The Limited Workspace Model for Geometric Algorithms

Space usage has been a concern since the very early days of algorithm design. The increased availability of devices with limited memory or power supply – such as smartphones, drones, or small sensors – as well as the proliferation of new storage media for which write access is comparatively slow and may have negative effects on the lifetime – such as flash drives – have led to renewed interest in the subject. As a result, the design of algorithms for the limited workspace model has seen a significant rise in popularity in computational geometry over the last decade. In this setting, we typically have a large amount of data that needs to be processed. Although we may access the data in any way and as often as we like, write-access to the main storage is limited and/or slow. Thus, we opt to use only higher level memory for intermediate data (e.g., CPU registers). Since the application areas of the devices mentioned above – sensors, smartphones, and drones – often handle a large amount of geographic (i.e., geometric) data, the scenario becomes particularly interesting from the viewpoint of computational geometry. Motivated by these considerations, we investigate geometric problems in the limited workspace model. In this model the input of size n resides in read-only memory, an algorithm may use a workspace of size s = {1, . . . , n} to read and write the intermediate data during its execution, and it reports the output to a write-only stream. The goal is to design algorithms whose running time decreases as s increases, which provides a time-space trade-off. In this thesis, we consider three fundamental geometric problems, namely, computing different types of Voronoi diagrams of a planar point set, computing the Euclidean minimum spanning tree of a planar point set, and computing the k-visibility region of a point inside a polygonal domain. Using several innovative techniques, we either achieve the first time-space trade-offs for those problems or improve the previous results.Der Speicherplatzbedarf ist seit den Anfängen des Algorithmenentwurfs von Interesse. Die erhöhte Verfügbarkeit von Geräten mit begrenztem Speicherplatz oder begrenzter Stromversorgung – wie Smartphones, Drohnen oder kleine Sensoren – sowie die Verbreitung neuer Speichermedien, bei denen der Schreibzugriff vergleichsweise langsam ist und negative Auswirkungen auf die Lebensdauer haben kann – wie beispielsweise Flash-Laufwerken – haben zu erneuter Aufmerksamkeit für dieses Thema geführt. In der Folge hat der Entwurf von Algorithmen für das Limited Workspace Model (Modell mit begrenztem Arbeitsspeicher) in den letzten zehn Jahren einen signifikanten Anstieg an Popularität in der algorithmischen Geometrie erfahren. In diesem Setting haben wir in der Regel eine große Menge an Daten, die verarbeitet werden müssen. Obwohl wir auf die Daten beliebig oft und in beliebiger Weise zugreifen können, ist der Schreibzugriff auf den Hauptspeicher begrenzt und/oder langsam. Zwischenergebnisse werden daher nur in einem kleineren, übergeordneten Speicher (z. B. CPU-Register) abgelegt. Da die Anwendungsbereiche der oben genannten Geräte – Sensoren, Smartphones und Drohnen – oft mit einer großen Menge an geografischen (d. h., geometrischen) Daten umgehen, ist dieses Szenario aus Sicht der algorithmischen Geometrie besonders interessant. Motiviert durch diese Überlegungen haben wir geometrische Probleme im Limited Workspace Model untersucht. In diesem Modell befindet sich die Eingabe der Größe n in einem schreibgeschützten Speicher, ein Algorithmus kann einen Arbeitsspeicher der Größe s = {1, . . . , n} verwenden, um die Zwischendaten während der Ausführung zu lesen und zu schreiben. Die Ausgabe sendet er an einen lesegeschützten Stream. Ziel ist es, Algorithmen zu entwickeln, deren Laufzeit mit zunehmender Verfügbarkeit an Arbeitsspeicher abnimmt, was einen Time-Space Trade-Off (Laufzeit-Speicher-Abwägung) darstellt. In dieser Arbeit betrachten wir drei grundlegende geometrische Probleme, nämlich die Berechnung verschiedener Arten von Voronoi-Diagrammen einer Punktmenge in der Ebene, die Berechnung des euklidischen minimalen Spannbaums einer ebenen Punktmenge und die Bestimmung der k-Sichtbarkeitsregion (k-visibility region) eines Punkts innerhalb eines polygonalen Gebiets. Mit mehreren innovativen Techniken entwickeln wir entweder die ersten Time-Space Trade-Offs für diese Probleme oder verbessern die bisherigen Ergebnisse

