[pt] Pesquisa de cunho micro-etnográfico, realizada em aulas de ciências exatas numa universidade do Rio de Janeiro, descreve e analisa o surgimento e gerenciamento de conflitos entre participantes em sala de aula. A fundamentação teórica se baseia nos pressupostos da Sociolingüística Interacional para análise do discurso oral. Realizou-se uma triangulação metodológica que incluiu o método de observação participante, gravações em vídeo/áudio e entrevistas. Os resultados mostram que os conflitos entre os participantes decorrem de: relações paradoxais criadas por alinhamentos contraditórios; distintas expectativas em relação à aula e ao programa do curso; diferentes interpretações acerca da função dos alinhamentos, e relativização da assimetria entre professores e alunos o que permite a expressão de alinhamentos humorísticos e agressivos. Outros resultados mostram como os conflitos são movimentos importantes para os participantes construírem novas relações com os outros membros do grupo. Este estudo é uma reflexão acerca dos enquadres de conflito o que pode contribuir para a prática do professor como educador. / [en] This micro-analytical research, conducted in a formal course at a graduate school of computer science in Rio de Janeiro, describes and analyzes the appearance and management of conflicts between participants in the classroom. An Interactional Sociolinguistic theoretical perspective is taken up to analyze oral discourse. Methodological triangulation, which included participant-observation, video/audio recording, and interviewing, was carried out. Results show that conflicts between participants are brought about by: paradoxical relationships due to contradictory alignments; different expectations associated to the course and its agenda; different interpretations related to alignment functions, and mitigated asymmetrical relationships allowing humorous and aggressive alignments to become evident. Other results reveal how conflicts can be important movements in the construction of new relationships with other members of the group. This study is a reflection about conflict frames, which can contribute to the teacher`s practice as an educator.

A computational grid is a hardware and software infrastructure that provides dependable, consistent, pervasive, and inexpensive access to high-end computational capabilities. This talk is divided into three parts. Firstly, we give an overview of the main issues in grid computing. Next, we introduce ALiCE (Adaptive and Scalable Internet-based Computing Engine), a platform independent and lightweight grid. ALiCE exploits object-level parallelism using our Object Network Transport Architecture (ONTA). Grid applications are written using ALiCE Object Programming Template that hides the complexities of the underlying grid fabric. Lastly, we present some performance results of ALiCE applications including the geo-rectification of satellite images and the progressive multiple sequence alignments problem. / Singapore-MIT Alliance (SMA)

Grapheme-to-phoneme conversion (G2P) is the task of converting a word, represented by a sequence of graphemes, to its pronunciation, represented by a sequence of phonemes. The G2P task plays a crucial role in speech synthesis systems, and is an important part of other applications, including spelling correction and speech-to-speech machine translation. G2P conversion is a complex task, for which a number of diverse solutions have been proposed. In general, the problem is challenging because the source string does not unambiguously specify the target representation. In addition, the training data include only example word pairs without the structural information of subword alignments. In this thesis, I introduce several novel approaches for G2P conversion. My contributions can be categorized into (1) new alignment models and (2) new output generation models. With respect to alignment models, I present techniques including many-to-many alignment, phonetic-based alignment, alignment by integer linear programing and alignment-by-aggregation. Many-to-many alignment is designed to replace the one-to-one alignment that has been used almost exclusively in the past. The new many-to-many alignments are more precise and accurate in expressing grapheme-phoneme relationships. The other proposed alignment approaches attempt to advance the training method beyond the use of Expectation-Maximization (EM). With respect to generation models, I first describe a framework for integrating many-to-many alignments and language models for grapheme classification. I then propose joint processing for G2P using online discriminative training. I integrate a generative joint n-gram model into the discriminative framework. Finally, I apply the proposed G2P systems to name transliteration generation and mining tasks. Experiments show that the proposed system achieves state-of-the-art performance in both the G2P and name transliteration tasks.

