8,071 research outputs found
A Data Transformation System for Biological Data Sources
Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data
Building Efficient Query Engines in a High-Level Language
Abstraction without regret refers to the vision of using high-level
programming languages for systems development without experiencing a negative
impact on performance. A database system designed according to this vision
offers both increased productivity and high performance, instead of sacrificing
the former for the latter as is the case with existing, monolithic
implementations that are hard to maintain and extend. In this article, we
realize this vision in the domain of analytical query processing. We present
LegoBase, a query engine written in the high-level language Scala. The key
technique to regain efficiency is to apply generative programming: LegoBase
performs source-to-source compilation and optimizes the entire query engine by
converting the high-level Scala code to specialized, low-level C code. We show
how generative programming allows to easily implement a wide spectrum of
optimizations, such as introducing data partitioning or switching from a row to
a column data layout, which are difficult to achieve with existing low-level
query compilers that handle only queries. We demonstrate that sufficiently
powerful abstractions are essential for dealing with the complexity of the
optimization effort, shielding developers from compiler internals and
decoupling individual optimizations from each other. We evaluate our approach
with the TPC-H benchmark and show that: (a) With all optimizations enabled,
LegoBase significantly outperforms a commercial database and an existing query
compiler. (b) Programmers need to provide just a few hundred lines of
high-level code for implementing the optimizations, instead of complicated
low-level code that is required by existing query compilation approaches. (c)
The compilation overhead is low compared to the overall execution time, thus
making our approach usable in practice for compiling query engines
Distributed top-k aggregation queries at large
Top-k query processing is a fundamental building block for efficient ranking in a large number of applications. Efficiency is a central issue, especially for distributed settings, when the data is spread across different nodes in a network. This paper introduces novel optimization methods for top-k aggregation queries in such distributed environments. The optimizations can be applied to all algorithms that fall into the frameworks of the prior TPUT and KLEE methods. The optimizations address three degrees of freedom: 1) hierarchically grouping input lists into top-k operator trees and optimizing the tree structure, 2) computing data-adaptive scan depths for different input sources, and 3) data-adaptive sampling of a small subset of input sources in scenarios with hundreds or thousands of query-relevant network nodes. All optimizations are based on a statistical cost model that utilizes local synopses, e.g., in the form of histograms, efficiently computed convolutions, and estimators based on order statistics. The paper presents comprehensive experiments, with three different real-life datasets and using the ns-2 network simulator for a packet-level simulation of a large Internet-style network
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