There are a variety of chromosomal abnormalities such as translocation, duplication, deletion, insertion and inversion, which may cause severe diseases, e.g., cancers and birth defects. Multi-color fluorescence in-situ hybridization (M-FISH) is an imaging technique popularly used for simultaneously detecting and visualizing these complex abnormalities in a single hybridization. In spite of the advancement of fluorescence microscopy for chromosomal abnormality detection, the quality of the fluorescence images is still limited, due to the spectral overlap, uneven intensity level across multiple channels, variations of background and inhomogeneous intensity within intra-channels. Therefore, it is critical but challenging to distinguish the different types of chromosomes accurately in order to detect the chromosomal abnormalities from M-FISH images. The main contribution of this dissertation is to develop an M-FISH image analysis pipeline by taking full advantage of spatial and spectral information from M-FISH imaging. In addition, novel image analysis approaches such as the sparse representation are applied in this work. The pipeline starts with the image preprocessing to extract the background to improve the quality of the raw images by low-rank plus group lasso decomposition. Then, the image segmentation is performed by incorporating both spatial and spectral information by total variation (TV) and row-wise constraints. Finally image classification is conducted by considering the structural information of neighboring pixels with a row-wise sparse representation model. In each step, new methods and sophisticated algorithms were developed and compared with several popularly used methods, It shows that (1) the preprocessing model improves the quality of the raw images; (2) the segmentation model outperforms than both fuzzy c-means (FCM) and improved adaptive fuzzy c-means (IAFCM) models in terms of correct ratio and false rate; and (3) the classification model corrects the misclassification to improve the accuracy of chromosomal abnormalities detection, especially for the complex inter-chromosomal rearrangements. / 1 / Jingyao Li

The World Wide Web is a rich source of information and continues to expand in size and complexity. Mainly because the data on the web is lack of rigid and uniform data models or schemas, how to effectively and efficiently manage web data and retrieve information is becoming a challenge problem. Discovering web page communities, which capture the features of the web and web-based data to find intrinsic relationships among the data, is one of the effective ways to solve this problem. A web page community is a set of web pages that has its own logical and semantic structures. In this work, we concentrate on the web data in web page format and exploit hyperlink information to discover (construct) web page communities. Three main web page communities are studied in this work: the first one is consisted of hub and authority pages, the second one is composed of relevant web pages with respect to a given page (URL), and the last one is the community with hierarchical cluster structures. For analysing hyperlinks, we establish a mathematical framework, especially the matrix-based framework, to model hyperlinks. Within this mathematical framework, hyperlink analysis is placed on a solid mathematic base and the results are reliable. For the web page community that is consisted of hub and authority pages, we focus on eliminating noise pages from the concerned page source to obtain another good quality page source, and in turn improve the quality of web page communities. We propose an innovative noise page elimination algorithm based on the hyperlink matrix model and mathematic operations, especially the singular value decomposition (SVD) of matrix. The proposed algorithm exploits hyperlink information among the web pages, reveals page relationships at a deeper level, and numerically defines thresholds for noise page elimination. The experiment results show the effectiveness and feasibility of the algorithm. This algorithm could also be used solely for web-based data management systems to filter unnecessary web pages and reduce the management cost. In order to construct a web page community that is consisted of relevant pages with respect to a given page (URL), we propose two hyperlink based relevant page finding algorithms. The first algorithm comes from the extended co-citation analysis of web pages. It is intuitive and easy to be implemented. The second one takes advantage of linear algebra theories to reveal deeper relationships among the web pages and identify relevant pages more precisely and effectively. The corresponding page source construction for these two algorithms can prevent the results from being affected by malicious hyperlinks on the web. The experiment results show the feasibility and effectiveness of the algorithms. The research results could be used to enhance web search by caching the relevant pages for certain searched pages. For the purpose of clustering web pages to construct a community with its hierarchical cluster structures, we propose an innovative web page