Efficient data representation for XML in peer-based systems

Purpose - New directions in the provision of end-user computing experiences mean that the best way to share data between small mobile computing devices needs to be determined. Partitioning large structures so that they can be shared efficiently provides a basis for data-intensive applications on such platforms. The partitioned structure can be compressed using dictionary-based approaches and then directly queried without firstly decompressing the whole structure. Design/methodology/approach - The paper describes an architecture for partitioning XML into structural and dictionary elements and the subsequent manipulation of the dictionary elements to make the best use of available space. Findings - The results indicate that considerable savings are available by removing duplicate dictionaries. The paper also identifies the most effective strategy for defining dictionary scope. Research limitations/implications - This evaluation is based on a range of benchmark XML structures and the approach to minimising dictionary size shows benefit in the majority of these. Where structures are small and regular, the benefits of efficient dictionary representation are lost. The authors' future research now focuses on heuristics for further partitioning of structural elements. Practical implications - Mobile applications that need access to large data collections will benefit from the findings of this research. Traditional client/server architectures are not suited to dealing with high volume demands from a multitude of small mobile devices. Peer data sharing provides a more scalable solution and the experiments that the paper describes demonstrate the most effective way of sharing data in this context. Social implications - Many services are available via smartphone devices but users are wary of exploiting the full potential because of the need to conserve battery power. The approach mitigates this challenge and consequently expands the potential for users to benefit from mobile information systems. This will have impact in areas such as advertising, entertainment and education but will depend on the acceptability of file sharing being extended from the desktop to the mobile environment. Originality/value - The original work characterises the most effective way of sharing large data sets between small mobile devices. This will save battery power on devices such as smartphones, thus providing benefits to users of such devices

Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being widely applied to the large sets of sequences often encountered as the outcome of DNA sequencing experiments. In previous work, we presented a novel algorithm that allows the BWT of human genome scale data to be computed on very moderate hardware, thus enabling us to investigate the BWT as a tool for the compression of such datasets. Results We first used simulated reads to explore the relationship between the level of compression and the error rate, the length of the reads and the level of sampling of the underlying genome and compare choices of second-stage compression algorithm. We demonstrate that compression may be greatly improved by a particular reordering of the sequences in the collection and give a novel `implicit sorting' strategy that enables these benefits to be realised without the overhead of sorting the reads. With these techniques, a 45x coverage of real human genome sequence data compresses losslessly to under 0.5 bits per base, allowing the 135.3Gbp of sequence to fit into only 8.2Gbytes of space (trimming a small proportion of low-quality bases from the reads improves the compression still further). This is more than 4 times smaller than the size achieved by a standard BWT-based compressor (bzip2) on the untrimmed reads, but an important further advantage of our approach is that it facilitates the building of compressed full text indexes such as the FM-index on large-scale DNA sequence collections.Comment: Version here is as submitted to Bioinformatics and is same as the previously archived version. This submission registers the fact that the advanced access version is now available at http://bioinformatics.oxfordjournals.org/content/early/2012/05/02/bioinformatics.bts173.abstract . Bioinformatics should be considered as the original place of publication of this article, please cite accordingl

Indexing large genome collections on a PC

Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key operation useful in such analyses is aligning sequencing reads against a collection of genomes, which is costly with the use of existing algorithms due to their large memory requirements. Results: We present MuGI, Multiple Genome Index, which reports all occurrences of a given pattern, in exact and approximate matching model, against a collection of thousand(s) genomes. Its unique feature is the small index size fitting in a standard computer with 16--32\,GB, or even 8\,GB, of RAM, for the 1000GP collection of 1092 diploid human genomes. The solution is also fast. For example, the exact matching queries are handled in average time of 39\,$\mu$s and with up to 3 mismatches in 373\,$\mu$s on the test PC with the index size of 13.4\,GB. For a smaller index, occupying 7.4\,GB in memory, the respective times grow to 76\,$\mu$s and 917\,$\mu$s. Availability: Software and Suuplementary material: \url{http://sun.aei.polsl.pl/mugi}

The Wiltshire Wills Feasibility Study

The Wiltshire and Swindon Record Office has nearly ninety thousand wills in its care. These records are neither adequately catalogued nor secured against loss by facsimile microfilm copies. With support from the Heritage Lottery Fund the Record Office has begun to produce suitable finding aids for the material. Beginning with this feasibility study the Record Office is developing a strategy to ensure the that facsimiles to protect the collection against risk of loss or damage and to improve public access are created.<p></p> This feasibility study explores the different methodologies that can be used to assist the preservation and conservation of the collection and improve public access to it. The study aims to produce a strategy that will enable the Record Office to create digital facsimiles of the Wills in its care for access purposes and to also create preservation quality microfilms. The strategy aims to seek the most cost effective and time efficient approach to the problem and identifies ways to optimise the processes by drawing on the experience of other similar projects. This report provides a set of guidelines and recommendations to ensure the best use of the resources available for to provide the most robust preservation strategy and to ensure that future access to the Wills as an information resource can be flexible, both local and remote, and sustainable

Decoding billions of integers per second through vectorization

In many important applications -- such as search engines and relational database systems -- data is stored in the form of arrays of integers. Encoding and, most importantly, decoding of these arrays consumes considerable CPU time. Therefore, substantial effort has been made to reduce costs associated with compression and decompression. In particular, researchers have exploited the superscalar nature of modern processors and SIMD instructions. Nevertheless, we introduce a novel vectorized scheme called SIMD-BP128 that improves over previously proposed vectorized approaches. It is nearly twice as fast as the previously fastest schemes on desktop processors (varint-G8IU and PFOR). At the same time, SIMD-BP128 saves up to 2 bits per integer. For even better compression, we propose another new vectorized scheme (SIMD-FastPFOR) that has a compression ratio within 10% of a state-of-the-art scheme (Simple-8b) while being two times faster during decoding.Comment: For software, see https://github.com/lemire/FastPFor, For data, see http://boytsov.info/datasets/clueweb09gap

TopSig: Topology Preserving Document Signatures

Performance comparisons between File Signatures and Inverted Files for text retrieval have previously shown several significant shortcomings of file signatures relative to inverted files. The inverted file approach underpins most state-of-the-art search engine algorithms, such as Language and Probabilistic models. It has been widely accepted that traditional file signatures are inferior alternatives to inverted files. This paper describes TopSig, a new approach to the construction of file signatures. Many advances in semantic hashing and dimensionality reduction have been made in recent times, but these were not so far linked to general purpose, signature file based, search engines. This paper introduces a different signature file approach that builds upon and extends these recent advances. We are able to demonstrate significant improvements in the performance of signature file based indexing and retrieval, performance that is comparable to that of state of the art inverted file based systems, including Language models and BM25. These findings suggest that file signatures offer a viable alternative to inverted files in suitable settings and from the theoretical perspective it positions the file signatures model in the class of Vector Space retrieval models.Comment: 12 pages, 8 figures, CIKM 201