Top-K Query Processing in Edge-Labeled Graph Data

Edge-labeled graphs have proliferated rapidly over the last decade due to the increased popularity of social networks and the Semantic Web. In social networks, relationships between people are represented by edges and each edge is labeled with a semantic annotation. Hence, a huge single graph can express many different relationships between entities. The Semantic Web represents each single fragment of knowledge as a triple (subject, predicate, object), which is conceptually identical to an edge from subject to object labeled with predicates. A set of triples constitutes an edge-labeled graph on which knowledge inference is performed. Subgraph matching has been extensively used as a query language for patterns in the context of edge-labeled graphs. For example, in social networks, users can specify a subgraph matching query to find all people that have certain neighborhood relationships. Heavily used fragments of the SPARQL query language for the Semantic Web and graph queries of other graph DBMS can also be viewed as subgraph matching over large graphs. Though subgraph matching has been extensively studied as a query paradigm in the Semantic Web and in social networks, a user can get a large number of answers in response to a query. These answers can be shown to the user in accordance with an importance ranking. In this thesis proposal, we present four different scoring models along with scalable algorithms to find the top-k answers via a suite of intelligent pruning techniques. The suggested models consist of a practically important subset of the SPARQL query language augmented with some additional useful features. The first model called Substitution Importance Query (SIQ) identifies the top-k answers whose scores are calculated from matched vertices' properties in each answer in accordance with a user-specified notion of importance. The second model called Vertex Importance Query (VIQ) identifies important vertices in accordance with a user-defined scoring method that builds on top of various subgraphs articulated by the user. Approximate Importance Query (AIQ), our third model, allows partial and inexact matchings and returns top-k of them with a user-specified approximation terms and scoring functions. In the fourth model called Probabilistic Importance Query (PIQ), a query consists of several sub-blocks: one mandatory block that must be mapped and other blocks that can be opportunistically mapped. The probability is calculated from various aspects of answers such as the number of mapped blocks, vertices' properties in each block and so on and the most top-k probable answers are returned. An important distinguishing feature of our work is that we allow the user a huge amount of freedom in specifying: (i) what pattern and approximation he considers important, (ii) how to score answers - irrespective of whether they are vertices or substitution, and (iii) how to combine and aggregate scores generated by multiple patterns and/or multiple substitutions. Because so much power is given to the user, indexing is more challenging than in situations where additional restrictions are imposed on the queries the user can ask. The proposed algorithms for the first model can also be used for answering SPARQL queries with ORDER BY and LIMIT, and the method for the second model also works for SPARQL queries with GROUP BY, ORDER BY and LIMIT. We test our algorithms on multiple real-world graph databases, showing that our algorithms are far more efficient than popular triple stores.

Semantic features for context organization

In recent years the technological world has grown by incorporating billions of small sensing devices, collecting and sharing real-world information. As the number of such devices grows, it becomes increasingly difficult to manage all these new information sources. There is no uniform way to share, process and understand context information. In previous publications we discussed efficient ways to organize context information that is independent of structure and representation. However, our previous solution suffers from semantic sensitivity. In this paper we review semantic methods that can be used to minimize this issue, and propose an unsupervised semantic similarity solution that combines distributional profiles with public web services. Our solution was evaluated against Miller-Charles dataset, achieving a correlation of 0.6.

Usefulness of social tagging in organizing and providing access to the web: An analysis of indexing consistency and quality