similarity measurement that incorporates hyperlink transitivity and page importance (weight).Based on this similarity measurement, two types of hierarchical web page clustering algorithms are proposed. The first one is the improvement of the conventional K-mean algorithms. It is effective in improving page clustering, but is sensitive to the predefined similarity thresholds for clustering. Another type is the matrix-based hierarchical algorithm. Two algorithms of this type are proposed in this work. One takes cluster-overlapping into consideration, another one does not. The matrix-based algorithms do not require predefined similarity thresholds for clustering, are independent of the order in which the pages are presented, and produce stable clustering results. The matrix-based algorithms exploit intrinsic relationships among web pages within a uniform matrix framework, avoid much influence of human interference in the clustering procedure, and are easy to be implemented for applications. The experiments show the effectiveness of the new similarity measurement and the proposed algorithms in web page clustering improvement. For applying above mathematical algorithms better in practice, we generalize the web page discovering as a special case of information retrieval and present a visualization system prototype, as well as technical details on visualization algorithm design, to support information retrieval based on linear algebra. The visualization algorithms could be smoothly applied to web applications. XML is a new standard for data representation and exchange on the Internet. In order to extend our research to cover this important web data, we propose an object representation model (ORM) for XML data. A set of transformation rules and algorithms are established to transform XML data (DTD and XML documents with DTD or without DTD) into this model. This model capsulizes elements of XML data and data manipulation methods. DTD-Tree is also defined to describe the logical structure of DTD. It also can be used as an application program interface (API) for processing DTD, such as transforming a DTD document into the ORM. With this data model, semantic meanings of the tags (elements) in XML data can be used for further research in XML data management and information retrieval, such as community construction for XML data.

The increasing variety of data mining tools offers a large palette of types and representation formats for predictive models. Managing the models then becomes a big challenge, as well as reusing the models and keeping the consistency of model and data repositories. Sustainable access and quality assessment of these models become limited to researchers. The approach for the Data and Model Governance (DMG) makes easier to process and support complex solutions. In this thesis, contributions are proposed towards ensembles of models with a focus on model representation, comparison and usage. Predictive Toxicology was chosen as an application field to demonstrate the proposed approach to represent predictive models linked to data for DMG. Further analysing methods such as predictive models comparison and predictive models combination for reusing the models from a collection of models were studied. Thus in this thesis, an original structure of the pool of models was proposed to represent predictive toxicology models called Predictive Toxicology Markup Language (PTML). PTML offers a representation scheme for predictive toxicology data and models generated by data mining tools. In this research, the proposed representation offers possibilities to compare models and select the relevant models based on different performance measures using proposed similarity measuring techniques. The relevant models were selected using a proposed cost function which is a composite of performance measures such as Accuracy (Acc), False Negative Rate (FNR) and False Positive Rate (FPR). The cost function will ensure that only quality models be selected as the candidate models for an ensemble. The proposed algorithm for optimisation and combination of Acc, FNR and FPR of ensemble models using double fault measure as the diversity measure improves Acc between 0.01 to 0.30 for all toxicology data sets compared to other ensemble methods such as Bagging, Stacking, Bayes and Boosting. The highest improvements for Acc were for data sets Bee (0.30), Oral Quail (0.13) and Daphnia (0.10). A small improvement (of about 0.01) in Acc was achieved for Dietary Quail and Trout. Important results by combining all the three performance measures are also related to reducing the distance between FNR and FPR for Bee, Daphnia, Oral Quail and Trout data sets for about 0.17 to 0.28. For Dietary Quail data set the improvement was about 0.01 though, but this data set is well known as a difficult learning exercise. For five UCI data sets tested, similar results were achieved with Acc improvement between 0.10 to 0.11, closing more the gaps between FNR and FPR. As a conclusion, the results show that by combining performance measures (Acc, FNR and FPR), as proposed within this thesis, the Acc increased and the distance between FNR and FPR decreased.

A Realidade Virtual é usada na produção de simulações complexas de ambientes virtuais 3D, envolvendo dispositivos de entrada e saída não triviais, para proporcionar aos usuários sensações de imersão em mundos simulados de tempo real. O projeto e o desenvolvimento de aplicações de realidade virtual caracterizam-se como tarefas complexas, devido à necessidade de integração de técnicas de diferentes áreas da computação e dispositivos não convencionais. Com o objetivo de aumentar o potencial de reutilização e compartilhamento de elementos de aplicações de realidade virtual, este trabalho propõe o RM-VRServices, um modelo conceitual de representação de aplicações de realidade virtual, e o VRServices, um modelo arquitetural para uma plataforma de software que apoia a produção, execução e compartilhamento de elementos de aplicações de realidade virtual em ambiente on-line. O RM-VRServices foi desenvolvido por meio da representação hierárquica de conceitos de mundos virtuais e aplicações de realidade virtual. A plataforma VRServices foi projetada com base no paradigma de computação orientada a serviços, com o objetivo de promover o compartilhamento de conteúdo, a interoperabilidade e a flexibilidade de acesso às funcionalidades da plataforma. O desenvolvimento de protótipos do modelo RM-VRServices e da plataforma VRServices, possibilitou a produção de aplicações de realidade virtual, em um ambiente on-line, acessível por meio de serviços, com interoperabilidade de linguagem de programação e plataforma computacional. / Virtual reality is used in the production of complex simulations of 3D virtual environments, involving nontrivial input and output devices, to provide users with sensations of immersion in the simulated world in real time. The design and development of virtual reality applications are characterized with complex tasks, due to the need to integrate techniques from different areas of computing and non-conventional devices. In order to increase the potential for reuse and sharing of elements of virtual reality applications, this work proposes the RM-VRServices, a conceptual model for representing virtual reality applications, and the VRServices, an architectural model for a software platform to support the production, implementation and element sharing of virtual reality applications in an online environment. The RM-VRServices was developed by using the hierarchical representation of virtual world concepts and virtual reality applications. The VRServices platform was designed based on the paradigm of service-oriented computing, with the goal of promoting content sharing, interoperability and flexibility of access to the features of the platform. The development of prototypes of the RM-VRServices model and the VRServices platform, enabled the production of virtual reality applications in an online environment, accessible through services, with interoperability of programming language and computing platform.

A Realidade Virtual é usada na produção de simulações complexas de ambientes virtuais 3D, envolvendo dispositivos de entrada e saída não triviais, para proporcionar aos usuários sensações de imersão em mundos simulados de tempo real. O projeto e o desenvolvimento de aplicações de realidade virtual caracterizam-se como tarefas complexas, devido à necessidade de integração de técnicas de diferentes áreas da computação e dispositivos não convencionais. Com o objetivo de aumentar o potencial de reutilização e compartilhamento de elementos de aplicações de realidade virtual, este trabalho propõe o RM-VRServices, um modelo conceitual de representação de aplicações de realidade virtual, e o VRServices, um modelo arquitetural para uma plataforma de software que apoia a produção, execução e compartilhamento de elementos de aplicações de realidade virtual em ambiente on-line. O RM-VRServices foi desenvolvido por meio da representação hierárquica de conceitos de mundos virtuais e aplicações de realidade virtual. A plataforma VRServices foi projetada com base no paradigma de computação orientada a serviços, com o objetivo de promover o compartilhamento de conteúdo, a interoperabilidade e a flexibilidade de acesso às funcionalidades da plataforma. O desenvolvimento de protótipos do modelo RM-VRServices e da plataforma VRServices, possibilitou a produção de aplicações de realidade virtual, em um ambiente on-line, acessível por meio de serviços, com interoperabilidade de linguagem de programação e plataforma computacional. / Virtual reality is used in the production of complex simulations of 3D virtual environments, involving nontrivial input and output devices, to provide users with sensations of immersion in the simulated world in real time. The design and development of virtual reality applications are characterized with complex tasks, due to the need to integrate techniques from different areas of computing and non-conventional devices. In order to increase the potential for reuse and sharing of elements of virtual reality applications, this work proposes the RM-VRServices, a conceptual model for representing virtual reality applications, and the VRServices, an architectural model for a software platform to support the production, implementation and element sharing of virtual reality applications in an online environment. The RM-VRServices was developed by using the hierarchical representation of virtual world concepts and virtual reality applications. The VRServices platform was designed based on the paradigm of service-oriented computing, with the goal of promoting content sharing, interoperability and flexibility of access to the features of the platform. The development of prototypes of the RM-VRServices model and the VRServices platform, enabled the production of virtual reality applications in an online environment, accessible through services, with interoperability of programming language and computing platform.

L’objectif du travail de thèse est de proposer un modèle de représentation des écritures dans les images de documents du patrimoine sans recourir à une transcription des textes. Ce modèle, issu d’une étude très complète des méthodes actuelles de caractérisation des écritures, est à la base d’une proposition de scénario de recherche par similarité de mots, indépendante du scripteur et ne nécessitant pas d’apprentissage. La recherche par similarité proposée repose sur une structure de graphes intégrant des informations sur la topologie, la morphologie locale des mots et sur le contexte extrait du voisinage de chaque point d’intérêt. Un graphe est construit à partir du squelette décrit en chaque point sommet par le contexte de formes, descripteur riche et compact. L’extraction de mots est assurée par une première étape de localisation grossière de régions candidates, décrites par une séquence déduite d’une représentation par graphes liée à des critères topologiques de voisinage. L’appariement entre mots repose ensuite sur une distance dynamique et un usage adapté du coût d’édition approximé entre graphes rendant compte de la nature bi-dimensionnelle de l’écriture. L’approche a été conçue pour être robuste aux distorsions de l’écriture et aux changements de scripteurs. Les expérimentations sont réalisées sur des bases de documents manuscrits patrimoniaux exploitées dans les compétitions de word-spotting. Les performances illustrent la pertinence de la proposition et ouvrent des voies nouvelles d’investigation dans des domaines d’applications autour de la reconnaissance de symboles et d’écritures iconographiques / As more and more documents, especially historical handwritten documents, are converted into digitized version for long-term preservation, the demands for efficient information retrieval techniques in such document images are increasing. The objective of this research is to establish an effective representation model for handwriting, especially historical manuscripts. The proposed model is supposed to help the navigation in historical document collections. Specifically speaking, we developed our handwriting representation model with regards to word spotting application. As a specific pattern recognition task, handwritten word spotting faces many challenges such as the high intra-writer and inter-writer variability. Nowadays, it has been admitted that OCR techniques are unsuccessful in handwritten offline documents, especially historical ones. Therefore, the particular characterization and comparison methods dedicated to handwritten word spotting are strongly required. In this work, we explore several techniques that allow the retrieval of singlestyle handwritten document images with query image. The proposed representation model contains two facets of handwriting, morphology and topology. Based on the skeleton of handwriting, graphs are constructed with the structural points as the vertexes and the strokes as the edges. By signing the Shape Context descriptor as the label of vertex, the contextual information of handwriting is also integrated. Moreover, we develop a coarse-to-fine system for the large-scale handwritten word spotting using our representation model. In the coarse selection, graph embedding is adapted with consideration of simple and fast computation. With selected regions of interest, in the fine selection, a specific similarity measure based on graph edit distance is designed. Regarding the importance of the order of handwriting, dynamic time warping assignment with block merging is added. The experimental results using benchmark handwriting datasets demonstrate the power of the proposed representation model and the efficiency of the developed word spotting approach. The main contribution of this work is the proposed graph-based representation model, which realizes a comprehensive description of handwriting, especially historical script. Our structure-based model captures the essential characteristics of handwriting without redundancy, and meanwhile is robust to the intra-variation of handwriting and specific noises. With additional experiments, we have also proved the potential of the proposed representation model in other symbol recognition applications, such as handwritten musical and architectural classification

Les piles à combustible à membrane échangeuse de protons (PEMFC) constituent une alternative aux moteurs thermiques utilisés dans le cadre d’applications transport ou dans le cadre d’applications stationnaires. Cependant, une large commercialisation des PEMFC dépend des progrès qui peuvent être réalisés pour améliorer leur fiabilité et leur durabilité. La PEMFC est sujette à plusieurs types de dégradations complexes et non entièrement maitrisées qui varient en fonction des conditions de fonctionnement. Cependant, il est admis qu’il est souhaitable de faire fonctionner la PEMFC à distributions de courant uniformes car des distributions de courant hétérogènes entraînent une mauvaise utilisation des réactifs et des catalyseurs, une diminution des performances globales et une possible dégradation des matériaux constitutifs du coeur de la pile. De nouvelles stratégies de diagnostic doivent donc être proposées en s’appuyant sur les distributions de courant. Mes travaux de recherche consistent à développer un nouvel outil de diagnostic s’appuyant sur une mesure du champ électromagnétique externe (non invasive) rayonné par la pile PEMFC. Le champ magnétique possède l’intérêt d’être corrélé à la distribution locale du courant circulant à l’intérieur de la pile, et