Polyhedral computational geometry for averaging metric phylogenetic trees

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 measures on spaces of nonpositive curvature developed by Sturm. We show that the combinatorics of geodesics with a specified fixed endpoint in tree space are determined by the location of the varying endpoint in a certain polyhedral subdivision of tree space. The variance function associated to a finite subset of tree space has a fixed $C^\infty$ algebraic formula within each cell of the corresponding subdivision, and is continuously differentiable in the interior of each orthant of tree space. We use this subdivision to establish two iterative methods for producing sequences that converge to the Frechet mean: one based on Sturm's Law of Large Numbers, and another based on descent algorithms for finding optima of smooth functions on convex polyhedra. We present properties and biological applications of Frechet means and extend our main results to more general globally nonpositively curved spaces composed of Euclidean orthants.Comment: 43 pages, 6 figures; v2: fixed typos, shortened Sections 1 and 5, added counter example for polyhedrality of vistal subdivision in general CAT(0) cubical complexes; v1: 43 pages, 5 figure

Fraisse Limits, Ramsey Theory, and Topological Dynamics of Automorphism Groups

We study in this paper some connections between the Fraisse theory of amalgamation classes and ultrahomogeneous structures, Ramsey theory, and topological dynamics of automorphism groups of countable structures.Comment: 73 pages, LaTeX 2e, to appear in Geom. Funct. Ana

Lehmer's Problem, McKay's Correspondence, and 2,3,72,3,7

This paper addresses a long standing open problem due to Lehmer in which the triple 2,3,7 plays a notable role. Lehmer's problem asks whether there is a gap between 1 and the next smallest algebraic integer with respect to Mahler measure. The question has been studied in a wide range of contexts including number theory, ergodic theory, hyperbolic geometry, and knot theory; and relates to basic questions such as describing the distribution of heights of algebraic integers, and of lengths of geodesics on arithmetic surfaces. This paper focuses on the role of Coxeter systems in Lehmer's problem. The analysis also leads to a topological version of McKay's correspondence

Freeness theorems for operads via Gr\"obner bases

We show how to use Groebner bases for operads to prove various freeness theorems: freeness of certain operads as nonsymmetric operads, freeness of an operad Q as a P-module for an inclusion P into Q, freeness of a suboperad. This gives new proofs of many known results of this type and helps to prove some new results.Comment: 15 pages, no figures, corrected typos and changed in parts the structure of the pape

Notions of Relative Ubiquity for Invariant Sets of Relational Structures

Given a finite lexicon L of relational symbols and equality, one may view the collection of all L-structures on the set of natural numbers w as a space in several different ways. We consider it as: (i) the space of outcomes of certain infinite two-person games; (ii) a compact metric space; and (iii) a probability measure space. For each of these viewpoints, we can give a notion of relative ubiquity, or largeness, for invariant sets of structures on w. For example, in every sense of relative ubiquity considered here, the set of dense linear orderings on w is ubiquitous in the set of linear orderings on w