Triangulating the Square and Squaring the Triangle: Quadtrees and Delaunay Triangulations are Equivalent

We show that Delaunay triangulations and compressed quadtrees are equivalent structures. More precisely, we give two algorithms: the first computes a compressed quadtree for a planar point set, given the Delaunay triangulation; the second finds the Delaunay triangulation, given a compressed quadtree. Both algorithms run in deterministic linear time on a pointer machine. Our work builds on and extends previous results by Krznaric and Levcopolous and Buchin and Mulzer. Our main tool for the second algorithm is the well-separated pair decomposition(WSPD), a structure that has been used previously to find Euclidean minimum spanning trees in higher dimensions (Eppstein). We show that knowing the WSPD (and a quadtree) suffices to compute a planar Euclidean minimum spanning tree (EMST) in linear time. With the EMST at hand, we can find the Delaunay triangulation in linear time. As a corollary, we obtain deterministic versions of many previous algorithms related to Delaunay triangulations, such as splitting planar Delaunay triangulations, preprocessing imprecise points for faster Delaunay computation, and transdichotomous Delaunay triangulations.Comment: 37 pages, 13 figures, full version of a paper that appeared in SODA 201

Preprocessing Imprecise Points for Delaunay Triangulation: Simplified and Extended

Suppose we want to compute the Delaunay triangulation of a set P whose points are restricted to a collection R of input regions known in advance. Building on recent work by Löffler and Snoeyink, we show how to leverage our knowledge of R for faster Delaunay computation. Our approach needs no fancy machinery and optimally handles a wide variety of inputs, e.g., overlapping disks of different sizes and fat regions. Keywords: Delaunay triangulation - Data imprecision - Quadtree

A Systematic Review of Algorithms with Linear-time Behaviour to Generate Delaunay and Voronoi Tessellations

Triangulations and tetrahedrizations are important geometrical discretization procedures applied to several areas, such as the reconstruction of surfaces and data visualization. Delaunay and Voronoi tessellations are discretization structures of domains with desirable geometrical properties. In this work, a systematic review of algorithms with linear-time behaviour to generate 2D/3D Delaunay and/or Voronoi tessellations is presented

Hierarchical Structures for High Dimensional Data Analysis

The volume of data is not the only problem in modern data analysis, data complexity is often more challenging. In many areas such as computational biology, topological data analysis, and machine learning, the data resides in high dimensional spaces which may not even be Euclidean. Therefore, processing such massive and complex data and extracting some useful information is a big challenge. Our methods will apply to any data sets given as a set of objects and a metric that measures the distance between them. In this dissertation, we first consider the problem of preprocessing and organizing such complex data into a hierarchical data structure that allows efficient nearest neighbor and range queries. There have been many data structures for general metric spaces, but almost all of them have construction time that can be quadratic in terms of the number of points. There are only two data structures with O(n log n) construction time, but both have very complex algorithms and analyses. Also, they cannot be implemented efficiently. Here, we present a simple, randomized incremental algorithm that builds a metric data structure in O(n log n) time in expectation. Thus, we achieve the best of both worlds, simple implementation with asymptotically optimal performance. Furthermore, we consider the close relationship between our metric data structure and point orderings used in applications such as k-center clustering. We give linear time algorithms to go back and forth between these orderings and our metric data structure. In the last part, we use metric data structures to extract topological features of a data set, such as the number of connected components, holes, and voids. We give an efficient algorithm for constructing a (1 + epsilon)-approximation to the so-called Nerve filtration of a metric space, a fundamental tool in topological data analysis

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis

BACKGROUND: Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2(-L )distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations. RESULTS: The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm. CONCLUSIONS: The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis

This work was partially supported by FCT through the PIDDAC Program funds (INESC-ID multiannual funding) and under grant PEst-OE/EEI/LA0008/2011 (IT multiannual funding). In addition, it was also partially funded by projects HIVCONTROL (PTDC/EEA-CRO/100128/2008, S. Vinga, PI), TAGS (PTDC/EIA-EIA/112283/2009) and NEUROCLINOMICS (PTDC/EIA-EIA/111239/2009) from FCT (Portugal).Background: Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2(-L) distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations. Results: The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm. Conclusions: The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems.publishersversionpublishe