Cette thèse traite d'une approche, guidée par une ontologie, conçue pour annoter les documents d'un corpus où chaque document décrit une entité de même type. Dans notre contexte, l'ensemble des documents doit être annoté avec des concepts qui sont en général trop spécifiques pour être explicitement mentionnés dans les textes. De plus, les concepts d'annotation ne sont représentés au départ que par leur nom, sans qu'aucune information sémantique ne leur soit reliée. Enfin, les caractéristiques des entités décrites dans les documents sont incomplètes. Pour accomplir ce processus particulier d'annotation de documents, nous proposons une approche nommée SAUPODOC (Semantic Annotation Using Population of Ontology and Definitions of Concepts) qui combine plusieurs tâches pour (1) peupler et (2) enrichir une ontologie de domaine. La phase de peuplement (1) ajoute dans l'ontologie des informations provenant des documents du corpus mais aussi du Web des données (Linked Open Data ou LOD). Le LOD représente aujourd'hui une source prometteuse pour de très nombreuses applications du Web sémantique à condition toutefois de développer des techniques adaptées d'acquisition de données. Dans le cadre de SAUPODOC, le peuplement de l'ontologie doit tenir compte de la diversité des données présentes dans le LOD : propriétés multiples, équivalentes, multi-valuées ou absentes. Les correspondances à établir, entre le vocabulaire de l'ontologie à peupler et celui du LOD, étant complexes, nous proposons un modèle pour faciliter leur spécification. Puis, nous montrons comment ce modèle est utilisé pour générer automatiquement des requêtes SPARQL et ainsi faciliter l'interrogation du LOD et le peuplement de l'ontologie. Celle-ci, une fois peuplée, est ensuite enrichie(2) avec les concepts d'annotation et leurs définitions qui sont apprises grâce à des exemples de documents annotés. Un raisonnement sur ces définitions permet enfin d'obtenir les annotations souhaitées. Des expérimentations ont été menées dans deux domaines d'application, et les résultats, comparés aux annotations obtenues avec des classifieurs, montrent l'intérêt de l'approche. / This thesis deals with an approach, guided by an ontology, designed to annotate documents from a corpus where each document describes an entity of the same type. In our context, all documents have to be annotated with concepts that are usually too specific to be explicitly mentioned in the texts. In addition, the annotation concepts are represented initially only by their name, without any semantic information connected to them. Finally, the characteristics of the entities described in the documents are incomplete. To accomplish this particular process of annotation of documents, we propose an approach called SAUPODOC (Semantic Annotation of Population Using Ontology and Definitions of Concepts) which combines several tasks to (1) populate and (2) enrich a domain ontology. The population step (1) adds to the ontology information from the documents in the corpus but also from the Web of Data (Linked Open Data or LOD). The LOD represents today a promising source for many applications of the Semantic Web, provided that appropriate techniques of data acquisition are developed. In the settings of SAUPODOC, the ontology population has to take into account the diversity of the data in the LOD: multiple, equivalent, multi-valued or absent properties. The correspondences to be established, between the vocabulary of the ontology to be populated and that of the LOD, are complex, thus we propose a model to facilitate their specification. Then, we show how this model is used to automatically generate SPARQL queries and facilitate the interrogation of the LOD and the population of the ontology. The latter, once populated, is then enriched (2) with the annotation concepts and definitions that are learned through examples of annotated documents. Reasoning on these definitions finally provides the desired annotations. Experiments have been conducted in two areas of application, and the results, compared with the annotations obtained with classifiers, show the interest of the approach.

