Дисертації з теми "Functional similarity"

Transcriptional regulation of genes is fundamental to all living organisms. The spatial, temporal and condition-specific expression levels of genes are in part determined by inherited regulatory codes in non-coding regions of the DNA. A large set of methods have been proposed to detect conserved regions of regulatory DNA by means of sequence alignments. However, it has become clear that some regulatory regions do not show statistically significant alignments even in the presence of functional conservation. Therefore, detecting and characterising elusive regulatory codes remains a challenging problem. In this thesis we develop and validate a novel computational alignment free model for detection of functional similarity of regulatory sequences. We show that our model can detect functional links between pairs of sequences that do not align with a significant score. We apply the model to a) detect enhancers within the same genome that are likely to have similar functions and b) to detect functionally conserved enhancer regions in orthologous genomes. Our method finds regulatory codes that are common to groups of similar enhancers and consistent with previous biological knowledge. The inputs for our model are two sequences that we wish to compare in terms of their functional similarity as well as a set of transcription factor motifs. The mathematical framework of our model is built on two main components: In the first model component, each sequence is mapped to a vector of estimated occupancy levels for all motifs. These vectors are representing which motifs at what multiplicity and specificity are present in each sequence. In the second model component, a statistical approach is established where we first estimate a probability distribution of motif occupancy levels for sequences that function similar to the template sequence. We then compute a statistical similarity score to evaluate if the sequences are more similar to each other than to random background sequences. Two applications of this model are presented: First it is applied to a set of experimentally validated non-alignable enhancers from D. melanogaster. We show that: • Our model can detect statistical links between these enhancers, • Weak binding sites can make a strong contribution to sequence similarity, • Our model treats statistically significant presence and absence of motifs symmetrically. Similarity of sequences, therefore, can be based on a combination of the two. We show examples of motifs making contributions to sequence similarity through their absence. • Using our model, we can create a network of similarities among the fly enhancers. Groups of enhancers in this network show common regulatory codes. One of these regulatory codes is strongly supported by existing experimental data. In the second application of our model we predict functional subregions of a known D. melanogaster enhancer. To achieve this, we first show that the model can detect the orthology of this enhancer between 10 Drosophila species. We then demonstrate how this statistical link can be used to predict functional subregions within this enhancer.

In this study, we identified one of the reasons of the low correlation between functional size and development effort which is overlooking the similarity of the functions during the mapping of the functional size and development effort. We developed a methodology (SiRFuS) that is based on the idea of the reuse of the similar functions internally to provide high correlation between functional size and development effort. The method is developed for the identification of the similar functions based on the method of Santillo and Abran. Similarity percentages among the functional processes and Similarity Reflective Functional Sizes are computed to attain adjusted functional sizes. The similarity reflective functional sizes were named as Discrete Similarity Reflective Functional Size and Continuous Similarity Reflective Functional Size based on the characteristics of the adjusted functional sizes. The SiRFuS method consists of three stages: measurement of the software product with COSMIC Functional Size Measurement (FSM) method
identification of the functional similarities bases on the measurement results and calculation of the similarity reflective functional sizes. In order to facilitate the detection of similar functions, calculation of the percentage of the similarities and similarity reflective functional sizes
a software tool is developed based on the SiRFuS method. Two case studies were performed in order to identify the improvement opportunities and evaluate the applicability of the method and the tool.

Gene functional annotations are an essential part of knowledge discovery in the analysis of large datasets, with the Gene Ontology [Ashburner et al., 2000] as the de facto standard for such annotations. A considerable number of approaches for quantifying functional similarity between gene products based on the semantic similarity between their annotations have been developed, but little guidance exists as to which of these measures are the most appropriate for different purposes. This was addressed here by comparing the performances of a number of similarity measures and associated parameters. This comparison provided some interesting new insights as well as confirming emerging trends from the literature. There is also a pressing need for novel ways of applying these measures to facilitate the functional analysis of lists of gene products. We developed a novel algorithm, FuSiGroups, to group GO terms based on their semantic similarity and genes based on their functional similarity. This two-fold grouping results in groups of not only functionally similar genes but also an associated set of related GO terms that characterise a single functional aspect relating the genes in the group, which facilitates analysis by creating more coherent groups. Each gene can belong to multiple groups, so the groups more accurately reflect the complexity of biological reality than clusters generated using traditional approaches. FuSiGroups was tested on a number of scenarios and in each case, successfully generated biologically relevant groups, identifying the key functional aspects of the dataset. The algorithm also managed to eliminate genes that were functionally unrelated to the bulk of the dataset and distinguish between different biological pathways. Although dataset size is currently a limiting factor, with smaller datasets performing the best, FuSiGroups has been demonstrated as a promising approach for the functional analysis of gene products.

L’objectif de ce travail de thèse était d’approfondir les connaissances actuelles sur l’organisation des concepts d’objets fabriqués manipulables. Plus particulièrement, nous nous sommes intéressés au traitement implicite des relations thématiques (e.g., scie-bois) et des relations de similarité fonctionnelle spécifique (e.g., scie-hâche) et générale (e.g., scie-couteau) lors de l’identification des objets fabriqués manipulables. Les stimuli ont été sélectionnés par une tâche de génération de propriétés et le traitement implicite des relations sémantiques a été évalué grâce à l’enregistrement des mouvements oculaires dans le Paradigme du Monde Visuel. Tout d’abord, nous avons évalué le développement du traitement implicite des relations thématiques et de similarité fonctionnelle chez les enfants de 6-, 8- 10- ans et chez l’adulte. Les résultats ont montré que le traitement implicite des relations de similarité fonctionnelle générale évolue progressivement avec l’âge, alors que les relations thématiques sont déjà implicitement traitées dès 6-ans. Ensuite, nous avons testé le rôle de l’action dans le traitement de ces relations. Chez l’adulte, les résultats ont montré que l’action amorce le traitement des relations thématiques différemment en fonction du niveau de représentation de l’action impliqué. Le traitement thématique est facilité par l’action représentée au niveau du geste mais gêné par l’action représentée au niveau de l’intention. Chez l’enfant, les données ont montré que le traitement de relations de similarité fonctionnelle générale est facilité par l’action représentée au niveau de l’intention. Les données préliminaires chez le patient cérébro-lésé renforcent l’idée d’une structure conceptuelle multidéterminée et graduelle. Dans l’ensemble, ce travail démontre que les connaissances sur les objets fabriqués manipulables sont organisées selon des relations sémantiques distinctes qui présentent des trajectoires développementales différentes et correspondent à diffèrent niveaux de représentation d’action
The general aim of this work was to provide a better understanding of the cognitive mechanisms underlying manipulable artifact object conceptual organization. Specifically, we investigated implicit processing of thematic (e.g., saw-wood) and functional similarity relations at the specific (e.g., saw-axe) and general (e.g., saw-knife) levels during manipulable artifact object identification. Stimuli were selected from property generation and implicit semantic processing was investigated using eye-tracking in the Visual World Paradigm. First, we assessed the development of thematic and functional similarity processing in 6-, 8-, 10- year-old children and adults. Results demonstrated progressive emergence of general function similarity processing with age, while thematic and specific function similarity processing was already present from 6. Findings support a graded involvement of distinct mechanisms in object semantic processing and development. In the second series of experiments, we investigated the role of action in thematic and functional similarity processing by combining action priming with the Visual World Paradigm in adults and 6-year-olds. In adults, action primed thematic processing differently depending on the level of action representation entailed. Thematic processing was facilitated by gesture-level action representations but disturbed by intention-level action representations. In 6-year-olds, intention-level action representations improved general functional similarity relation implicit processing. Findings highlight the role of different action representation levels in manipulable artifact object semantic processing. Finally, preliminary data collected in 8 stroke patients provided additional evidence in favor of a multidetermined and graded manipulable artifact semantic structure. Together, findings demonstrate that knowledge about manipulable artifacts is organized along distinct types of semantic relations that show different developmental trajectories and relate to different levels of action representations

Simultaneous measurement of the expression levels of thousands to ten thousand genes in multiple tissue types is a result of advancement in microarray technology. These expression levels provide clues about the gene functions and that have enabled better diagnosis and treatment of serious disease like cancer. To solve the mystery of unknown gene functions, biological to statistical mapping is needed in terms of classifying the genes. Here we introduce a novel approach of combining both statistical consistency and biological relevance of the clusters produced by a clustering method. Here we employ two performance measures in combination for measuring statistical stability and functional similarity of the cluster members using a set of gene expressions with known biological functions. Through this analysis we construct a platform to predict about unknown gene functions using the outperforming clustering algorithm.

The problem of species diversity and co-existence in hyper-diverse communities remains. Traditionally ecologists have approached this problem from examining patterns of co-occurrence, interaction matrices and abundance distributions. This work, while productive, generally has rarely explored the role of shared ancestry and species-specific quantitative function in promoting species diversity and co-existence. This has been a critical oversight as simply analyzing the list of Latin binomials in an assemblage ignores the relatedness between taxa as well as the diversity in organismal form and function--the very information relevant to evolutionary, ecological, and historical hypotheses about the distribution of diversity and community assembly. The following research is designed to investigate the role of phylogenetic and functional similarity on species diversity and co-existence through space and time in diverse tropical tree communities. Specifically, I investigate: (i) the role of phylogenetic relatedness in determining community structure from very local to large regional spatial scales; (ii) the role of phylogeny in determining the structure of tree communities at different strategraphic levels in the canopy; (iii) the power of recently developed phylogenetic analyses to detect non-random patterns of co-existence in communities when the phylogenetic tree used is not completely resolved; (iv) the role of functional similarity in promoting co-existence in a Neotropical dry forest through space and across body sizes; (v) whether decadal long trends in forest composition can be explained on the basis of species-specific function; and (vi) variability in a key functional trait across New World forest communities and along the Angiosperm phylogeny.

