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

Tropical polar cones, hypergraph transversals, and mean payoff games

We discuss the tropical analogues of several basic questions of convex duality. In particular, the polar of a tropical polyhedral cone represents the set of linear inequalities that its elements satisfy. We characterize the extreme rays of the polar in terms of certain minimal set covers which may be thought of as weighted generalizations of minimal transversals in hypergraphs. We also give a tropical analogue of Farkas lemma, which allows one to check whether a linear inequality is implied by a finite family of linear inequalities. Here, the certificate is a strategy of a mean payoff game. We discuss examples, showing that the number of extreme rays of the polar of the tropical cyclic polyhedral cone is polynomially bounded, and that there is no unique minimal system of inequalities defining a given tropical polyhedral cone.Comment: 27 pages, 6 figures, revised versio

Approximation of norms on Banach spaces

Relatively recently it was proved that if $\Gamma$ is an arbitrary set, then any equivalent norm on $c_0(\Gamma)$ can be approximated uniformly on bounded sets by polyhedral norms and $C^\infty$ smooth norms, with arbitrary precision. We extend this result to more classes of spaces having uncountable symmetric bases, such as preduals of the `discrete' Lorentz spaces $d(w,1,\Gamma)$, and certain symmetric Nakano spaces and Orlicz spaces. We also show that, given an arbitrary ordinal number $\alpha$, there exists a scattered compact space $K$ having Cantor-Bendixson height at least $\alpha$, such that every equivalent norm on $C(K)$ can be approximated as above

Tight Bounds for Consensus Systems Convergence

We analyze the asymptotic convergence of all infinite products of matrices taken in a given finite set, by looking only at finite or periodic products. It is known that when the matrices of the set have a common nonincreasing polyhedral norm, all infinite products converge to zero if and only if all infinite periodic products with period smaller than a certain value converge to zero, and bounds exist on that value. We provide a stronger bound holding for both polyhedral norms and polyhedral seminorms. In the latter case, the matrix products do not necessarily converge to 0, but all trajectories of the associated system converge to a common invariant space. We prove our bound to be tight, in the sense that for any polyhedral seminorm, there is a set of matrices such that not all infinite products converge, but every periodic product with period smaller than our bound does converge. Our technique is based on an analysis of the combinatorial structure of the face lattice of the unit ball of the nonincreasing seminorm. The bound we obtain is equal to half the size of the largest antichain in this lattice. Explicitly evaluating this quantity may be challenging in some cases. We therefore link our problem with the Sperner property: the property that, for some graded posets, -- in this case the face lattice of the unit ball -- the size of the largest antichain is equal to the size of the largest rank level. We show that some sets of matrices with invariant polyhedral seminorms lead to posets that do not have that Sperner property. However, this property holds for the polyhedron obtained when treating sets of stochastic matrices, and our bound can then be easily evaluated in that case. In particular, we show that for the dimension of the space $n \geq 8$, our bound is smaller than the previously known bound by a multiplicative factor of $\frac{3}{2 \sqrt{\pi n}}$

A-Tint: A polymake extension for algorithmic tropical intersection theory

In this paper we study algorithmic aspects of tropical intersection theory. We analyse how divisors and intersection products on tropical cycles can actually be computed using polyhedral geometry. The main focus of this paper is the study of moduli spaces, where the underlying combinatorics of the varieties involved allow a much more efficient way of computing certain tropical cycles. The algorithms discussed here have been implemented in an extension for polymake, a software for polyhedral computations.Comment: 32 pages, 5 figures, 4 tables. Second version: Revised version, to be published in European Journal of Combinatoric

Group field theories for all loop quantum gravity

Group field theories represent a 2nd quantized reformulation of the loop quantum gravity state space and a completion of the spin foam formalism. States of the canonical theory, in the traditional continuum setting, have support on graphs of arbitrary valence. On the other hand, group field theories have usually been defined in a simplicial context, thus dealing with a restricted set of graphs. In this paper, we generalize the combinatorics of group field theories to cover all the loop quantum gravity state space. As an explicit example, we describe the GFT formulation of the KKL spin foam model, as well as a particular modified version. We show that the use of tensor model tools allows for the most effective construction. In order to clarify the mathematical basis of our construction and of the formalisms with which we deal, we also give an exhaustive description of the combinatorial structures entering spin foam models and group field theories, both at the level of the boundary states and of the quantum amplitudes.Comment: version published in New Journal of Physic

Minimal external representations of tropical polyhedra

Tropical polyhedra are known to be representable externally, as intersections of finitely many tropical half-spaces. However, unlike in the classical case, the extreme rays of their polar cones provide external representations containing in general superfluous half-spaces. In this paper, we prove that any tropical polyhedral cone in R^n (also known as "tropical polytope" in the literature) admits an essentially unique minimal external representation. The result is obtained by establishing a (partial) anti-exchange property of half-spaces. Moreover, we show that the apices of the half-spaces appearing in such non-redundant external representations are vertices of the cell complex associated with the polyhedral cone. We also establish a necessary condition for a vertex of this cell complex to be the apex of a non-redundant half-space. It is shown that this condition is sufficient for a dense class of polyhedral cones having "generic extremities".Comment: v1: 32 pages, 10 figures; v2: minor revision, 34 pages, 10 figure