves of Equal Depth) tree. LED trees can be used in computational phylogeny, since they are a natural representative of the time evolution of a set of species in a…
Decision trees are widely used for interpretable machine learning due to their clearly structured reasoning process. However, this structure belies a challenge we refer to as predictive equivalence: a given tree's decision boundary can be…
A split-by-edges tree of a graph G on n vertices is a binary tree T where the root = V(G), every leaf is an independent set in G, and for every other node N in T with children L and R there is a pair of vertices {u, v} in N such that L = N…
In Francis and Steel (2015), it was shown that there exists non-trivial networks on $4$ leaves upon which the distance metric affords a metric on a tree which is not the base tree of the network. In this paper we extend this result in two…
We explicitly determine the automorphism groups of all self-similar trees (a.k.a. trees with finitely many cone types). We show that any such automorphism group is a direct limit of certain finite products of finite symmetric groups, which…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…
Several indices that measure the degree of balance of a rooted phylogenetic tree have been proposed so far in the literature. In this work we define and study a new index of this kind, which we call the total cophenetic index: the sum, over…
Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on…
Place value numbers, such as the binary or decimal numbers can be represented by the end vertices (leaf or pendant vertices) of rooted symmetrical trees. Numbers that consist of at most a fixed number of digits are represented by vertices…
Stochastic modeling of phylogenies raises five questions that have received varying levels of attention from quantitatively inclined biologists. 1) How large do we expect (from the model) the ration of maximum historical diversity to…
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 reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…
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…
We survey the definition and some elementary properties of real trees. There are no new results, as far as we know. One purpose is to give a number of different definitions and show the equivalence between them. We discuss also, for…
Motivated by geometric origami and the straight skeleton construction, we outline a map between spaces of phylogenetic trees and spaces of planar polygons. The limitations of this map is studied through explicit examples, culminating in…
In this manuscript, we show that any neural network with any activation function can be represented as a decision tree. The representation is equivalence and not an approximation, thus keeping the accuracy of the neural network exactly as…
Phylogenetic trees summarize evolutionary relationships. The Billera-Holmes-Vogtmann (BHV) space for comparing phylogenetic trees has many elegant mathematical properties, but it does not encompass trees with differing leaf sets. To…