Esta tese apresenta soluções para o gerenciamento e otimização de temperatura para sistemas de codificação de vídeo baseados nas características da aplicação e no conteúdo dos vídeos digitais. Diferente dos trabalhos estado-da-arte, as soluções propostas nesta tese focam em técnicas de gerenciamento de temperatura no nível da aplicação e características da aplicação codificação de vídeo e as propriedades dos vídeos digitais são explorados para desenvolver soluções termais para a codificação de vídeo com baixas perdas na qualidade de serviço das aplicações. Diversas análises são realizadas considerando a aplicação de codificação de vídeo para entender o comportamento da temperatura durante o processo de codificação para diferentes sequências de vídeo. Com base nos resultados das análises, soluções com diferentes abordagens são propostas para atenuar os efeitos da temperatura nos sistemas de codificação de vídeo. Gerenciamento de temperatura baseado nas características da aplicação para o padrão de codificação HEVC usa uma técnica de seleção de configuração em tempo de execução para manter a temperatura abaixo dos limites seguros de operação com bons resultados de qualidade de vídeo. Otimização de temperatura baseado em computação imprecisa usa aproximações baseadas em conteúdo para reduzir a temperatura de chips executando o HEVC. Um escalonador de tarefas que usa características da aplicação para guiar o escalonamento de threads focando na redução dos gradientes espaciais de temperatura que são resultantes do desbalanceamento natural de cargas entre as threads da aplicação. As soluções propostas são capazes de reduzir em até 10 ºC a temperatura do chip com perdas insignificantes na eficiência de compressão. Os resultados de qualidade objetiva (medida usando PSNR) são de 12 dBs até 20 dBs maiores quando comparados com trabalhos da literatura. Além disso, o escalonador de tarefas proposto é capaz de eliminar os gradientes espaciais de temperatura maiores que 5 ºC para arquitetura multi-cores. Como principal conclusão, esta tese demonstra que as técnicas de gerenciamento de temperatura que usam o conhecimento da aplicação de maneira conjunta com as propriedades dos vídeos digitais tem um alto potencial para melhorar os resultados de temperatura de sistemas de codificação de vídeo mantendo bons resultados de qualidade visual dos vídeos codificados. / This thesis presents application-driven temperature-aware solutions for next generation video coding systems, such as the High Efficiency Video Coding (HEVC). Different from state-of-the-art works, the proposed solutions raise the abstraction of temperature management to the application-level, where video coding characteristics and video content properties are used to leverage thermal-aware solutions for video coding with low QoS (Quality of Service) degradation. Several video coding and temperature analyses are performed to understand the behavior of temperature when encoding different video sequences. Based on the analyses results, different approaches are proposed to mitigate the temperature effects on video coding systems. Application-driven temperature management for HEVC uses run-time encoder configuration selection to keep temperature under safe operational state while providing good visual quality results. Temperature optimization using approximate computing uses content-driven approximations to reduce the on-chip temperature of HEVC encoding. Application-driven temperature-aware scheduler leverages application-specific knowledge to guide a scheduling technique targeting reducing the spatial temperature gradients that are resulted from the unbalance workload nature of multi-threaded video coding application. The proposed solutions are able to provide up to 10 °C of chip temperature reduction with negligible compression efficiency loss. Besides, when compared with previous works the resulted objective video quality (PSNR) is from 12 dB up to 20 dB higher. Moreover, the proposed scheduler eliminates spatial temperature gradients greater than 5 ºC of multi-core architectures. As conclusion, this thesis demonstrates that leveraging application-specific knowledge and video content properties has a significant potential to improve temperature profiles of video coding systems while still keeping good quality results.

Esta tese apresenta soluções para o gerenciamento e otimização de temperatura para sistemas de codificação de vídeo baseados nas características da aplicação e no conteúdo dos vídeos digitais. Diferente dos trabalhos estado-da-arte, as soluções propostas nesta tese focam em técnicas de gerenciamento de temperatura no nível da aplicação e características da aplicação codificação de vídeo e as propriedades dos vídeos digitais são explorados para desenvolver soluções termais para a codificação de vídeo com baixas perdas na qualidade de serviço das aplicações. Diversas análises são realizadas considerando a aplicação de codificação de vídeo para entender o comportamento da temperatura durante o processo de codificação para diferentes sequências de vídeo. Com base nos resultados das análises, soluções com diferentes abordagens são propostas para atenuar os efeitos da temperatura nos sistemas de codificação de vídeo. Gerenciamento de temperatura baseado nas características da aplicação para o padrão de codificação HEVC usa uma técnica de seleção de configuração em tempo de execução para manter a temperatura abaixo dos limites seguros de operação com bons resultados de qualidade de vídeo. Otimização de temperatura baseado em computação imprecisa usa aproximações baseadas em conteúdo para reduzir a temperatura de chips executando o HEVC. Um escalonador de tarefas que usa características da aplicação para guiar o escalonamento de threads focando na redução dos gradientes espaciais de temperatura que são resultantes do desbalanceamento natural de cargas entre as threads da aplicação. As soluções propostas são capazes de reduzir em até 10 ºC a temperatura do chip com perdas insignificantes na eficiência de compressão. Os resultados de qualidade objetiva (medida usando PSNR) são de 12 dBs até 20 dBs maiores quando comparados com trabalhos da literatura. Além disso, o escalonador de tarefas proposto é capaz de eliminar os gradientes espaciais de temperatura maiores que 5 ºC para arquitetura multi-cores. Como principal conclusão, esta tese demonstra que as técnicas de gerenciamento de temperatura que usam o conhecimento da aplicação de maneira conjunta com as propriedades dos vídeos digitais tem um alto potencial para melhorar os resultados de temperatura de sistemas de codificação de vídeo mantendo bons resultados de qualidade visual dos vídeos codificados. / This thesis presents application-driven temperature-aware solutions for next generation video coding systems, such as the High Efficiency Video Coding (HEVC). Different from state-of-the-art works, the proposed solutions raise the abstraction of temperature management to the application-level, where video coding characteristics and video content properties are used to leverage thermal-aware solutions for video coding with low QoS (Quality of Service) degradation. Several video coding and temperature analyses are performed to understand the behavior of temperature when encoding different video sequences. Based on the analyses results, different approaches are proposed to mitigate the temperature effects on video coding systems. Application-driven temperature management for HEVC uses run-time encoder configuration selection to keep temperature under safe operational state while providing good visual quality results. Temperature optimization using approximate computing uses content-driven approximations to reduce the on-chip temperature of HEVC encoding. Application-driven temperature-aware scheduler leverages application-specific knowledge to guide a scheduling technique targeting reducing the spatial temperature gradients that are resulted from the unbalance workload nature of multi-threaded video coding application. The proposed solutions are able to provide up to 10 °C of chip temperature reduction with negligible compression efficiency loss. Besides, when compared with previous works the resulted objective video quality (PSNR) is from 12 dB up to 20 dB higher. Moreover, the proposed scheduler eliminates spatial temperature gradients greater than 5 ºC of multi-core architectures. As conclusion, this thesis demonstrates that leveraging application-specific knowledge and video content properties has a significant potential to improve temperature profiles of video coding systems while still keeping good quality results.

Les applications modernes s’appuient sur des architectures qui combinent de plus en plus de composants logiciels émanant de plusieurs éditeurs, implantant des fonctions de plus en plus spécialisées, et très souvent déployés dans le « cloud ». De ce fait, ces applications nécessitent une dynamique et une adaptation certaines vis-à-vis des flux de données que leurs composants échangent et des besoins de qualité de service (QdS) que ces flux requièrent. Pour la majorité des applications, il s’avère difficile d’identifier à l’avance l’ensemble des flux et/ou d’exprimer précisément les besoins de QdS associés. Ainsi, fournir un service de communication réseau capable de répondre et de suivre les besoins de ces applications sans gaspiller, par surdimensionnement, l’utilisation des ressources réseau, pose plusieurs défis aux réseaux de communication supports, notamment un haut degré de flexibilité, largement au-delà des possibilités des réseaux de communication actuels. L’objectif de ce travail de thèse est de développer le concept de réseau guidé par les applications (ADN : Application Driven Networking), réseau capable d’offrir des services de communication personnalisés et dynamiques aux applications. Le qualificatif personnalisé signifie que le service ADN répond à des besoins de communication applicatifs exprimés avec un niveau de granularité très fin pouvant aller jusqu’aux flux élémentaires. Ces besoins peuvent être exprimés explicitement par l’application ou inférés par le réseau par analyse du trafic. L’aspect dynamique signifie que le service ADN est reprogrammé et ajusté pour suivre l’évolution des besoins de l’application dans le temps. Les contributions de ce travail de thèse couvrent plusieurs points. Nous avons défini l’architecture générale d’un réseau ADN bâti sur une infrastructure réseau de type SDN (Software Defined Network) en explicitant ses composants fonctionnels et en spécifiant les interfaces entre composants. Nous avons développé les algorithmes de ses principaux composants, notamment deux algorithmes d’allocation de ressources réseau qui calculent les chemins de données et les ressources réseau à y réserver pour satisfaire les exigences de bande passante et de délai des services ADN, tout en optimisant l’utilisation de ressources. Nous avons mis au point deux heuristiques de migration des services ADN afin de répartir aux mieux la charge du réseau et d’augmenter l’admissibilité des requêtes des services ADN à venir. Nous avons développé un prototype démonstrateur de réseau ADN qui fournit un ensemble de services ADN à des applications dynamiques basées sur le middleware temps réel DDS (Data Distribution Service). / Modern applications are typically composed of lots of software components that tend to implement self-contained specialized functions. These components are often supplied by many software editors and provisioned and accessed via the cloud. As a consequence, the data flows that are exchanged between applications’ components and their QoS requirements vary over time. Moreover, in many situations, it is quite difficult to pre-identify this set of data flows and/or express precisely the associated QoS. Hence, providing a network service that meets application requirements and dynamically evolves with their needs without uselessly wasting network resources poses several challenges to the underlying communication network. Notably, the necessity of a high level of flexibility, far beyond the capabilities of today’s communication networks. The aim of this PhD is to develop the Application Driven Networking (ADN) concept, which is able to provide tailored and dynamic network services to applications. Tailored means that the ADN service captures a fine-grained description of application needs, which can consider elementary flows. These needs can be expressed, either, explicitly by the application or inferred by the network by traffic analysis. The dynamic facet means that the ADN service is reprogrammed and adjusted to fit to evolving application needs. The main contributions of this thesis are the following. First, a general architecture of the ADN network built on top of a Software Defined Network (SDN) infrastructure is proposed. Algorithms related to the ADN functional components are also proposed, in particular two network resource allocation algorithms that calculate the optimal (in terms of network resource utilization) data paths and the required network resources that meet application requirements. Two ADN service migration heuristics are also proposed to efficiently distribute the network load and increase the acceptance of forthcoming network service requests. An ADN network prototype is developed as proof of concept. It provides ADN services to dynamic applications with QoS requirements built on top of the DDS (Data Distribution Service) middleware.

Esta tese apresenta soluções para o gerenciamento e otimização de temperatura para sistemas de codificação de vídeo baseados nas características da aplicação e no conteúdo dos vídeos digitais. Diferente dos trabalhos estado-da-arte, as soluções propostas nesta tese focam em técnicas de gerenciamento de temperatura no nível da aplicação e características da aplicação codificação de vídeo e as propriedades dos vídeos digitais são explorados para desenvolver soluções termais para a codificação de vídeo com baixas perdas na qualidade de serviço das aplicações. Diversas análises são realizadas considerando a aplicação de codificação de vídeo para entender o comportamento da temperatura durante o processo de codificação para diferentes sequências de vídeo. Com base nos resultados das análises, soluções com diferentes abordagens são propostas para atenuar os efeitos da temperatura nos sistemas de codificação de vídeo. Gerenciamento de temperatura baseado nas características da aplicação para o padrão de codificação HEVC usa uma técnica de seleção de configuração em tempo de execução para manter a temperatura abaixo dos limites seguros de operação com bons resultados de qualidade de vídeo. Otimização de temperatura baseado em computação imprecisa usa aproximações baseadas em conteúdo para reduzir a temperatura de chips executando o HEVC. Um escalonador de tarefas que usa características da aplicação para guiar o escalonamento de threads focando na redução dos gradientes espaciais de temperatura que são resultantes do desbalanceamento natural de cargas entre as threads da aplicação. As soluções propostas são capazes de reduzir em até 10 ºC a temperatura do chip com perdas insignificantes na eficiência de compressão. Os resultados de qualidade objetiva (medida usando PSNR) são de 12 dBs até 20 dBs maiores quando comparados com trabalhos da literatura. Além disso, o escalonador de tarefas proposto é capaz de eliminar os gradientes espaciais de temperatura maiores que 5 ºC para arquitetura multi-cores. Como principal conclusão, esta tese demonstra que as técnicas de gerenciamento de temperatura que usam o conhecimento da aplicação de maneira conjunta com as propriedades dos vídeos digitais tem um alto potencial para melhorar os resultados de temperatura de sistemas de codificação de vídeo mantendo bons resultados de qualidade visual dos vídeos codificados. / This thesis presents application-driven temperature-aware solutions for next generation video coding systems, such as the High Efficiency Video Coding (HEVC). Different from state-of-the-art works, the proposed solutions raise the abstraction of temperature management to the application-level, where video coding characteristics and video content properties are used to leverage thermal-aware solutions for video coding with low QoS (Quality of Service) degradation. Several video coding and temperature analyses are performed to understand the behavior of temperature when encoding different video sequences. Based on the analyses results, different approaches are proposed to mitigate the temperature effects on video coding systems. Application-driven temperature management for HEVC uses run-time encoder configuration selection to keep temperature under safe operational state while providing good visual quality results. Temperature optimization using approximate computing uses content-driven approximations to reduce the on-chip temperature of HEVC encoding. Application-driven temperature-aware scheduler leverages application-specific knowledge to guide a scheduling technique targeting reducing the spatial temperature gradients that are resulted from the unbalance workload nature of multi-threaded video coding application. The proposed solutions are able to provide up to 10 °C of chip temperature reduction with negligible compression efficiency loss. Besides, when compared with previous works the resulted objective video quality (PSNR) is from 12 dB up to 20 dB higher. Moreover, the proposed scheduler eliminates spatial temperature gradients greater than 5 ºC of multi-core architectures. As conclusion, this thesis demonstrates that leveraging application-specific knowledge and video content properties has a significant potential to improve temperature profiles of video coding systems while still keeping good quality results.

A prevalent morphology in the microscopic world of artificial microswimmers, bacteria and viruses is that of a helix. The intriguingly different physics at play at the small scale level make it necessary for bacteria to employ swimming strategies different from our everyday experience, such as the rotation of a helical filament. Bio-inspired microswimmers that mimic bacterial locomotion achieve propulsion at the microscale level using magnetically actuated, rotating helical filaments. A promising application of these artificial microswimmers is in non-invasive medicine, for drug delivery to tumours or microsurgery. Two crucial features need to be addressed in the design of microswimmers. First, the ability to selectively control large ensembles and second, the adaptivity to move through complex conduit geometries, such as the constrictions and curves of the tortuous tumour microvasculature. In this dissertation, a mechanics-based selective control mechanism for magnetic microswimmers is proposed, and a model and simulation of an elastic helix passing through a constricted microchannel are developed. Thereafter, a theoretical framework is developed for the propulsion by stiff elastic filaments in viscous fluids. In order to address this fluid-structure problem, a pertubative, asymptotic, elastohydrodynamic approach is used to characterise the deformation that arises from and in turn affects the motion. This framework is applied to the helical filaments of bacteria and magnetically actuated microswimmers. The dissertation then turns to the sub-bacterial scale of bacteriophage viruses, 'phages' for short, that infect bacteria by ejecting their genetic material and replicating inside their host. The valuable insight that phages can offer in our fight against pathogenic bacteria and the possibility of phage therapy as an alternative to antibiotics, are of paramount importance to tackle antibiotics resistance. In contrast to typical phages, flagellotropic phages first attach to bacterial flagella, and have the striking ability to reach the cell body for infection, despite their lack of independent motion. The last part of the dissertation develops the first theoretical model for the nut-and-bolt mechanism (proposed by Berg and Anderson in 1973). A nut being rotated will move along a bolt. Similarly, a phage wraps itself around a flagellum possessing helical grooves, and exploits the rotation of the flagellum in order to passively travel along and towards the cell body, according to this mechanism. The predictions from the model agree with experimental observations with respect to directionality, speed and the requirements for succesful translocation.