A Polynomial Time Algorithm to Compute Geodesics in CAT(0) Cubical Complexes

This paper presents the first polynomial time algorithm to compute geodesics in a CAT(0) cubical complex in general dimension. The algorithm is a simple iterative method to update breakpoints of a path joining two points using Miller, Owen and Provan\u27s algorithm (Adv. in Appl. Math, 2015) as a subroutine. Our algorithm is applicable to any CAT(0) space in which geodesics between two close points can be computed, not limited to CAT(0) cubical complexes

Geodesics in CAT(0) Cubical Complexes

We describe an algorithm to compute the geodesics in an arbitrary CAT(0) cubical complex. A key tool is a correspondence between cubical complexes of global non-positive curvature and posets with inconsistent pairs. This correspondence also gives an explicit realization of such a complex as the state complex of a reconfigurable system, and a way to embed any interval in the integer lattice cubing of its dimension.Comment: 27 pages, 7 figure

Hierarchically hyperbolic spaces I: curve complexes for cubical groups

In the context of CAT(0) cubical groups, we develop an analogue of the theory of curve complexes and subsurface projections. The role of the subsurfaces is played by a collection of convex subcomplexes called a \emph{factor system}, and the role of the curve graph is played by the \emph{contact graph}. There are a number of close parallels between the contact graph and the curve graph, including hyperbolicity, acylindricity of the action, the existence of hierarchy paths, and a Masur--Minsky-style distance formula. We then define a \emph{hierarchically hyperbolic space}; the class of such spaces includes a wide class of cubical groups (including all virtually compact special groups) as well as mapping class groups and Teichm\"{u}ller space with any of the standard metrics. We deduce a number of results about these spaces, all of which are new for cubical or mapping class groups, and most of which are new for both. We show that the quasi-Lipschitz image from a ball in a nilpotent Lie group into a hierarchically hyperbolic space lies close to a product of hierarchy geodesics. We also prove a rank theorem for hierarchically hyperbolic spaces; this generalizes results of Behrstock--Minsky, Eskin--Masur--Rafi, Hamenst\"{a}dt, and Kleiner. We finally prove that each hierarchically hyperbolic group admits an acylindrical action on a hyperbolic space. This acylindricity result is new for cubical groups, in which case the hyperbolic space admitting the action is the contact graph; in the case of the mapping class group, this provides a new proof of a theorem of Bowditch.Comment: To appear in "Geometry and Topology". This version incorporates the referee's comment

The space of ultrametric phylogenetic trees

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. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods.Comment: Minor changes. This version has been published in JTB. 27 pages, 9 figure

Acylindrical hyperbolicity of cubical small-cancellation groups

We provide an analogue of Strebel's classification of geodesic triangles in classical $C'(\frac16)$ groups for groups given by Wise's cubical presentations satisfying sufficiently strong metric cubical small cancellation conditions. Using our classification, we prove that, except in specific degenerate cases, such groups are acylindrically hyperbolic.Comment: Added figures. Exposition improved in Section 3, correction/simplification in Section 5, background added and citations updated in Section