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

Maximum Likelihood Estimation of Log-Concave Densities on Tree Space

Phylogenetic trees are key data objects in biology, and the method of phylogenetic reconstruction has been highly developed. The space of phylogenetic trees is a nonpositively curved metric space. Recently, statistical methods to analyze the set of trees on this space are being developed utilizing this property. Meanwhile, in Euclidean space, the log-concave maximum likelihood method has emerged as a new nonparametric method for probability density estimation. In this paper, we derive a sufficient condition for the existence and uniqueness of the log-concave maximum likelihood estimator on tree space. We also propose an estimation algorithm for one and two dimensions. Since various factors affect the inferred trees, it is difficult to specify the distribution of sample trees. The class of log-concave densities is nonparametric, and yet the estimation can be conducted by the maximum likelihood method without selecting hyperparameters. We compare the estimation performance with a previously developed kernel density estimator numerically. In our examples where the true density is log-concave, we demonstrate that our estimator has a smaller integrated squared error when the sample size is large. We also conduct numerical experiments of clustering using the Expectation-Maximization (EM) algorithm and compare the results with k-means++ clustering using Fr\'echet mean.Comment: 41 pages, 10 figure

Bounded geometry for Kleinian groups

We show that a Kleinian surface group, or hyperbolic 3-manifold with a cusp-preserving homotopy-equivalence to a surface, has bounded geometry if and only if there is an upper bound on an associated collection of coefficients that depend only on its end invariants. Bounded geometry is a positive lower bound on the lengths of closed geodesics. When the surface is a once-punctured torus, the coefficients coincide with the continued fraction coefficients associated to the ending laminations. Applications include an improvement to the bounded geometry versions of Thurston's ending lamination conjecture, and of Bers' density conjecture.Comment: 49 pages, 13 figures. Revised from IMS preprint version, with additional introductory material. To appear in Invent. Mat

Investigations in Hadamard spaces

Kjo tezë e doktoratës hulumton ndërveprimin midis gjeometrisë dhe analizës konvekse në hapësirat Hadamard. E motivuar nga aplikime të shumta të gjeometrisë CAT(0), puna jonë bazohet në rezultatet e shumë autorëve të mëparshëmnë mbi analizën konvekse dhe gjeometrinë në sensin e Alexandrovit. Hetimet tona u përgjigjen disa pyetjeve në teorinë e hapësirave CAT(0) prej të cilave disa janë parashtruar si probleme të hapura në literaturën e fundit. Teza jonë e doktoratës zhvillohet sipas linjave të mëposhtme: 1. Topologjitë e dobëta në hapësirat Hadamard, 2. Konveksifikimi i bashkësive kompakte, 3. Problemi i pemës mesatare në hapësirat e pemëve filogjenetike, 4. Konvergjenca Mosko në hapësirat Hadamard, 5. Operatorët (plotësisht) jo-ekspansivë dhe aplikimet e tyre në hapësirat Hadamard.Diese Doktorarbeit untersucht das Zusammenspiel zwischen Geometrie und konvexer Analyse in Hadamardräumen. Motiviert durch zahlreiche Anwendungen der CAT(0)-Geometrie baut unsere Arbeit auf den Ergebnissen vieler früherer Autoren in der konvexen Analysis und der Alexandrov-Geometrie auf. Unsere Untersuchungen beantworten mehrere Fragen in der Theorie von CAT(0)-Räumen, von denen einige in der neueren Literatur als offene Probleme gestellt wurden. Zusammengefasst entwickelt sich unsere Dissertation in folgende Richtungen: 1. Schwache Topologien in Hadamard-Räumen, 2. Konvexe Hüllen kompakter Mengen, 3. Mittleres Baumproblem in phylogenetischen Baumräumen, 4. Mosco-Konvergenz in Hadamard-Räumen, 5. Fest nichtexpansive Operatoren und ihre Anwendungen in Hadamard-Räumen.This thesis investigates the interplay between geometry and convex analysis in Hadamard spaces. Motivated by numerous applications of CAT(0) geometry, our work builds upon the results in convex analysis and Alexandrov geometry of many previous authors. Our investigations answer several questions in the theory of CAT(0) spaces some of which were posed as open problems in recent literature. In a nutshell our thesis develops along the following lines: 1. Weak topologies in Hadamard spaces, 2. Convex hulls of compact sets, 3. Mean tree problem in phylogenetic tree spaces, 4. Mosco convergence in Hadamard spaces, 5. Firmly nonexpansive operators and their applications in Hadamard spaces

Abstracts for the twentyfirst European workshop on Computational geometry, Technische Universiteit Eindhoven, The Netherlands, March 9-11, 2005

This volume contains abstracts of the papers presented at the 21st European Workshop on Computational Geometry, held at TU Eindhoven (the Netherlands) on March 9–11, 2005. There were 53 papers presented at the Workshop, covering a wide range of topics. This record number shows that the field of computational geometry is very much alive in Europe. We wish to thank all the authors who submitted papers and presented their work at the workshop. We believe that this has lead to a collection of very interesting abstracts that are both enjoyable and informative for the reader. Finally, we are grateful to TU Eindhoven for their support in organizing the workshop and to the Netherlands Organisation for Scientific Research (NWO) for sponsoring the workshop