Vues de sécurité xml : requêtes, mises à jour, et schémas. Les évolutions technologiques ont consacré l'émergence des services web et du stockage des données en ligne, en complément des bases de données traditionnelles. Ces évolutions facilitent l'accès aux données, mais en contrepartie soulèvent de nouvelles problématiques de sécurité. La mise en œuvre de politiques de contrôle d'accès appropriées est une des approches permettant de réduire ces risques.Nous étudions ici les politiques de contrôle d'accès au niveau d'un document XML, politiques que nous modélisons par des vues de sécurité XML (non matérialisées) à l'instar de Fan et al. Ces vues peuvent être représentées facilement par des alignements d'arbres grâce à l'absence d'opérateurs arithmétiques ou de restructuration. Notre objectif est par conséquent d'examiner comment manipuler efficacement ce type de vues, à l'aide des méthodes formelles, et plus particulièrement des techniques de réécriture de requêtes et la théorie des automates d'arbres. Trois directions principales ont orienté nos recherches: nous avons tout d'abord élaboré des algorithmes pour évaluer l'expressivité d'une vue, en fonction des requêtes qui peuvent être exprimées à travers cette vue. Il s'avère que l'on ne peut décider en général si une vue permet d'exprimer une requête particulière, mais cela devient possible lorsque la vue satisfait des hypothèses générales. En second lieu, nous avons considéré les problèmes soulevés par la mises à jour du document à travers une vue. Enfin, nous proposons des solutions pour construire automatiquement un schéma de la vue. En particulier, nous présentons différentes techniques pour représenter de façon approchée l'ensemble des documents au moyen d'une DTD.

The focus of this thesis is to develop computational techniques for analysis of protein structures. We model protein structures as points in 3-dimensional space which in turn are modeled as weighted graphs. The problem of protein structure comparison is posed as a weighted graph matching problem and an algorithm motivated from the spectral graph matching techniques is developed. The thesis also proposes novel similarity measures by deriving kernel functions. These kernel functions allow the data to be mapped to a suitably defined Reproducing kernel Hilbert Space(RKHS), paving the way for efficient algorithms for protein structure classification. Protein structure comparison (structure alignment)is a classical method of determining overall similarity between two protein structures. This problem can be posed as the approximate weighted subgraph matching problem, which is a well known NP-Hard problem. Spectral graph matching techniques provide efficient heuristic solution for the weighted graph matching problem using eigenvectors of adjacency matrices of the graphs. We propose a novel and efficient algorithm for protein structure comparison using the notion of neighborhood preserving projections (NPP) motivated from spectral graph matching. Empirically, we demonstrate that comparing the NPPs of two protein structures gives the correct equivalences when the sizes of proteins being compared are roughly similar. Also, the resulting algorithm is 3 -20 times faster than the existing state of the art techniques. This algorithm was used for retrieval of protein structures from standard databases with accuracies comparable to the state of the art. A limitation of the above method is that it gives wrong results when the number of unmatched residues, also called insertions and deletions (indels), are very high. This problem was tackled by matching neighborhoods, rather than entire structures. For each pair of neighborhoods, we grow the neighborhood alignments to get alignments for entire structures. This results in a robust method that has outperformed the existing state of the art methods on standard benchmark datasets. This method was also implemented using MPI on a cluster for database search. Another important problem in computational biology is classification of protein structures into classes exhibiting high structural similarity. Many manual and semi-automatic structural classification databases exist. Kernel methods along with support vector machines (SVM) have proved to be a robust and principled tool for classification. We have proposed novel positive semidefinite kernel functions on protein structures based on spatial neighborhoods. The kernels were derived using a general technique called convolution kernel, and showed to be related to the spectral alignment score in a limiting case. These kernels have outperformed the existing tools when validated on a well known manual classification scheme called SCOP. The kernels were designed keeping the general problem of capturing structural similarity in mind, and have been successfully applied to problems in other domains, e.g. computer vision.

No description available.

[pt] Baseando-se em teorias da Sociolingüística Interacional e Análise da Conversa, mais especificamente, da Fala-em-interação em contexto institucional, analisa-se o papel do mediador no gerenciamento de conflitos entre consumidor e empresas reclamadas em um Juizado Especial Cível de Relações de Consumo. Utiliza-se, como dados, gravações de fala-em-interação em audiências de conciliação desse juizado. A resolução de conflitos em ambiente institucional difere da disputa informal por contar com um mandato institucional particular que direciona uma organização interacional, na qual os direitos de participação são restritos, diferentemente da conversa cotidiana. Expectativas de normas, status de participação diferenciados e seqüência de procedimentos caracterizam a audiência de conciliação e possibilitam a sua divisão em dois momentos principais: a narrativa e a negociação. Analisando o papel do mediador nesses dois momentos, observa-se que ele co- constrói a história do consumidor, por meio de perguntas e de formulações. Assim, durante o relato do conflito, o mediador se alinha, na maior parte das vezes, com o consumidor. Durante a negociação, o mediador pode mudar o seu alinhamento com a finalidade de cumprir a sua tarefa institucional de negociar e conseguir conciliar os adversários. Desse modo, pode-se concluir que os alinhamentos do mediador são direcionados para a sua tarefa institucional. / [en] Based on Interactional Sociolinguistics and Conversation Analysis theories, this work investigates the mediator role in conflict management between costumers and product and services suppliers in conciliation hearings in a brazilian Small Claim Court (Juizado Especial de Relações de Consumo). The date consist of tape recordings of talk-in-interaction in work place. Conflict resolution in institutional settings is distinct from informal dispute because its procedures define especific roles for each interaction participant. A particular institutional mandate determine a interactional organization where the participants rigths suffer restrictions that are absent in ordinary conversation. Norms expectations, distinct participation status and sequence of procedures are features of conciliation hearings that make possible to identify two moments in the hearings: narrative and negociation. Analysing the mediator role in the narrative moment, it was observed his co-contruction of the consumer narrative by questions and formulations. Thus, the mediator align himself most of the time with the consumer side during the conflict narrative. In the negotiation moment, he may change his alignment in order to do a institutional task of making agreement between disputants. Finally, there is an argument that mediator alignments are oriented by his institutional work.

No description available.

Protein sequencing has produced overwhelming amount of protein sequences, especially in the last decade. Nevertheless, the majority of the proteins' functional and structural classes are still unknown, and experimental methods currently used to determine these properties are very expensive, laborious and time consuming. Therefore, automated computational methods are urgently required to accurately and reliably predict functional and structural classes of the proteins. Several bioinformatics methods have been developed to determine such properties of the proteins directly from their sequence information. Such methods that involve signal processing methods have recently become popular in the bioinformatics area and been investigated for the analysis of DNA and protein sequences and shown to be useful and generally help better characterise the sequences. However, there are various technical issues that need to be addressed in order to overcome problems associated with the signal processing methods for the analysis of the proteins sequences. Amino acid indices that are used to transform the protein sequences into signals have various applications and can represent diverse features of the protein sequences and amino acids. As the majority of indices have similar features, this project proposes a new set of computationally derived indices that better represent the original group of indices. A study is also carried out that resulted in finding a unique and universal set of best discriminating amino acid indices for the characterisation of allergenic proteins. This analysis extracts features directly from the protein sequences by using Discrete Fourier Transform (DFT) to build a classification model based on Support Vector Machines (SVM) for the allergenic proteins. The proposed predictive model yields a higher and more reliable accuracy than those of the existing methods. A new method is proposed for performing a multiple sequence alignment. For this method, DFT-based method is used to construct a new distance matrix in combination with multiple amino acid indices that were used to encode protein sequences into numerical sequences. Additionally, a new type of substitution matrix is proposed where the physicochemical similarities between any given amino acids is calculated. These similarities were calculated based on the 25 amino acids indices selected, where each one represents a unique biological protein feature. The proposed multiple sequence alignment method yields a better and more reliable alignment than the existing methods. In order to evaluate complex information that is generated as a result of DFT, Complex Informational Spectrum Analysis (CISA) is developed and presented. As the results show, when protein classes present similarities or differences according to the Common Frequency Peak (CFP) in specific amino acid indices, then it is probable that these classes are related to the protein feature that the specific amino acid represents. By using only the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient, as biologically related features can appear individually either in the real or the imaginary spectrum. This is successfully demonstrated over the analysis of influenza neuraminidase protein sequences. Upon identification of a new protein, it is important to single out amino acid responsible for the structural and functional classification of the protein, as well as the amino acids contributing to the protein's specific biological characterisation. In this work, a novel approach is presented to identify and quantify the relationship between individual amino acids and the protein. This is successfully demonstrated over the analysis of influenza neuraminidase protein sequences. Characterisation and identification problem of the Influenza A virus protein sequences is tackled through a Subgroup Discovery (SD) algorithm, which can provide ancillary knowledge to the experts. The main objective of the case study was to derive interpretable knowledge for the influenza A virus problem and to consequently better describe the relationships between subtypes of this virus. Finally, by using DFT-based sequence-driven features a Support Vector Machine (SVM)-based classification model was built and tested, that yields higher predictive accuracy than that of SD. The methods developed and presented in this study yield promising results and can be easily applied to proteomic fields.

