Speeding up RDF aggregate discovery through sampling

International audienceRDF graphs can be large and complex; finding out interesting information within them is challenging. One easy method for users to discover such graphs is to be shown interesting aggregates (un-der the form of two-dimensional graphs, i.e., bar charts), where interestingness is evaluated through statistics criteria. Dagger [5] pioneered this approach, however its is quite inefficient, in particular due to the need to evaluate numerous, expensive aggregation queries. In this work, we describe Dagger + , which builds upon Dagger and leverages sampling to speed up the evaluation of potentially interesting aggregates. We show that Dagger + achieves very significant execution time reductions, while reaching results very close to those of the original, less efficient system

Towards a Linked Semantic Web: Precisely, Comprehensively and Scalably Linking Heterogeneous Data in the Semantic Web

The amount of Semantic Web data is growing rapidly today. Individual users, academic institutions and businesses have already published and are continuing to publish their data in Semantic Web standards, such as RDF and OWL. Due to the decentralized nature of the Semantic Web, the same real world entity may be described in various data sources with different ontologies and assigned syntactically distinct identifiers. Furthermore, data published by each individual publisher may not be complete. This situation makes it difficult for end users to consume the available Semantic Web data effectively. In order to facilitate data utilization and consumption in the Semantic Web, without compromising the freedom of people to publish their data, one critical problem is to appropriately interlink such heterogeneous data. This interlinking process is sometimes referred to as Entity Coreference, i.e., finding which identifiers refer to the same real world entity. In the Semantic Web, the owl:sameAs predicate is used to link two equivalent (coreferent) ontology instances. An important question is where these owl:sameAs links come from. Although manual interlinking is possible on small scales, when dealing with large-scale datasets (e.g., millions of ontology instances), automated linking becomes necessary. This dissertation summarizes contributions to several aspects of entity coreference research in the Semantic Web. First of all, by developing the EPWNG algorithm, we advance the performance of the state-of-the-art by 1% to 4%. EPWNG finds coreferent ontology instances from different data sources by comparing every pair of instances and focuses on achieving high precision and recall by appropriately collecting and utilizing instance context information domain-independently. We further propose a sampling and utility function based context pruning technique, which provides a runtime speedup factor of 30 to 75. Furthermore, we develop an on-the-fly candidate selection algorithm, P-EPWNG, that enables the coreference process to run 2 to 18 times faster than the state-of-the-art on up to 1 million instances while only making a small sacrifice in the coreference F1-scores. This is achieved by utilizing the matching histories of the instances to prune instance pairs that are not likely to be coreferent. We also propose Offline, another candidate selection algorithm, that not only provides similar runtime speedup to P-EPWNG but also helps to achieve higher candidate selection and coreference F1-scores due to its more accurate filtering of true negatives. Different from P-EPWNG, Offline pre-selects candidate pairs by only comparing their partial context information that is selected in an unsupervised, automatic and domain-independent manner.In order to be able to handle really heterogeneous datasets, a mechanism for automatically determining predicate comparability is proposed. Combing this property matching approach with EPWNG and Offline, our system outperforms state-of-the-art algorithms on the 2012 Billion Triples Challenge dataset on up to 2 million instances for both coreference F1-score and runtime. An interesting project, where we apply the EPWNG algorithm for assisting cervical cancer screening, is discussed in detail. By applying our algorithm to a combination of different patient clinical test results and biographic information, we achieve higher accuracy compared to its ablations. We end this dissertation with the discussion of promising and challenging future work