Geometric Algorithms and Data Structures for Simulating Diffusion Limited Reactions

Radiation therapy is one of the most effective means for treating cancers. An important calculation in radiation therapy is the estimation of dose distribution in the treated patient, which is key to determining the treatment outcome and potential side effects of the therapy. Biological dose — the level of biological damage (e.g., cell killing ratio, DNA damage, etc.) inflicted by the radiation is the best measure of treatment quality, but it is very difficult to calculate. Therefore, most clinics today use physical dose - the energy deposited by incident radiation per unit body mass - for planning radiation therapy, which can be calculated accurately using kinetic Monte Carlo simulations. Studies have found that physical dose correlates with biological dose, but exhibits a very complex relationship that is not yet well understood. Generally speaking, the calculation of biological dose involves four steps: (1) the calculation of physical dose distribution, (2) the generation of radiochemicals based on the physical dose distribution, (3) the simulation of interactions between radiochemicals and bio-matter in the body, and (4) the estimation of biological damage based on the distribution of radiochemicals. This dissertation focuses on the development of a more efficient and effective simulation algorithm to speed up step (3). The main contribution of this research is the development of an efficient and effective kinetic Monte Carlo (KMC) algorithm for simulating diffusion-limited chemical reactions in the context of radiation therapy. The central problem studied is - given n particles distributed among a small number of particle species, all allowed to diffuse and chemically react according to a small number of chemical reaction equations - predict the radiochemical yield over time. The algorithm presented makes use of a sparse grid structure, with one grid per species per radiochemical reactant used to group particles in a way that makes the nearest neighbor search efficient, where particles are stored only once, yet are represented in grids of all appropriate reaction radii. A kinetic data structure is used as the time stepping mechanism, which provides spatially local updates to the simulation at a frequency which captures all events - retaining accuracy. A serial and three parallel versions of the algorithm have been developed. The parallel versions implement the kinetic data structure using both a standard priority queue and a treap data structure in order to investigate the algorithms scalability. The treap provides a way for each thread of execution to do more work in a particular region of space. A comparison with a spatial discretization variant of the algorithm is also provided

Efficient geometric algorithms for preference top-k queries, stochastic line arrangements, and proximity problems

University of Minnesota Ph.D. dissertation. June 2017. Major: Computer Science. Advisor: Ravi Janardan. 1 computer file (PDF); x, 150 pages.Problems arising in diverse real-world applications can often be modeled by geometric objects such as points, lines, and polygons. The goal of this dissertation research is to design efficient algorithms for such geometric problems and provide guarantees on their performance via rigorous theoretical analysis. Three related problems are discussed in this thesis. The first problem revisits the well-known problem of answering preference top-k queries, which arise in a wide range of applications in databases and computational geometry. Given a set of n points, each with d real-valued attributes, the goal is to organize the points into a suitable data structure so that user preference queries can be answered efficiently. A query consists of a d-dimensional vector w, representing a user's preference for each attribute, and an integer k, representing the number of data points to be retrieved. The answer to a query is the k highest-scoring points relative to w, where the score of a point, p, is designed to reflect how well it captures, in aggregate, the user's preferences for the different attributes. This thesis contributes efficient exact solutions in low dimensions (2D and 3D), and a new sampling-based approximation algorithm in higher dimensions. The second problem extends the fundamental geometric concept of a line arrangement to stochastic data. A line arrangement in the plane is a partition of the plane into vertices, edges, and faces. Surprisingly, diverse problems, including the preference top-k query and k-order Voronoi Diagram, essentially boil down to answering questions about the set of k-topmost lines at some abscissa. This thesis considers line arrangements in a new setting, where each line has an associated existence probability representing uncertainty that is inherent in real-world data. An upper-bound is derived on the expected number of changes in the set of k-topmost lines, taken over the entire x-axis, and a worst-case upper bound is given for k = 1. Also, given is an efficient algorithm to compute the most likely k-topmost lines in the arrangement. Applications of this problem including the most likely Voronoi Diagram in R^1 and stochastic preference top-k query are discussed. The third problem discussed is geometric proximity search in both the stochastic setting and the query-retrieval setting. Under the stochastic setting, the thesis considers two fundamental problems, namely, the stochastic closest pair problem and the k most likely nearest neighbor search. In both problems, the data points are assumed to lie on a tree embedded in R^2 and distances are measured along the tree (a so-called tree space). For the former, efficient solutions are given to compute the probability that the closest pair distance of a realization of the input is at least l and to compute the expected closest pair distance. For the latter, the thesis generalizes the concept of most likely Voronoi Diagram from R^1 to tree space and bounds its combinatorial complexity. A data structure for the diagram and an algorithm to construct it are also given. For the query-retrieval version which is considered in R^2, the goal is to retrieve the closest pair within a user-specified query range. The contributions here include efficient data structures and algorithms that have fast query time while using linear or near-linear space for a variety of query shapes. In addition, a generic framework is presented, which returns a closest pair that is no farther apart than the closest pair in a suitably shrunken version of the query range

