Advance of the Access Methods

The goal of this paper is to outline the advance of the access methods in the last ten years as well as to make review of all available in the accessible bibliography methods

Exploring Bit-Difference for Approximate KNN Search in High-dimensional Databases

In this paper, we develop a novel index structure to support efficient approximate k-nearest neighbor (KNN) query in high-dimensional databases. In high-dimensional spaces, the computational cost of the distance (e.g., Euclidean distance) between two points contributes a dominant portion of the overall query response time for memory processing. To reduce the distance computation, we first propose a structure (BID) using BIt-Difference to answer approximate KNN query. The BID employs one bit to represent each feature vector of point and the number of bit-difference is used to prune the further points. To facilitate real dataset which is typically skewed, we enhance the BID mechanism with clustering, cluster adapted bitcoder and dimensional weight, named the BID⁺. Extensive experiments are conducted to show that our proposed method yields significant performance advantages over the existing index structures on both real life and synthetic high-dimensional datasets.Singapore-MIT Alliance (SMA

DisC Diversity: Result Diversification based on Dissimilarity and Coverage

Recently, result diversification has attracted a lot of attention as a means to improve the quality of results retrieved by user queries. In this paper, we propose a new, intuitive definition of diversity called DisC diversity. A DisC diverse subset of a query result contains objects such that each object in the result is represented by a similar object in the diverse subset and the objects in the diverse subset are dissimilar to each other. We show that locating a minimum DisC diverse subset is an NP-hard problem and provide heuristics for its approximation. We also propose adapting DisC diverse subsets to a different degree of diversification. We call this operation zooming. We present efficient implementations of our algorithms based on the M-tree, a spatial index structure, and experimentally evaluate their performance.Comment: To appear at the 39th International Conference on Very Large Data Bases (VLDB), August 26-31, 2013, Riva del Garda, Trento, Ital

Data sensitive approximate query approaches in metric spaces

Ankara : The Department of Computer Engineering and the Graduate School of Engineering and Science of Bilkent University, 2011.Thesis (Master's) -- Bilkent University, 2011.Includes bibliographical references leaves 56-59.Similarity searching is the task of retrieval of relevant information from datasets. We are particularly interested in datasets that contain complex and unstructured data such as images, videos, audio recordings, protein and DNA sequences. The relevant information is typically defined using one of two common query types: a range query involves retrieval of all the objects within a specified distance to the query object; whereas a k-nearest neighbor query deals with obtaining k closest database objects to the query object. A variety of index structures based on the notion of metric spaces have been offered to process these two query types. The query performances of the proposed index structures have not been satisfactory particularly for high dimensional datasets. As a solution, various approximate similarity search methods offering the users a quality/time trade-off have been proposed. The rationale is that the users might be willing to tolerate query precision to retrieve query results relatively faster. The proposed approximate searching schemes usually have strong connections to the underlying data structures, making the comparison of the quality of the essence of their ideas difficult. In this thesis we investigate various approximation approaches to decrease the response time of similarity queries. These approaches use a variety of statistics about the dataset in order to obtain dynamic (at the time of querying) and specific guidance on the approximation for each query object individually. The experiments are performed on top of a simple underlying pivot-based index structure to minimize the effects of the index to our approximation schemes. The results show that it is possible to improve the performance/precision of the approximation based on data and query object sensitive guidance.Dilek, MerveM.S

Recognition of short functional motifs in protein sequences

The main goal of this study was to develop a method for computational de novo prediction of short linear motifs (SLiMs) in protein sequences that would provide advantages over existing solutions for the users. The users are typically biological laboratory researchers, who want to elucidate the function of a protein that is possibly mediated by a short motif. Such a process can be subcellular localization, secretion, post-translational modification or degradation of proteins. Conducting such studies only with experimental techniques is often associated with high costs and risks of uncertainty. Preliminary prediction of putative motifs with computational methods, them being fast and much less expensive, provides possibilities for generating hypotheses and therefore, more directed and efficient planning of experiments. To meet this goal, I have developed HH-MOTiF – a web-based tool for de novo discovery of SLiMs in a set of protein sequences. While working on the project, I have also detected patterns in sequence properties of certain SLiMs that make their de novo prediction easier. As some of these patterns are not yet described in the literature, I am sharing them in this thesis. While evaluating and comparing motif prediction results, I have identified conceptual gaps in theoretical studies, as well as existing practical solutions for comparing two sets of positional data annotating the same set of biological sequences. To close this gap and to be able to carry out in-depth performance analyses of HH-MOTiF in comparison to other predictors, I have developed a corresponding statistical method, SLALOM (for StatisticaL Analysis of Locus Overlap Method). It is currently available as a standalone command line tool

An Efficient Algorithm for Bulk-Loading xBR+ -trees

A major part of the interface to a database is made up of the queries that can be addressed to this database and answered (processed) in an efficient way, contributing to the quality of the developed software. Efficiently processed spatial queries constitute a fundamental part of the interface to spatial databases due to the wide area of applications that may address such queries, like geographical information systems (GIS), location-based services, computer visualization, automated mapping, facilities management, etc. Another important capability of the interface to a spatial database is to offer the creation of efficient index structures to speed up spatial query processing. The xBR + -tree is a balanced disk-resident quadtree-based index structure for point data, which is very efficient for processing such queries. Bulk-loading refers to the process of creating an index from scratch, when the dataset to be indexed is available beforehand, instead of creating the index gradually (and more slowly), when the dataset elements are inserted one-by-one. In this paper, we present an algorithm for bulk-loading xBR + -trees for big datasets residing on disk, using a limited amount of main memory. The resulting tree is not only built fast, but exhibits high performance in processing a broad range of spatial queries, where one or two datasets are involved. To justify these characteristics, using real and artificial datasets of various cardinalities, first, we present an experimental comparison of this algorithm vs. a previous version of the same algorithm and STR, a popular algorithm of bulk-loading R-trees, regarding tree creation time and the characteristics of the trees created, and second, we experimentally compare the query efficiency of bulk-loaded xBR + -trees vs. bulk-loaded R-trees, regarding I/O and execution time. Thus, this paper contributes to the implementation of spatial database interfaces and the efficient storage organization for big spatial data management