Antibiotics are the crux of modern medicine, and antibiotic resistance (AbR) is a challenge to overcome. It has long been known that antibiotic production by soil microbiota is a natural process. Antibiotics such as streptomycin and penicillin come from common soil microorganisms. AbR is said to spread readily and rapidly through the environment, but its natural occurrence is poorly constrained. In studies analyzing natural AbR across a variety of habitats, researchers have found resistance in agricultural fields, human and animal feces, soils, deep caves, prehistoric ice cores, marine habitats, and reclaimed wastewater. Permafrost soils represent a pristine (human-unimpacted) environment capable of serving as a model system for natural AbR. I compared a functionality-based approach to a traditional identity-based approach to identify AbR sequences in permafrost microbial community genomes. The functionality-based approach yielded better quality results overall, and identified sequences more likely to be mappable to molecular pathways with the KEGG database.

Les avancées dans l'analyse de l'expression différentielle de gènes ont suscité un vif intérêt pour l'étude d'ensembles de gènes présentant une similarité d'expression au cours d'une même condition expérimentale. Les approches classiques pour interpréter l'information biologique reposent sur l'utilisation de méthodes statistiques. Cependant, ces méthodes se focalisent sur les gènes les plus connus tout en générant des informations redondantes qui peuvent être éliminées en prenant en compte la structure des ressources de connaissances qui fournissent l'annotation. Au cours de cette thèse, nous avons exploré différentes méthodes permettant l'annotation d'ensembles de gènes.Premièrement, nous présentons les solutions visuelles développées pour faciliter l'interprétation des résultats d'annota-tion d'un ou plusieurs ensembles de gènes. Dans ce travail, nous avons développé un prototype de visualisation, appelé MOTVIS, qui explore l'annotation d'une collection d'ensembles des gènes. MOTVIS utilise ainsi une combinaison de deux vues inter-connectées : une arborescence qui fournit un aperçu global des données mais aussi des informations détaillées sur les ensembles de gènes, et une visualisation qui permet de se concentrer sur les termes d'annotation d'intérêt. La combinaison de ces deux visualisations a l'avantage de faciliter la compréhension des résultats biologiques lorsque des données complexes sont représentées.Deuxièmement, nous abordons les limitations des approches d'enrichissement statistique en proposant une méthode originale qui analyse l'impact d'utiliser différentes mesures de similarité sémantique pour annoter les ensembles de gènes. Pour évaluer l'impact de chaque mesure, nous avons considéré deux critères comme étant pertinents pour évaluer une annotation synthétique de qualité d'un ensemble de gènes : (i) le nombre de termes d'annotation doit être réduit considérablement tout en gardant un niveau suffisant de détail, et (ii) le nombre de gènes décrits par les termes sélectionnés doit être maximisé. Ainsi, neuf mesures de similarité sémantique ont été analysées pour trouver le meilleur compromis possible entre réduire le nombre de termes et maintenir un niveau suffisant de détails fournis par les termes choisis. Tout en utilisant la Gene Ontology (GO) pour annoter les ensembles de gènes, nous avons obtenu de meilleurs résultats pour les mesures de similarité sémantique basées sur les nœuds qui utilisent les attributs des termes, par rapport aux mesures basées sur les arêtes qui utilisent les relations qui connectent les termes. Enfin, nous avons développé GSAn, un serveur web basé sur les développements précédents et dédié à l'annotation d'un ensemble de gènes a priori. GSAn intègre MOTVIS comme outil de visualisation pour présenter conjointement les termes représentatifs et les gènes de l'ensemble étudié. Nous avons comparé GSAn avec des outils d'enrichissement et avons montré que les résultats de GSAn constituent un bon compromis pour maximiser la couverture de gènes tout en minimisant le nombre de termes.Le dernier point exploré est une étape visant à étudier la faisabilité d'intégrer d'autres ressources dans GSAn. Nous avons ainsi intégré deux ressources, l'une décrivant les maladies humaines avec Disease Ontology (DO) et l'autre les voies métaboliques avec Reactome. Le but était de fournir de l'information supplémentaire aux utilisateurs finaux de GSAn. Nous avons évalué l'impact de l'ajout de ces ressources dans GSAn lors de l'analyse d’ensembles de gènes. L'intégration a amélioré les résultats en couvrant d'avantage de gènes sans pour autant affecter de manière significative le nombre de termes impliqués. Ensuite, les termes GO ont été mis en correspondance avec les termes DO et Reactome, a priori et a posteriori des calculs effectués par GSAn. Nous avons montré qu'un processus de mise en correspondance appliqué a priori permettait d'obtenir un plus grand nombre d'inter-relations entre les deux ressources
The revolution in new sequencing technologies, by strongly improving the production of omics data, is greatly leading to new understandings of the relations between genotype and phenotype. To interpret and analyze data grouped according to a phenotype of interest, methods based on statistical enrichment became a standard in biology. However, these methods synthesize the biological information by a priori selecting the over-represented terms and focus on the most studied genes that may represent a limited coverage of annotated genes within a gene set. During this thesis, we explored different methods for annotating gene sets. In this frame, we developed three studies allowing the annotation of gene sets and thus improving the understanding of their biological context.First, visualization approaches were applied to represent annotation results provided by enrichment analysis for a gene set or a repertoire of gene sets. In this work, a visualization prototype called MOTVIS (MOdular Term VISualization) has been developed to provide an interactive representation of a repertoire of gene sets combining two visual metaphors: a treemap view that provides an overview and also displays detailed information about gene sets, and an indented tree view that can be used to focus on the annotation terms of interest. MOTVIS has the advantage to solve the limitations of each visual metaphor when used individually. This illustrates the interest of using different visual metaphors to facilitate the comprehension of biological results by representing complex data.Secondly, to address the issues of enrichment analysis, a new method for analyzing the impact of using different semantic similarity measures on gene set annotation was proposed. To evaluate the impact of each measure, two relevant criteria were considered for characterizing a "good" synthetic gene set annotation: (i) the number of annotation terms has to be drastically reduced while maintaining a sufficient level of details, and (ii) the number of genes described by the selected terms should be as large as possible. Thus, nine semantic similarity measures were analyzed to identify the best possible compromise between both criteria while maintaining a sufficient level of details. Using GO to annotate the gene sets, we observed better results with node-based measures that use the terms’ characteristics than with edge-based measures that use the relations terms. The annotation of the gene sets achieved with the node-based measures did not exhibit major differences regardless of the characteristics of the terms used. Then, we developed GSAn (Gene Set Annotation), a novel gene set annotation web server that uses semantic similarity measures to synthesize a priori GO annotation terms. GSAn contains the interactive visualization MOTVIS, dedicated to visualize the representative terms of gene set annotations. Compared to enrichment analysis tools, GSAn has shown excellent results in terms of maximizing the gene coverage while minimizing the number of terms.At last, the third work consisted in enriching the annotation results provided by GSAn. Since the knowledge described in GO may not be sufficient for interpreting gene sets, other biological information, such as pathways and diseases, may be useful to provide a wider biological context. Thus, two additional knowledge resources, being Reactome and Disease Ontology (DO), were integrated within GSAn. In practice, GO terms were mapped to terms of Reactome and DO, before and after applying the GSAn method. The integration of these resources improved the results in terms of gene coverage without affecting significantly the number of involved terms. Two strategies were applied to find mappings (generated or extracted from the web) between each new resource and GO. We have shown that a mapping process before computing the GSAn method allowed to obtain a larger number of inter-relations between the two knowledge resources

Cette thèse présente: 1) le développement d'une nouvelle approche pour trouver des associations directes entre des paires d'éléments liés indirectement à travers diverses caractéristiques communes, 2) l'utilisation de cette approche pour associer directement des fonctions biologiques aux domaines protéiques (ECDomainMiner et GODomainMiner) et pour découvrir des interactions domaine-domaine, et enfin 3) l'extension de cette approche pour annoter de manière complète à partir des domaines les structures et les séquences des protéines. Au total, 20 728 et 20 318 associations EC-Pfam et GO-Pfam non redondantes ont été découvertes, avec des F-mesures de plus de 0,95 par rapport à un ensemble de référence Gold Standard extrait d'une source d'associations connues (InterPro). Par rapport à environ 1500 associations déterminées manuellement dans InterPro, ECDomainMiner et GODomainMiner produisent une augmentation de 13 fois le nombre d'associations EC-Pfam et GO-Pfam disponibles. Ces associations domaine-fonction sont ensuite utilisées pour annoter des milliers de structures de protéines et des millions de séquences de protéines pour lesquelles leur composition de domaine est connue mais qui manquent actuellement d'annotations fonctionnelles. En utilisant des associations de domaines ayant acquis des annotations fonctionnelles inférées, et en tenant compte des informations de taxonomie, des milliers de règles d'annotation ont été générées automatiquement. Ensuite, ces règles ont été utilisées pour annoter des séquences de protéines dans la base de données TrEMBL
This thesis presents: 1) the development of a novel approach to find direct associations between pairs of elements linked indirectly through various common features, 2) the use of this approach to directly associate biological functions to protein domains (ECDomainMiner and GODomainMiner), and to discover domain-domain interactions, and finally 3) the extension of this approach to comprehensively annotate protein structures and sequences. ECDomainMiner and GODomainMiner are two applications to discover new associations between EC Numbers and GO terms to protein domains, respectively. They find a total of 20,728 and 20,318 non-redundant EC-Pfam and GO-Pfam associations, respectively, with F-measures of more than 0.95 with respect to a “Gold Standard” test set extracted from InterPro. Compared to around 1500 manually curated associations in InterPro, ECDomainMiner and GODomainMiner infer a 13-fold increase in the number of available EC-Pfam and GO-Pfam associations. These function-domain associations are then used to annotate thousands of protein structures and millions of protein sequences for which their domain composition is known but that currently lack experimental functional annotations. Using inferred function-domain associations and considering taxonomy information, thousands of annotation rules have automatically been generated. Then, these rules have been utilized to annotate millions of protein sequences in the TrEMBL database