This dissertation research points out major challenging problems with current Knowledge Organization (KO) systems, such as subject gateways or web directories: (1) the current systems use traditional knowledge organization systems based on controlled vocabulary which is not very well suited to web resources, and (2) information is organized by professionals not by users, which means it does not reflect intuitively and instantaneously expressed users’ current needs. In order to explore users’ needs, I examined social tags which are user-generated uncontrolled vocabulary. As investment in professionally-developed subject gateways and web directories diminishes (support for both BUBL and Intute, examined in this study, is being discontinued), understanding characteristics of social tagging becomes even more critical. Several researchers have discussed social tagging behavior and its usefulness for classification or retrieval; however, further research is needed to qualitatively and quantitatively investigate social tagging in order to verify its quality and benefit. This research particularly examined the indexing consistency of social tagging in comparison to professional indexing to examine the quality and efficacy of tagging. The data analysis was divided into three phases: analysis of indexing consistency, analysis of tagging effectiveness, and analysis of tag attributes. Most indexing consistency studies have been conducted with a small number of professional indexers, and they tended to exclude users. Furthermore, the studies mainly have focused on physical library collections. This dissertation research bridged these gaps by (1) extending the scope of resources to various web documents indexed by users and (2) employing the Information Retrieval (IR) Vector Space Model (VSM) - based indexing consistency method since it is suitable for dealing with a large number of indexers. As a second phase, an analysis of tagging effectiveness with tagging exhaustivity and tag specificity was conducted to ameliorate the drawbacks of consistency analysis based on only the quantitative measures of vocabulary matching. Finally, to investigate tagging pattern and behaviors, a content analysis on tag attributes was conducted based on the FRBR model. The findings revealed that there was greater consistency over all subjects among taggers compared to that for two groups of professionals. The analysis of tagging exhaustivity and tag specificity in relation to tagging effectiveness was conducted to ameliorate difficulties associated with limitations in the analysis of indexing consistency based on only the quantitative measures of vocabulary matching. Examination of exhaustivity and specificity of social tags provided insights into particular characteristics of tagging behavior and its variation across subjects. To further investigate the quality of tags, a Latent Semantic Analysis (LSA) was conducted to determine to what extent tags are conceptually related to professionals’ keywords and it was found that tags of higher specificity tended to have a higher semantic relatedness to professionals’ keywords. This leads to the conclusion that the term’s power as a differentiator is related to its semantic relatedness to documents. The findings on tag attributes identified the important bibliographic attributes of tags beyond describing subjects or topics of a document. The findings also showed that tags have essential attributes matching those defined in FRBR. Furthermore, in terms of specific subject areas, the findings originally identified that taggers exhibited different tagging behaviors representing distinctive features and tendencies on web documents characterizing digital heterogeneous media resources. These results have led to the conclusion that there should be an increased awareness of diverse user needs by subject in order to improve metadata in practical applications. This dissertation research is the first necessary step to utilize social tagging in digital information organization by verifying the quality and efficacy of social tagging. This dissertation research combined both quantitative (statistics) and qualitative (content analysis using FRBR) approaches to vocabulary analysis of tags which provided a more complete examination of the quality of tags. Through the detailed analysis of tag properties undertaken in this dissertation, we have a clearer understanding of the extent to which social tagging can be used to replace (and in some cases to improve upon) professional indexing.

'An Artificial Immune System as a Recommender System for Web Sites'

Artificial Immune Systems have been used successfully to build recommender systems for film databases. In this research, an attempt is made to extend this idea to web site recommendation. A collection of more than 1000 individuals' web profiles (alternatively called preferences / favourites / bookmarks file) will be used. URLs will be classified using the DMOZ (Directory Mozilla) database of the Open Directory Project as our ontology. This will then be used as the data for the Artificial Immune Systems rather than the actual addresses. The first attempt will involve using a simple classification code number coupled with the number of pages within that classification code. However, this implementation does not make use of the hierarchical tree-like structure of DMOZ. Consideration will then be given to the construction of a similarity measure for web profiles that makes use of this hierarchical information to build a better-informed Artificial Immune System.

EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.

Una aproximación basada en Linked Data para la detección de potenciales redes de colaboración científica a partir de la anotación semántica de producción científica: Piloto aplicado con producción científica de investigadores ecuatorianos

En este documento se propone un marco de trabajo basado en tecnologías de la Web Semántica para detectar potenciales redes de colaboración, mediante el enriquecimiento semántico de artículos científicos producidos por investigadores que publican con afiliaciones ecuatorianas. El marco de trabajo se describe a través de un ciclo de publicación de datos enlazados. Como alcance se consideraron publicaciones que tienen al menos un autor con afiliación ecuatoriana. Las redes de colaboración detectadas son un insumo importante para fortalecer los esfuerzos del gobierno ecuatoriano y las autoridades universitarias del país, priorizar los esfuerzos y recursos invertidos en investigación y determinar la pertinencia o coherencia de los programas de investigación.

