相关论文: Types of Stickiness in BHV Phylogenetic Tree Space…

We describe the use of the Frechet mean and variance in the Billera-Holmes-Vogtmann (BHV) treespace to summarize and explore the diversity of a set of phylogenetic trees. We show that the Frechet mean is comparable to other summary methods,…

Samples of phylogenetic trees arise in a variety of evolutionary and biomedical applications, and the Fr\'echet mean in Billera-Holmes-Vogtmann tree space is a summary tree shown to have advantages over other mean or consensus trees.…

The Fr\'echet mean, a generalization to a metric space of the expectation of a random variable in a vector space, can exhibit unexpected behavior for a wide class of random variables. For instance, it can stick to a point (more generally to…

Billera-Holmes-Vogtmann (BHV) tree space is a geodesic metric space of edge-weighted phylogenetic trees with a fixed leaf set. Constructing parametric distributions on this space is challenging due to its non-Euclidean geometry and the…

Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…

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…

The phylogenetic tree space introduced by Billera, Holmes, and Vogtmann (BHV tree space) is a CAT(0) continuous space that represents trees with edge weights with an intrinsic geodesic distance measure. The geodesic distance measure unique…

We analyze the structure and stickiness in the chaotic components of generic Hamiltonian systems with divided phase space. Following the method proposed recently in Lozej and Robnik [Phys. Rev. E 98, 022220 (2018)], the sticky regions are…

The Billera-Holmes-Vogtmann (BHV) space of weighted trees can be embedded in Euclidean space, but the extrinsic Euclidean mean often lies outside of treespace. Sturm showed that the intrinsic Frechet mean exists and is unique in treespace.…

Based on the probability distributions of products of random variables, we propose a simple stringy mechanism that prefers the meta-stable vacua with a small cosmological constant. We state some relevant properties of the probability…

As demonstrated in our previous work on ${\boldsymbol T}_{4}$, the space of phylogenetic trees with four leaves, the global, as well as the local, topological structure of the space plays an important role in the non-classical limiting…

The inference of evolutionary histories is a central problem in evolutionary biology. The analysis of a sample of phylogenetic trees can be conducted in Billera-Holmes-Vogtmann tree space, which is a CAT(0) metric space of phylogenetic…

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…

We consider a Bayesian approach to variable selection in the presence of high dimensional covariates based on a hierarchical model that places prior distributions on the regression coefficients as well as on the model space. We adopt the…

Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…

We propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than…

Possibilities for using geometry and topology to analyze statistical problems in biology raise a host of novel questions in geometry, probability, algebra, and combinatorics that demonstrate the power of biology to influence the future of…

Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering…

We are interested in measures of central tendency for a population on a network, which is modeled by a metric tree. The location parameters that we study are generalized Fr\'echet means obtained by minimizing the objective function $\alpha…

We study the distribution of occupation times for a one-dimensional random walk restricted to a finite interval by reflecting boundary conditions. At short times the classical bimodal distribution due to L\'evy is reproduced with walkers…