相关论文: Tropical Fermat-Weber Points over Spaces of $M$-Ul…
In a metric space, the Fermat-Weber points of a sample are statistics to measure the central tendency of the sample and it is well-known that the Fermat-Weber point of a sample is not necessarily unique in the metric space. We investigate…
We study a parametric version of the Fermat-Weber problem with respect to an asymmetric distance function, which occurs naturally in tropical geometry. Our results yield a method for constructing phylogenetic supertrees.
We study the geometry of tropical Fermat--Weber points, that is, optimal solutions to a location problem over a projective space using a dissimilarity measure derived from the tropical metric. It is well-known that for a given sample, such…
Fermat-Weber points with respect to an asymmetric tropical distance function are studied. It turns out that they correspond to the optimal solutions of a transportation problem. The results are applied to obtain a new method for computing…
Given a matroid M on the ground set E, the Bergman fan B(M), or space of M-ultrametrics, is a polyhedral complex in R^E which arises in several different areas, such as tropical algebraic geometry, dynamical systems, and phylogenetics.…
Let $\mathbf{v}_1,\ldots,\mathbf{v}_m$ be points in a metric space with distance $d$, and let $w_1,\ldots,w_m$ be positive real weights. The weighted Fermat-Weber points are those points $\mathbf{x}$ which minimize $\sum w_i d(\mathbf{v}_i,…
Ultametrics are an important class of distances used in applications such as phylogenetics, clustering and classification theory. Ultrametrics are essentially distances that can be represented by an edge-weighted rooted tree so that all of…
Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
We investigate uniqueness issues that arise in $l^\infty$-optimization to linear spaces and Bergman fans of matroids. For linear spaces, we give a polyhedral decomposition of $\mathbb{R}^n$ based on the dimension of the set of…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
We study the geometry of metrics and convexity structures on the space of phylogenetic trees, which is here realized as the tropical linear space of all \ ultrametrics. The ${\rm CAT}(0)$-metric of Billera-Holmes-Vogtman arises from the…
We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
In the tropical projective torus, it is not guaranteed that the projection of a Fermat-Weber point of a given data set is a Fermat-Weber point of the projection of the data set. In this paper, we focus on the projection on the tropical…
Phylogenetic trees provide a fundamental representation of evolutionary relationships, yet the combinatorial explosion of possible tree topologies renders inference computationally challenging. Classical approaches to characterizing tree…
Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain Monte Carlo (MCMC) analyses used in Bayesian phylogenetic tree reconstruction. The…
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…
This paper investigates the computational geometry relevant to calculations of the Frechet mean and variance for probability distributions on the phylogenetic tree space of Billera, Holmes and Vogtmann, using the theory of probability…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…