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PhD theses

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  1. Dataflows and Provenance: From Nested Relational Calculus to the Open Provenance Model

    Kwasnikowska, Natalia
    Excerpt from the introduction: ... A conceptual data model for dataflow repositories should offer a precise specification of the types of data (including the data flows themselves) stored in the repository, and of the relationships among them. Such a data model is important because it provides a formal framework that allows: • Analyzing, in a rigorous manner, the possibilities and limitations of dataflow repositories. • Comparing, again in a rigorous manner, the functionality of different existing systems. • Highlighting differences in meaning of common notions as used by different authors or in different systems, such as "workflow" , "provenance" ,...

  2. An Extensible Simulation Framework Supporting Physically-based Interactive Painting

    Van Laerhoven, Tom
    Since the introduction of computers, a lot of effort has gone into the research on applications that enable a user to create images for their artistic value. In case of interactive systems that try to provide a digital equivalent of the traditional painting process, however, most still produce images that appear too artificial and lack the \natural look" and complexity that can be found in real paintings. Especially capturing the ambient behavior of watery paints like watercolor, gouache and Oriental ink, which run, drip and diffuse, is a challenging task to perform in real-time. For this reason, artists still prefer...

  3. DNA and Databases: The Sticker Complex Model

    Gillis, Joris
    Desoxyribonucle¨ınezuur (DNA) is de drager van genetische informatie in grote en kleine organismen. Een DNA-streng is opgebouwd uit vier verschillende basisdeeltjes, nucleotiden of basen genoemd: A, C, T, en G (zie Figuur 1). Bindingen kunnen ontstaan tussen complementaire basen, A-T en C-G. Twee DNA-strengen die volledig gebonden zijn, vormen de beroemde dubbele helix. Het vormen van bindingen tussen complementaire basen wordt hybridizatie genoemd. Afhankelijk van de lengte en de omgevingsfactoren, kunnen twee niet perfect complementaire DNA-strengen toch binden. Bijvoorbeeld, DNAstrengen CCCACCC en GGGGGGG zijn niet perfect complementair, want basen A en G zijn niet complementair. Toch is het mogelijk dat...

  4. Declarative Networking: Models and Conjectures

    Ameloot, Tom
    Deze thesis gaat over declarative networking, een onderzoeksgebied waarin men gedistribueerde programma’s implementeert met beschrijvende talen zoals Datalog [2], waarin men voornamelijk specificeert wat de uitvoer is, en niet zozeer hoe deze uitvoer moet berekend worden. Het voordeel van zulke talen is dat complexe algoritmen kunnen beschreven worden met redelijk korte programma’s [45, 37]. Ter vergelijking, om gegevensbanken te ondervragen gebruikt men standaard de beschrijvende taal SQL in plaats van een imperatieve programmeertaal zoals Java, omdat men voor deze toepassing vaak veel kortere en overzichtelijkere programma’s kan schrijven in SQL. In deze thesis gebruiken we twee bestaande modellen. Het eerste...

  5. Statistical models for high-throughput proteomic and genomic data

    Claesen, Jürgen
    The advent of high-throughput techniques such as micro-arrays, mass spectrometry, and next-generation sequencing, expedited in biology and life science, the shift towards \-omics" oriented studies. These techniques generate large datasets, which are often complex, and require appropriate statistical analysis. The main goal of this dissertation was the development of statistical models which allow analysis of high-throughput proteomic and genomic data. In the first part of this thesis, the focus is on mass-spectrometry-based proteomics. More specifically, on the (aggregated) isotopic distribution and how this characteristic signal can be used to interprete mass spectral data. The different peaks of the isotopic distribution...

  6. Flexible modeling tools for hierarchical and incomplete data, with applications in comet assays and clinical trials

    Ghebretinsae, Aklilu Habteab
    In this thesis, some modeling issues and design aspects that arise in toxicological studies and clinical trials are addressed. The text is structured in two parts. The first part of the thesis is motivated by a comet assay, a toxicological study design to assess DNA damage, which has been a standard tool in the pharmaceutical industry for the assessment of the safety of potential new drugs. In this part, a flexible modeling tool is proposed addressing the different modeling issues and an estimation technique is explored. In particular, various models, i.e., a flexible model for hierarchically clustered and overdispersed outcomes,...

  7. Statistical Methods for Analysis of High Throughput Experiments in Early Drug Development

    Khamiakova, Tatsiana
    Introduction: Advances in biotechnology and the ability to obtain molecular profiles of biological samples, and in particular, the transcriptomic data, have been transforming the way biomedical research and early drug development are carried out for more than a decade (Clarke et al., 2004; Chengalvala et al., 2007; Hughes et al., 2011). In view of increasing costs of the drug development and nevertheless a large number of drugs which fail the clinical trials either due to the lack of efficacy or side effects, novel technologies can potentially assist the selection of the most promising compounds for later stages in the drug...

  8. Exploiting Context-awareness and Social Interaction to Provide Help in Large–scale Environments

    Mahmud, Nasim

  9. Pseudo-likelihood and Estimating Equation Methodology for Incomplete Data

    Teshome Ayele, Birhanu
    In applied research such as clinical trials, two general lines of attack have been employed to address the problem of incomplete data. The first is simply to design and carry out the study in a manner that limits the amount of incomplete data. Better implementation of a more appropiate design could reduce the frequency of missing values substantially. A variety of techniques for doing this has been proposed for clinical trials (National Research Council, 2010). The second line of attack for the treatment of incomplete data, and the focus of this thesis, is to apply analysis methods that exploit partial...

