XML Matchers: approaches and challenges

Schema Matching, i.e. the process of discovering semantic correspondences between concepts adopted in different data source schemas, has been a key topic in Database and Artificial Intelligence research areas for many years. In the past, it was largely investigated especially for classical database models (e.g., E/R schemas, relational databases, etc.). However, in the latest years, the widespread adoption of XML in the most disparate application fields pushed a growing number of researchers to design XML-specific Schema Matching approaches, called XML Matchers, aiming at finding semantic matchings between concepts defined in DTDs and XSDs. XML Matchers do not just take well-known techniques originally designed for other data models and apply them on DTDs/XSDs, but they exploit specific XML features (e.g., the hierarchical structure of a DTD/XSD) to improve the performance of the Schema Matching process. The design of XML Matchers is currently a well-established research area. The main goal of this paper is to provide a detailed description and classification of XML Matchers. We first describe to what extent the specificities of DTDs/XSDs impact on the Schema Matching task. Then we introduce a template, called XML Matcher Template, that describes the main components of an XML Matcher, their role and behavior. We illustrate how each of these components has been implemented in some popular XML Matchers. We consider our XML Matcher Template as the baseline for objectively comparing approaches that, at first glance, might appear as unrelated. The introduction of this template can be useful in the design of future XML Matchers. Finally, we analyze commercial tools implementing XML Matchers and introduce two challenging issues strictly related to this topic, namely XML source clustering and uncertainty management in XML Matchers.Comment: 34 pages, 8 tables, 7 figure

A Framework for Top-K Queries over Weighted RDF Graphs

abstract: The Resource Description Framework (RDF) is a specification that aims to support the conceptual modeling of metadata or information about resources in the form of a directed graph composed of triples of knowledge (facts). RDF also provides mechanisms to encode meta-information (such as source, trust, and certainty) about facts already existing in a knowledge base through a process called reification. In this thesis, an extension to the current RDF specification is proposed in order to enhance RDF triples with an application specific weight (cost). Unlike reification, this extension treats these additional weights as first class knowledge attributes in the RDF model, which can be leveraged by the underlying query engine. Additionally, current RDF query languages, such as SPARQL, have a limited expressive power which limits the capabilities of applications that use them. Plus, even in the presence of language extensions, current RDF stores could not provide methods and tools to process extended queries in an efficient and effective way. To overcome these limitations, a set of novel primitives for the SPARQL language is proposed to express Top-k queries using traditional query patterns as well as novel predicates inspired by those from the XPath language. Plus, an extended query processor engine is developed to support efficient ranked path search, join, and indexing. In addition, several query optimization strategies are proposed, which employ heuristics, advanced indexing tools, and two graph metrics: proximity and sub-result inter-arrival time. These strategies aim to find join orders that reduce the total query execution time while avoiding worst-case pattern combinations. Finally, extensive experimental evaluation shows that using these two metrics in query optimization has a significant impact on the performance and efficiency of Top-k queries. Further experiments also show that proximity and inter-arrival have an even greater, although sometimes undesirable, impact when combined through aggregation functions. Based on these results, a hybrid algorithm is proposed which acknowledges that proximity is more important than inter-arrival time, due to its more complete nature, and performs a fine-grained combination of both metrics by analyzing the differences between their individual scores and performing the aggregation only if these differences are negligible.Dissertation/ThesisM.S. Computer Science 201

edge2vec: Representation learning using edge semantics for biomedical knowledge discovery

Representation learning provides new and powerful graph analytical approaches and tools for the highly valued data science challenge of mining knowledge graphs. Since previous graph analytical methods have mostly focused on homogeneous graphs, an important current challenge is extending this methodology for richly heterogeneous graphs and knowledge domains. The biomedical sciences are such a domain, reflecting the complexity of biology, with entities such as genes, proteins, drugs, diseases, and phenotypes, and relationships such as gene co-expression, biochemical regulation, and biomolecular inhibition or activation. Therefore, the semantics of edges and nodes are critical for representation learning and knowledge discovery in real world biomedical problems. In this paper, we propose the edge2vec model, which represents graphs considering edge semantics. An edge-type transition matrix is trained by an Expectation-Maximization approach, and a stochastic gradient descent model is employed to learn node embedding on a heterogeneous graph via the trained transition matrix. edge2vec is validated on three biomedical domain tasks: biomedical entity classification, compound-gene bioactivity prediction, and biomedical information retrieval. Results show that by considering edge-types into node embedding learning in heterogeneous graphs, \textbf{edge2vec}\ significantly outperforms state-of-the-art models on all three tasks. We propose this method for its added value relative to existing graph analytical methodology, and in the real world context of biomedical knowledge discovery applicability.Comment: 10 page