Motion planning for self-reconfiguring robotic systems

Robots that can actively change morphology offer many advantages over fixed shape, or monolithic, robots: flexibility, increased maneuverability and modularity. So called self-reconfiguring systems (SRS) are endowed with a shape changing ability enabled by an active connection mechanism. This mechanism allows a mechanical link to be engaged or disengaged between two neighboring robotic subunits. Through utilization of embedded joints to change the geometry plus the connection mechanism to change the topology of the kinematics, a collection of robotic subunits can drastically alter the overall kinematics. Thus, an SRS is a large robot comprised of many small cooperating robots that is able to change its morphology on demand. By design, such a system has many and variable degrees of freedom (DOF). To gain the benefits of self-reconfiguration, the process of morphological change needs to be controlled in response to the environment. This is a motion planning problem in a high dimensional configuration space. This problem is complex because each subunit only has a few internal DOFs, and each subunit's range of motion depends on the state of its connected neighbors. Together with the high dimensionality, the problem may initially appear to be intractable, because as the number of subunits grow, the state space expands combinatorially. However, there is hope. If individual robotic subunits are identical, then there will exist some form of regularity in the resulting state space of the conglomerate. If this regularity can be exploited, then there may exist tractable motion planning algorithms for self-reconfiguring system. Existing approaches in the literature have been successful in developing algorithms for specific SRSs. However, it is not possible to transfer one motion planning algorithm onto another system. SRSs share a similar form of regularity, so one might hope that a tool from mathematical literature would identify the common properties that are exploitable for motion planning. So, while there exists a number of algorithms for certain subsets of possible SRS instantiations, there is no general motion planning methodology applicable to all SRSs. In this thesis, firstly, the best existing general motion planning techniques were evaluated to the SRS motion planning problem. Greedy search, simulated annealing, rapidly exploring random trees and probabilistic roadmap planning were found not to scale well, requiring exponential computation time, as the number of subunits in the SRS increased. The planners performance was limited by the availability of a good general purpose heuristic. There does not currently exist a heuristic which can accurately guide a path through the search space toward a far away goal configuration. Secondly, it is shown that a computationally efficient reconfiguration algorithms do exist by development of an efficient motion planning algorithm for an exemplary SRS, the Claytronics formulation of the Hexagonal Metamorphic Robot (HMR). The developed algorithm was able to solve a randomly generated shape-to-shape planning task for the SRS in near linear time as the number of units in the configuration grew. Configurations containing 20,000 units were solvable in under ten seconds on modest computational hardware. The key to the success of the approach was discovering a subspace of the motion planning space that corresponded with configurations with high mobility. Plans could be discovered in this sub-space much more readily because the risk of the search entering a blind alley was greatly reduced. Thirdly, in order to extract general conclusions, the efficient subspace, and other efficient subspaces utilized in other works, are analyzed using graph theoretic methods. The high mobility is observable as an increase in the state space's Cheeger constant, which can be estimated with a local sampling procedure. Furthermore, state spaces associated with an efficient motion planning algorithm are well ordered by the graph minor relation. These qualitative observations are discoverable by machine without human intervention, and could be useful components in development of a general purpose SRS motion planner compiler

Data Structures & Algorithm Analysis in C++

This is the textbook for CSIS 215 at Liberty University.https://digitalcommons.liberty.edu/textbooks/1005/thumbnail.jp