Timos K. Sellis

Multiple-query optimization

Some recently proposed extensions to relational database systems, as well as to deductive database systems, require support for multiple-query processing. For example, in a database system enhanced with inference capabilities, a simple query involving a rule with multiple definitions may expand to more than one actual query that has to be run over the database. It is an interesting problem then to come up with algorithms that process these queries together instead of one query at a time. The main motivation for performing such an interquery optimization lies in the fact that queries may share common data. We examine the problem of multiple-query optimization in this paper. The first major contribution of the paper is a systematic look at the problem, along with the presentation and analysis of algorithms that can be used for multiple-query optimization. The second contribution lies in the presentation of experimental results. Our results show that using multiple-query processing algorithms may reduce execution cost considerably.

DIANA-microT web server: elucidating microRNA functions through target prediction

Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT.

Accurate microRNA target prediction correlates with protein repression levels.

BackgroundMicroRNAs are small endogenously expressed non-coding RNA molecules that regulate target gene expression through translation repression or messenger RNA degradation. MicroRNA regulation is performed through pairing of the microRNA to sites in the messenger RNA of protein coding genes. Since experimental identification of miRNA target genes poses difficulties, computational microRNA target prediction is one of the key means in deciphering the role of microRNAs in development and disease.ResultsDIANA-microT 3.0 is an algorithm for microRNA target prediction which is based on several parameters calculated individually for each microRNA and combines conserved and non-conserved microRNA recognition elements into a final prediction score, which correlates with protein production fold change. Specifically, for each predicted interaction the program reports a signal to noise ratio and a precision score which can be used as an indication of the false positive rate of the prediction.ConclusionRecently, several computational target prediction programs were benchmarked based on a set of microRNA target genes identified by the pSILAC method. In this assessment DIANA-microT 3.0 was found to achieve the highest precision among the most widely used microRNA target prediction programs reaching approximately 66%. The DIANA-microT 3.0 prediction results are available online in a user friendly web server at http://www.microrna.gr/microT

A survey of logical models for OLAP databases

In this paper, we present different proposals for multidimensional data cubes, which are the basic logical model for OLAP applications. We have grouped the work in the field in two categories: commercial tools (presented along with terminology and standards) and academic efforts. We further divide the academic efforts in two subcategories: the relational model extensions and the cube-oriented approaches. Finally, we attempt a comparative analysis of the various efforts.

Spatio-temporal indexing for large multimedia applications

Multimedia applications usually involve a large number of multimedia objects (texts, images, sounds, etc.). Spatial and temporal relationships among these objects should be efficiently supported and retrieved within a multimedia authoring tool. In this paper, we present several spatial, temporal and spatio-temporal relationships of interest, and propose efficient indexing schemes, based on multidimensional (spatial) data structures, for large multimedia applications that involve thousands of objects. Evaluation models of the proposed schemes are also presented, as well as hints for the selection of the most appropriate one, according to the multimedia authors requirements.

A model for the prediction of R-tree performance

In this paper we present an analytical model that predicts the performance of R-trees (and its variants) when a range query needs to be answered. The cost model uses knowledge of the dataset only i.e., the proposed formula that estimates the number of disk accesses is a function of data properties, namely, the amount of data and their density in the work space. In other words, the proposed model is applicable even before the construction of the R-tree index, a fact that makes it a useful tool for dynamic spatial databases. Several experiments on synthetic and real datasets show that the proposed analytical model is very accurate, the relative error being usually around 10%-15%, for uniform and non-uniform distributions. We believe that this error is involved with the gap between efficient R-tree variants, like the R*-tree, and an optimum, not implemented yet, method. Our work extends previous research concerning R-tree analysis and constitutes a useful tool for spatial query optimizers that need to evaluate the cost of a complex spatial query and its execution procedure.

Topological relations in the world of minimum bounding rectangles: a study with R-trees

Recent developments in spatial relations have led to their use in numerous applications involving spatial databases. This paper is concerned with the retrieval of topological relations in Minimum Bounding Rectangle-based data structures. We study the topological information that Minimum Bounding Rectangles convey about the actual objects they enclose, using the concept of projections. Then we apply the results to R-trees and their variations, R+-trees and R*-trees in order to minimise disk accesses for queries involving topological relations. We also investigate queries that involve complex spatial conditions in the form of disjunctions and conjunctions and we discuss possible extensions.

An efficient pictorial database system for PSQL

Pictorial databases require efficient and direct spatial search based on the analog form of spatial objects and relationships instead of search based on some cumbersome alphanumeric encodings of the pictures. A description is given of PSQL, a query language that allows pictorial domains to be presented to the user in their analog form and allows him or her to do direct manipulation on the objects found on those domains. Direct spatial search and computation on the pictures is done using efficient data structures, R- and R/sup +/-trees (multidimensional B-trees), which are excellent devices for searching spatial objects and relationships found on pictures. >

The Lowell database research self-assessment

Database needs are changing, driven by the Internet and increasing amounts of scientific and sensor data. In this article, the authors propose research into several important new directions for database management systems.

A methodology for clustering XML documents by structure

The processing and management of XML data are popular research issues. However, operations based on the structure of XML data have not received strong attention. These operations involve, among others, the grouping of structurally similar XML documents. Such grouping results from the application of clustering methods with distances that estimate the similarity between tree structures. This paper presents a framework for clustering XML documents by structure. Modeling the XML documents as rooted ordered labeled trees, we study the usage of structural distance metrics in hierarchical clustering algorithms to detect groups of structurally similar XML documents. We suggest the usage of structural summaries for trees to improve the performance of the distance calculation and at the same time to maintain or even improve its quality. Our approach is tested using a prototype testbed.