The estimation of effort is at the heart of project tasks, since it is used for many purposes such as cost estimation, budgeting, monitoring, project planning, control and software investments. Researchers analyze problems of the estimation, propose new models and use new techniques to improve accuracy. However up to now, there is no comprehensive estimation methodology to guide companies in their effort estimation tasks. Effort estimation problem is not only a computational but also a managerial problem. It requires estimation goals, execution steps, applied measurement methods and updating mechanisms to be properly defined. Besides project teams should have motivation and responsibilities to build a reliable database. If such methodology is not defined, common interpretation will not be constituted among software teams of the company, and variances in measurements and divergences in collected information prevents to collect sufficient historical information for building accurate models. This thesis proposes a methodology for organizations to manage and execute effort estimation processes. The approach is based on the reported best practices, v empirical results of previous studies and solutions to problems &
conflicts described in literature. Five integrated processes: Data Collection, Size Measurement, Data Analysis, Calibration, Effort Estimation processes are developed with their artifacts, procedures, checklists and templates. The validation and applicability of the methodology is checked in a middle-size software company. During the validation of methodology we also evaluated some concepts such as Functional Similarity (FS) and usage of Base Functional Components (BFC) in effort model on a reliable dataset. By this way we evaluated whether these subjects should be a part of methodology or not. Besides in this study it is the first time that the COSMIC has been used for Artificial Neural Network models.

Software project managers usually use benchmarking repositories to estimate effort, cost, and duration of the software development which will be used to appropriately plan, monitor and control the project activities. In addition, precision of benchmarking repositories is a critical factor in software effort estimation process which plays subsequently a critical role in the success of the software development project. In order to construct such a precise benchmarking data repository, it is important to have defined benchmarking data attributes and data characteristics and to have collected project data accordingly. On the other hand, studies show that data characteristics of benchmark data sets have impact on generalizing the studies which are based on using these datasets. Quality of data repository is not only depended on quality of collected data, but also it is related to how these data are collected. In this thesis, a benchmarking methodology is proposed for organizations to collect benchmarking data for effort estimation purposes. This methodology consists of three main components: benchmarking measures, benchmarking data collection processes, and benchmarking data collection tool. In this approach results of previous studies from the literature were used too. In order to verify and validate the methodology project data were collected in two middle size software organizations and one small size organization by using automated benchmarking data collection tool. Also, effort estimation models were constructed and evaluated for these projects data and impact of different characteristics of the projects was inspected in effort estimation models.

MicroRNAs (miRNAs) são pequenos RNAs não codificadores de proteínas que atuam principalmente como silenciadores pós-transcricionais, inibindo a tradução de RNAs mensageiros. Evidências crescentes revelam que tais moléculas desempenham papéis críticos em muitos processos biológicos importantes. Uma vez que não existem anotações de termos de miRNAs na Gene Ontology (GO), tampouco um banco de dados de referência com anotações funcionais dos mesmos, o cálculo da medida de similaridade entre miRNAs de forma direta não possui um padrão estabelecido. Por outro lado, a existência de bancos de dados de genes-alvo de miRNAs, como o TarBase, e bases de dados contendo informações sobre associações de miRNAs e doenças humanas, como o HMDD, nos permite inferir a similaridade funcional dos miRNAs indiretamente, por meio da análise de seus genes-alvo na GO ou entre suas doenças relacionadas na ontologia MeSH. Além disso, de acordo com a estrutura da ontologia de miRNAs OMIT, um miRNA também pode ser anotado com outras informações, tais como a sua natureza de atuação como oncogênico ou supressor de tumor, o organismo em que se encontra, o tipo de experimento em que foi encontrado, suas associações com doenças, genes-alvo, proteínas e eventos patológicos. Dessa forma, a similaridade entre miRNAs pode ser inferida com base na combinação de um conjunto de informações contidas nas respectivas anotações, de forma que possamos obter um aproveitamento de várias informações existentes, definindo assim um cálculo de similaridade funcional composta. Assim, neste trabalho, propomos a criação e aplicação de um método chamado CFSim, aplicado sobre a OMIT e que utiliza a ontologia de doenças, MeSH, e a ontologia de genes, GO, para calcular a similaridade entre dois miRNAs, juntamente com informações contidas em suas anotações. A validação de nosso método foi realizada por meio da comparação com a similaridade funcional inferida considerando diferentes famílias de miRNAs e os resultados obtidos mostraram que nosso método é eficiente, no sentido de que a similaridade entre miRNAs pertencentes à mesma família é maior que a similaridade entre miRNAs de famílias distintas. Ainda, em comparação com os métodos de similaridade funcional já existentes na literatura, o CFSim obteve melhores resultados. Adicionalmente, para tornarmos viável a utilização do método proposto, foi projetado e implementado um ambiente contendo a infraestrutura necessária para que pesquisadores possam incluir dados obtidos de novas descobertas e consultar as informações sobre um determinado miRNA, assim como calcular a similaridade entre dois miRNAs, baseada no método proposto.
MicroRNAs (miRNAs) are small non-coding RNA that mainly negatively regulate gene expression by inhibiting translation of target RNAs. Increasing evidences show that such molecules play critical roles in many important biological processes. Since there are no terms of miRNAs annotations in Gene Ontology (GO), nor a database with microRNAs functional annotations, directly calculating the functional similarity between miRNAs does not have an estabilished pattern aproach. However, the existence of miRNAs target genes database, such as TarBase, and a miRNAs-disease associations database, such as HMDD, allow us to indirectly infer functional similarity of miRNAs through the analysis of their target genes in GO or between their related diseases in MeSH. Moreover, according to the structure of the ontology of miRNAs OMIT, a miRNA can also be annotated with other information, such as if it acts as an oncogene or a tumor suppressor, the organism that it belongs, the experiment in which it was found, its associations with diseases, target genes, proteins and pathological events. Thus, miRNAs similarity can be inferred based on the combination of a broad set of information contained in their annotations, indeed, we can use all available information defining the calculation of a composed functional similarity. In this study, we propose the creation and application of CFSim method applied to the OMIT using the diseases ontology, MeSH, and gene ontology, GO, to compute miRNAs similarity based on different information in their annotations. We validated our method by comparing with functional similarity inferred by miRNA families and the results showed that our method is efficient in sense that the functional similarity between miRNAs in the same family was greater compared to other miRNAs from distinct families. Furthermore, in comparison with existing methods of functional similarity in the literature until the present day, the CFSim showed better results. Finally, to make feasible the use of the proposed method, an environment was designed and implemented, containing the necessary infrastructure so that researchers can include data from new discoveries and see information about a particular miRNA, as well as calculate the similarity between two miRNAs, based in the proposed method.

