Grid-based semantic integration of heterogeneous data resources: Implementation on a HealthGrid

This thesis was submitted for the degree of Doctor of Philosophy and was awarded by Brunel University.The semantic integration of geographically distributed and heterogeneous data resources still remains a key challenge in Grid infrastructures. Today's mainstream Grid technologies hold the promise to meet this challenge in a systematic manner, making data applications more scalable and manageable. The thesis conducts a thorough investigation of the problem, the state of the art, and the related technologies, and proposes an Architecture for Semantic Integration of Data Sources (ASIDS) addressing the semantic heterogeneity issue. It defines a simple mechanism for the interoperability of heterogeneous data sources in order to extract or discover information regardless of their different semantics. The constituent technologies of this architecture include Globus Toolkit (GT4) and OGSA-DAI (Open Grid Service Architecture Data Integration and Access) alongside other web services technologies such as XML (Extensive Markup Language). To show this, the ASIDS architecture was implemented and tested in a realistic setting by building an exemplar application prototype on a HealthGrid (pilot implementation). The study followed an empirical research methodology and was informed by extensive literature surveys and a critical analysis of the relevant technologies and their synergies. The two literature reviews, together with the analysis of the technology background, have provided a good overview of the current Grid and HealthGrid landscape, produced some valuable taxonomies, explored new paths by integrating technologies, and more importantly illuminated the problem and guided the research process towards a promising solution. Yet the primary contribution of this research is an approach that uses contemporary Grid technologies for integrating heterogeneous data resources that have semantically different. data fields (attributes). It has been practically demonstrated (using a prototype HealthGrid) that discovery in semantically integrated distributed data sources can be feasible by using mainstream Grid technologies, which have been shown to have some Significant advantages over non-Grid based approaches

Quality of experience aware adaptive hypermedia system

The research reported in this thesis proposes, designs and tests a novel Quality of Experience Layer (QoE-layer) for the classic Adaptive Hypermedia Systems (AHS) architecture. Its goal is to improve the end-user perceived Quality of Service in different operational environments suitable for residential users. While the AHS’ main role of delivering personalised content is not altered, its functionality and performance is improved and thus the user satisfaction with the service provided. The QoE Layer takes into account multiple factors that affect Quality of Experience (QoE), such as Web components and network connection. It uses a novel Perceived Performance Model that takes into consideration a variety of performance metrics, in order to learn about the Web user operational environment characteristics, about changes in network connection and the consequences of these changes on the user’s quality of experience. This model also considers the user’s subjective opinion about his/her QoE, increasing its effectiveness and suggests strategies for tailoring Web content in order to improve QoE. The user related information is modelled using a stereotype-based technique that makes use of probability and distribution theory. The QoE-Layer has been assessed through both simulations and qualitative evaluation in the educational area (mainly distance learning), when users interact with the system in a low bit rate operational environment. The simulations have assessed “learning” and “adaptability” behaviour of the proposed layer in different and variable home connections when a learning task is performed. The correctness of Perceived Performance Model (PPM) suggestions, access time of the learning process and quantity of transmitted data were analysed. The results show that the QoE layer significantly improves the performance in terms of the access time of the learning process with a reduction in the quantity of data sent by using image compression and/or elimination. A visual quality assessment confirmed that this image quality reduction does not significantly affect the viewers’ perceived quality that was close to “good” perceptual level. For qualitative evaluation the QoE layer has been deployed on the open-source AHA! system. The goal of this evaluation was to compare the learning outcome, system usability and user satisfaction when AHA! and QoE-ware AHA systems were used. The assessment was performed in terms of learner achievement, learning performance and usability assessment. The results indicate that QoE-aware AHA system did not affect the learning outcome (the students have similar-learning achievements) but the learning performance was improved in terms of study time. Most significantly, QoE-aware AHA provides an important improvement in system usability as indicated by users’ opinion about their satisfaction related to QoE

Architectures and GPU-Based Parallelization for Online Bayesian Computational Statistics and Dynamic Modeling

Recent work demonstrates that coupling Bayesian computational statistics methods with dynamic models can facilitate the analysis of complex systems associated with diverse time series, including those involving social and behavioural dynamics. Particle Markov Chain Monte Carlo (PMCMC) methods constitute a particularly powerful class of Bayesian methods combining aspects of batch Markov Chain Monte Carlo (MCMC) and the sequential Monte Carlo method of Particle Filtering (PF). PMCMC can flexibly combine theory-capturing dynamic models with diverse empirical data. Online machine learning is a subcategory of machine learning algorithms characterized by sequential, incremental execution as new data arrives, which can give updated results and predictions with growing sequences of available incoming data. While many machine learning and statistical methods are adapted to online algorithms, PMCMC is one example of the many methods whose compatibility with and adaption to online learning remains unclear. In this thesis, I proposed a data-streaming solution supporting PF and PMCMC methods with dynamic epidemiological models and demonstrated several successful applications. By constructing an automated, easy-to-use streaming system, analytic applications and simulation models gain access to arriving real-time data to shorten the time gap between data and resulting model-supported insight. The well-defined architecture design emerging from the thesis would substantially expand traditional simulation models' potential by allowing such models to be offered as continually updated services. Contingent on sufficiently fast execution time, simulation models within this framework can consume the incoming empirical data in real-time and generate informative predictions on an ongoing basis as new data points arrive. In a second line of work, I investigated the platform's flexibility and capability by extending this system to support the use of a powerful class of PMCMC algorithms with dynamic models while ameliorating such algorithms' traditionally stiff performance limitations. Specifically, this work designed and implemented a GPU-enabled parallel version of a PMCMC method with dynamic simulation models. The resulting codebase readily has enabled researchers to adapt their models to the state-of-art statistical inference methods, and ensure that the computation-heavy PMCMC method can perform significant sampling between the successive arrival of each new data point. Investigating this method's impact with several realistic PMCMC application examples showed that GPU-based acceleration allows for up to 160x speedup compared to a corresponding CPU-based version not exploiting parallelism. The GPU accelerated PMCMC and the streaming processing system can complement each other, jointly providing researchers with a powerful toolset to greatly accelerate learning and securing additional insight from the high-velocity data increasingly prevalent within social and behavioural spheres. The design philosophy applied supported a platform with broad generalizability and potential for ready future extensions. The thesis discusses common barriers and difficulties in designing and implementing such systems and offers solutions to solve or mitigate them

