LinkedScales : bases de dados em multiescala

Orientador: André SantanchèTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: As ciências biológicas e médicas precisam cada vez mais de abordagens unificadas para a análise de dados, permitindo a exploração da rede de relacionamentos e interações entre elementos. No entanto, dados essenciais estão frequentemente espalhados por um conjunto cada vez maior de fontes com múltiplos níveis de heterogeneidade entre si, tornando a integração cada vez mais complexa. Abordagens de integração existentes geralmente adotam estratégias especializadas e custosas, exigindo a produção de soluções monolíticas para lidar com formatos e esquemas específicos. Para resolver questões de complexidade, essas abordagens adotam soluções pontuais que combinam ferramentas e algoritmos, exigindo adaptações manuais. Abordagens não sistemáticas dificultam a reutilização de tarefas comuns e resultados intermediários, mesmo que esses possam ser úteis em análises futuras. Além disso, é difícil o rastreamento de transformações e demais informações de proveniência, que costumam ser negligenciadas. Este trabalho propõe LinkedScales, um dataspace baseado em múltiplos níveis, projetado para suportar a construção progressiva de visões unificadas de fontes heterogêneas. LinkedScales sistematiza as múltiplas etapas de integração em escalas, partindo de representações brutas (escalas mais baixas), indo gradualmente para estruturas semelhantes a ontologias (escalas mais altas). LinkedScales define um modelo de dados e um processo de integração sistemático e sob demanda, através de transformações em um banco de dados de grafos. Resultados intermediários são encapsulados em escalas reutilizáveis e transformações entre escalas são rastreadas em um grafo de proveniência ortogonal, que conecta objetos entre escalas. Posteriormente, consultas ao dataspace podem considerar objetos nas escalas e o grafo de proveniência ortogonal. Aplicações práticas de LinkedScales são tratadas através de dois estudos de caso, um no domínio da biologia -- abordando um cenário de análise centrada em organismos -- e outro no domínio médico -- com foco em dados de medicina baseada em evidênciasAbstract: Biological and medical sciences increasingly need a unified, network-driven approach for exploring relationships and interactions among data elements. Nevertheless, essential data is frequently scattered across sources with multiple levels of heterogeneity. Existing data integration approaches usually adopt specialized, heavyweight strategies, requiring a costly upfront effort to produce monolithic solutions for handling specific formats and schemas. Furthermore, such ad-hoc strategies hamper the reuse of intermediary integration tasks and outcomes. This work proposes LinkedScales, a multiscale-based dataspace designed to support the progressive construction of a unified view of heterogeneous sources. It departs from raw representations (lower scales) and goes towards ontology-like structures (higher scales). LinkedScales defines a data model and a systematic, gradual integration process via operations over a graph database. Intermediary outcomes are encapsulated as reusable scales, tracking the provenance of inter-scale operations. Later, queries can combine both scale data and orthogonal provenance information. Practical applications of LinkedScales are discussed through two case studies on the biology domain -- addressing an organism-centric analysis scenario -- and the medical domain -- focusing on evidence-based medicine dataDoutoradoCiência da ComputaçãoDoutor em Ciência da Computação141353/2015-5CAPESCNP

Query Processing in a P2P Network of Taxonomy-based Information Sources

In this study we address the problem of answering queries over a peer-to-peer system of taxonomy-based sources. A taxonomy states subsumption relationships between negation-free DNF formulas on terms and negation-free conjunctions of terms. To the end of laying the foundations of our study, we first consider the centralized case, deriving the complexity of the decision problem and of query evaluation. We conclude by presenting an algorithm that is efficient in data complexity and is based on hypergraphs. We then move to the distributed case, and introduce a logical model of a network of taxonomy-based sources. On such network, a distributed version of the centralized algorithm is then presented, based on a message passing paradigm, and its correctness is proved. We finally discuss optimization issues, and relate our work to the literature

Integration of heterogeneous multidimensional data marts

 Data analysts often require access to integrated multidimensional data from local and external data warehouses. The integration process is often undertaken by expert database practitioners who will need to analyze the structure of the data, and match schemas and data before creating an integrated view of the data for visualization and analysis. Such a manual process may be acceptable for databases used in transaction processing applications but does not help decision makers who need access to the information quickly and cost effective in a constantly changing environment. This thesis addresses several challenges towards automating the integration of data warehouses based on a dimensional model known as Star schema. We recognize that the structure of multidimensional data, namely dimension hierarchies, is critical to the accuracy of the integration but is not always available or accessible. To address this problem, we infer dimension hierarchies from their instances, and demonstrate that they are sufficient to ensure the accuracy of the integration even though they may vary from the intended hierarchies. To improve the accuracy of matching Star schemas, we propose a more precise representation of Star schemas and demonstrate its effectiveness by comparing it against the existing approaches that treat Star schemas as relational models. To match instances of dimensions, we demonstrate that a graph matching algorithm is effective and performs with a high level of accuracy. We propose algorithms which enforce the tree structure of integrated data which is necessary for correct aggregation, and reduce false positive cases occurring during the instance matching. The effectiveness of our algorithms is shown through experiments with real life data. Despite perfectly matching schemas and hierarchies, there are often dimensions with mismatching data which restrict the scope of the integration. We propose to relax the requirement for dimension compatibility, and introduce measures that quantify the loss of data resulting from the less strict requirement. These measures enable data analysts to identify lossless fragments of data, and thereby, extend the scope of the integrated data. To provide a more comprehensive view of data for analysis, we link the integrated data with the data exclusive to each source by extending the navigation operation for multidimensional data. These contributions help towards shifting the integration problem away from expert database practitioners to empowered data analysts in combining multidimensional data from multiple sources in real time, and in a cost effective manner