ExpRalytics: analyse expressive et efficace de graphes RDF

Large (Linked) Open Data are increasingly shared as RDF graphs today. However, such data does not yet reach its full potential in terms of sharing and reuse. We provide new methods to meaningfully summarize data graphs, with a particular focus on RDF graphs. One class of tools for this task are structural RDF graph summaries, which allow users to grasp the different connections between RDF graph nodes. To this end, we introduce our novel RDFQuotient tool that finds compact yet informative RDF graph summaries that can serve as first-sight visualizations of an RDF graph’s structure. We also consider the problem of automatically identifying the k most interesting aggregate queries that can be evaluated on an RDF graph, given an integer k and a user-specified interestingness function. Aggregate queries are routinely used to learn insights from relational data warehouses, and some prior research has addressed the problem of automatically recommending interesting aggregate queries.Les données ouvertes sont souvent partagées sous la forme de graphes RDF, qui sont une incarnation du principe Linked Open Data (données ouvertes liées). De telles données n’ont toutefois pas atteint leur entier potentiel d’utilisation et de partage. L’obstacle pour ce faire réside principalement au niveau de la capacité des utilisateurs à explorer, découvrir et saisir le contenu et des graphes RDF; cette tâche est complexe car les graphes sont naturellement hétérogènes, et peuvent être à la fois volumineux et complexes. Nous proposons de nouvelles méthodes pour résumer de grands graphes de données, avec un accent particulier sur les graphes RDF. A cette fin, nous avons proposé une nouvelle approché pour la construction de résumés structurels de graphes RDF, à savoir RDFQuotient.Nous considérons aussi le problème d’identifier automatiquement les requêtes d’agrégation les plus intéressantes qui peuvent être évaluées sur un graphe RDF