Tous les systèmes biologiques sont formés d’atomes et de molécules qui interagissent et dont émergent des propriétés subtiles et complexes. Par ces interactions, les organismes vivants peuvent subvenir à toutes leurs fonctions vitales. Ces propriétés apparaissent dans tous les systèmes biologiques à des niveaux différents, du niveau des molécules et gènes jusqu’aux niveau des cellules et tissus. Ces dernières années, les physiciens se sont impliqués dans la compréhension de ces aspects particulièrement intrigants, en particulier en étudiant les systèmes vivants dans le cadre de la théorie des réseaux, théorie qui offre des outils d’analyse très puissants. Il est possible aujourd’hui d’identifier deux classes d’approches qui sont utilisée pour étudier ces types de systèmes complexes : les méthodes directes de modélisation et les approches inverses d’inférence. Dans cette thèse, mon travail est basé sur les deux types d’approches appliquées à trois niveaux de systèmes biologiques. Dans la première partie de la thèse, je me concentre sur les premières étapes du développement des tissus biologiques des plantes. Je propose un nouveau modèle pour comprendre la dynamique collective des transporteurs de l’hormone auxine et qui permet la croissance non-homogène des tissu dans l’espace et le temps. Dans la deuxième partie de la thèse, j’analyse comment l’évolution contraint la diversité́ de séquence des protéines tout en conservant leur fonction dans différents organismes. En particulier, je propose une nouvelle méthode pour inférer les sites essentiels pour la fonction ou la structure de protéines à partir d’un ensemble de séquences biologiques. Finalement, dans la troisième partie de la thèse, je travaille au niveau cellulaire et étudie les réseaux de signalisation associés à l’auxine. Dans ce contexte, je reformule un modèle préexistant et propose une nouvelle technique qui permet de définir et d’étudier la réponse du système aux signaux externes pour des topologies de réseaux différentes. J’exploite ce cadre théorique pour identifier le rôle fonctionnel de différentes topologies dans ces systèmes. / All biological systems are made of atoms and molecules interacting in a non- trivial manner. Such non-trivial interactions induce complex behaviours allow- ing organisms to fulfill all their vital functions. These features can be found in all biological systems at different levels, from molecules and genes up to cells and tissues. In the past few decades, physicists have been paying much attention to these intriguing aspects by framing them in network approaches for which a number of theoretical methods offer many powerful ways to tackle systemic problems. At least two different ways of approaching these challenges may be considered: direct modeling methods and approaches based on inverse methods. In the context of this thesis, we made use of both methods to study three different problems occurring on three different biological scales. In the first part of the thesis, we mainly deal with the very early stages of tissue development in plants. We propose a model aimed at understanding which features drive the spontaneous collective behaviour in space and time of PINs, the transporters which pump the phytohormone auxin out of cells. In the second part of the thesis, we focus instead on the structural properties of proteins. In particular we ask how conservation of protein function across different organ- isms constrains the evolution of protein sequences and their diversity. Hereby we propose a new method to extract the sequence positions most relevant for protein function. Finally, in the third part, we study intracellular molecular networks that implement auxin signaling in plants. In this context, and using extensions of a previously published model, we examine how network structure affects network function. The comparison of different network topologies provides insights into the role of different modules and of a negative feedback loop in particular. Our introduction of the dynamical response function allows us to characterize the systemic properties of the auxin signaling when external stimuli are applied.