L'objectif de cette thèse est d'étudier le comportement de différentes représentations d'images, notamment apprentissage profond, dans le contexte d'application en imagerie médicale. Le but est de développer une méthode unifiée efficace pour les applications visées que sont la super résolution, la segmentation et la synthèse. La super-résolution est un procès d'estimation d'une image haute-résolution à partir d'une ou plusieurs images basses résolutions. Dans cette thèse, nous nous concentrons sur la super résolutionunique, c'est-à-dire que l'image haute résolution (HR) est estimée par une image basse-résolution (LR) correspondante. Augmenter la résolution de l'image grâce à la super-résolution est la clé d'une compréhension plus précise de l'anatomie. L'application de la super résolution permet d'obtenir des cartes de segmentation plus précises. Étant donné que deux bases de données qui contiennent les images différentes (par exemple, les images d'IRM et les images de CT), la synthèse est un procès d'estimation d'une image qui est approximative aux images dans la base de données de cible à partir d'une image de la base de données de source. Parfois, certains contrastes tissulaires ne peuvent pas être acquis pendant la séance d'imagerie en raison du temps et des coûts élevés ou de l'absence d'appareils. Une solution possible est à utiliser des méthodes de synthèse d'images médicales pour générer les images avec le contraste différent qui est manquée dans le domaine à cible à partir de l'image du domaine donnée. L'objectif des images synthétiques est d'améliorer d'autres étapes du traitement automatique des images médicales telles que la segmentation, la super-résolution ou l'enregistrement. Dans cette thèse, nous proposons les réseaux neurones pour la super résolutionet la synthèse d'image médicale. Les résultats démontrent le potentiel de la méthode que nous proposons en ce qui concerne les applications médicales pratiques. / In this thesis, our motivation is dedicated to studying the behaviors of different image representations and developing a method for super-resolution, cross-modal synthesis and segmentation of medical imaging. Super-Resolution aims to enhance the image resolution using single or multiple data acquisitions. In this work, we focus on single image super-resolution (SR) that estimates the high-resolution (HR) image from one corresponding low-resolution (LR) image. Increasing image resolution through SR is a key to more accurate understanding of the anatomy. The applications of super-resolution have been shown that applying super-resolution techniques leads to more accurate segmentation maps. Sometimes, certain tissue contrasts may not be acquired during the imaging session because of time-consuming, expensive costor lacking of devices. One possible solution is to use medical image cross-modal synthesis methods to generate the missing subject-specific scans in the desired target domain from the given source image domain. The objective of synthetic images is to improve other automatic medical image processing steps such as segmentation, super-resolution or registration. In this thesis, convolutional neural networks are applied to super-resolution and cross-modal synthesis in the context of supervised learning. In addition, an attempt to apply generative adversarial networks for unpaired cross-modal synthesis brain MRI is described. Results demonstrate the potential of deep learning methods with respect to practical medical applications.

