scholarly journals Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures

Author(s):  
Tetsuo Shibuya
Keyword(s):  
2007 ◽  
Vol 32 (2) ◽  
pp. 283-294 ◽  
Author(s):  
Liang Zuopeng ◽  
Hu Kongfa ◽  
Ye Ning ◽  
Dong Yisheng
Keyword(s):  

Signals ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 336-352
Author(s):  
Frank Zalkow ◽  
Julian Brandner ◽  
Meinard Müller

Flexible retrieval systems are required for conveniently browsing through large music collections. In a particular content-based music retrieval scenario, the user provides a query audio snippet, and the retrieval system returns music recordings from the collection that are similar to the query. In this scenario, a fast response from the system is essential for a positive user experience. For realizing low response times, one requires index structures that facilitate efficient search operations. One such index structure is the K-d tree, which has already been used in music retrieval systems. As an alternative, we propose to use a modern graph-based index, denoted as Hierarchical Navigable Small World (HNSW) graph. As our main contribution, we explore its potential in the context of a cross-version music retrieval application. In particular, we report on systematic experiments comparing graph- and tree-based index structures in terms of the retrieval quality, disk space requirements, and runtimes. Despite the fact that the HNSW index provides only an approximate solution to the nearest neighbor search problem, we demonstrate that it has almost no negative impact on the retrieval quality in our application. As our main result, we show that the HNSW-based retrieval is several orders of magnitude faster. Furthermore, the graph structure also works well with high-dimensional index items, unlike the tree-based structure. Given these merits, we highlight the practical relevance of the HNSW graph for music information retrieval (MIR) applications.


2021 ◽  
Vol 11 (5) ◽  
pp. 2405
Author(s):  
Yuxiang Sun ◽  
Tianyi Zhao ◽  
Seulgi Yoon ◽  
Yongju Lee

Semantic Web has recently gained traction with the use of Linked Open Data (LOD) on the Web. Although numerous state-of-the-art methodologies, standards, and technologies are applicable to the LOD cloud, many issues persist. Because the LOD cloud is based on graph-based resource description framework (RDF) triples and the SPARQL query language, we cannot directly adopt traditional techniques employed for database management systems or distributed computing systems. This paper addresses how the LOD cloud can be efficiently organized, retrieved, and evaluated. We propose a novel hybrid approach that combines the index and live exploration approaches for improved LOD join query performance. Using a two-step index structure combining a disk-based 3D R*-tree with the extended multidimensional histogram and flash memory-based k-d trees, we can efficiently discover interlinked data distributed across multiple resources. Because this method rapidly prunes numerous false hits, the performance of join query processing is remarkably improved. We also propose a hot-cold segment identification algorithm to identify regions of high interest. The proposed method is compared with existing popular methods on real RDF datasets. Results indicate that our method outperforms the existing methods because it can quickly obtain target results by reducing unnecessary data scanning and reduce the amount of main memory required to load filtering results.


2008 ◽  
Vol 20 (2) ◽  
pp. 276-285 ◽  
Author(s):  
Hai Zhuge ◽  
Liang Feng
Keyword(s):  

Author(s):  
Muhammad Attahir Jibril ◽  
Philipp Götze ◽  
David Broneske ◽  
Kai-Uwe Sattler

AbstractAfter the introduction of Persistent Memory in the form of Intel’s Optane DC Persistent Memory on the market in 2019, it has found its way into manifold applications and systems. As Google and other cloud infrastructure providers are starting to incorporate Persistent Memory into their portfolio, it is only logical that cloud applications have to exploit its inherent properties. Persistent Memory can serve as a DRAM substitute, but guarantees persistence at the cost of compromised read/write performance compared to standard DRAM. These properties particularly affect the performance of index structures, since they are subject to frequent updates and queries. However, adapting each and every index structure to exploit the properties of Persistent Memory is tedious. Hence, we require a general technique that hides this access gap, e.g., by using DRAM caching strategies. To exploit Persistent Memory properties for analytical index structures, we propose selective caching. It is based on a mixture of dynamic and static caching of tree nodes in DRAM to reach near-DRAM access speeds for index structures. In this paper, we evaluate selective caching on the OLAP-optimized main-memory index structure Elf, because its memory layout allows for an easy caching. Our experiments show that if configured well, selective caching with a suitable replacement strategy can keep pace with pure DRAM storage of Elf while guaranteeing persistence. These results are also reflected when selective caching is used for parallel workloads.


Atmosphere ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 564
Author(s):  
Hong Shen ◽  
Longkun Yu ◽  
Xu Jing ◽  
Fengfu Tan

The turbulence moment of order m (μm) is defined as the refractive index structure constant Cn2 integrated over the whole path z with path-weighting function zm. Optical effects of atmospheric turbulence are directly related to turbulence moments. To evaluate the optical effects of atmospheric turbulence, it is necessary to measure the turbulence moment. It is well known that zero-order moments of turbulence (μ0) and five-thirds-order moments of turbulence (μ5/3), which correspond to the seeing and the isoplanatic angles, respectively, have been monitored as routine parameters in astronomical site testing. However, the direct measurement of second-order moments of turbulence (μ2) of the whole layer atmosphere has not been reported. Using a star as the light source, it has been found that μ2 can be measured through the covariance of the irradiance in two receiver apertures with suitable aperture size and aperture separation. Numerical results show that the theoretical error of this novel method is negligible in all the typical turbulence models. This method enabled us to monitor μ2 as a routine parameter in astronomical site testing, which is helpful to understand the characteristics of atmospheric turbulence better combined with μ0 and μ5/3.


2014 ◽  
Vol 981 ◽  
pp. 175-178
Author(s):  
Run Tao Liu ◽  
Yuan Jing Chen ◽  
Da Yong Cao ◽  
De Yu Liu

In this paper, the index structure, PR-quadtree for spatial data, is used to store data for a database. The properties of the quadtree are studied. With the properties prunning rules are set up for searching the Skyline set of the data stored in the quadtree. Through detailed analysis for the tree the method of finding some approximate skyline points is designed, by which a new skyline searching algorithm is given. The new algorithm is more effective.


2013 ◽  
Vol 756-759 ◽  
pp. 916-921
Author(s):  
Ye Liang

The amount of data in our industry and the world is exploding. Data is being collected and stored at unprecedented rates. The challenge is not only to store and manage the vast volume of data, which is also called big data, but also to analyze and query from it. In order to put forward the universal method to response mobile big data query, queries are separated and grouped according to kinds of query for massive mobile objects in the space. The indexing method for grouping the mobile objects with Grid (GG TPR-tree) has great efficiency to manage a massive capacity of mobile objects within a limited area, but it only could meet a part of requirements for mobile big data query if the GG TPR-tree was used solely. This thesis offers solutions to simple immediate query, simple continuous query, active window query, and continuous window query, dynamic condition query and other query requests by employing DTDI index structure. The experiments prove that with the support of DTDI index structure, query of massive mobile objects has higher precision and better query performance.


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