The Weight Function in the Subtree Kernel is Decisive

Tree data are ubiquitous because they model a large variety of situations, e.g., the architecture of plants, the secondary structure of RNA, or the hierarchy of XML files. Nevertheless, the analysis of these non-Euclidean data is difficult per se. In this paper, we focus on the subtree kernel that is a convolution kernel for tree data introduced by Vishwanathan and Smola in the early 2000's. More precisely, we investigate the influence of the weight function from a theoretical perspective and in real data applications. We establish on a 2-classes stochastic model that the performance of the subtree kernel is improved when the weight of leaves vanishes, which motivates the definition of a new weight function, learned from the data and not fixed by the user as usually done. To this end, we define a unified framework for computing the subtree kernel from ordered or unordered trees, that is particularly suitable for tuning parameters. We show through eight real data classification problems the great efficiency of our approach, in particular for small datasets, which also states the high importance of the weight function. Finally, a visualization tool of the significant features is derived.Comment: 36 page

Rewriting Declarative Query Languages

Queries against databases are formulated in declarative languages. Examples are the relational query language SQL and XPath or XQuery for querying data stored in XML. Using a declarative query language, the querist does not need to know about or decide on anything about the actual strategy a system uses to answer the query. Instead, the system can freely choose among the algorithms it employs to answer a query. Predominantly, query processing in the relational context is accomplished using a relational algebra. To this end, the query is translated into a logical algebra. The algebra consists of logical operators which facilitate the application of various optimization techniques. For example, logical algebra expressions can be rewritten in order to yield more efficient expressions. In order to query XML data, XPath and XQuery have been developed. Both are declarative query languages and, hence, can benefit from powerful optimizations. For instance, they could be evaluated using an algebraic framework. However, in general, the existing approaches are not directly utilizable for XML query processing. This thesis has two goals. The first goal is to overcome the above-mentioned misfits of XML query processing, making it ready for industrial-strength settings. Specifically, we develop an algebraic framework that is designed for the efficient evaluation of XPath and XQuery. To this end, we define an order-aware logical algebra and a translation of XPath into this algebra. Furthermore, based on the resulting algebraic expressions, we present rewrites in order to speed up the execution of such queries. The second goal is to investigate rewriting techniques in the relational context. To this end, we present rewrites based on algebraic equivalences that unnest nested SQL queries with disjunctions. Specifically, we present equivalences for unnesting algebraic expressions with bypass operators to handle disjunctive linking and correlation. Our approach can be applied to quantified table subqueries as well as scalar subqueries. For all our results, we present experiments that demonstrate the effectiveness of the developed approaches

Modelling molecular networks: relationships between different formalisms and levels of details

This document is the deliverable 1.3 of French ANR CALAMAR. It presents a study of different formalisms used for modelling and analyzing large molecular regulation networks, their formal links, in terms of mutual encodings and of abstractions, and the corresponding levels of detail captured

Online Analysis of Dynamic Streaming Data

Die Arbeit zum Thema "Online Analysis of Dynamic Streaming Data" beschäftigt sich mit der Distanzmessung dynamischer, semistrukturierter Daten in kontinuierlichen Datenströmen um Analysen auf diesen Datenstrukturen bereits zur Laufzeit zu ermöglichen. Hierzu wird eine Formalisierung zur Distanzberechnung für statische und dynamische Bäume eingeführt und durch eine explizite Betrachtung der Dynamik von Attributen einzelner Knoten der Bäume ergänzt. Die Echtzeitanalyse basierend auf der Distanzmessung wird durch ein dichte-basiertes Clustering ergänzt, um eine Anwendung des Clustering, einer Klassifikation, aber auch einer Anomalieerkennung zu demonstrieren. Die Ergebnisse dieser Arbeit basieren auf einer theoretischen Analyse der eingeführten Formalisierung von Distanzmessungen für dynamische Bäume. Diese Analysen werden unterlegt mit empirischen Messungen auf Basis von Monitoring-Daten von Batchjobs aus dem Batchsystem des GridKa Daten- und Rechenzentrums. Die Evaluation der vorgeschlagenen Formalisierung sowie der darauf aufbauenden Echtzeitanalysemethoden zeigen die Effizienz und Skalierbarkeit des Verfahrens. Zudem wird gezeigt, dass die Betrachtung von Attributen und Attribut-Statistiken von besonderer Bedeutung für die Qualität der Ergebnisse von Analysen dynamischer, semistrukturierter Daten ist. Außerdem zeigt die Evaluation, dass die Qualität der Ergebnisse durch eine unabhängige Kombination mehrerer Distanzen weiter verbessert werden kann. Insbesondere wird durch die Ergebnisse dieser Arbeit die Analyse sich über die Zeit verändernder Daten ermöglicht

The Weight Function in the Subtree Kernel is Decisive

Tree data are ubiquitous because they model a large variety of situations, e.g., the architecture of plants, the secondary structure of RNA, or the hierarchy of XML files. Nevertheless, the analysis of these non-Euclidean data is difficul per se. In this paper, we focus on the subtree kernel that is a convolution kernel for tree data introduced by Vishwanathan and Smola in the early 2000's. More precisely, we investigate the influence of the weight function from a theoretical perspective and in real data applications. We establish on a 2-classes stochastic model that the performance of the subtree kernel is improved when the weight of leaves vanishes, which motivates the definition of a new weight function, learned from the data and not fixed by the user as usually done. To this end, we define a unified framework for computing the subtree kernel from ordered or unordered trees, that is particularly suitable for tuning parameters. We show through two real data classification problems the great efficiency of our approach, in particular with respect to the ones considered in the literature, which also states the high importance of the weight function. Finally, a visualization tool of the significant features is derived.Comment: 28 page

Machine Learning-Based Ontology Mapping Tool to Enable Interoperability in Coastal Sensor Networks

In today’s world, ontologies are being widely used for data integration tasks and solving information heterogeneity problems on the web because of their capability in providing explicit meaning to the information. The growing need to resolve the heterogeneities between different information systems within a domain of interest has led to the rapid development of individual ontologies by different organizations. These ontologies designed for a particular task could be a unique representation of their project needs. Thus, integrating distributed and heterogeneous ontologies by finding semantic correspondences between their concepts has become the key point to achieve interoperability among different representations. In this thesis, an advanced instance-based ontology matching algorithm has been proposed to enable data integration tasks in ocean sensor networks, whose data are highly heterogeneous in syntax, structure, and semantics. This provides a solution to the ontology mapping problem in such systems based on machine-learning methods and string-based methods