Sistema colaborativo para monitoramento remoto de equipamentos biomédicos para a videolaparoscopia através do framework web-engineering e o padrão MVC sistema vera-3C

Dissertação (mestrado)—Universidade de Brasília, Faculdade de Tecnologia, Departamento de Engenharia Mecânica, 2015.

Adicionando temporalidade à linguagem OWL 2 : um estudo a partir da linguagem tOWL e sua decibilidade

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Exatas, Departamento de Ciência da Computação, Programa de Pós-Graducação em Informática, 2016.

POPLAR GENE EXPRESSION DATA ANALYSIS PIPELINES

Analyzing large-scale gene expression data is a labor-intensive and time-consuming process. To make data analysis easier, we developed a set of pipelines for rapid processing and analysis poplar gene expression data for knowledge discovery. Of all pipelines developed, differentially expressed genes (DEGs) pipeline is the one designed to identify biologically important genes that are differentially expressed in one of multiple time points for conditions. Pathway analysis pipeline was designed to identify the differentially expression metabolic pathways. Protein domain enrichment pipeline can identify the enriched protein domains present in the DEGs. Finally, Gene Ontology (GO) enrichment analysis pipeline was developed to identify the enriched GO terms in the DEGs. Our pipeline tools can analyze both microarray gene data and high-throughput gene data. These two types of data are obtained by two different technologies. A microarray technology is to measure gene expression levels via microarray chips, a collection of microscopic DNA spots attached to a solid (glass) surface, whereas high throughput sequencing, also called as the next-generation sequencing, is a new technology to measure gene expression levels by directly sequencing mRNAs, and obtaining each mRNA’s copy numbers in cells or tissues. We also developed a web portal (http://sys.bio.mtu.edu/) to make all pipelines available to public to facilitate users to analyze their gene expression data. In addition to the analyses mentioned above, it can also perform GO hierarchy analysis, i.e. construct GO trees using a list of GO terms as an input.

DATA DRIVEN INTELLIGENT AGENT NETWORKS FOR ADAPTIVE MONITORING AND CONTROL

To analyze the characteristics and predict the dynamic behaviors of complex systems over time, comprehensive research to enable the development of systems that can intelligently adapt to the evolving conditions and infer new knowledge with algorithms that are not predesigned is crucially needed. This dissertation research studies the integration of the techniques and methodologies resulted from the fields of pattern recognition, intelligent agents, artificial immune systems, and distributed computing platforms, to create technologies that can more accurately describe and control the dynamics of real-world complex systems. The need for such technologies is emerging in manufacturing, transportation, hazard mitigation, weather and climate prediction, homeland security, and emergency response. Motivated by the ability of mobile agents to dynamically incorporate additional computational and control algorithms into executing applications, mobile agent technology is employed in this research for the adaptive sensing and monitoring in a wireless sensor network. Mobile agents are software components that can travel from one computing platform to another in a network and carry programs and data states that are needed for performing the assigned tasks. To support the generation, migration, communication, and management of mobile monitoring agents, an embeddable mobile agent system (Mobile-C) is integrated with sensor nodes. Mobile monitoring agents visit distributed sensor nodes, read real-time sensor data, and perform anomaly detection using the equipped pattern recognition algorithms. The optimal control of agents is achieved by mimicking the adaptive immune response and the application of multi-objective optimization algorithms. The mobile agent approach provides potential to reduce the communication load and energy consumption in monitoring networks. The major research work of this dissertation project includes: (1) studying effective feature extraction methods for time series measurement data; (2) investigating the impact of the feature extraction methods and dissimilarity measures on the performance of pattern recognition; (3) researching the effects of environmental factors on the performance of pattern recognition; (4) integrating an embeddable mobile agent system with wireless sensor nodes; (5) optimizing agent generation and distribution using artificial immune system concept and multi-objective algorithms; (6) applying mobile agent technology and pattern recognition algorithms for adaptive structural health monitoring and driving cycle pattern recognition; (7) developing a web-based monitoring network to enable the visualization and analysis of real-time sensor data remotely. Techniques and algorithms developed in this dissertation project will contribute to research advances in networked distributed systems operating under changing environments.

