Clear and Compress: Computing Persistent Homology in Chunks

We present a parallelizable algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then simplifying the unpaired columns, and finally applying standard reduction on the simplified matrix. The approach generalizes a technique by G\"unther et al., which uses discrete Morse Theory to compute persistence; we derive the same worst-case complexity bound in a more general context. The algorithm employs several practical optimization techniques which are of independent interest. Our sequential implementation of the algorithm is competitive with state-of-the-art methods, and we improve the performance through parallelized computation.Comment: This result was presented at TopoInVis 2013 (http://www.sci.utah.edu/topoinvis13.html

Finding Pairwise Intersections Inside a Query Range

We study the following problem: preprocess a set O of objects into a data structure that allows us to efficiently report all pairs of objects from O that intersect inside an axis-aligned query range Q. We present data structures of size $O(n({\rm polylog} n))$ and with query time $O((k+1)({\rm polylog} n))$ time, where k is the number of reported pairs, for two classes of objects in the plane: axis-aligned rectangles and objects with small union complexity. For the 3-dimensional case where the objects and the query range are axis-aligned boxes in R^3, we present a data structures of size $O(n\sqrt{n}({\rm polylog} n))$ and query time $O((\sqrt{n}+k)({\rm polylog} n))$. When the objects and query are fat, we obtain $O((k+1)({\rm polylog} n))$ query time using $O(n({\rm polylog} n))$ storage

Computing and reducing slope complexes

In this paper we provide a new characterization of cell de- composition (called slope complex) of a given 2-dimensional continuous surface. Each patch (cell) in the decomposition must satisfy that there exists a monotonic path for any two points in the cell. We prove that any triangulation of such surface is a slope complex and explain how to obtain new slope complexes with a smaller number of slope regions decomposing the surface. We give the minimal number of slope regions by counting certain bounding edges of a triangulation of the surface obtained from its critical points.Ministerio de Economía y Competitividad MTM2015-67072-

Semi-dynamic connectivity in the plane

Motivated by a path planning problem we consider the following procedure. Assume that we have two points $s$ and $t$ in the plane and take $\mathcal{K}=\emptyset$. At each step we add to $\mathcal{K}$ a compact convex set that does not contain $s$ nor $t$. The procedure terminates when the sets in $\mathcal{K}$ separate $s$ and $t$. We show how to add one set to $\mathcal{K}$ in $O(1+k\alpha(n))$ amortized time plus the time needed to find all sets of $\mathcal{K}$ intersecting the newly added set, where $n$ is the cardinality of $\mathcal{K}$, $k$ is the number of sets in $\mathcal{K}$ intersecting the newly added set, and $\alpha(\cdot)$ is the inverse of the Ackermann function

Mind the Gap: A Study in Global Development through Persistent Homology

The Gapminder project set out to use statistics to dispel simplistic notions about global development. In the same spirit, we use persistent homology, a technique from computational algebraic topology, to explore the relationship between country development and geography. For each country, four indicators, gross domestic product per capita; average life expectancy; infant mortality; and gross national income per capita, were used to quantify the development. Two analyses were performed. The first considers clusters of the countries based on these indicators, and the second uncovers cycles in the data when combined with geographic border structure. Our analysis is a multi-scale approach that reveals similarities and connections among countries at a variety of levels. We discover localized development patterns that are invisible in standard statistical methods

Topological characteristics of oil and gas reservoirs and their applications

We demonstrate applications of topological characteristics of oil and gas reservoirs considered as three-dimensional bodies to geological modeling.Comment: 12 page

Categorification of persistent homology

We redevelop persistent homology (topological persistence) from a categorical point of view. The main objects of study are diagrams, indexed by the poset of real numbers, in some target category. The set of such diagrams has an interleaving distance, which we show generalizes the previously-studied bottleneck distance. To illustrate the utility of this approach, we greatly generalize previous stability results for persistence, extended persistence, and kernel, image and cokernel persistence. We give a natural construction of a category of interleavings of these diagrams, and show that if the target category is abelian, so is this category of interleavings.Comment: 27 pages, v3: minor changes, to appear in Discrete & Computational Geometr

A Bichromatic Incidence Bound and an Application

We prove a new, tight upper bound on the number of incidences between points and hyperplanes in Euclidean d-space. Given n points, of which k are colored red, there are O_d(m^{2/3}k^{2/3}n^{(d-2)/3} + kn^{d-2} + m) incidences between the k red points and m hyperplanes spanned by all n points provided that m = \Omega(n^{d-2}). For the monochromatic case k = n, this was proved by Agarwal and Aronov. We use this incidence bound to prove that a set of n points, no more than n-k of which lie on any plane or two lines, spans \Omega(nk^2) planes. We also provide an infinite family of counterexamples to a conjecture of Purdy's on the number of hyperplanes spanned by a set of points in dimensions higher than 3, and present new conjectures not subject to the counterexample.Comment: 12 page

On the maximum size of an anti-chain of linearly separable sets and convex pseudo-discs

We show that the maximum cardinality of an anti-chain composed of intersections of a given set of n points in the plane with half-planes is close to quadratic in n. We approach this problem by establishing the equivalence with the problem of the maximum monotone path in an arrangement of n lines. For a related problem on antichains in families of convex pseudo-discs we can establish the precise asymptotic bound: it is quadratic in n. The sets in such a family are characterized as intersections of a given set of n points with convex sets, such that the difference between the convex hulls of any two sets is nonempty and connected.Comment: 10 pages, 3 figures. revised version correctly attributes the idea of Section 3 to Tverberg; and replaced k-sets by "linearly separable sets" in the paper and the title. Accepted for publication in Israel Journal of Mathematic

Computation of protein geometry and its applications: Packing and function prediction

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure