13 resultados para Conditional Directed Graph

em Doria (National Library of Finland DSpace Services) - National Library of Finland, Finland


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Main purpose of this thesis is to introduce a new lossless compression algorithm for multispectral images. Proposed algorithm is based on reducing the band ordering problem to the problem of finding a minimum spanning tree in a weighted directed graph, where set of the graph vertices corresponds to multispectral image bands and the arcs’ weights have been computed using a newly invented adaptive linear prediction model. The adaptive prediction model is an extended unification of 2–and 4–neighbour pixel context linear prediction schemes. The algorithm provides individual prediction of each image band using the optimal prediction scheme, defined by the adaptive prediction model and the optimal predicting band suggested by minimum spanning tree. Its efficiency has been compared with respect to the best lossless compression algorithms for multispectral images. Three recently invented algorithms have been considered. Numerical results produced by these algorithms allow concluding that adaptive prediction based algorithm is the best one for lossless compression of multispectral images. Real multispectral data captured from an airplane have been used for the testing.

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With the shift towards many-core computer architectures, dataflow programming has been proposed as one potential solution for producing software that scales to a varying number of processor cores. Programming for parallel architectures is considered difficult as the current popular programming languages are inherently sequential and introducing parallelism is typically up to the programmer. Dataflow, however, is inherently parallel, describing an application as a directed graph, where nodes represent calculations and edges represent a data dependency in form of a queue. These queues are the only allowed communication between the nodes, making the dependencies between the nodes explicit and thereby also the parallelism. Once a node have the su cient inputs available, the node can, independently of any other node, perform calculations, consume inputs, and produce outputs. Data ow models have existed for several decades and have become popular for describing signal processing applications as the graph representation is a very natural representation within this eld. Digital lters are typically described with boxes and arrows also in textbooks. Data ow is also becoming more interesting in other domains, and in principle, any application working on an information stream ts the dataflow paradigm. Such applications are, among others, network protocols, cryptography, and multimedia applications. As an example, the MPEG group standardized a dataflow language called RVC-CAL to be use within reconfigurable video coding. Describing a video coder as a data ow network instead of with conventional programming languages, makes the coder more readable as it describes how the video dataflows through the different coding tools. While dataflow provides an intuitive representation for many applications, it also introduces some new problems that need to be solved in order for data ow to be more widely used. The explicit parallelism of a dataflow program is descriptive and enables an improved utilization of available processing units, however, the independent nodes also implies that some kind of scheduling is required. The need for efficient scheduling becomes even more evident when the number of nodes is larger than the number of processing units and several nodes are running concurrently on one processor core. There exist several data ow models of computation, with different trade-offs between expressiveness and analyzability. These vary from rather restricted but statically schedulable, with minimal scheduling overhead, to dynamic where each ring requires a ring rule to evaluated. The model used in this work, namely RVC-CAL, is a very expressive language, and in the general case it requires dynamic scheduling, however, the strong encapsulation of dataflow nodes enables analysis and the scheduling overhead can be reduced by using quasi-static, or piecewise static, scheduling techniques. The scheduling problem is concerned with nding the few scheduling decisions that must be run-time, while most decisions are pre-calculated. The result is then an, as small as possible, set of static schedules that are dynamically scheduled. To identify these dynamic decisions and to find the concrete schedules, this thesis shows how quasi-static scheduling can be represented as a model checking problem. This involves identifying the relevant information to generate a minimal but complete model to be used for model checking. The model must describe everything that may affect scheduling of the application while omitting everything else in order to avoid state space explosion. This kind of simplification is necessary to make the state space analysis feasible. For the model checker to nd the actual schedules, a set of scheduling strategies are de ned which are able to produce quasi-static schedulers for a wide range of applications. The results of this work show that actor composition with quasi-static scheduling can be used to transform data ow programs to t many different computer architecture with different type and number of cores. This in turn, enables dataflow to provide a more platform independent representation as one application can be fitted to a specific processor architecture without changing the actual program representation. Instead, the program representation is in the context of design space exploration optimized by the development tools to fit the target platform. This work focuses on representing the dataflow scheduling problem as a model checking problem and is implemented as part of a compiler infrastructure. The thesis also presents experimental results as evidence of the usefulness of the approach.

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The amount of biological data has grown exponentially in recent decades. Modern biotechnologies, such as microarrays and next-generation sequencing, are capable to produce massive amounts of biomedical data in a single experiment. As the amount of the data is rapidly growing there is an urgent need for reliable computational methods for analyzing and visualizing it. This thesis addresses this need by studying how to efficiently and reliably analyze and visualize high-dimensional data, especially that obtained from gene expression microarray experiments. First, we will study the ways to improve the quality of microarray data by replacing (imputing) the missing data entries with the estimated values for these entries. Missing value imputation is a method which is commonly used to make the original incomplete data complete, thus making it easier to be analyzed with statistical and computational methods. Our novel approach was to use curated external biological information as a guide for the missing value imputation. Secondly, we studied the effect of missing value imputation on the downstream data analysis methods like clustering. We compared multiple recent imputation algorithms against 8 publicly available microarray data sets. It was observed that the missing value imputation indeed is a rational way to improve the quality of biological data. The research revealed differences between the clustering results obtained with different imputation methods. On most data sets, the simple and fast k-NN imputation was good enough, but there were also needs for more advanced imputation methods, such as Bayesian Principal Component Algorithm (BPCA). Finally, we studied the visualization of biological network data. Biological interaction networks are examples of the outcome of multiple biological experiments such as using the gene microarray techniques. Such networks are typically very large and highly connected, thus there is a need for fast algorithms for producing visually pleasant layouts. A computationally efficient way to produce layouts of large biological interaction networks was developed. The algorithm uses multilevel optimization within the regular force directed graph layout algorithm.

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Viimeisten vuosien aikana laajakaistaoperaattoreiden laajakaistaverkot ovat nopeiden ja kiinteähintaisten laajakaistaliittymien johdosta kasvaneet suuriksi kokonaisuuksiksi. Kokonaisuuksia hallitaan erilaisilla verkonhallintatyökaluilla. Verkonhallintatyökalut sisältävät suuren määrän eri tasoista tietoa laitteista ja laitteiden välisistä suhteista. Kokonaisuuksien hahmottaminen ilman tiedoista rakennettua kuvaa on vaikeaa ja hidasta. Laajakaistaverkon topologian visualisoinnissa muodostetaan kuva laitteista ja niiden välisistä suhteista. Visualisoitua kuvaa voidaan käyttää osana verkonhallintatyökalua, jolloin käyttäjälle muodostuu nopeasti näkymä verkon laitteista ja rakenteesta eli topologiasta. Visualisoinnissa kuvan piirto-ongelma täytyy muuttaa graafin piirto-ongelmaksi. Graafin piirto-ongelmassa verkon rakennetta käsitellään graafina, joka mahdollistaa kuvan muodostamisen automaattisia piirtomenetelmiä hyväksikäyttäen. Halutunlainen ulkoasu kuvalle muodostetaan automaattisilla piirtomenetelmillä, joilla laitteiden ja laitteiden välisten suhteiden esitystapoja voidaan muuttaa. Esitystavoilla voidaan muuttaa esimerkiksi laitteiden muotoa, väriä ja kokoa. Esitystapojen lisäksi piirtomenetelmien tärkein tehtävä on laskea laitteiden sijaintien koordinaattien arvot, jotka loppujen lopuksi määräävät koko kuvan rakenteen. Koordinaattien arvot lasketaan piirtoalgoritmeilla, joista voimiin perustuvat algoritmit sopivat parhaiten laajakaistaverkkojen laitteiden sijaintien laskemiseen. Tämän diplomityön käytännön työssä toteutettiin laajakaistaverkon topologian visualisointityökalu.

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This study investigates the relationship between the time-varying risk premiums and conditional market risk in the stock markets of the ten member countries of Economy and Monetary Union. Second, it examines whether the conditional second moments change over time and are there asymmetric effects in the conditional covariance matrix. Third, it analyzes the possible effects of the chosen testing framework. Empirical analysis is conducted using asymmetric univariate and multivariate GARCH-in-mean models and assuming three different degrees of market integration. For a daily sample period from 1999 to 2007, the study shows that the time-varying market risk alone is not enough to explain the dynamics of risk premiums and indications are found that the market risk is detected only when its price is allowed to change over time. Also asymmetric effects in the conditional covariance matrix, which is found to be time-varying, are clearly present and should be recognized in empirical asset pricing analyses.

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The use of domain-specific languages (DSLs) has been proposed as an approach to cost-e ectively develop families of software systems in a restricted application domain. Domain-specific languages in combination with the accumulated knowledge and experience of previous implementations, can in turn be used to generate new applications with unique sets of requirements. For this reason, DSLs are considered to be an important approach for software reuse. However, the toolset supporting a particular domain-specific language is also domain-specific and is per definition not reusable. Therefore, creating and maintaining a DSL requires additional resources that could be even larger than the savings associated with using them. As a solution, di erent tool frameworks have been proposed to simplify and reduce the cost of developments of DSLs. Developers of tool support for DSLs need to instantiate, customize or configure the framework for a particular DSL. There are di erent approaches for this. An approach is to use an application programming interface (API) and to extend the basic framework using an imperative programming language. An example of a tools which is based on this approach is Eclipse GEF. Another approach is to configure the framework using declarative languages that are independent of the underlying framework implementation. We believe this second approach can bring important benefits as this brings focus to specifying what should the tool be like instead of writing a program specifying how the tool achieves this functionality. In this thesis we explore this second approach. We use graph transformation as the basic approach to customize a domain-specific modeling (DSM) tool framework. The contributions of this thesis includes a comparison of di erent approaches for defining, representing and interchanging software modeling languages and models and a tool architecture for an open domain-specific modeling framework that e ciently integrates several model transformation components and visual editors. We also present several specific algorithms and tool components for DSM framework. These include an approach for graph query based on region operators and the star operator and an approach for reconciling models and diagrams after executing model transformation programs. We exemplify our approach with two case studies MICAS and EFCO. In these studies we show how our experimental modeling tool framework has been used to define tool environments for domain-specific languages.

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Protein engineering aims to improve the properties of enzymes and affinity reagents by genetic changes. Typical engineered properties are affinity, specificity, stability, expression, and solubility. Because proteins are complex biomolecules, the effects of specific genetic changes are seldom predictable. Consequently, a popular strategy in protein engineering is to create a library of genetic variants of the target molecule, and render the population in a selection process to sort the variants by the desired property. This technique, called directed evolution, is a central tool for trimming protein-based products used in a wide range of applications from laundry detergents to anti-cancer drugs. New methods are continuously needed to generate larger gene repertoires and compatible selection platforms to shorten the development timeline for new biochemicals. In the first study of this thesis, primer extension mutagenesis was revisited to establish higher quality gene variant libraries in Escherichia coli cells. In the second study, recombination was explored as a method to expand the number of screenable enzyme variants. A selection platform was developed to improve antigen binding fragment (Fab) display on filamentous phages in the third article and, in the fourth study, novel design concepts were tested by two differentially randomized recombinant antibody libraries. Finally, in the last study, the performance of the same antibody repertoire was compared in phage display selections as a genetic fusion to different phage capsid proteins and in different antibody formats, Fab vs. single chain variable fragment (ScFv), in order to find out the most suitable display platform for the library at hand. As a result of the studies, a novel gene library construction method, termed selective rolling circle amplification (sRCA), was developed. The method increases mutagenesis frequency close to 100% in the final library and the number of transformants over 100-fold compared to traditional primer extension mutagenesis. In the second study, Cre/loxP recombination was found to be an appropriate tool to resolve the DNA concatemer resulting from error-prone RCA (epRCA) mutagenesis into monomeric circular DNA units for higher efficiency transformation into E. coli. Library selections against antigens of various size in the fourth study demonstrated that diversity placed closer to the antigen binding site of antibodies supports generation of antibodies against haptens and peptides, whereas diversity at more peripheral locations is better suited for targeting proteins. The conclusion from a comparison of the display formats was that truncated capsid protein three (p3Δ) of filamentous phage was superior to the full-length p3 and protein nine (p9) in obtaining a high number of uniquely specific clones. Especially for digoxigenin, a difficult hapten target, the antibody repertoire as ScFv-p3Δ provided the clones with the highest affinity for binding. This thesis on the construction, design, and selection of gene variant libraries contributes to the practical know-how in directed evolution and contains useful information for scientists in the field to support their undertakings.