  10. Mining Correlated Motif Pairs from Protein-Protein Interaction Networks

    Boyen, Peter

  11. Acquiring the World through Photographs

    Haber, Tom
    Applications in entertainment, augmented/virtual reality, architecture and digital museums require the creation, or rendering of realistic computer-generated images of real-world objects from novel viewpoints and with novel illumination. These images should be indistinguishable from real photographs taken under similar conditions. In this dissertation, we will explore methods to acquire accurate input models, for photorealistic rendering, from the real-world using cameras and photographs. The capture step should be as simple as possible. We will describe a system for capturing detailed geometry within a cinematographic setting. The system uses a compact and simple set-up of cameras and a projector that illuminates the scene with...

  12. Discovering structure in semi-structured data

    Bex, Geert Jan
    Excerpt of introduction: Unfortunately, in spite of the above mentioned advantages, the presence of a schema is not mandatory and many XML documents are not accompanied by one. For instance, in a recent study, Barbosa et al. have shown that approximately half of the XML documents available on the web do not refer to a schema. In another study, we have noted that about two-thirds of XSDs gathered from schema repositories and from the web are not valid with respect to the W3C XML Schema specification, rendering them essentially useless for immediate application (see Chapter 6). A similar observation was...

  13. Service Quality Improvement and User Experience Optimization by Introducing Intelligence in the Network

    Wijnants, Maarten
    The majority of present-day distributed applications demand a certain level of service from the transportation network and impose a number of performance requirements on it. Failure to meet these requirements will typically degrade the efficiency of the application and, more importantly, will likely have a detrimental impact on the experience of the end-user. Over the years, a number of frameworks has therefore been proposed that enable transportation networks to guarantee a certain Quality of Service (QoS) and the positive implications of these frameworks on application performance have been established. Due to the growing attention to human factors however, the focus...

  14. An Architecture for Large-scale Virtual Interactive Communities

    Quax, Peter
    Following the popularity of text-based Internet chat channels and instant messaging applications, virtual interactive communities are often advertised as ‘revolutionary’ applications that allow large groups of people to share ideas, experiences and make new friends. What is largely unknown by the general public is that these applications share the underlying technology with networked computer games, and were founded in research for military purposes. We start this dissertation by analyzing the behavior (in terms of bandwidth usage) of applications based on networked virtual environments technology, such as networked games and virtual interactive communities. Also, the impact of common network-related problems, in...

  15. Dynamic User Interface Generation for Mobile and Embedded Systems with Model-Based User Interface Development

    Luyten, Kris
    A user’s physical and virtual environments are becoming increasingly interwoven. Mobile and embedded devices have become more the rule than the exception: many present-day users are inexperienced when it comes to traditional computers, but are in daily contact with computerized systems. The increasing diversity of all kinds of devices, together with the possibilities of running arbitrary software autonomously, result in a thousand-and-one potential areas of use, whether mobile or not. The possibility of communicating with the (in)direct environment using other devices and observing that same environment allow us to develop ambient intelligent software which has knowledge of the environment and...

  16. New techniques for subdivision modelling

    BEETS, Koen
    In this dissertation, several tools and techniques for modelling with subdivision surfaces are presented. Based on the huge amount of theoretical knowledge about subdivision surfaces, we present techniques to facilitate practical 3D modelling which make subdivision surfaces even more useful. Subdivision surfaces have reclaimed attention several years ago after their application in full-featured 3D animation movies, such as Toy Story. Since then and due to their attractive properties an ever increasing amount of research papers emerged, both in theoretical as well as in practical fields. The main contributions of this work are: • a subdivision scheme, which locally minimizes curvature...

  17. Modelling and querying spatio-temporal data

    Haesevoets, Sofie
    In this thesis, we started with defining spatio-temporal databases as a special type of constraint databases, meaning that we defined spatio-temporal objects to be semialgebraic subsets of (Rn × R). A consequence of this choice is that spatio-temporal data can be described by Boolean combinations of polynomial equations, which can be expressed in the language FO(+, ×, <, 0, 1). Although spatio-temporal databases have been studied for a decade already, the question “What are spatio-temporal database queries” is still actual. In relational database theory, it is common to require queries to be generic. A generic query asks only for properties...

  18. Realism In Environment Sensitive Plant Models and their Animation

    VAN HAEVRE, William
    For computer related visualization purposes, the beauty of plants and trees plays an important role in the representation of the world we live in. Many techniques exist to model and to animate them, but often these result in an “unnatural” look. Especially representing the structural complexity of an aged tree in a convincing way, in many cases still remains a challenging task to perform. For these reasons, many modelers/animators prefer to use traditional methods, which are very labor-intensive and require a good knowledge of the underlying phenomena involved. In this dissertation we present two main contributions to facilitate this cumbersome...

  19. Static analysis of XML transformation and schema languages

    Martens, Wim
    XML Typechecking; XML Schema; Chain Regular Expressions; XML Schema Languages

  20. New approaches in the modeling of subdivision surfaces

    CLAES, Johan
    Recursive subdivision surfaces allow considerable freedom in designing surfaces of arbitrary topology. Tools to manipulate them, however, are still not as powerful as existing tools for longer established modeling paradigms, such as B-spline surfaces. Furthermore, the most well-behaved and most widely used schemes are approximating schemes, which do not interpolate their initial control points. This dissertation describes a new modeling paradigm, providing the possibility of locally choosing an interpolating variant of the conventionally approximating subdivision scheme. Our approach combines the advantages of approximating schemes with the precise control of interpolating schemes. Unlike other solutions that mostly focus on locally changing...

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