105,574 research outputs found
Scalable Similarity Search for Molecular Descriptors
Similarity search over chemical compound databases is a fundamental task in
the discovery and design of novel drug-like molecules. Such databases often
encode molecules as non-negative integer vectors, called molecular descriptors,
which represent rich information on various molecular properties. While there
exist efficient indexing structures for searching databases of binary vectors,
solutions for more general integer vectors are in their infancy. In this paper
we present a time- and space- efficient index for the problem that we call the
succinct intervals-splitting tree algorithm for molecular descriptors (SITAd).
Our approach extends efficient methods for binary-vector databases, and uses
ideas from succinct data structures. Our experiments, on a large database of
over 40 million compounds, show SITAd significantly outperforms alternative
approaches in practice.Comment: To be appeared in the Proceedings of SISAP'1
Compressing DNA sequence databases with coil
Background: Publicly available DNA sequence databases such as GenBank are large, and are
growing at an exponential rate. The sheer volume of data being dealt with presents serious storage
and data communications problems. Currently, sequence data is usually kept in large "flat files,"
which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which
rarely achieves good compression ratios. While much research has been done on compressing
individual DNA sequences, surprisingly little has focused on the compression of entire databases
of such sequences. In this study we introduce the sequence database compression software coil.
Results: We have designed and implemented a portable software package, coil, for compressing
and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared
towards achieving high compression ratios at the expense of execution time and memory usage
during compression – the compression time represents a "one-off investment" whose cost is
quickly amortised if the resulting compressed file is transmitted many times. Decompression
requires little memory and is extremely fast. We demonstrate a 5% improvement in compression
ratio over state-of-the-art general-purpose compression tools for a large GenBank database file
containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental
additions to a sequence database.
Conclusion: coil presents a compelling alternative to conventional compression of flat files for the
storage and distribution of DNA sequence databases having a narrow distribution of sequence
lengths, such as EST data. Increasing compression levels for databases having a wide distribution of
sequence lengths is a direction for future work
Using Visualization to Support Data Mining of Large Existing Databases
In this paper. we present ideas how visualization technology can be used to improve the difficult process of querying very large databases. With our VisDB system, we try to provide visual support not only for the query specification process. but also for evaluating query results and. thereafter, refining the query accordingly. The main idea of our system is to represent as many data items as possible by the pixels of the display device. By arranging and coloring the pixels according to the relevance for the query, the user gets a visual impression of the resulting data set and of its relevance for the query. Using an interactive query interface, the user may change the query dynamically and receives immediate feedback by the visual representation of the resulting data set. By using multiple windows for different parts of the query, the user gets visual feedback for each part of the query and, therefore, may easier understand the overall result. To support complex queries, we introduce the notion of approximate joins which allow the user to find data items that only approximately fulfill join conditions. We also present ideas how our technique may be extended to support the interoperation of heterogeneous databases. Finally, we discuss the performance problems that are caused by interfacing to existing database systems and present ideas to solve these problems by using data structures supporting a multidimensional search of the database
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