Binary RDF for Scalable Publishing, Exchanging and Consumption in the Web of Data

El actual diluvio de datos está inundando la web con grandes volúmenes de datos representados en RDF, dando lugar a la denominada 'Web de Datos'. En esta tesis proponemos, en primer lugar, un estudio profundo de aquellos textos que nos permitan abordar un conocimiento global de la estructura real de los conjuntos de datos RDF, HDT, que afronta la representación eficiente de grandes volúmenes de datos RDF a través de estructuras optimizadas para su almacenamiento y transmisión en red. HDT representa efizcamente un conjunto de datos RDF a través de su división en tres componentes: la cabecera (Header), el diccionario (Dictionary) y la estructura de sentencias RDF (Triples). A continuación, nos centramos en proveer estructuras eficientes de dichos componentes, ocupando un espacio comprimido al tiempo que se permite el acceso directo a cualquier dat

Stream-dashboard : a big data stream clustering framework with applications to social media streams.

Data mining is concerned with detecting patterns of data in raw datasets, which are then used to unearth knowledge that might not have been discovered using conventional querying or statistical methods. This discovered knowledge has been used to empower decision makers in countless applications spanning across many multi-disciplinary areas including business, education, astronomy, security and Information Retrieval to name a few. Many applications generate massive amounts of data continuously and at an increasing rate. This is the case for user activity over social networks such as Facebook and Twitter. This flow of data has been termed, appropriately, a Data Stream, and it introduced a set of new challenges to discover its evolving patterns using data mining techniques. Data stream clustering is concerned with detecting evolving patterns in a data stream using only the similarities between the data points as they arrive without the use of any external information (i.e. unsupervised learning). In this dissertation, we propose a complete and generic framework to simultaneously mine, track and validate clusters in a big data stream (Stream-Dashboard). The proposed framework consists of three main components: an online data stream clustering algorithm, a component for tracking and validation of pattern behavior using regression analysis, and a component that uses the behavioral information about the detected patterns to improve the quality of the clustering algorithm. As a first component, we propose RINO-Streams, an online clustering algorithm that incrementally updates the clustering model using robust statistics and incremental optimization. The second component is a methodology that we call TRACER, which continuously performs a set of statistical tests using regression analysis to track the evolution of the detected clusters, their characteristics and quality metrics. For the last component, we propose a method to build some behavioral profiles for the clustering model over time, that can be used to improve the performance of the online clustering algorithm, such as adapting the initial values of the input parameters. The performance and effectiveness of the proposed framework were validated using extensive experiments, and its use was demonstrated on a challenging real word application, specifically unsupervised mining of evolving cluster stories in one pass from the Twitter social media streams

Bench-Ranking: ettekirjutav analüüsimeetod suurte teadmiste graafide päringutele

Relatsiooniliste suurandmete (BD) töötlemisraamistike kasutamine suurte teadmiste graafide töötlemiseks kätkeb endas võimalust päringu jõudlust optimeerimida. Kaasaegsed BD-süsteemid on samas keerulised andmesüsteemid, mille konfiguratsioonid omavad olulist mõju jõudlusele. Erinevate raamistike ja konfiguratsioonide võrdlusuuringud pakuvad kogukonnale parimaid tavasid parema jõudluse saavutamiseks. Enamik neist võrdlusuuringutest saab liigitada siiski vaid kirjeldavaks ja diagnostiliseks analüütikaks. Lisaks puudub ühtne standard nende uuringute võrdlemiseks kvantitatiivselt järjestatud kujul. Veelgi enam, suurte graafide töötlemiseks vajalike konveierite kavandamine eeldab täiendavaid disainiotsuseid mis tulenevad mitteloomulikust (relatsioonilisest) graafi töötlemise paradigmast. Taolisi disainiotsuseid ei saa automaatselt langetada, nt relatsiooniskeemi, partitsioonitehnika ja salvestusvormingute valikut. Käesolevas töös käsitleme kuidas me antud uurimuslünga täidame. Esmalt näitame disainiotsuste kompromisside mõju BD-süsteemide jõudluse korratavusele suurte teadmiste graafide päringute tegemisel. Lisaks näitame BD-raamistike jõudluse kirjeldavate ja diagnostiliste analüüside piiranguid suurte graafide päringute tegemisel. Seejärel uurime, kuidas lubada ettekirjutavat analüütikat järjestamisfunktsioonide ja mitmemõõtmeliste optimeerimistehnikate (nn "Bench-Ranking") kaudu. See lähenemine peidab kirjeldava tulemusanalüüsi keerukuse, suunates praktiku otse teostatavate teadlike otsusteni.Leveraging relational Big Data (BD) processing frameworks to process large knowledge graphs yields a great interest in optimizing query performance. Modern BD systems are yet complicated data systems, where the configurations notably affect the performance. Benchmarking different frameworks and configurations provides the community with best practices for better performance. However, most of these benchmarking efforts are classified as descriptive and diagnostic analytics. Moreover, there is no standard for comparing these benchmarks based on quantitative ranking techniques. Moreover, designing mature pipelines for processing big graphs entails considering additional design decisions that emerge with the non-native (relational) graph processing paradigm. Those design decisions cannot be decided automatically, e.g., the choice of the relational schema, partitioning technique, and storage formats. Thus, in this thesis, we discuss how our work fills this timely research gap. Particularly, we first show the impact of those design decisions’ trade-offs on the BD systems’ performance replicability when querying large knowledge graphs. Moreover, we showed the limitations of the descriptive and diagnostic analyses of BD frameworks’ performance for querying large graphs. Thus, we investigate how to enable prescriptive analytics via ranking functions and Multi-Dimensional optimization techniques (called ”Bench-Ranking”). This approach abstracts out from the complexity of descriptive performance analysis, guiding the practitioner directly to actionable informed decisions.https://www.ester.ee/record=b553332