Scalable, Data- intensive Network Computation

To enable groups of collaborating researchers at different locations to effectively share large datasets and investigate their spontaneous hypotheses on the fly, we are interested in de- veloping a distributed system that can be easily leveraged by a variety of data intensive applications. The system is composed of (i) a number of best effort logistical depots to en- able large-scale data sharing and in-network data processing, (ii) a set of end-to-end tools to effectively aggregate, manage and schedule a large number of network computations with attendant data movements, and (iii) a Distributed Hash Table (DHT) on top of the generic depot services for scalable data management. The logistical depot is extended by following the end-to-end principles and is modeled with a closed queuing network model. Its performance characteristics are studied by solving the steady state distributions of the model using local balance equations. The modeling results confirm that the wide area network is the performance bottleneck and running concurrent jobs can increase resource utilization and system throughput. As a novel contribution, techniques to effectively support resource demanding data- intensive applications using the ¯ne-grained depot services are developed. These techniques include instruction level scheduling of operations, dynamic co-scheduling of computation and replication, and adaptive workload control. Experiments in volume visualization have proved the effectiveness of these techniques. Due to the unique characteristic of data- intensive applications and our co-scheduling algorithm, a DHT is implemented on top of the basic storage and computation services. It demonstrates the potential of the Logistical Networking infrastructure to serve as a service creation platform

Grid-based semantic integration of heterogeneous data resources : implementation on a HealthGrid

The semantic integration of geographically distributed and heterogeneous data resources still remains a key challenge in Grid infrastructures. Today's mainstream Grid technologies hold the promise to meet this challenge in a systematic manner, making data applications more scalable and manageable. The thesis conducts a thorough investigation of the problem, the state of the art, and the related technologies, and proposes an Architecture for Semantic Integration of Data Sources (ASIDS) addressing the semantic heterogeneity issue. It defines a simple mechanism for the interoperability of heterogeneous data sources in order to extract or discover information regardless of their different semantics. The constituent technologies of this architecture include Globus Toolkit (GT4) and OGSA-DAI (Open Grid Service Architecture Data Integration and Access) alongside other web services technologies such as XML (Extensive Markup Language). To show this, the ASIDS architecture was implemented and tested in a realistic setting by building an exemplar application prototype on a HealthGrid (pilot implementation). The study followed an empirical research methodology and was informed by extensive literature surveys and a critical analysis of the relevant technologies and their synergies. The two literature reviews, together with the analysis of the technology background, have provided a good overview of the current Grid and HealthGrid landscape, produced some valuable taxonomies, explored new paths by integrating technologies, and more importantly illuminated the problem and guided the research process towards a promising solution. Yet the primary contribution of this research is an approach that uses contemporary Grid technologies for integrating heterogeneous data resources that have semantically different. data fields (attributes). It has been practically demonstrated (using a prototype HealthGrid) that discovery in semantically integrated distributed data sources can be feasible by using mainstream Grid technologies, which have been shown to have some Significant advantages over non-Grid based approaches.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Proceedings of the First PhD Symposium on Sustainable Ultrascale Computing Systems (NESUS PhD 2016)

Proceedings of the First PhD Symposium on Sustainable Ultrascale Computing Systems (NESUS PhD 2016) Timisoara, Romania. February 8-11, 2016.The PhD Symposium was a very good opportunity for the young researchers to share information and knowledge, to present their current research, and to discuss topics with other students in order to look for synergies and common research topics. The idea was very successful and the assessment made by the PhD Student was very good. It also helped to achieve one of the major goals of the NESUS Action: to establish an open European research network targeting sustainable solutions for ultrascale computing aiming at cross fertilization among HPC, large scale distributed systems, and big data management, training, contributing to glue disparate researchers working across different areas and provide a meeting ground for researchers in these separate areas to exchange ideas, to identify synergies, and to pursue common activities in research topics such as sustainable software solutions (applications and system software stack), data management, energy efficiency, and resilience.European Cooperation in Science and Technology. COS

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

Emergency Response Information System Interoperability: Development of Chemical Incident Response Data Model

Emergency response requires an efficient information supply chain for the smooth operations of intra- and inter-organizational emergency management processes. However, the breakdown of this information supply chain due to the lack of consistent data standards presents a significant problem. In this paper, we adopt a theory- driven novel approach to develop an XML-based data model that prescribes a comprehensive set of data standards (semantics and internal structures) for emergency management to better address the challenges of information interoperability. Actual documents currently being used in mitigating chemical emergencies from a large number of incidents are used in the analysis stage. The data model development is guided by Activity Theory and is validated through a RFC-like process used in standards development. This paper applies the standards to the real case of a chemical incident scenario. Further, it complies with the national leading initiatives in emergency standards (National Information Exchange Model