Cache-Optimal Data-Structures for Hierarchical Methods on Adaptively Refined Space-Partitioning Grids

Author(s):  
Miriam Mehl

Author(s):  
F. Çetin ◽  
M. O. Kulekci

Abstract. This paper presents a study that compares the three space partitioning and spatial indexing techniques, KD Tree, Quad KD Tree, and PR Tree. KD Tree is a data structure proposed by Bentley (Bentley and Friedman, 1979) that aims to cluster objects according to their spatial location. Quad KD Tree is a data structure proposed by Berezcky (Bereczky et al., 2014) that aims to partition objects using heuristic methods. Unlike Bereczky’s partitioning technique, a new partitioning technique is presented based on dividing objects according to space-driven, in the context of this study. PR Tree is a data structure proposed by Arge (Arge et al., 2008) that is an asymptotically optimal R-Tree variant, enables data-driven segmentation. This study mainly aimed to search and render big spatial data in real-time safety-critical avionics navigation map application. Such a real-time system needs to efficiently reach the required records inside a specific boundary. Performing range query during the runtime (such as finding the closest neighbors) is extremely important in performance. The most crucial purpose of these data structures is to reduce the number of comparisons to solve the range searching problem. With this study, the algorithms’ data structures are created and indexed, and worst-case analyses are made to cover the whole area to measure the range search performance. Also, these techniques’ performance is benchmarked according to elapsed time and memory usage. As a result of these experimental studies, Quad KD Tree outperformed in range search analysis over the other techniques, especially when the data set is massive and consists of different geometry types.



2017 ◽  
Vol 28 (3-4) ◽  
pp. e1780 ◽  
Author(s):  
Erik Herrmann ◽  
Martin Manns ◽  
Han Du ◽  
Somayeh Hosseini ◽  
Klaus Fischer


2009 ◽  
Vol 106 (37) ◽  
pp. 15544-15548 ◽  
Author(s):  
Zia Khan ◽  
Joshua S. Bloom ◽  
Benjamin A. Garcia ◽  
Mona Singh ◽  
Leonid Kruglyak

Quantitative studies of protein abundance rarely span more than a small number of experimental conditions and replicates. In contrast, quantitative studies of transcript abundance often span hundreds of experimental conditions and replicates. This situation exists, in part, because extracting quantitative data from large proteomics datasets is significantly more difficult than reading quantitative data from a gene expression microarray. To address this problem, we introduce two algorithmic advances in the processing of quantitative proteomics data. First, we use space-partitioning data structures to handle the large size of these datasets. Second, we introduce techniques that combine graph-theoretic algorithms with space-partitioning data structures to collect relative protein abundance data across hundreds of experimental conditions and replicates. We validate these algorithmic techniques by analyzing several datasets and computing both internal and external measures of quantification accuracy. We demonstrate the scalability of these techniques by applying them to a large dataset that comprises a total of 472 experimental conditions and replicates.





1994 ◽  
Vol 9 (3) ◽  
pp. 127
Author(s):  
X.-B. Lu ◽  
F. Stetter
Keyword(s):  






Disputatio ◽  
2019 ◽  
Vol 11 (55) ◽  
pp. 345-369
Author(s):  
Peter Ludlow

AbstractDavid Chalmers argues that virtual objects exist in the form of data structures that have causal powers. I argue that there is a large class of virtual objects that are social objects and that do not depend upon data structures for their existence. I also argue that data structures are themselves fundamentally social objects. Thus, virtual objects are fundamentally social objects.



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