permet d’avoir des informations sur les performances locales. Cette distribution est liée aux conditions opératoires de la pile. Il est alors possible, à partir d’une signature magnétique de remonter à une information locale et à la cause des distributions de courant non uniformes. Des bases (vecteurs) qui contiennent les données des champs magnétiques issues des 30 capteurs disposés autour de la PAC sont construites à partir de distributions de courant spécifiques. Ces bases constituent un espace de représentation du comportement anormal de la PEMFC et permettront de d’élaborer des signatures caractérisant les fonctionnements indésirables. Ainsi, deux méthodes ont été développées pour permettre : (i) d’extraire des paramètres pertinents sur la répartition de la densité de courant traduisant les performances locales de la PAC, (ii) de classifier les différents modes de fonctionnements indésirables. La première méthode consiste à générer des résidus vectoriels en comparant le comportement réel du système (caractérisé par un vecteur mesure) avec les bases générées. Des variables qualitatives ont été élaborées pour classifier les modes de fonctionnement indésirables de la pile. La deuxième méthode consiste à extraire des paramètres à partir de la projection du vecteur mesure dans la direction des bases. La classification est réalisée dans des espaces 2D. Une validation des deux méthodes proposées a été effectuée à partir de mesures expérimentales sur une PEMFC de taille industrielle (stack GENEPAC de 40 cellules construit par le CEA et PSA). La pertinence des paramètres extraits a été vérifiée en s’appuyant sur des distributions de courant mesurées directement. Les modes de fonctionnement indésirables prédéfinis permettent de localiser les paramètres opératoires ayant conduit à l’évolution de la distribution de courant. Les outils ainsi réalisés sont très facilement transposables à d’autres piles PEMFC. / Proton exchange membrane fuel cell (PEMFC) is a potential alternative energy conversion device for stationary and automotive applications. Wide commercialization of PEMFC depends on progress that can be achieved to enhance its reliability and durability. The PEM fuel cell is subject to several types of complex and not fully mastered degradations which vary with operating conditions. It is desirable to operate the PEMFC at uniform current distribution because non uniform current distribution over the MEA could result in poor reactant and catalyst utilization, overall cell performance degradation as well as corrosion processes inside the PEM fuel cell. Therefore, new diagnostic strategies must be proposed, including choice of information gathered on the system and the fuel cell operation representation. My research is to develop a new diagnostic tool based on a measure of the external electromagnetic field (non-invasive) radiated by the fuel cell. The magnetic field has the advantage of being correlated to the local distribution of the current flowing inside the fuel cell (a physical indicator to obtain information on local performance of a fuel cell); it is linked to the local operating conditions: relative humidity level, temperature etc. It is then possible, from a magnetic signature to trace local information. Baselines (vectors) which contain the magnetic fields data generated by specific current distribution are built to characterize the magnetic field generated by the undesirable operation of the fuel cell. Baselines constitute a representation space of abnormal system behavior. Two methods have been developed to enable: (i) to extract the relevant parameters on the distribution of the current density resulting from PEM fuel cell stack local performance, (ii) to classify different types of undesirables operations. The first method is to generate vector residuals by comparing the actual behavior of the system (characterized by a measurement vector) with the baselines generated. Qualitative variables were created to classify the undesirable modes of PEM fuel cell stack operation. The second method is to extract parameters from the projection of the vector in the direction of measurement baselines. The classification is performed in 2D space. Validation from experimental measurements of the two proposed methods has been carried out on a commercial scale PEMFC (GENEPAC stack of 40 cells built by the CEA and PSA). The relevance of the extracted parameters was verified based on current density distributions measured directly. The undesirable predefined operating modes were used to locate the operating conditions parameters that led to the evolution of the current density distribution. The tools are made easily transferable to other PEMFC stack.

This work describes important periods of making application on editing 3D scene. It concerns a program which makes possible visualization of objects and simulation graphic scene. The introduction of this document is dedicated to theorical analysis, which is oriented on objects presentation in computer graphic with detailed orientation on Boundary Representation. The following chapter is about transformations and manipulators. Design part introduces basic problems and apprises with exercise solutions on general level. In the part of the implementation, we find detailed description of actual solution for particular phase of proposal. It states description of advanced camera system and transformation of objects by the help of graphic manipulators. The next chapter discuss implement effects, modifications and solution for graphical user interface.