Compact semantic representations of observational data

Das Konzept des Internet der Dinge (IoT) ist in mehreren Bereichen weit verbreitet, damit Geräte miteinander interagieren und bestimmte Aufgaben erfüllen können. IoT-Geräte umfassen verschiedene Konzepte, z.B. Sensoren, Programme, Computer und Aktoren. IoT-Geräte beobachten ihre Umgebung, um Informationen zu sammeln und miteinander zu kommunizieren, um gemeinsame Aufgaben zu erfüllen. Diese Vorrichtungen erzeugen kontinuierlich Beobachtungsdatenströme, die zu historischen Daten werden, wenn diese Beobachtungen gespeichert werden. Durch die Zunahme der Anzahl der IoT-Geräte wird eine große Menge an Streaming- und historischen Beobachtungsdaten erzeugt. Darüber hinaus wurden mehrere Ontologien, wie die Semantic Sensor Network (SSN) Ontologie, für die semantische Annotation von Beobachtungsdaten vorgeschlagen - entweder Stream oder historisch. Das Resource Description Framework (RDF) ist ein weit verbreitetes Datenmodell zur semantischen Beschreibung der Datensätze. Semantische Annotation bietet ein gemeinsames Verständnis für die Verarbeitung und Analyse von Beobachtungsdaten. Durch das Hinzufügen von Semantik wird die Datengröße jedoch weiter erhöht, insbesondere wenn die Beobachtungswerte von mehreren Geräten redundant erfasst werden. So können beispielsweise mehrere Sensoren Beobachtungen erzeugen, die den gleichen Wert für die relative Luftfeuchtigkeit in einem bestimmten Zeitstempel und einer bestimmten Stadt anzeigen. Diese Situation kann in einem RDF-Diagramm mit vier RDF-Tripel dargestellt werden, wobei Beobachtungen als Tripel dargestellt werden, die das beobachtete Phänomen, die Maßeinheit, den Zeitstempel und die Koordinaten beschreiben. Die RDF-Tripel einer Beobachtung sind mit dem gleichen Thema verbunden. Solche Beobachtungen teilen sich die gleichen Objekte in einer bestimmten Gruppe von Eigenschaften, d.h. sie entsprechen einem Sternmuster, das sich aus diesen Eigenschaften und Objekten zusammensetzt. Wenn die Anzahl dieser Subjektentitäten oder Eigenschaften in diesen Sternmustern groß ist, wird die Größe des RDF-Diagramms und der Abfrageverarbeitung negativ beeinflusst; wir bezeichnen diese Sternmuster als häufige Sternmuster. Diese Arbeit befasst sich mit dem Problem der Identifizierung von häufigen Sternenmustern in RDF-Diagrammen und entwickelt Berechnungsmethoden, um häufige Sternmuster zu identifizieren und ein faktorisiertes RDF-Diagramm zu erzeugen, bei dem die Anzahl der häufigen Sternmuster minimiert wird. Darüber hinaus wenden wir diese faktorisierten RDF-Darstellungen über historische semantische Sensordaten an, die mit der SSN-Ontologie beschrieben werden, und präsentieren tabellarische Darstellungen von faktorisierten semantischen Sensordaten, um Big Data-Frameworks auszunutzen. Darüber hinaus entwickelt diese Arbeit einen wissensbasierten Ansatz namens DESERT, der in der Lage ist, bei Bedarf Streamdaten zu faktorisieren und semantisch anzureichern (on-Demand factorizE and Semantically Enrich stReam daTa). Wir bewerten die Leistung unserer vorgeschlagenen Techniken anhand mehrerer RDF-Diagramm-Benchmarks. Die Ergebnisse zeigen, dass unsere Techniken in der Lage sind, häufige Sternmuster effektiv und effizient zu erkennen, und die Größe der RDF-Diagramme kann um bis zu 66,56% reduziert werden, während die im ursprünglichen RDF-Diagramm dargestellten Daten erhalten bleiben. Darüber hinaus sind die kompakten Darstellungen in der Lage, die Anzahl der RDF-Tripel um mindestens 53,25% in historischen Beobachtungsdaten und bis zu 94,34% in Beobachtungsdatenströmen zu reduzieren. Darüber hinaus reduzieren die Ergebnisse der Anfrageauswertung über historische Daten die Ausführungszeit der Anfrage um bis zu drei Größenordnungen. In Beobachtungsdatenströmen wird die Größe der zur Beantwortung der Anfrage benötigten Daten um 92,53% reduziert, wodurch der Speicherplatzbedarf zur Beantwortung der Anfragen reduziert wird. Diese Ergebnisse belegen, dass IoT-Daten mit den vorgeschlagenen kompakten Darstellungen effizient dargestellt werden können, wodurch die negativen Auswirkungen semantischer Annotationen auf das IoT-Datenmanagement reduziert werden.The Internet of Things (IoT) concept has been widely adopted in several domains to enable devices to interact with each other and perform certain tasks. IoT devices encompass different concepts, e.g., sensors, programs, computers, and actuators. IoT devices observe their surroundings to collect information and communicate with each other in order to perform mutual tasks. These devices continuously generate observational data streams, which become historical data when these observations are stored. Due to an increase in the number of IoT devices, a large amount of streaming and historical observational data is being produced. Moreover, several ontologies, like the Semantic Sensor Network (SSN) Ontology, have been proposed for semantic annotation of observational data-either streams or historical. Resource Description Framework (RDF) is widely adopted data model to semantically describe the datasets. Semantic annotation provides a shared understanding for processing and analysis of observational data. However, adding semantics, further increases the data size especially when the observation values are redundantly sensed by several devices. For example, several sensors can generate observations indicating the same value for relative humidity in a given timestamp and city. This situation can be represented in an RDF graph using four RDF triples where observations are represented as triples that describe the observed phenomenon, the unit of measurement, the timestamp, and the coordinates. The RDF triples of an observation are associated with the same subject. Such observations share the same objects in a certain group of properties, i.e., they match star patterns composed of these properties and objects. In case the number of these subject entities or properties in these star patterns is large, the size of the RDF graph and query processing are negatively impacted; we refer these star patterns as frequent star patterns. This thesis addresses the problem of identifying frequent star patterns in RDF graphs and develop computational methods to identify frequent star patterns and generate a factorized RDF graph where the number of frequent star patterns is minimized. Furthermore, we apply these factorized RDF representations over historical semantic sensor data described using the SSN ontology and present tabular-based representations of factorized semantic sensor data in order to exploit Big Data frameworks. In addition, this thesis devises a knowledge-driven approach named DESERT that is able to on-Demand factorizE and Semantically Enrich stReam daTa. We evaluate the performance of our proposed techniques on several RDF graph benchmarks. The outcomes show that our techniques are able to effectively and efficiently detect frequent star patterns and RDF graph size can be reduced by up to 66.56% while data represented in the original RDF graph is preserved. Moreover, the compact representations are able to reduce the number of RDF triples by at least 53.25% in historical observational data and upto 94.34% in observational data streams. Additionally, query evaluation results over historical data reduce query execution time by up to three orders of magnitude. In observational data streams the size of the data required to answer the query is reduced by 92.53% reducing the memory space requirements to answer the queries. These results provide evidence that IoT data can be efficiently represented using the proposed compact representations, reducing thus, the negative impact that semantic annotations may have on IoT data management