Neste trabalho foram investigados dois sistemas de multicamadas de semicondutores amorfos, a-SI:h/SI IND.1-XC IND.X:h e a-SI:h/a-GE:h, crescidos pela técnica de plasma enhanced chemical vapor deposition (PECVD). A difração de raios x a baixo angulo (SAXRD) foi a técnica utilizada para estudo das propriedades estruturais destas super-redes. Os objetivos deste trabalho foram: a) determinar as propriedades estruturais destes sistemas, no que tange a periodicidade da super-rede, uniformidade em espessura e tipo de interface; b) desenvolver modelos teóricos de simulação das intensidades difratadas; e c) avaliar o processo de difusão e cristalização dos componentes das multicamadas, através de tratamentos térmicos. As multicamadas de a-SI:h/a-SI IND.1-XC IND.X:h foram crescidas variando-se dois parâmetros de deposição: a concentração de metano na mistura gasosa e o tempo de plasma etching de hidrogênio entre deposições consecutivas. A combinação dos resultados de espectroscopia de eletrons auger (aes) e saxrd permitiram avaliar a espessura das interfaces. Interfaces mais abruptas foram obtidas em sistemas crescidos sobre uma camada buffer, tempos de plasma etching de hidrogênio de, pelo menos, 2min, e camadas de a-SI IND.1-XC IND.X:H crescidas com mais alta concentração de CH IND.4 na mistura gasosa e em condições de baixo fluxo de silano. / In this work, two types of amorphous semiconductor multilayers were investigated, a-SI:h/SI IND.1-XC IND.X:h and a-SI:h/a-GE:h, deposited by the Plasma Enhanced Chemical Vapor Deposition (PECVD) method. The Small Angle X-Ray Diffraction (SAXRD) technique was used to study the structural properties of these super-lattices. The aim of this work was: a) to determine the structural properties of these systems, including the periodicity, thickness uniformity and interface sharpness; b) to develop theoretical models to simulate the diffracted intensities; and c) to evaluate the diffusion and crystallization processes of the multilayer components, by means of heat treatments. The a-SI:h/a-SI IND.1-XC IND.X multilayers were deposited, varying two growth parameters: the methane concentration in the gaseous mixture and the intermediate plasma etching time between consecutive depositions. The Auger Electron Spectroscopy (AES) and SAXRD results were combined to evaluate the interface thickness. The sharpest interfaces were obtained on samples deposited on top of a buffer layer, plasma etching times of at least 2 min. and a-SI IND.1-XC IND.X:H layers deposited with a higher CH IND.4. concentration in the gaseous mixture and in conditions of low silane flow.

Made available in DSpace on 2016-07-27T14:21:45Z (GMT). No. of bitstreams: 1 Laura Drummond de Azeredo Coutinho Jardim.pdf: 625995 bytes, checksum: 003129089832e8f2fc79846f74a3472e (MD5) Previous issue date: 2009-04-25 / The present study has the objective of analyzing the possibility of including in Psychological Assistance Institutions, because of the huge demand, Super Heroes Therapeutic Groups. This idea has emerge from the perception of a necessity of group work in institutions, aiming to decrease the waiting list of patients, adding the possibility of inserting the theme Super Heroes as therapeutic mediator, observing that, nowadays, children have been presenting in their speech and play, interest in histories and films about them. The technique developed in this research is an adaptation of Gutfreind (2003) experience with fairytales therapeutic groups. Six children, of both sexes, going to school, age range between five and seven year s old and parents with low income were the group attended. All these kids were in the waiting list of patients, and had claimed of familiar relationship difficulties. These Therapeutic Groups happened in ten dates: two were designated to interview the parents and the other eight to meet and be with the children. At the end of the research, even though some considerations were made, could be seen that the Therapeutic Group helped in the emotional development and also offered some tools to the kids to work with reality. / O presente estudo tem como objetivo analisar a possibilidade de incluir em instituições de atendimento psicológico, onde a demanda é grande, Oficinas Terapêuticas com Super Heróis. Essa idéia surgiu a partir de uma percepção da necessidade de trabalhos em grupos em instituições visando diminuir a espera do atendimento, somado a questão da possibilidade de inserção dos Super Heróis como mediadores terapêuticos, visto que atualmente a criança, tanto em seu discurso quanto em suas brincadeiras, apresenta um grande interesse pelas suas histórias e filmes. A técnica desenvolvida na pesquisa é uma adaptação a partir de a experiência de Gutfreind (2003), com ateliês de contos de fadas. Participaram da pesquisa seis crianças de ambos os sexos e com idades entre cinco e sete anos, de baixa renda e que frequentam escola. Todas essas crianças haviam buscado atendimento na instituição com queixas ligadas a problemas de relacionamento familiar. As Oficinas Terapêuticas aconteceram em dez encontros, no qual dois foram reservados para entrevistas com os pais e os outros oito encontros com as crianças. Ao final da pesquisa, apesar de algumas considerações terem sido levantadas, percebeu-se que as Oficinas auxiliaram no desenvolvimento emocional e também ofereceram recursos para as crianças lidarem com a realidade.