RSLT: trasformazione di Open LinkedData in testi in linguaggio naturaletramite template dichiarativi

La diffusione del Semantic Web e di dati semantici in formato RDF, ha creato la necessità di un meccanismo di trasformazione di tali informazioni, semplici da interpretare per una macchina, in un linguaggio naturale, di facile comprensione per l'uomo. Nella dissertazione si discuterà delle soluzioni trovate in letteratura e, nel dettaglio, di RSLT, una libreria JavaScript che cerca di risolvere questo problema, consentendo la creazione di applicazioni web in grado di eseguire queste trasformazioni tramite template dichiarativi. Verranno illustrati, inoltre, tutti i cambiamenti e tutte le modi�che introdotte nella versione 1.1 della libreria, la cui nuova funzionalit�à principale �è il supporto a SPARQL 1.0.

Edoxaban versus enoxaparin–warfarin in patients undergoing cardioversion of atrial fibrillation (ENSURE-AF): a randomised, open-label, phase 3b trial

Background Edoxaban, an oral factor Xa inhibitor, is non-inferior for prevention of stroke and systemic embolism in patients with atrial fibrillation and is associated with less bleeding than well controlled warfarin therapy. Few safety data about edoxaban in patients undergoing electrical cardioversion are available. Methods We did a multicentre, prospective, randomised, open-label, blinded-endpoint evaluation trial in 19 countries with 239 sites comparing edoxaban 60 mg per day with enoxaparin–warfarin in patients undergoing electrical cardioversion of non-valvular atrial fibrillation. The dose of edoxaban was reduced to 30 mg per day if one or more factors (creatinine clearance 15–50 mL/min, low bodyweight [≤60 kg], or concomitant use of P-glycoprotein inhibitors) were present. Block randomisation (block size four)—stratified by cardioversion approach (transoesophageal echocardiography [TEE] or not), anticoagulant experience, selected edoxaban dose, and region—was done through a voice-web system. The primary efficacy endpoint was a composite of stroke, systemic embolic event, myocardial infarction, and cardiovascular mortality, analysed by intention to treat. The primary safety endpoint was major and clinically relevant non-major (CRNM) bleeding in patients who received at least one dose of study drug. Follow-up was 28 days on study drug after cardioversion plus 30 days to assess safety. This trial is registered with ClinicalTrials.gov, number NCT02072434. Findings Between March 25, 2014, and Oct 28, 2015, 2199 patients were enrolled and randomly assigned to receive edoxaban (n=1095) or enoxaparin–warfarin (n=1104). The mean age was 64 years (SD 10·54) and mean CHA2DS2-VASc score was 2·6 (SD 1·4). Mean time in therapeutic range on warfarin was 70·8% (SD 27·4). The primary efficacy endpoint occurred in five (<1%) patients in the edoxaban group versus 11 (1%) in the enoxaparin–warfarin group (odds ratio [OR] 0·46, 95% CI 0·12–1·43). The primary safety endpoint occurred in 16 (1%) of 1067 patients given edoxaban versus 11 (1%) of 1082 patients given enoxaparin–warfarin (OR 1·48, 95% CI 0·64–3·55). The results were independent of the TEE-guided strategy and anticoagulation status. Interpretation ENSURE-AF is the largest prospective randomised clinical trial of anticoagulation for cardioversion of patients with non-valvular atrial fibrillation. Rates of major and CRNM bleeding and thromboembolism were low in the two treatment groups. Funding Daiichi Sankyo provided financial support for the study. © 2016 Elsevier Ltd

URIs and Intertextuality: Incumbent Philosophical Commitments in the Development of the Semantic Web

Examines two commitments inherent in Resource Description Framework (RDF): intertextuality and rationalism. After introducing how rationalism has been studied in knowledge organization, this paper then introduces the concept of bracketed-rationalism. This paper closes with a discussion of ramifications of intertextuality and bracketed rationalism on evaluation of RDF.