Molecular Simulation Studies of Chromonic Mesogens in Aqueous Solution

This thesis focuses on understanding the aggregation behaviour of lyotropic chromonic liquid crystals in aqueous solution. Molecular simulation methods are used to provide structural and thermodynamic information on the self-assembly of chromonic mesogens, and the results used to re-interpret data from previous experimental studies of these systems. Extensive atomistic level molecular dynamic simulations have been performed on three chromonic dyes in solution: 5,5'-dimethyoxy-bis-(3,3'-di-sulphopropyl)- thiacyanine triethylammonium salt (Dye A), 5,5'-dichloro-bis-(3,3'-di-sulphopropyl)- thiacyanine triethylammonium salt (Dye B), and Bordeaux dye. The results are compared to key experimental data, such as X-ray scattering and cross-sectional areas and aggregation free energies. Previously suggested chromonic aggregation models, such as a double-width column and a brickwork layer structure, have been discounted based on the simulation results. Instead the simulations of dyes A and B demonstrate an anti-parallel stacking arrangement providing columns in which solubilizing sulphonate groups lie on alternate sides of the column as the column is traversed. In addition, a new type of chromonic smectic layered phase is predicted for these molecules. For dye A, a novel chiral column structure is seen within isolated columns in isotropic solution. For Bordeaux dye a stable single-molecule column is seen, along with a number of meta-stable structures including a double-width column in which two single-molecule columns are linked via a salt bridge. In an attempt to simulate larger time and length scales, two bottom-up coarsegraining techniques, iterative Boltzmann inversion (IBI) and force matching (FM), were tested on simple hexane/water systems and then applied to Dye A. Both of these methods proved to be largely unsuccessful in reproducing the same aggregation behaviour seen in the atomistic simulation work

Instance-Based Lossless Summarization of Knowledge Graph With Optimized Triples and Corrections (IBA-OTC)

Knowledge graph (KG) summarization facilitates efficient information retrieval for exploring complex structural data. For fast information retrieval, it requires processing on redundant data. However, it necessitates the completion of information in a summary graph. It also saves computational time during data retrieval, storage space, in-memory visualization, and preserving structure after summarization. State-of-the-art approaches summarize a given KG by preserving its structure at the cost of information loss. Additionally, the approaches not preserving the underlying structure, compromise the summarization ratio by focusing only on the compression of specific regions. In this way, these approaches either miss preserving the original facts or the wrong prediction of inferred information. To solve these problems, we present a novel framework for generating a lossless summary by preserving the structure through super signatures and their corresponding corrections. The proposed approach summarizes only the naturally overlapped instances while maintaining its information and preserving the underlying Resource Description Framework RDF graph. The resultant summary is composed of triples with positive, negative, and star corrections that are optimized by the smart calling of two novel functions namely merge and disperse . To evaluate the effectiveness of our proposed approach, we perform experiments on nine publicly available real-world knowledge graphs and obtain a better summarization ratio than state-of-the-art approaches by a margin of 10% to 30% with achieving its completeness, correctness, and compactness. In this way, the retrieval of common events and groups by queries is accelerated in the resultant graph

A Survey on Graph Kernels

Graph kernels have become an established and widely-used technique for solving classification tasks on graphs. This survey gives a comprehensive overview of techniques for kernel-based graph classification developed in the past 15 years. We describe and categorize graph kernels based on properties inherent to their design, such as the nature of their extracted graph features, their method of computation and their applicability to problems in practice. In an extensive experimental evaluation, we study the classification accuracy of a large suite of graph kernels on established benchmarks as well as new datasets. We compare the performance of popular kernels with several baseline methods and study the effect of applying a Gaussian RBF kernel to the metric induced by a graph kernel. In doing so, we find that simple baselines become competitive after this transformation on some datasets. Moreover, we study the extent to which existing graph kernels agree in their predictions (and prediction errors) and obtain a data-driven categorization of kernels as result. Finally, based on our experimental results, we derive a practitioner's guide to kernel-based graph classification

Deployment and Operation of Complex Software in Heterogeneous Execution Environments

This open access book provides an overview of the work developed within the SODALITE project, which aims at facilitating the deployment and operation of distributed software on top of heterogeneous infrastructures, including cloud, HPC and edge resources. The experts participating in the project describe how SODALITE works and how it can be exploited by end users. While multiple languages and tools are available in the literature to support DevOps teams in the automation of deployment and operation steps, still these activities require specific know-how and skills that cannot be found in average teams. The SODALITE framework tackles this problem by offering modelling and smart editing features to allow those we call Application Ops Experts to work without knowing low level details about the adopted, potentially heterogeneous, infrastructures. The framework offers also mechanisms to verify the quality of the defined models, generate the corresponding executable infrastructural code, automatically wrap application components within proper execution containers, orchestrate all activities concerned with deployment and operation of all system components, and support on-the-fly self-adaptation and refactoring