L’objectif de ce travail est de mettre au point une nouvelle approche automatique pour identifier les réseaux de gènes concourant à une même fonction biologique. Ceci permet une meilleure compréhension des phénomènes biologiques et notamment des processus impliqués dans les maladies telles que les cancers. Différentes stratégies ont été développées pour essayer de regrouper les gènes d’un organisme selon leurs relations fonctionnelles : génétique classique et génétique moléculaire. Ici, nous utilisons une propriété connue des réseaux de gènes fonctionnellement liés à savoir que ces gènes sont généralement co-régulés et donc co-exprimés. Cette co-régulation peut être mise en évidence par des méta-analyses de données de puces à ADN (micro-arrays) telles que Gemma ou COXPRESdb. Dans un travail précédent [Al Adhami et al., 2015], la topologie d’un réseau de co-expression de gènes a été caractérisé en utilisant deux paramètres de description des réseaux qui discriminent des groupes de gènes sélectionnés aléatoirement (modules aléatoires, RM) de groupes de gènes avec des liens fonctionnels connus (modules fonctionnels, FM), c’est-à-dire des gènes appartenant au même processus biologique GO. Dans le présent travail, nous avons cherché à généraliser cette approche et à proposer une méthode, appelée TopoFunc, pour améliorer l’annotation existante de la fonction génique. Nous avons d’abord testé différents descripteurs topologiques du réseau de co-expression pour sélectionner ceux qui identifient le mieux des modules fonctionnels. Puis, nous avons constitué une base de données rassemblant des modules fonctionnels et aléatoires, pour lesquels, sur la base des descripteurs sélectionnés, nous avons construit un modèle de discrimination LDA [Friedman et al., 2001] permettant, pour un sous-ensemble de gènes donné, de prédire son type (fonctionnel ou non). Basée sur la méthode de similarité de gènes travaillée par Wang et ses collègues [Wang et al., 2007], nous avons calculé un score de similarité fonctionnelle entre les gènes d’un module. Nous avons combiné ce score avec celui du modèle LDA dans une fonction de fitness implémenté dans un algorithme génétique (GA). À partir du processus biologique d’ontologie de gènes donné (GO-BP), AG visait à éliminer les gènes faiblement co-exprimés avec la plus grande clique de GO-BP et à ajouter des gènes «améliorant» la topologie et la fonctionnalité du module. Nous avons testé TopoFunc sur 193 GO-BP murins comprenant 50-100 gènes et avons montré que TopoFunc avait agrégé un certain nombre de nouveaux gènes avec le GO-BP initial tout en améliorant la topologie des modules et la similarité fonctionnelle. Ces études peuvent être menées sur plusieurs espèces (homme, souris, rat, et possiblement poulet et poisson zèbre) afin d’identifier des modules fonctionnels conservés au cours de l’évolution
The aim of this work is to develop a new automatic approach to identify networks of genes involved in the same biological function. This allows a better understanding of the biological phenomena and in particular of the processes involved in diseases such as cancers. Various strategies have been developed to try to cluster genes of an organism according to their functional relationships : classical genetics and molecular genetics. Here we use a well-known property of functionally related genes mainly that these genes are generally co-regulated and therefore co-expressed. This co-regulation can be detected by microarray meta-analyzes databases such as Gemma or COXPRESdb. In a previous work [Al Adhami et al., 2015], the topology of a gene coexpression network was characterized using two description parameters of networks that discriminate randomly selected groups of genes (random modules, RM) from groups of genes with known functional relationship (functional modules, FM), e.g. genes that belong to the same GO Biological Process. We first tested different topological descriptors of the co-expression network to select those that best identify functional modules. Then, we built a database of functional and random modules for which, based on the selected descriptors, we constructed a discrimination model (LDA)[Friedman et al., 2001] allowing, for a given subset of genes, predict its type (functional or not). Based on the similarity method of genes worked by Wang and co-workers [Wang et al., 2007], we calculated a functional similarity score between the genes of a module. We combined this score with that of the LDA model in a fitness function implemented in a genetic algorithm (GA). Starting from a given Gene Ontology Biological Process (GO-BP), AG aimed to eliminate genes that were weakly coexpressed with the largest clique of the GO-BP and to add genes that "improved" the topology and functionality of the module. We tested TopoFunc on the 193 murine GO-BPs comprising 50-100 genes and showed that TopoFunc aggregated a number of novel genes to the initial GO-BP while improving module topology and functional similarity. These studies can be conducted on several species (humans, mice, rats, and possibly chicken and zebrafish) to identify functional modules preserved during evolution

Functional characterization of biochemically-isolated proteins is a central task in the biochemical and genetic description of the biology of cells and tissues. Protein identification by mass spectrometry consists of associating an isolated protein with a specific gene or protein sequence in silico, thus inferring its specific biochemical function based upon previous characterizations of that protein or a similar protein having that sequence identity. By performing this analysis on a large scale in conjunction with biochemical experiments, novel biological knowledge can be developed. The study presented here focuses on mass spectrometry-based proteomics of organisms with unsequenced genomes and corresponding developments in biological sequence database searching with mass spectrometry data. Conventional methods to identify proteins by mass spectrometry analysis have employed proteolytic digestion, fragmentation of resultant peptides, and the correlation of acquired tandem mass spectra with database sequences, relying upon exact matching algorithms; i.e. the analyzed peptide had to previously exist in a database in silico to be identified. One existing sequence-similarity protein identification method was applied (MS BLAST, Shevchenko 2001) and one alternative novel method was developed (MultiTag), for searching protein and EST databases, to enable the recognition of proteins that are generally unrecognizable by conventional softwares but share significant sequence similarity with database entries (~60-90%). These techniques and available database sequences enabled the characterization of the Xenopus laevis microtubule-associated proteome and the Dunaliella salina soluble salt-induced proteome, both organisms with unsequenced genomes and minimal database sequence resources. These sequence-similarity methods extended protein identification capabilities by more than two-fold compared to conventional methods, making existing methods virtually superfluous. The proteomics of Dunaliella salina demonstrated the utility of MS BLAST as an indispensable method for characterization of proteins in organisms with unsequenced genomes, and produced insight into Dunaliella?s inherent resilience to high salinity. The Xenopus study was the first proteomics project to simultaneously use all three central methods of representation for peptide tandem mass spectra for protein identification: sequence tags, amino acids sequences, and mass lists; and it is the largest proteomics study in Xenopus laevis yet completed, which indicated a potential relationship between the mitotic spindle of dividing cells and the protein synthesis machinery. At the beginning of these experiments, the identification of proteins was conceptualized as using ?conventional? versus ?sequence-similarity? techniques, but through the course of experiments, a conceptual shift in understanding occurred along with the techniques developed and employed to encompass variations in mass spectrometry instrumentation, alternative mass spectrum representation forms, and the complexities of database resources, producing a more systematic description and utilization of available resources for the characterization of proteomes by mass spectrometry and advanced informatic approaches. The experiments demonstrated that proteomics technologies are only as powerful in the field of biology as the biochemical experiments are precise and meaningful.

