11,186 research outputs found

    Scalable Construction of Text Indexes with Thrill

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    The suffix array is the key to efficient solutions for myriads of string processing problems in different application domains, like data compression, data mining, or bioinformatics. With the rapid growth of available data, suffix array construction algorithms have to be adapted to advanced computational models such as external memory and distributed computing. In this article, we present five suffix array construction algorithms utilizing the new algorithmic big data batch processing framework Thrill, which allows scalable processing of input sizes on distributed systems in orders of magnitude that have not been considered before

    Prospects and limitations of full-text index structures in genome analysis

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    The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

    Streaming Similarity Self-Join

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    We introduce and study the problem of computing the similarity self-join in a streaming context (SSSJ), where the input is an unbounded stream of items arriving continuously. The goal is to find all pairs of items in the stream whose similarity is greater than a given threshold. The simplest formulation of the problem requires unbounded memory, and thus, it is intractable. To make the problem feasible, we introduce the notion of time-dependent similarity: the similarity of two items decreases with the difference in their arrival time. By leveraging the properties of this time-dependent similarity function, we design two algorithmic frameworks to solve the sssj problem. The first one, MiniBatch (MB), uses existing index-based filtering techniques for the static version of the problem, and combines them in a pipeline. The second framework, Streaming (STR), adds time filtering to the existing indexes, and integrates new time-based bounds deeply in the working of the algorithms. We also introduce a new indexing technique (L2), which is based on an existing state-of-the-art indexing technique (L2AP), but is optimized for the streaming case. Extensive experiments show that the STR algorithm, when instantiated with the L2 index, is the most scalable option across a wide array of datasets and parameters

    Online Self-Indexed Grammar Compression

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    Although several grammar-based self-indexes have been proposed thus far, their applicability is limited to offline settings where whole input texts are prepared, thus requiring to rebuild index structures for given additional inputs, which is often the case in the big data era. In this paper, we present the first online self-indexed grammar compression named OESP-index that can gradually build the index structure by reading input characters one-by-one. Such a property is another advantage which enables saving a working space for construction, because we do not need to store input texts in memory. We experimentally test OESP-index on the ability to build index structures and search query texts, and we show OESP-index's efficiency, especially space-efficiency for building index structures.Comment: To appear in the Proceedings of the 22nd edition of the International Symposium on String Processing and Information Retrieval (SPIRE2015
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