When integrating data from autonomous sources, exact matches of data items that represent the same real-world object often fail due to a lack of common keys. Yet in many cases structural information is available and can be used to match such data. Typically the matching must be approximate since the representations in the sources differ.We propose pq-grams to approximately match hierarchical data from autonomous sources and define the pq-gram distance between ordered labeled trees as an effective and efficient approximation of the fanout weighted tree edit distance. We prove that the pq-gram distance is a lower bound of the fanout weighted tree edit distance and give a normalization of the pq-gram distance for which the triangle inequality holds. Experiments on synthetic and real-world data (residential addresses and XML) confirm the scalability of our approach and show the effectiveness of pq-grams. ACM Reference Format:Augsten, N., Böhlen, M., and Gamper, J. 2010. The pq-gram distance between ordered labeled trees.

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In order to process interval timestamped data, the sequenced semantics has been proposed. This paper presents a relational algebra solution that provides native support for the three properties of the sequenced semantics: snapshot reducibility, extended snapshot reducibility, and change preservation. We introduce two temporal primitives, temporal splitter and temporal aligner, and define rules that use these primitives to reduce the operators of a temporal algebra to their nontemporal counterparts. Our solution supports the three properties of the sequenced semantics through interval adjustment and timestamp propagation. We have implemented the temporal primitives and reduction rules in the kernel of PostgreSQL to get native database support for processing interval timestamped data. The support is comprehensive and includes outer joins, antijoins, and aggregations with predicates and functions over the time intervals of argument relations. The implementation and empirical evaluation confirms effectiveness and scalability of our solution that leverages existing database query optimization techniques.

Because of its flexibility, intuitiveness, and expressivity, the graph edit distance (GED) is one of the most widely used distance measures for labeled graphs. Since exactly computing GED is NP-hard, over the past years, various heuristics have been proposed. They use techniques such as transformations to the linear sum assignment problem with error-correction, local search, and linear programming to approximate GED via upper or lower bounds. In this paper, we provide a systematic overview of the most important heuristics. Moreover, we empirically evaluate all compared heuristics within an integrated implementation.

Many databases contain temporal, or time-referenced, data and use intervals to capture the temporal aspect. While SQL-based database management systems (DBMSs) are capable of supporting the management of interval data, the support they offer can be improved considerably. A range of proposed temporal data models and query languages offer ample evidence to this effect. Natural queries that are very difficult to formulate in SQL are easy to formulate in these temporal query languages. The increased focus on analytics over historical data where queries are generally more complex exacerbates the difficulties and thus the potential benefits of a temporal query language. Commercial DBMSs have recently started to offer limited temporal functionality in a step-by-step manner, focusing on the representation of intervals and neglecting the implementation of the query evaluation engine. This article demonstrates how it is possible to extend the relational database engine to achieve a full-fledged, industrial-strength implementation of sequenced temporal queries, which intuitively are queries that are evaluated at each time point. Our approach reduces temporal queries to nontemporal queries over data with adjusted intervals, and it leaves the processing of nontemporal queries unaffected. Specifically, the approach hinges on three concepts: interval adjustment, timestamp propagation, and attribute scaling. Interval adjustment is enabled by introducing two new relational operators, a temporal normalizer and a temporal aligner, and the latter two concepts are enabled by the replication of timestamp attributes and the use of so-called scaling functions. By providing a set of reduction rules, we can transform any temporal query, expressed in terms of temporal relational operators, to a query expressed in terms of relational operators and the two new operators. We prove that the size of a transformed query is linear in the number of temporal operators in the original query. An integration of the new operators and the transformation rules, along with query optimization rules, into the kernel of PostgreSQL is reported. Empirical studies with the resulting temporal DBMS are covered that offer insights into pertinent design properties of the article's proposal. Many databases contain temporal, or time-referenced, data and use intervals to capture the temporal aspect. While SQL-based database management systems (DBMSs) are capable of supporting the management of interval data, the support they offer can be improved considerably. A range of proposed temporal data models and query languages offer ample evidence to this effect. Natural queries that are very difficult to formulate in SQL are easy to formulate in these temporal query languages. The increased focus on analytics over historical data where queries are generally more complex exacerbates the difficulties and thus the potential benefits of a temporal query language. Commercial DBMSs have recently started to offer limited temporal functionality in a step-by-step manner, ...

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Abstract. Business Intelligence solutions, encompassing technologies such as multi-dimensional data modeling and aggregate query processing, are being applied increasingly to non-traditional data. This paper extends multi-dimensional aggregation to apply to data with associated interval values that capture when the data hold. In temporal databases, intervals typically capture the states of reality that the data apply to, or capture when the data are, or were, part of the current database state. This paper proposes a new aggregation operator that addresses several challenges posed by interval data. First, the intervals to be associated with the result tuples may not be known in advance, but depend on the actual data. Such unknown intervals are accommodated by allowing result groups that are specified only partially. Second, the operator contends with the case where an interval associated with data expresses that the data holds for each point in the interval, as well as the case where the data holds only for the entire interval, but must be adjusted to apply to sub-intervals. The paper reports on an implementation of the new operator and on an empirical study that indicates that the operator scales to large data sets and is competitive with respect to other temporal aggregation algorithms.

BackgroundThe new sequencing technologies enable to scan very long and dense genetic sequences, obtaining datasets of genetic markers that are an order of magnitude larger than previously available. Such genetic sequences are characterized by common alleles interspersed with multiple rarer alleles. This situation has renewed the interest for the identification of haplotypes carrying the rare risk alleles. However, large scale explorations of the linkage-disequilibrium (LD) pattern to identify haplotype blocks are not easy to perform, because traditional algorithms have at least Θ(n2) time and memory complexity.ResultsWe derived three incremental optimizations of the widely used haplotype block recognition algorithm proposed by Gabriel et al. in 2002. Our most efficient solution, called MIG ++, has only Θ(n) memory complexity and, on a genome-wide scale, it omits >80% of the calculations, which makes it an order of magnitude faster than the original algorithm. Differently from the existing software, the MIG ++ analyzes the LD between SNPs at any distance, avoiding restrictions on the maximal block length. The haplotype block partition of the entire HapMap II CEPH dataset was obtained in 457 hours. By replacing the standard likelihood-based D′ variance estimator with an approximated estimator, the runtime was further improved. While producing a coarser partition, the approximate method allowed to obtain the full-genome haplotype block partition of the entire 1000 Genomes Project CEPH dataset in 44 hours, with no restrictions on allele frequency or long-range correlations. These experiments showed that LD-based haplotype blocks can span more than one million base-pairs in both HapMap II and 1000 Genomes datasets. An application to the North American Rheumatoid Arthritis Consortium (NARAC) dataset shows how the MIG ++ can support genome-wide haplotype association studies.ConclusionsThe MIG ++ enables to perform LD-based haplotype block recognition on genetic sequences of any length and density. In the new generation sequencing era, this can help identify haplotypes that carry rare variants of interest. The low computational requirements open the possibility to include the haplotype block structure into genome-wide association scans, downstream analyses, and visual interfaces for online genome browsers.