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Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.

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This thesis estimates long-run time variant conditional correlation between stock and bond returns of CIVETS (Colombia, Indonesia, Vietnam, Egypt, Turkey, and South Africa) nations. Further, aims to analyse the presence of asymmetric volatility effect in both asset returns, as well as, obverses increment or decrement in conditional correlation during pre-crisis and crisis period, which lead to make a reliable diversification decision. The Constant Conditional Correlation (CCC) GARCH model of Bollerslev (1990), the Dynamic Conditional Correlation (DCC) GARCH model (Engle 2002), and the Asymmetric Dynamic Conditional Correlation (ADCC) GARCH model of Cappiello, Engle, and Sheppard (2006) were implemented in the study. The analyses present strong evidence of time-varying conditional correlation in CIVETS markets, excluding Vietnam, during 2005-2013. In addition, negative innovation effects were found in both conditional variance and correlation of the asset returns. The results of this study recommend investors to include financial assets from these markets in portfolios, in order to obtain better stock-bond diversification benefits, especially during high volatility periods.

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This thesis studies the impact of the latest Russian crisis on global markets, and especially Central and Eastern Europe. The results are compared to other shocks and crises over the last twenty years to see how significant they have been. The cointegration process of Central and Eastern European financial markets is also reviewed and updated. Using three separate conditional correlation GARCH models, the latest crisis is not found to have initiated similar surges in conditional correlations to previous crises over the last two decades. Market cointegration for Central and Eastern Europe is found to have stalled somewhat after initial correlation increases post EU accession.

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The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates’ gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems’ rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

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The purpose of this study is to find out how laser based Directed Energy Deposition processes can benefit from different types of monitoring. DED is a type of additive manufacturing process, where parts are manufactured in layers by using metallic powder or metallic wire. DED processes can be used to manufacture parts that are not possible to manufacture with conventional manufacturing processes, when adding new geometries to existing parts or when wanting to minimize the scrap material that would result from machining the part. The aim of this study is to find out why laser based DED-processes are monitored, how they are monitored and what devices are used for monitoring. This study has been done in the form of a literature review. During the manufacturing process, the DED-process is highly sensitive to different disturbances such as fluctuations in laser absorption, powder feed rate, temperature, humidity or the reflectivity of the melt pool. These fluctuations can cause fluctuations in the size of the melt pool or its temperature. The variations in the size of the melt pool have an effect on the thickness of individual layers, which have a direct impact on the final surface quality and dimensional accuracy of the parts. By collecting data from these fluctuations and adjusting the laser power in real-time, the size of the melt pool and its temperature can be kept within a specified range that leads to significant improvements in the manufacturing quality. The main areas of monitoring can be divided into the monitoring of the powder feed rate, the temperature of the melt pool, the height of the melt pool and the geometry of the melt pool. Monitoring the powder feed rate is important when depositing different material compositions. Monitoring the temperature of the melt pool can give information about the microstructure and mechanical properties of the part. Monitoring the height and the geometry of the melt pool is an important factor in achieving the desired dimensional accuracy of the part. By combining multiple different monitoring devices, the amount of fluctuations that can be controlled will be increased. In addition, by combining additive manufacturing with machining, the benefits of both processes could be utilized.