Pseudo-contractions as Gentle Repairs

Updating a knowledge base to remove an unwanted consequence is a challenging task. Some of the original sentences must be either deleted or weakened in such a way that the sentence to be removed is no longer entailed by the resulting set. On the other hand, it is desirable that the existing knowledge be preserved as much as possible, minimising the loss of information. Several approaches to this problem can be found in the literature. In particular, when the knowledge is represented by an ontology, two different families of frameworks have been developed in the literature in the past decades with numerous ideas in common but with little interaction between the communities: applications of AGM-like Belief Change and justification-based Ontology Repair. In this paper, we investigate the relationship between pseudo-contraction operations and gentle repairs. Both aim to avoid the complete deletion of sentences when replacing them with weaker versions is enough to prevent the entailment of the unwanted formula. We show the correspondence between concepts on both sides and investigate under which conditions they are equivalent. Furthermore, we propose a unified notation for the two approaches, which might contribute to the integration of the two areas

On the Discovery of Semantically Meaningful SQL Constraints from Armstrong Samples: Foundations, Implementation, and Evaluation

A database is said to be C-Armstrong for a finite set Σ of data dependencies in a class C if the database satisfies all data dependencies in Σ and violates all data dependencies in C that are not implied by Σ. Therefore, Armstrong databases are concise, user-friendly representations of abstract data dependencies that can be used to judge, justify, convey, and test the understanding of database design choices. Indeed, an Armstrong database satisfies exactly those data dependencies that are considered meaningful by the current design choice Σ. Structural and computational properties of Armstrong databases have been deeply investigated in Codd’s Turing Award winning relational model of data. Armstrong databases have been incorporated in approaches towards relational database design. They have also been found useful for the elicitation of requirements, the semantic sampling of existing databases, and the specification of schema mappings. This research establishes a toolbox of Armstrong databases for SQL data. This is challenging as SQL data can contain null marker occurrences in columns declared NULL, and may contain duplicate rows. Thus, the existing theory of Armstrong databases only applies to idealized instances of SQL data, that is, instances without null marker occurrences and without duplicate rows. For the thesis, two popular interpretations of null markers are considered: the no information interpretation used in SQL, and the exists but unknown interpretation by Codd. Furthermore, the study is limited to the popular class C of functional dependencies. However, the presence of duplicate rows means that the class of uniqueness constraints is no longer subsumed by the class of functional dependencies, in contrast to the relational model of data. As a first contribution a provably-correct algorithm is developed that computes Armstrong databases for an arbitrarily given finite set of uniqueness constraints and functional dependencies. This contribution is based on axiomatic, algorithmic and logical characterizations of the associated implication problem that are also established in this thesis. While the problem to decide whether a given database is Armstrong for a given set of such constraints is precisely exponential, our algorithm computes an Armstrong database with a number of rows that is at most quadratic in the number of rows of a minimum-sized Armstrong database. As a second contribution the algorithms are implemented in the form of a design tool. Users of the tool can therefore inspect Armstrong databases to analyze their current design choice Σ. Intuitively, Armstrong databases are useful for the acquisition of semantically meaningful constraints, if the users can recognize the actual meaningfulness of constraints that they incorrectly perceived as meaningless before the inspection of an Armstrong database. As a final contribution, measures are introduced that formalize the term “useful” and it is shown by some detailed experiments that Armstrong tables, as computed by the tool, are indeed useful. In summary, this research establishes a toolbox of Armstrong databases that can be applied by database designers to concisely visualize constraints on SQL data. Such support can lead to database designs that guarantee efficient data management in practice