Related papers: Polyhedral Combinatorics of UPGMA Cones
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a widely used clustering method. Here we show that UPGMA is a greedy heuristic for the normalized equidistant minimum evolution (NEME) problem, that is, finding a rooted tree that…
The Neighbor-Joining algorithm is a popular distance-based phylogenetic method that computes a tree metric from a dissimilarity map arising from biological data. Realizing dissimilarity maps as points in Euclidean space, the algorithm…
UPGMA is a heuristic method identifying the least squares equidistant phylogenetic tree given empirical distance data among $n$ taxa. We study this classic algorithm using the geometry of the space of all equidistant trees with $n$ leaves,…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
This paper introduces an algebraic combinatorial approach to simplicial cone decompositions, a key step in solving inhomogeneous linear Diophantine systems and counting lattice points in polytopes. We use constant term manipulation on the…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
This paper is about the combinatorics of finite point configurations in the tropical projective space or, dually, of arrangements of finitely many tropical hyperplanes. Moreover, arrangements of finitely many tropical halfspaces can be…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
The volume and the number of lattice points of the permutohedron P_n are given by certain multivariate polynomials that have remarkable combinatorial properties. We give several different formulas for these polynomials. We also study a more…
The metric space of phylogenetic trees defined by Billera, Holmes, and Vogtmann, which we refer to as BHV space, provides a natural geometric setting for describing collections of trees on the same set of taxa. However, it is sometimes…
Ultrametric matrices are a class of covariance matrices that arise in latent tree models. As a parameter space in a statistical model, the set of ultrametric matrices is neither convex nor a smooth manifold. Focus in the literature has…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
In this paper we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster…
Ultrametric trees are trees whose leaves lie at the same distance from the root. They are used to model the genealogy of a population of particles co-existing at the same point in time. We show how the boundary of an ultrametric tree, like…
In 2019, Yoshida et al. developed tropical Principal Component Analysis (PCA), that is, an analogue of the classical PCA in the setting of tropical geometry and applied it to visualize a set of gene trees over a space of phylogenetic trees…
An elimination tree for a connected graph $G$ is a rooted tree on the vertices of $G$ obtained by choosing a root $x$ and recursing on the connected components of $G-x$ to produce the subtrees of $x$. Elimination trees appear in many guises…
An important application of distance geometry to biochemistry studies the embeddings of the vertices of a weighted graph in the three-dimensional Euclidean space such that the edge weights are equal to the Euclidean distances between…
We develop an algorithmic theory of convex optimization over discrete sets. Using a combination of algebraic and geometric tools we are able to provide polynomial time algorithms for solving broad classes of convex combinatorial…
Solutions to a linear Diophantine system, or lattice points in a rational convex polytope, are important concepts in algebraic combinatorics and computational geometry. The enumeration problem is fundamental and has been well studied,…