Les modèles d'occupation de niche au sein des communautés locales, la variabilité spatiale de la biodiversité le long des gradients environnementaux du stress et des perturbations, et les processus de succession végétale sont plusieurs sujets fondamentaux en écologie. Récemment, l'approche basée sur les traits est apparue comme un moyen prometteur de comprendre les processus structurant les communautés végétales et cette approche a même été proposée comme méthode pour reconstruire l'écologie communautaire en fonction des traits fonctionnels. Par conséquent, lier ces thèmes fondamentaux en utilisant une lentille fonctionnelle devrait nous donner un aperçu de certaines questions fondamentales en écologie et sera l'objectif principal de ma thèse. En général, mon projet de doctorat vise à étudier les structures de l'occupation de l'espace fonctionnel dans les gradients spatio-temporels. Plus précisément, l'objectif du chapitre 2 est (i) d'étudier les modèles d'occupation de la niche fonctionnelle en calculant trois métriques clés de niche (le volume total de niche fonctionnelle , le chevauchement des niches fonctionnelles et le volume de niche fonctionnel moyen) des communautés pauvres en espèces aux communautés riches en espèces et (ii) de déterminer le principal facteur de la structure observée de l'occupation de la niche fonctionnelle dans les communautés végétales du monde entier. Dans le chapitre 3, je vise à prédire et à expliquer la variation de la richesse en espèces selon les gradients de stress et de perturbation, en reliant le modèle d'équilibre dynamique et l'occupation de la niche fonctionnelle en fonction du cadre développé au chapitre 2. L'objectif du chapitre 4 est de tester expérimentalement l’application d'une méthode d'ordination CSR évaluée globalement en fonction de trois traits de feuilles (surface foliaire, teneur en matière sèche des feuilles et surface foliaire spécifique) dans les études locales. Enfin, l'objectif du chapitre 5 est de tester expérimentalement les hypothèses qui concilient les points de vue déterministes et historiquement contingents de la succession végétale, en étudiant la variation des divergences taxonomiques et fonctionnelles entre les communautés selon des gradients de stress et de perturbation. L'étude globale (chapitre 2) est basée sur une collection de 21 jeux de données, couvrant les biomes tropicaux et tempérés, et se compose de 313 communautés végétales représentant différentes formes de croissance. Les études locales (chapitre 3, 4 et 5) sont basées sur le même système expérimental constitué de 24 mésocosmes présentant différents niveaux de stress et de perturbation. L'expérience a commencé en 2009 avec le même mélange de graines de 30 espèces herbacées semées sur les 24 mésocosmes et s'est terminée en 2016. Nous avons permis la colonisation naturelle de graines de la banque commune de graines de sol et de l'environnement pendant la succession de sept ans. Dix traits ont été mesurés sur cinq individus (échantillonnés directement à partir des mésocosmes) par espèce par mésocosme en 2014 (chapitre 3 et 4). Un autre ensemble de traits (16 traits, y compris certains traits qui ne pouvaient pas être mesurés directement dans les mésocosmes), ont été mesurés au niveau de l'espèce (valeurs moyennes des traits) pour les 34 espèces les plus abondantes (certaines espèces disparues dans les mésocosmes) au cours des sept Ans, en les regroupant séparément pour une saison de croissance. Au chapitre 2, nous avons constaté que les communautés étaient plus diverses en termes fonctionnels (une augmentation du volume fonctionnel total) dans les communautés riches en espèces et que les espèces se chevauchaient davantage au sein de la communauté (augmentation du chevauchement fonctionnel), mais ne divisaient pas plus finement l'espace fonctionnel (aucune réduction du volume fonctionnel moyen). En outre, le filtrage de l'habitat est un processus répandu qui conduit à la caractérisation de l'occupation de niche fonctionnelle dans les communautés végétales. Dans le chapitre 3, nous avons trouvé un modèle similaire d'occupation de niche fonctionnelle sur un système expérimental avec une taille spatiale communautaire constante et un effort d'échantillonnage des traits, qui, avec le chapitre 2, nous a fourni une image plus complète et plus solide de l'occupation de niche fonctionnelle dans les communautés végétales. De plus, nous avons réussi à relier le modèle de l'occupation de la niche fonctionnelle et le modèle d'équilibre dynamique et avons constaté que le filtrage concurrentiel était le processus dominant qui détermine le mode d'occupation de la niche fonctionnelle et la richesse des espèces le long du stress et de la perturbation des gradients. Au chapitre 4, nous fournissons un soutien empirique à une méthode d'ordination CSR calibrée globalement en montrant une relation entre l'abondance relative d'espèces en croissance dans les mésocosmes ayant différents niveaux de fertilité du sol et mortalité indépendante de la densité et leur classification CSR. Au chapitre 5, nous avons montré que la succession d'installations au cours de sept ans dans ces mésocosmes était plus déterministe d'un point de vue fonctionnel, mais plus historiquement contingent d'un point de vue taxonomique et que l'importance relative de la contingence historique a diminué à mesure que l'environnement devenait plus stressé ou perturbé. En conclusion, les structures de l'occupation de l'espace fonctionnel dans (le volume fonctionnel total, le chevauchement fonctionnel et le volume fonctionnel moyen, les Chapitre 2 et 3) ou entre les communautés locales (dissimilarité fonctionnelle, chapitre 5) sont déterministes plutôt que neutres (ou contingence historique ). Les espèces tolératrices de stress sont plus avantagées dans les mésocosmes moins fertiles tandis que les espèces rudérales sont plus avantagées dans les mésocosmes avec plus de mortalité indépendante de la densité.
Abstract : The patterns of niche occupancy within local communities, the spatial variability of biodiversity along environmental gradients of stress and disturbance, and the processes of plant succession are several fundamental topics in ecology. Recently, the trait-based approach has emerged as a promising way to understand the processes structuring plant communities and has even been proposed as a method to rebuild community ecology based on functional traits. Therefore, linking these fundamental themes through a functional lens should give us more insight into some basic questions in ecology and will be the main objective of my thesis. Generally, my PhD project is to investigate the structures of functional space occupancy along both spatial and temporal gradients. Specifically, the objective of Chapter 2 is to investigate the patterns of functional niche occupancy by calculating three key niche metrics (the total functional niche volume, the functional niche overlap and the average functional niche volume) from speciespoor communities to species-rich communities and to determine the main driver of the observed pattern of functional niche occupancy across plant communities worldwide. In Chapter 3, I aim to predict and explain the variation of species richness along gradients of stress and disturbance, by linking the dynamic equilibrium model and functional niche occupancy based on the framework developed in Chapter 2. The objective of Chapter 4 is to experimentally test the application of a globally calibrated CSR ordination method based on three leaf traits (leaf area, leaf dry matter content and specific leaf area) in local studies. Finally, the aim of Chapter 5 is to experimentally test the hypotheses reconciling the deterministic and historically contingent views of plant succession, by investigating the variation of taxonomic and functional dissimilarities between communities along gradients of stress and disturbance. The global study (Chapter 2) is based on a collection 21 trait datasets, spanning tropical to temperate biomes, and consisting of 313 plant communities representing different growth forms. The local studies (Chapter 3, 4 and 5) are based on the same experimental system consisting of 24 mesocosms experiencing different levels of stress and disturbance. The experiment started in 2009 with the same seed mixture of 30 herbaceous species broadcast over the 24 mesocosms and ended in 2016. We allowed natural colonization of seeds from the common soil seed bank and from the surroundings during the seven-year succession. Ten traits were measured on five individuals (sampled directly from the mesocosms) per species per mesocosms in 2014 (Chapter 3 and 4). Another set of traits (16 traits including some traits that were not able to measured directly in the mesocosms) were measured at the species level (species mean traits values) for the 34 most abundant species (some species disappeared in the mesocosms) over the seven years, by regrowing them separately for one growing season. In Chapter 2, we found communities were more functionally diverse (an increase in total functional volume) in species-rich communities, and species overlapped more within the community (an increase in functional overlap) but did not more finely divide the functional space (no decline in average functional volume). Moreover, habitat filtering is a widespread process driving the pattern of functional niche occupancy across plant communities. In Chapter 3, we found a similar pattern of functional niche occupancy on an experimental system with a constant community spatial size and trait-sampling effort, which together with Chapter 2 provided us a more comprehensive and robust picture of functional niche occupancy across plant communities. In addition, we succeeded in linking the pattern of functional niche occupancy and the dynamic equilibrium model and found that habitat filtering was the dominant process determining the pattern of functional niche occupancy and species richness along the gradients stress and disturbance. In Chapter 4, we provide empirical support for a globally calibrated CSR ordination method by showing a relationship between the relative abundance of species growing in mesocosms having different levels of soil fertility and density-independent mortality and their CSR classification. In Chapter 5, we showed that plant succession over seven years in these mesocosms was more deterministic from a functional perspective but more historically contingent from a taxonomic perspective, and that the relative importance of historical contingency decreased as the environment became more stressed or disturbed. In conclusion, the structures of functional space occupancy within (the total functional volume, the functional overlap and the average functional volume; Chapter 2 and 3) or between local communities (functional dissimilarity, Chapter 5) are deterministic rather than neutral (or historical contingency). Stress-tolerators were more favored in high stress communities, while ruderals are more favored in high disturbed mesocosms (Chapter 4).

Fundação de Amparo a Pesquisa do Estado de Minas Gerais
This thesis deals with the study of the tree component in a seasonal semideciduous forest (FES) with a good state of conservation. Initially, it was prepare a general introduction, showing the importance of the detailing study of forests well preserved, as comparative basis with disturbed forests. After this context, the thesis has been divided into two chapters. The first chapter tries to characterize the tree component of a hectare of FES, through the studies of floristic composition and horizontal and vertical structure, and the characterization of the soil. The species were classified accord the dominant stratum and in sucessional group. In this chapter were calculate the floristic similarities with other FES southeastern Brazil, based on the richness and abundance. In the second chapter was searched the formation of functional groups based on ecological attributes of the species. Therefore, it was used a similarity s dendrogram based on the presence/absence of attributes. The results showed that even in preserved forests have high spatial heterogeneity caused by natural gaps. The division of groups successional point to the concentration of late secondary species and low presence of pioneers in the strata. The similarity s analysis based on richness allowed the formation of four groups, and the similarity based on the abundance allowed closer areas with similar degree of conservation, even approaching the FES studied with other FESs in well conserved stage. These results demonstrate the high degree of maturity of the FES studied. In the delimitation of functional groups, four major groups were determined by their attributes: G1 - ornitocoric and light-demanding group; G2 - mastocoric and canopy light-demanding group; G3 - canopy, abiotic dispersion group and G4 - ornitocoric, shade-tolerant and the only group predominant in the understory. The G4 was the more abundant group. It was concluded that the tree community, although present natural gaps, is in a mature stage; the proximity between fragments of FES is a determinant factor in the floristic composition; fragments in similar conservation state have higher floristic similarity; the community tree has, at least, four big functional groups, which play different function in the ecosystem. The results obtained here have great contribution to the understanding of the ecological patterns and processes involved in these ecosystems. But there is a need for further studies that can for detail the communities tree structure and involves the formation of functional groups for better understanding of high diversity forests.
Esta dissertação trata do estudo do componente arbóreo em uma floresta estacional semidecidual (FES) em bom estado de conservação. Inicialmente, foi elaborada uma introdução geral, ressaltando a importância de estudos ecológicos detalhados em florestas preservadas, como base comparativa com florestas alteradas. Após esta contextualização, a dissertação foi dividida em dois capítulos. O primeiro buscou caracterizar, por meio da composição florística e da estrutura, horizontal e vertical, o componente arbóreo de um hectare de FES; além da caracterização do solo da área. As espécies foram classificadas conforme seu estrato dominante e quanto ao grupo sucessional. No mesmo capitulo, também foram calculadas similaridades florísticas, baseadas na riqueza e na abundância, com outras FES do sudeste brasileiro. No segundo capitulo buscou-se a formação de grupos funcionais baseados em atributos ecológicos das espécies. Para isso, foi utilizado um dendrograma de similaridade com base na presença/ausência dos atributos. Os resultados apontaram que mesmo florestas preservadas possuem alta heterogeneidade espacial, causada pelas clareiras naturais. A delimitação dos grupos sucessionais apontou para uma maior concentração de espécies secundárias tardias e pouca presença de pioneiras nos estratos formados. A análise de similaridade baseada na riqueza permitiu a formação de quatro grupos, e a similaridade baseado na abundância permitiu aproximar áreas com semelhante grau de conservação, inclusive aproximando a FES estudada com outras FESs em bom estágio de conservação. Foi possível, assim, determinar o elevado grau de maturidade da FES estudada. Na delimitação de grupos funcionais formaram-se quatro grandes grupos, determinados pelos seus atributos: G1 - grupo ornitocórico, demandante de luz direta, G2 - grupo mastocórico, de dossel demandante de luz direta, G3 - grupo formado por dispersão abiótica e do dossel e G4 - grupo ornitocórico, predominante do subdossel e sub-bosque e único grupo tolerante à sombra e o mais abundante em número de indivíduos. Concluiu-se que a comunidade arbórea, apesar de apresentar clareiras naturais, encontra-se em um estágio maduro; a proximidade entre fragmentos de FES é um fator importante na similaridade na composição florística; fragmentos em semelhante estado de conservação podem ter sua similaridade florística aproximada; a comunidade arbórea apresenta pelo menos quatro grandes grupos funcionais, que desempenham papeis distintos no ecossistema. Os resultados aqui obtidos trazem uma contribuição importante para o entendimento sobre os padrões e processos ecológicos envolvidos nesses ecossistemas, e reforça a necessidade de novos estudos, tanto para detalhamento da estrutura das comunidades arbóreas, quanto estudos que envolvam a formação de grupos funcionais para uma maior compreensão das florestas com alta diversidade.
Mestre em Ecologia e Conservação de Recursos Naturais

La présente thèse couvre deux principaux thèmes de recherche qui seront présentés dans deux parties et précédés par un prolegomenon commun. Dans ce dernier nous introduisons les concepts essentiels et nous exploitons aussi le lien entre les deux parties.

Dans la première partie, le principal objet d’intérêt est la soi-disant fonctionnelle exponentielle de processus de Lévy. La loi de cette variable aléatoire joue un rôle primordial dans de nombreux domaines divers tant sur le plan théorique que dans des domaines appliqués. Doney dérive une factorisation de la loi arc-sinus en termes de suprema de processus stables indépendants et de même index. Une factorisation similaire de la loi arc-sinus en termes de derniers temps de passage au niveau 1 de processus de Bessel peut aussi être établie en utilisant un résultat dû à Getoor. Des factorisations semblables d’une variable de Pareto en termes des mêmes objets peut également être obtenue. Le but de cette partie est de donner une preuve unifiée et une généralisation de ces factorisations qui semblent n’avoir aucun lien à première vue. Même s’il semble n’y avoir aucune connexion entre le supremum d’un processus stable et le dernier temps de passage d’un processus de Bessel, il peut être montré que ces variables aleatoires sont liées à des fonctionnelles exponentielles de processus de Lévy spécifiques. Notre contribution principale dans cette partie et aussi au niveau de caractérisations de la loi de la fonctionnelle exponentielle sont des factorisations de la loi arc-sinus et de variables de Pareto généralisées. Notre preuve s’appuie sur une factorisation de Wiener-Hopf récente de Patie et Savov.

Dans la deuxième partie, motivée par le fait que la dérivée fractionnaire de Caputo et d’autres opérateurs fractionnaires classiques coïncident avec le générateur de processus de Markov auto-similaires positifs particuliers, nous introduisons des opérateurs généralisés de Caputo et nous étudions certaines propriétés. Nous nous intéressons particulièrement aux conditions sous lesquelles ces opérateurs coïncident avec les générateurs infinitésimaux de processus de Markov auto-similaires positifs généraux. Dans ce cas, nous étudions les fonctions invariantes de ces opérateurs qui admettent une représentation en termes de séries entières. Nous précisons que cette classe de fonctions contient les fonctions de Bessel modifiées, les fonctions de Mittag-Leffler ainsi que plusieurs fonctions hypergéométriques. Nous proposons une étude unifiant et en profondeur de cette classe de fonctions.
Doctorat en Sciences
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Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq
Abiotic and biotic factors determine the species diversity along environmental gradients, but are not yet determined how these factors modulate changes in richness and ecological (functional) characteristics of communities along environmental gradients related to heterogeneity and amount of resources. There are studies which support that resources heterogeneity and/or resources amount influence the variations of animal diversity, but often, these studies do not distinguish clearly between these effects. On the other hand, species and ecological characteristics that coexist along environmental gradients should be affected by competition, niche overlap and/or environmental filters that influence the richness and functional redundancy (FR) of communities, and a greater niches heterogeneity and amount should promote functional differentiation among species. Because of their importance in ecosystems, their high diversity and close evolutionary relationship with plants at the Neotropics; I chose the arboreal ants as an object of study to test: 1) There is an increase in arboreal ants richness linked to an increase in the heterogeneity and amount of food and structural niches 2) The arboreal ants FR decreases with increasing heterogeneity and decreases with quantity of niches.Samples were taken in 42 plots of 100 m2 forming a heterogeneity and amount of resources gradient at Emas National Park, Mineiros, GO. After sampling and identification of organisms - plants and ants – I take nine functional characteristics measures for ants and a team of experts measured six variables of the community of woody plants. From the plots sampling, I got the ant richness and FR, and described biotic parameters related to heterogeneity and quantity of resources from the characteristics of the vegetation. Using the technique of PCA, I calculated the principal axes of environmental variables for the heterogeneity and amount of resources. These axes were related to arboreal ant richness and FR employing the Akaike criterion. Once the effect of heterogeneity and amount of resources was separated, the richness of ants was explained by the resources amount and the FR by the resources heterogeneity and amount. A greater amount of food and structural niches may encourage the coexistence of a large number of ant species possibly by a decreasing competitive exclusion and an improved distribution of resources among species. An increase in habitat heterogeneity and a decrease in food resources quantity may enable ant species to distinguished functionally, this may cause a decrease in FR; little diversification of structural resources and higheramount of food may promote that environment and competitive exclusion diminish the variety of functional features present in the community.
Os fatores abióticos e bióticos determinam a diversidade de espécies ao longo de gradientes ambientais, porém ainda não está determinado como esses fatores modulam as mudanças da riqueza e características ecológicas (funcionais) das comunidades ao longo de gradientes de heterogeneidade e quantidade de recursos. Existem estudos que apoiam que a heterogeneidade e/ou quantidade recursos influenciam as variações da diversidade animal, mas com frequência, estes estudos não separam com nitidez estes efeitos. Por outro lado, as espécies e características ecológicas que coexistem ao longo de gradientes ambientais devem ser afetadas pela competição, sobreposição de nichos e/ou filtros ambientais que influenciam a riqueza e redundância funcional (RF) das comunidades, e uma maior heterogeneidade e menor quantidadede nichos deve promover a diferenciação funcional das espécies. Devido sua importância nos ecossistemas, sua alta diversidade e a estreita relação evolutiva com as plantas nos Neotrópicos, escolhi as formigas arborícolas como objeto de estudo para testar se: 1) Existe um aumento da riqueza de formigas arborícolas ligado a um aumento na heterogeneidade e quantidade de nichos alimentares e estruturais 2) A RF das formigas arborícolas diminui conforme aumenta a heterogeneidade e diminui a quantidade nichos.Amostrei 42 parcelas de 100 m2que formam um gradiente de heterogeneidade e quantidade de recursosno Parque Nacional das Emas, Mineiros, GO. Após a amostragem e identificação dos organismos - plantas e formigas -, mensureinove características funcionais para as formigas e uma equipe de especialistas mensurou seis variáveis da comunidade das plantas lenhosas. A partir da amostragem das parcelas obtive a riqueza e RF das formigas, e descrevi parâmetros bióticos de heterogeneidade e quantidade de recursos a partir das características da vegetação. Usando a técnica da PCA, calculei os eixos principais das variáveis ambientais para a heterogeneidade e quantidade de recursos. Estes eixos foram relacionados com a riqueza e RF das formigasarborícolas mediante o critério Akaike. Uma vez separado o efeito da heterogeneidade e quantidade de recursos, a riqueza das formigas foi explicada pela quantidade de recursos e a RF pela heterogeneidade e quantidade de recursos. Uma maior quantidade de nichos alimentares e estruturais deve fomentar a coexistência de um maior número de espécies de formigas possivelmente por uma diminuição da exclusão competitiva e uma melhor divisão dos recursos entre as espécies. Um aumento na heterogeneidade do habitat e diminuição da quantidade de recurso alimentar deve permitirque as espécies de formigas se diferenciem funcionalmente, isto pode provocaruma diminuição da RF; pouca diversificação dos recursos estruturais e maior quantidade de alimento pode fomentar que o ambiente e a exclusão competitiva diminuam a variedade de características funcionais presentes na comunidade.

The present study investigates lexical similarity perceptions by students of Swedish as a foreign language (L3) with a good yet non-native proficiency in English (L2). The general theoretical framework is provided by studies in transfer of learning and its specific instance, transfer in language acquisition.

It is accepted as true that all previous linguistic knowledge is facilitative in developing proficiency in a new language. However, a frequently reported phenomenon is that students see similarities between two systems in a different way than linguists and theoreticians of education do. As a consequence, the full facilitative potential of transfer remains unused.

The present research seeks to shed light on the similarity perceptions with the focus on the comprehension of a written text. In order to elucidate students’ views, a form involving similarity judgements and multiple choice questions for formally similar items has been designed, drawing on real language use as provided by corpora. 123 forms have been distributed in 6 groups of international students, 4 of them studying Swedish at Level I and 2 studying at Level II. 

The test items in the form vary in the degree of formal, semantic and functional similarity from very close cognates, to similar words belonging to different word classes, to items exhibiting category membership and/or being in subordinate/superordinate relation to each other, to deceptive cognates. The author proposes expected similarity ratings and compares them to the results obtained. The objective measure of formal similarity is provided by a string matching algorithm, Levenshtein distance.

The similarity judgements point at the fact that intermediate similarity values can be considered problematic. Similarity ratings between somewhat similar items are usually lower than could be expected. Besides, difference in grammatical meaning lowers similarity values significantly even if lexical meaning nearly coincides. Thus, the obtained results indicate that in order to utilize similarities to facilitate language learning, more attention should be paid to underlying similarities.