Des techniques variées de visualisation de molécules d’intérêt sur cellules vivantes ou fixées ont permis de suivre leur synthèse, localisation, dégradation et autres activités. Dans cette étude, nous avons développé deux outils de fluorescence pour étudier la synthèse des protéines sur bactéries vivantes. Le premier décrit l’utilisation du système Spinach pour l’imagerie du ribosome. Cette approche diffère des méthodes conventionnelles qui utilisent des protéines fluorescentes puisque l’ARN ribosomal 16S contient un aptamère qui rend fluorescent un composé fluorogène. Une étude comparative de la performance de différents aptamères Spinach a été réalisée. Un deuxième outil se focalise sur l’accumulation d’un antibiotique de la famille des aminoglycosides (ligand du ribosome) conjugué à un fluorophore. Ce nouveau conjugué, qui a conservé son activité bactéricide permet pour la première fois de visualiser l’accumulation de l’antibiotique sur bactérie vivante. Cela permet une analyse au niveau de la cellule unique d’une population bactérienne exposée à l’antibiotique. Nous avons également obtenu des données sur la localisation de l’antibiotique une fois qu’il a pénétré dans la bactérie à une résolution inégalée par microscopie super-résolutive. Nous espérons que ces deux méthodes vont maintenant permettre une meilleure compréhension de la synthèse des protéines et fournir une vue nouvelle de la pénétration des antibiotiques dans les bactéries pour y produire leur action bactéricide. / Various visualizing techniques have previously enabled monitoring the fate of molecules of interest: their expression, localization, degradation and other activities in live or fixed cells. In this study, we have developed two fluorescent tools to study protein synthesis in live bacterial cell. The first one describes the application of Spinach system to ribosomes imaging. This is different from conventional methods (that use fluorescent proteins) in that 16S rRNA contains an inserted RNA aptamer that elicits fluorescence of a fluorogenic compound. A comparative study of the performance of different Spinach aptamers was performed here. A second system focuses on the uptake of a fluorescently labeled ligand of the ribosome, an antibiotic of the class of aminoglycosides. This novel conjugate, which kept its bactericidal activity allows for the first time imaging of aminoglycoside uptake on live bacteria. This opened the door to a single cell analysis of bacterial cell populations. We also obtained data about the localization of the antibiotic once inside the bacteria to an unprecedented resolution using super resolution microscopy. We hope that both of these methods will contribute to a better understanding of protein synthesis as well as provide a novel view on the way antibiotics penetrate into cells and perform their bactericidal action.

Ce travail de thèse concerne l'amélioration du pouvoir de résolution de la microscopie optique en champ lointain. Nous avons développé des techniques qui tirent profit de la relation liant le champ électromagnétique émis par un objet à l’éclairement utilisé. En utilisant plusieurs images obtenues pour différents éclairements, et à l’aide d’un algorithme d'inversion approprié, il est possible d'accéder à des fréquences spatiales de l'objet habituellement filtrées par le microscope.Ce concept est d’abord appliqué à une technique de microscopie cohérente : la tomographique optique de diffraction. Elle permet d’obtenir numériquement une carte quantitative de la permittivité diélectrique de l'objet, avec une résolution supérieure à celle d'un microscope classique, à partir de plusieurs hologrammes de l'échantillon. Dans ce cadre, nous montrons que le phénomène de diffusion multiple permet d’atteindre des résolutions encore plus spectaculaires s’il est pris en compte. Nous étudions ensuite la microscopie de fluorescence par éclairement structuré, que nous proposons d’améliorer de deux manières différentes. Dans la première, nous utilisons un algorithme d’inversion capable de retrouver simultanément la densité de fluorescence et les éclairements utilisés. Grâce à celui-ci, nous pouvons remplacer l’illumination périodique et contrôlée généralement utilisée, par des speckles aléatoires formés avec un montage remarquablement simple. Nous montrons expérimentalement l'efficacité de cette approche. Dans un second temps, nous proposons de remplacer la lamelle de verre sur laquelle est repose l’échantillon par un réseau diélectrique nanométrique. Celui-ci crée à sa surface une grille de lumière de période inférieure à la limite de diffraction, ce qui permet d’améliorer d’avantage la résolution finale de l’image reconstruite. Nous détaillons la conception, la fabrication et la caractérisation expérimentale de ce substrat nanostructuré. / This PhD work focuses on the resolution improvement of far-field optical microscopy. We have studied and developed different techniques that take advantage of the relationship between the sample, the illumination and the diffracted (or emitted) field, in order to increase final band-pass of the image beyond that imposed by the diffraction phenomenon. In In these approaches, several images of the same sample are recorded under different illuminations. An inversion algorithm in then used to reconstruct a super-resolved map of the sample from the set of measurements.This concept is first applied to coherent microscopy. In tomographic diffraction microscopy, many holograms of the same unstained sample are obtained under various incidences, then used to numerically reconstruct a quantitative map of permittivity of the sample. The resolution is usually better than that of classical wide-field microscopy. We show theoretically and experimentally that, far from being a drawback, the presence of multiple scattering within the sample can, if properly accounted for, lead a to an even better resolution.We then study structured illumination fluorescence microscopy. We present two different ways for improving this method. The first one takes advantage of an inversion algorithm, which is able to retrieve the fluorescence density without knowing the illumination patterns. This algorithm permits one to replace the periodic light pattern classically used in structured illumination microscopy by unknown random speckle patterns. The implementation of the technique is thus considerably simplified while the resolution improvement remains. In the second approach, we propose to replace the coverslip on which the sample usually lays, by a sub-lambda grating. The latter is used to form, in near field, a light grid with sub-diffraction period that is able to probe the finest details of the sample. The design, fabrication and optical characterization of this key structure are detailed.

Neste trabalho foram investigados dois sistemas de multicamadas de semicondutores amorfos, a-SI:h/SI IND.1-XC IND.X:h e a-SI:h/a-GE:h, crescidos pela técnica de plasma enhanced chemical vapor deposition (PECVD). A difração de raios x a baixo angulo (SAXRD) foi a técnica utilizada para estudo das propriedades estruturais destas super-redes. Os objetivos deste trabalho foram: a) determinar as propriedades estruturais destes sistemas, no que tange a periodicidade da super-rede, uniformidade em espessura e tipo de interface; b) desenvolver modelos teóricos de simulação das intensidades difratadas; e c) avaliar o processo de difusão e cristalização dos componentes das multicamadas, através de tratamentos térmicos. As multicamadas de a-SI:h/a-SI IND.1-XC IND.X:h foram crescidas variando-se dois parâmetros de deposição: a concentração de metano na mistura gasosa e o tempo de plasma etching de hidrogênio entre deposições consecutivas. A combinação dos resultados de espectroscopia de eletrons auger (aes) e saxrd permitiram avaliar a espessura das interfaces. Interfaces mais abruptas foram obtidas em sistemas crescidos sobre uma camada buffer, tempos de plasma etching de hidrogênio de, pelo menos, 2min, e camadas de a-SI IND.1-XC IND.X:H crescidas com mais alta concentração de CH IND.4 na mistura gasosa e em condições de baixo fluxo de silano. / In this work, two types of amorphous semiconductor multilayers were investigated, a-SI:h/SI IND.1-XC IND.X:h and a-SI:h/a-GE:h, deposited by the Plasma Enhanced Chemical Vapor Deposition (PECVD) method. The Small Angle X-Ray Diffraction (SAXRD) technique was used to study the structural properties of these super-lattices. The aim of this work was: a) to determine the structural properties of these systems, including the periodicity, thickness uniformity and interface sharpness; b) to develop theoretical models to simulate the diffracted intensities; and c) to evaluate the diffusion and crystallization processes of the multilayer components, by means of heat treatments. The a-SI:h/a-SI IND.1-XC IND.X multilayers were deposited, varying two growth parameters: the methane concentration in the gaseous mixture and the intermediate plasma etching time between consecutive depositions. The Auger Electron Spectroscopy (AES) and SAXRD results were combined to evaluate the interface thickness. The sharpest interfaces were obtained on samples deposited on top of a buffer layer, plasma etching times of at least 2 min. and a-SI IND.1-XC IND.X:H layers deposited with a higher CH IND.4. concentration in the gaseous mixture and in conditions of low silane flow.

Num cenário em que dispositivos de aquisição de imagens e vídeo possuem recursos limitados ou as imagens disponíveis não possuem boa qualidade, as técnicas de super-resolução (SR) apresentam uma excelente alternativa para melhorar a qualidade das imagens. Nesta tese é apresentada uma proposta para super-resolução de imagem única que combina os benefícios da interpolação no domínio da transformada DCT e a eficiência dos métodos de reconstrução baseados no conceito de representação esparsa de sinais. A proposta busca aproveitar as melhorias já alcançadas na qualidade e eficiência computacional dos principais algoritmos de super-resolução existentes. O método de super-resolução proposto implementa algumas melhorias nas etapas de treinamento e reconstrução da imagem final. Na etapa de treinamento foi incluída uma nova etapa de extração de características utilizando técnicas de aguçamento por máscara de nitidez e construção de um novo dicionário. Esta estratégia busca extrair mais informações estruturais dos fragmentos de baixa e alta resolução do conjunto de treinamento e ao mesmo tempo reduzir o tamanho dos dicionários. Outra importante contribuição foi a inclusão de um processo iterativo e escalonável no algoritmo, reinserindo no conjunto de treinamento e na etapa de reconstrução, uma imagem de alta resolução obtida numa primeira iteração. Esta solução possibilitou uma melhora na qualidade da imagem de alta resolução final utilizando poucas imagens no conjunto de treinamento. As simulações computacionais demonstraram a capacidade do método proposto em produzir imagens com qualidade e com tempo computacional reduzido. / In a scenario in which the acquisition systems have limited resources or available images do not have good quality, the super-resolution (SR) techniques have become an excellent alternative for improving the image quality. In this thesis, we propose a single-image super-resolution (SR) method that combines the benefits of the DCT interpolation and efficiency of sparse representation method for image reconstruction. Also, the proposed method seeks to take advantage of the improvements already achieved in quality and computational efficiency of the existing SR algorithms. The proposed method implements some improvements in the dictionary training and the reconstruction process. A new dictionary was built by using an unsharp mask technique to characteristics extraction. Simultaneously, this strategy aim to extract more structural information of the low resolution and high resolution patches and reduce the dictionaries size. Another important contribution was the inclusion of an iterative and scalable process by reinserting the HR image obtained of first iteration. This solution aim to improve the quality of the final HR image using a few images in the training set. The results have demonstrated the ability of the proposed method to produce high quality images with reduced computational time.

Depuis quelques temps, les physiciens théoriciens de la matière condensée sont confrontés à un problème majeur : la puissance de calcul nécessaire pour simuler numériquement et étudier certains systèmes à N corps est insuffisante. Comme le contrôle et l’utilisation des systèmes d’atomes ultra-froids se sont développés de manière importante,principalement durant les deux dernières décennies, nous sommes peut-être en mesure d eproposer une solution alternative : utiliser des atomes ultra-froids piégés dans des réseaux optiques en tant que simulateur quantique. En effet, la physique des électrons se déplaçant sur la structure cristalline d’un solide, ainsi que celle des atomes piégés dans des réseaux optiques, sont toutes les deux décrites par le même modèle de Fermi-Hubbard, qui est une présentation simplifiée du comportement des fermions sur un réseau périodique. Les simulateurs quantiques peuvent donc simuler des propriétés électriques des matériaux, telle sque la conductivité ou le comportement isolant, et potentiellement aussi des propriété smagnétiques telles que l’ordre antiferromagnétique.L’expérience AUFRONS, sur laquelle j’ai travaillé pendant mon doctorat, a pour but d’étudie rla physique des fermions fortement corrélés, avec un simulateur quantique basé sur l’utilisation d’atomes ultra-froids de rubidium 87 et de potassium 40, piégés dans le potentiel nanostructuré des réseaux optiques bidimensionnels, générés en champ proche. Pour détecter la distribution atomique à d’aussi courtes distances, nous avons développé une technique d’imagerie novatrice, qui nous permettra de contourner la limite de diffraction. Une fois terminé, notre système d’imagerie pourrait potentiellement détecter et identifier des sites individuels du réseau optique sub-longueur d’onde.Dans ce manuscrit, je décris le travail que j’ai effectué pour construire l’expérience AUFRONS,ainsi que l’étude de faisabilité que j’ai réalisée pour la technique d’imagerie à super-résolution. / For some time now, theoretical physicists in condensed matter face a majorproblem: the computing power needed to numerically simulate and study some interactingmany-body systems is insufficient. As the control and use of ultracold atomic systems hasexperimented a significant development in recent years, an alternative to this problem is to usecold atoms trapped in optical lattices as a quantum simulator. Indeed, the physics of electronsmoving on a crystalline structure of a solid, and the one of trapped atoms in optical lattices areboth described by the same model, the Fermi-Hubbard model, which is a simplifiedrepresentation of fermions moving on a periodic lattice. The quantum simulators can thusreproduce the electrical properties of materials such as conductivity or insulating behavior, andpotentially also the magnetic ones such as antiferromagnetism.The AUFRONS experiment, in which I worked during my PhD, aims at building a quantumsimulator based on cooled atoms of 87Rb and 40K trapped in near field nanostructured opticalpotentials. In order to detect the atom distribution at such small distances, we have developedan innovative imaging technique for getting around the diffraction limit. This imaging systemcould potentially allow us to detect single-site trapped atoms in a sub-wavelength lattice.In this thesis, I introduce the work I have done for building the AUFRONS experiment, as wellas the feasability study that I did for the super-resolution imaging technique.

La ''super-résolution'' est définie comme une classe de techniques qui améliorent la résolution spatiale d’images. Les méthodes de super-résolution peuvent être subdivisés en méthodes à partir d’une seule image et à partir de multiple images. Cette thèse porte sur le développement d’algorithmes basés sur des théories mathématiques pour résoudre des problèmes de super-résolution à partir d’une seule image. En effet, pour estimer un’image de sortie, nous adoptons une approche mixte : nous utilisons soit un dictionnaire de « patches » avec des contraintes de parcimonie (typique des méthodes basées sur l’apprentissage) soit des termes régularisation (typiques des méthodes par reconstruction). Bien que les méthodes existantes donnent déjà de bons résultats, ils ne prennent pas en compte la géométrie des données dans les différentes tâches. Par exemple, pour régulariser la solution, pour partitionner les données (les données sont souvent partitionnées avec des algorithmes qui utilisent la distance euclidienne comme mesure de dissimilitude), ou pour apprendre des dictionnaires (ils sont souvent appris en utilisant PCA ou K-SVD). Ainsi, les méthodes de l’état de l’art présentent encore certaines limites. Dans ce travail, nous avons proposé trois nouvelles méthodes pour dépasser ces limites. Tout d’abord, nous avons développé SE-ASDS (un terme de régularisation basé sur le tenseur de structure) afin d’améliorer la netteté des bords. SE-ASDS obtient des résultats bien meilleurs que ceux de nombreux algorithmes de l’état de l’art. Ensuite, nous avons proposé les algorithmes AGNN et GOC pour déterminer un sous-ensemble local de données d’apprentissage pour la reconstruction d’un certain échantillon d’entrée, où l’on prend en compte la géométrie sous-jacente des données. Les méthodes AGNN et GOC surclassent dans la majorité des cas la classification spectrale, le partitionnement de données de type « soft », et la sélection de sous-ensembles basée sur la distance géodésique. Ensuite, nous avons proposé aSOB, une stratégie qui prend en compte la géométrie des données et la taille du dictionnaire. La stratégie aSOB surpasse les méthodes PCA et PGA. Enfin, nous avons combiné tous nos méthodes dans un algorithme unique, appelé G2SR. Notre algorithme montre de meilleurs résultats visuels et quantitatifs par rapport aux autres méthodes de l’état de l’art. / Image super-resolution is defined as a class of techniques that enhance the spatial resolution of images. Super-resolution methods can be subdivided in single and multi image methods. This thesis focuses on developing algorithms based on mathematical theories for single image super-resolution problems. Indeed, in order to estimate an output image, we adopt a mixed approach: i.e., we use both a dictionary of patches with sparsity constraints (typical of learning-based methods) and regularization terms (typical of reconstruction-based methods). Although the existing methods already perform well, they do not take into account the geometry of the data to: regularize the solution, cluster data samples (samples are often clustered using algorithms with the Euclidean distance as a dissimilarity metric), learn dictionaries (they are often learned using PCA or K-SVD). Thus, state-of-the-art methods still suffer from shortcomings. In this work, we proposed three new methods to overcome these deficiencies. First, we developed SE-ASDS (a structure tensor based regularization term) in order to improve the sharpness of edges. SE-ASDS achieves much better results than many state-of-the-art algorithms. Then, we proposed AGNN and GOC algorithms for determining a local subset of training samples from which a good local model can be computed for reconstructing a given input test sample, where we take into account the underlying geometry of the data. AGNN and GOC methods outperform spectral clustering, soft clustering, and geodesic distance based subset selection in most settings. Next, we proposed aSOB strategy which takes into account the geometry of the data and the dictionary size. The aSOB strategy outperforms both PCA and PGA methods. Finally, we combine all our methods in a unique algorithm, named G2SR. Our proposed G2SR algorithm shows better visual and quantitative results when compared to the results of state-of-the-art methods.

Protein sequence motifs are gathering more and more attention in the field of sequence analysis. The recurring patterns have the potential to determine the conformation, function and activities of the proteins. In our work, we obtained protein sequence motifs which are universally conserved across protein family boundaries. Therefore, unlike most popular motif discovering algorithms, our input dataset is extremely large. As a result, an efficient technique is essential. We use two granular computing models, Fuzzy Improved K-means (FIK) and Fuzzy Greedy K-means (FGK), in order to efficiently generate protein motif information. After that, we develop an efficient Super Granular SVM Feature Elimination model to further extract the motif information. During the motifs searching process, setting up a fixed window size in advance may simplify the computational complexity and increase the efficiency. However, due to the fixed size, our model may deliver a number of similar motifs simply shifted by some bases or including mismatches. We develop a new strategy named Positional Association Super-Rule to confront the problem of motifs generated from a fixed window size. It is a combination approach of the super-rule analysis and a novel Positional Association Rule algorithm. We use the super-rule concept to construct a Super-Rule-Tree (SRT) by a modified HHK clustering, which requires no parameter setup to identify the similarities and dissimilarities between the motifs. The positional association rule is created and applied to search similar motifs that are shifted some residues. By analyzing the motifs results generated by our approaches, we realize that these motifs are not only significant in sequence area, but also in secondary structure similarity and biochemical properties.