Polyhedral Combinatorics of UPGMA Cones

Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive orthant induced by classifying the input vectors according to tree topologies returned by the algorithm. The partition lattice informs the study of UPGMA trees. We give a closed form for the extreme rays of UPGMA cones on n taxa, and compute the normalized volumes of the UPGMA cones for small n. Keywords: phylogenetic trees, polyhedral combinatorics, partition lattic

VoroCrust: Voronoi Meshing Without Clipping

Polyhedral meshes are increasingly becoming an attractive option with particular advantages over traditional meshes for certain applications. What has been missing is a robust polyhedral meshing algorithm that can handle broad classes of domains exhibiting arbitrarily curved boundaries and sharp features. In addition, the power of primal-dual mesh pairs, exemplified by Voronoi-Delaunay meshes, has been recognized as an important ingredient in numerous formulations. The VoroCrust algorithm is the first provably-correct algorithm for conforming polyhedral Voronoi meshing for non-convex and non-manifold domains with guarantees on the quality of both surface and volume elements. A robust refinement process estimates a suitable sizing field that enables the careful placement of Voronoi seeds across the surface circumventing the need for clipping and avoiding its many drawbacks. The algorithm has the flexibility of filling the interior by either structured or random samples, while preserving all sharp features in the output mesh. We demonstrate the capabilities of the algorithm on a variety of models and compare against state-of-the-art polyhedral meshing methods based on clipped Voronoi cells establishing the clear advantage of VoroCrust output.Comment: 18 pages (including appendix), 18 figures. Version without compressed images available on https://www.dropbox.com/s/qc6sot1gaujundy/VoroCrust.pdf. Supplemental materials available on https://www.dropbox.com/s/6p72h1e2ivw6kj3/VoroCrust_supplemental_materials.pd

The Strominger-Yau-Zaslow conjecture: From torus fibrations to degenerations

This survey article begins with a discussion of the original form of the Strominger-Yau-Zaslow conjecture, surveys the state of knowledge concering this conjecture, and explains how thinking about this conjecture naturally leads to the program initiated by the author and Bernd Siebert to study mirror symmetry via degenerations of Calabi-Yau manifolds and log structures.Comment: 44 pages, to appear in the Proceedings of the 2005 AMS Symposium on Algebraic Geometry, Seattl