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Communities are assemblages of co-occurring species that potentially interact with each other. They are the result not only of a series of ecological processes or "assembly rules", but also of past and ongoing evolutionary processes. In recent years, the assembly rules have received increased attention from ecologists and two different processes have been explored: environmental filtering and limiting similarity. As the processes involved in the formation of the assemblages appear to vary in a manner dependent on scale, it is expected that such assembly rules have different effects over different spatial scales. Understanding this relationship between ecological processes and spatial scales in which they act has been a great challenge among scholars. In this context, the incorporation of phylogenetic and functional data to diversity classical approaches have established the basis for an emerging area of research in community ecology, promoting the development of many tools to detect the underlying structure of the assemblages and, therefore, to infer the processes assembly responsible for the formation of the assemblages. Here, we demonstrate how the use of different measures of phylogenetic and functional diversity along with the use of different null models can be a promising approach in solving paradigms still poorly understood, discussing how such methods can increase the predictive power of this growing area of research.
As comunidades são assembleias de espécies co-ocorrentes que interagem potencialmente umas com as outras. Elas são resultado não apenas de uma série de processos ecológicos ou regras de montagem , mas também de processos evolutivos passados e contínuos. Nos últimos anos, as regras de montagem têm recebido maior atenção dos ecólogos e dois processos diferentes têm sido explorados: os filtros ambientais e a similaridade limitante. Como os processos envolvidos na formação das assembleias parecem variar de uma forma dependente de escala, espera-se que tais regras de montagem tenham diferentes efeitos ao longo de diferentes escalas espaciais. Compreender essa relação entre os processos ecológicos e as escalas espaciais nas quais eles atuam tem sido um grande desafio entre os estudiosos. Nesse contexto, a incorporação de dados filogenéticos e funcionais às abordagens clássicas de diversidade tem estabelecido a base de uma emergente área de pesquisa em ecologia de comunidades, impulsionando o desenvolvimento de muitas ferramentas para detectar a subjacente estrutura das assembleias e, portanto, inferir os processos de montagem responsáveis pela formação das assembleias. Aqui, demonstramos como a utilização de diferentes medidas de diversidade filogenética e funcional juntamente com o uso de diferentes modelos nulos pode ser uma abordagem promissora na solução de paradigmas ainda pouco compreendidos, discutindo como tais métodos podem aumentar o poder preditivo dessa crescente área de pesquisa.

L'explosion de la quantité de données produites chaque jour a fait de l' l'Apprentissage Automatique un outil vital pour extraire des motifs de haute valeur à partir de celles-là. Concrètement, un algorithme d'apprentissage automatique apprend de tels motifs après avoir été entraîné sur un jeu de données appelé données d'entraînement, et sa performance est évaluée sur échantillon différent, appelé données de test. L'Adaptation de Domaine est une branche de l'apprentissage automatique, dans lequel les données d'entraînement et de test ne sont plus supposées provenir de la même distribution de probabilité. Dans ce cas, les deux distributions des données d'entraînement et de test correspondent respectivement aux domaines source et cible. Nos contributions se focalisent sur trois aspects théoriques en relation avec l'adaptation de domaine pour les tâches de classification. Le premier est l'apprentissage avec des fonctions de similarité, qui traite les algorithmes de classification basés sur la comparaison d'une instance à d'autres exemples pour décider sa classe. Le deuxième est la classification à vaste marge qui concerne l'apprentissage d'un classifieur maximisant la séparation entre classes. Le troisième aspect est le Transport Optimal qui formalise un principe d'effort minimal pour le transport de masses de probabilité entre distributions. Au début de cette thèse, nous nous intéressions à l'apprentissage avec ce que l'on appelle fonctions de similarités (epsilon,gamma,tau)-bonnes dans le cadre de l'adaptation de domaine, puisque ces fonctions ont été introduites dans la littérature dans le cadre classique de l'apprentissage supervisé. C'est le sujet de notre première contribution dans laquelle nous étudions théoriquement la performance d'une fonction de similarité sur une distribution cible, étant donné qu'elle est adéquate pour la source. Puis, nous abordons plus généralement le thème de la classification à vaste marge pour l'adaptation de domaine, avec des hypothèses de départ plus faibles que celles adoptées dans la première contribution. Dans ce contexte, nous proposons une nouvelle étude théorique et un algorithme d'adaptation de domaine, ce qui constitue notre deuxième contribution. Nous dérivons de nouvelles bornes prenant en compte la marge de classification dans le domaine cible, que nous convexifions en tirant profit de la théorie du Transport Optimal, en vue de dériver un algorithme d'adaptation de domaine présentant une variation adversariale du problème classique de Kantorovitch. Finalement, nous dédions notre dernière contribution aux variations adversariales ou minimax du problème du transport optimal, où nous démontrons l'adaptabilité de notre approche
The surge in the quantity of data produced nowadays made of Machine Learning, a subfield of Artificial Intelligence, a vital tool used to extract valuable patterns from them and allowed it to be integrated into almost every aspect of our everyday activities. Concretely, a machine learning algorithm learns such patterns after being trained on a dataset called the training set, and its performance is assessed on a different set called the testing set. Domain Adaptation is an active research area of machine learning, in which the training and testing sets are not assumed to stem from the same probability distribution, as opposed to Supervised Learning. In this case, the two distributions generating the training and testing data correspond respectively to the source and target domains. Our contributions focus on three theoretical aspects related to domain adaptation for classification tasks. The first one is learning with similarity functions, which deals with classification algorithms based on comparing an instance to other examples in order to decide its class. The second is large-margin classification, which concerns learning classifiers that maximize the separation between classes. The third is Optimal Transport that formalizes the principle of least effort for transporting probability masses between two distributions. At the beginning of the thesis, we were interested in learning with so-called (epsilon,gamma,tau)-good similarity functions in the domain adaptation framework, since these functions have been introduced in the literature in the classical framework of supervised learning. This is the subject of our first contribution in which we theoretically study the performance of a similarity function on a target distribution, given it is suitable for the source one. Then, we tackle the more general topic of large-margin classification in domain adaptation, with weaker assumptions than those adopted in the first contribution. In this context, we proposed a new theoretical study and a domain adaptation algorithm, which is our second contribution. We derive novel bounds taking the classification margin on the target domain into account, that we convexify by leveraging the appealing Optimal Transport theory, in order to derive a domain adaptation algorithm with an adversarial variation of the classic Kantorovich problem. Finally, after noticing that our adversarial formulation can be generalized to include several other cases of interest, we dedicate our last contribution to adversarial or minimax variations of the optimal transport problem, where we demonstrate the versatility of our approach

Living cells are controlled by proteins and genes that interact through complex molecular pathways to achieve a specific function. Therefore, determination of protein-protein interaction is fundamental for the understanding of the cell’s lifecycle and functions. The function of a protein is also largely determined by its interactions with other proteins. The amount of protein-protein interaction data available has multiplied by the emergence of large-scale technologies for detecting them, but the drawback of such measures is the relatively high amount of noise present in the data. It is time consuming to experimentally determine protein-protein interactions and therefore the aim of this project is to create a computational method that predicts interactions with high sensitivity and specificity. Semantic similarity measures were applied across the Gene Ontology terms assigned to proteins in S. cerevisiae to predict protein-protein interactions. Three semantic similarity measures were tested to see which one performs best in predicting such interactions. Based on the results, a method that predicts function of proteins in connection with connectivity was devised. The results show that semantic similarity is a useful measure for predicting protein-protein interactions.

Dans de nombreux problèmes d’apprentissage automatique et de reconnaissance des formes, il y a toujours un besoin de fonctions métriques appropriées pour mesurer la distance ou la similarité entre des données. La fonction métrique est une fonction qui définit une distance ou une similarité entre chaque paire d’éléments d’un ensemble de données. Dans cette thèse, nous proposons une nouvelle methode, Triangular Similarity Metric Learning (TSML), pour spécifier une fonction métrique de données automatiquement. Le système TSML proposée repose une architecture Siamese qui se compose de deux sous-systèmes identiques partageant le même ensemble de paramètres. Chaque sous-système traite un seul échantillon de données et donc le système entier reçoit une paire de données en entrée. Le système TSML comprend une fonction de coût qui définit la relation entre chaque paire de données et une fonction de projection permettant l’apprentissage des formes de haut niveau. Pour la fonction de coût, nous proposons d’abord la similarité triangulaire (Triangular Similarity), une nouvelle similarité métrique qui équivaut à la similarité cosinus. Sur la base d’une version simplifiée de la similarité triangulaire, nous proposons la fonction triangulaire (the triangular loss) afin d’effectuer l’apprentissage de métrique, en augmentant la similarité entre deux vecteurs dans la même classe et en diminuant la similarité entre deux vecteurs de classes différentes. Par rapport aux autres distances ou similarités, la fonction triangulaire et sa fonction gradient nous offrent naturellement une interprétation géométrique intuitive et intéressante qui explicite l’objectif d’apprentissage de métrique. En ce qui concerne la fonction de projection, nous présentons trois fonctions différentes: une projection linéaire qui est réalisée par une matrice simple, une projection non-linéaire qui est réalisée par Multi-layer Perceptrons (MLP) et une projection non-linéaire profonde qui est réalisée par Convolutional Neural Networks (CNN). Avec ces fonctions de projection, nous proposons trois systèmes de TSML pour plusieurs applications: la vérification par paires, l’identification d’objet, la réduction de la dimensionnalité et la visualisation de données. Pour chaque application, nous présentons des expérimentations détaillées sur des ensembles de données de référence afin de démontrer l’efficacité de notre systèmes de TSML
In many machine learning and pattern recognition tasks, there is always a need for appropriate metric functions to measure pairwise distance or similarity between data, where a metric function is a function that defines a distance or similarity between each pair of elements of a set. In this thesis, we propose Triangular Similarity Metric Learning (TSML) for automatically specifying a metric from data. A TSML system is loaded in a siamese architecture which consists of two identical sub-systems sharing the same set of parameters. Each sub-system processes a single data sample and thus the whole system receives a pair of data as the input. The TSML system includes a cost function parameterizing the pairwise relationship between data and a mapping function allowing the system to learn high-level features from the training data. In terms of the cost function, we first propose the Triangular Similarity, a novel similarity metric which is equivalent to the well-known Cosine Similarity in measuring a data pair. Based on a simplified version of the Triangular Similarity, we further develop the triangular loss function in order to perform metric learning, i.e. to increase the similarity between two vectors in the same class and to decrease the similarity between two vectors of different classes. Compared with other distance or similarity metrics, the triangular loss and its gradient naturally offer us an intuitive and interesting geometrical interpretation of the metric learning objective. In terms of the mapping function, we introduce three different options: a linear mapping realized by a simple transformation matrix, a nonlinear mapping realized by Multi-layer Perceptrons (MLP) and a deep nonlinear mapping realized by Convolutional Neural Networks (CNN). With these mapping functions, we present three different TSML systems for various applications, namely, pairwise verification, object identification, dimensionality reduction and data visualization. For each application, we carry out extensive experiments on popular benchmarks and datasets to demonstrate the effectiveness of the proposed systems

A kernel function is an important component in the support vector machine (SVM) kernel-based classifier. This is due to the elegant mathematical characteristics of a kernel, which amount to the mapping of non-linearly separable classes to an implicit higher-dimensional feature space where they can become linearly separable, and hence easier to classify. Such characteristics are those prescribed by the underpinning positive semi-definite (PSD) property. The properties of this feature space can, however, be difficult to interpret, to customize or select an appropriate kernel for the classification task at hand. Moreover, the high-dimensionality of the feature space does not usually provide apparent and intuitive information about the natural representations of the data in the input space, as the construction of this feature space is only implicit. On the other hand, SVM kernels have also been regarded as similarity functions in many contexts to measure the resemblance between two patterns, which can be from the same or different classes. However, despite the elegant theory of PSD kernels, and its remarkable implications on the performance of many learning algorithms, limited research efforts seem to have studied kernels from this similarity perspective. Given that patterns from the same class share more similar characteristics than those belonging to different classes, this similarity perspective can therefore provide more tangible means to craft or select appropriate kernels than the properties of the implicit high-dimensional feature spaces that one might not even be able to calculate. This thesis therefore aims to: (i) investigate the similarity-based properties, which can be exploited to characterise kernels (with focus on the so-called “orthogonal polynomial kernels”) when used as similarity functions, and (ii) assess the influence of these properties on the performance of the SVM classifier. An appropriate similarity-based model is therefore defined in the thesis based on how the shape of an SVM kernel should ideally look like when used to measure the similarity between its two inputs. The model proposes that the similarity curve should be maximized when the two kernel inputs are identical, and it should decay monotonically as they differ more and more from each other. Motivated by the pictorial characteristics of the Chebyshev kernels reported in the literature, the thesis adopts this kernel-shape perspective to also study some other orthogonal polynomial kernels (such as the Legendre kernels and Hermite kernels), to underpin the assessment of the proposed ideal shape of the similarity curve for kernel-based pattern classification by SVMs. The analysis of these polynomial kernels revealed that they are naturally constructed from smaller kernel building blocks, which are combined by summation and multiplication operations. A novel similarity fusion framework is therefore developed in this thesis to investigate the effect of these fusion operations on the shape characteristics of the kernels and on their classification performance. This framework is developed in three stages, where Stage 1 kernels are those building blocks constructed from only the polynomial order n (the highest order under consideration), whereas Stage 2 kernels combine all the Stage 1 kernel blocks (from order 0 to n) using a summation fusion operation. The Stage 3 kernels finally combine Stage 2 kernels with another kernel via a multiplication fusion operation. The analysis of the shape characteristics of these three-stage polynomial kernels revealed that their inherent fusion operations are synergistic in nature, as they bring their shapes closer to the ideal similarity function model, and hence enable the calculation of more accurate similarity measures, and accordingly score better classification performance. Experimental results showed that these summative and multiplicative fusion operations improved the classification accuracy by average factors of 17.35% and 19.16%, respectively, depending on the dataset and the polynomial function employed. On the other hand, the shapes of the Stage 2 polynomial kernels have also been shown to oscillate after a certain threshold within the standard normalized input space of [-1,1]. A simple adaptive data normalization approach is therefore proposed to confine the data to the threshold window where these kernels exhibit the sought after ideal shape characteristics, hence eliminate the possibility of any data point to be located outside the range where these oscillations are observed. The implementation of the adaptive data normalization approach accordingly leads to a more accurate calculation of similarity measures and improves the classification performance. When compared to the standard normalized input space, experimental results (performed on the Stage 2 kernels) demonstrate the effectiveness of the proposed adaptive data normalization approach, with an average accuracy improvement factor of 11.772%, depending on the dataset and the polynomial function utilized. Finally, a new perspective is also introduced whereby the utilization of orthogonal polynomials is perceived as a way of transforming the input space to another vector space, of the same dimensionality as the input space, prior to the kernel calculation step. Based on this perspective, a novel processing approach, based on vector concatenation, is proposed which, unlike the previous approaches, ensures that the quantities processed by each polynomial order are always formulated in vector form. This way, the attributes embedded in the structure of the original vectors are maintained intact. The proposed concatenated processing approach can also be used with any polynomial function, regardless of the parity combination of its monomials, whether they are only odd, only even, or a combination of both. Moreover, the Gaussian kernel is also proposed to be evaluated on vectors processed by the polynomial kernels (instead of the linear kernel used in the previous approaches), due to the more accurate similarity shape characteristics of the Gaussian kernel, as well as its renowned ability to implicitly map the input space to a feature space of higher dimensionality. Experimental results demonstrate the superiority of the concatenated approach for all the three polynomial-kernel stages of the developed similarity fusion framework and for all the polynomial functions under investigation. When the Gaussian kernel is evaluated on the vectors processed using the concatenated approach, the observed results show a statistically significant improvement in the average classification accuracy of 22.269%, compared to when the linear kernel is evaluated on the vectors processed using the previously proposed approaches.

Em sistemas reais, os dados armazenados tipicamente apresentam inconsistências causadas por erros de gra a, abreviações, caracteres trocados, entre outros. Isto faz com que diferentes representações do mesmo objeto do mundo real sejam registrados como elementos distintos, causando um problema no momento de consultar os dados. Portanto, o problema investigado nesta tese refere-se às consultas por abrangência, que procuram encontrar objetos que representam o mesmo objeto real consultado . Esse tipo de consulta não pode ser processado por coincidência exata, necessitando de um mecanismo de consulta com suporte à similaridade. Para cada consulta submetida a uma determinada coleção, a função de similaridade produz um ranking dos elementos dessa coleção ordenados pelo valor de similaridade entre cada elemento e o objeto consulta. Como somente os elementos que são variações do objeto consulta são relevantes e deveriam ser retornados, é necessário o uso de um limiar para delimitar o resultado. O primeiro desa o das consultas por abrangência é a de nição do limiar. Geralmente é o especialista humano que faz a estimativa manualmente através da identi - cação de elementos relevantes e irrelevantes para cada consulta e em seguida, utiliza uma medida como revocação e precisão (R&P). A alta dependência do especialista humano di culta o uso de consultas por abrangência na prática, principalmente em grandes coleções. Por esta razão, o método apresentado nesta tese tem por objetivo estimar R&P para vários limiares com baixa dependência do especialista humano. Como um sub-produto do método, também é possível selecionar o limiar mais adequado para uma função sobre uma determinada coleção. Considerando que as funções de similaridade são imperfeitas e que apresentam níveis diferentes de qualidade, é necessário avaliar a função de similaridade para cada coleção, pois o resultado é dependente dos dados. Um limiar para uma coleção pode ser totalmente inadequado para outra coleção, embora utilizando a mesma função de similaridade. Como forma de medir a qualidade de funções de similaridade no contexto de consultas por abrangência, esta tese apresenta a discernibilidade. Trata-se de uma medida que de ne a habilidade da função de similaridade de separar elementos relevantes e irrelevantes. Comparando com a precisão média, a discernibilidade captura variações que não são percebidas pela precisão média, o que mostra que a discernibilidade é mais apropriada para consultas por abrangência. Uma extensa avaliação experimental usando dados reais mostra a viabilidade tanto do método de estimativas como da medida de discernibilidade para consultas por abrangência.
In real systems, stored data typically have inconsistencies caused by typing errors, abbreviations, transposed characters, amongst others. For this reason, di erent representations of the same real world object are stored as distinct elements, causing problems during query processing. In this sense, this thesis investigates range queries which nd objects that represent the same real world object being queried . This type of query cannot be processed by exact matching, thus requiring the support for querying by similarity. For each query submitted to a given collection, the similarity function produces a ranked list of all elements in this collection. This ranked list is sorted decreasingly by the similarity score value with the query object. Only the variations of the query object should be part of the result as only those items are relevant. For this reason, it is necessary to apply a threshold value to properly split the ranking. The rst challenge of range queries is the de nition of a proper threshold. Usually, a human specialist makes the estimation manually through the identi cation of relevant and irrelevant elements for each query. Then, he/she uses measures such as recall and precision (R&P). The high dependency on the human specialist is the main di culty related to use of range queries in real situations, specially for large collections. In this sense, the method presented in this thesis has the objective of estimating R&P at several thresholds with low human intervention. As a by-product of this method, it is possible to select the optimal threshold for a similarity function in a given collection. Considering the fact that the similarity functions are imperfect and vary in quality, it is necessary to evaluate the similarity function for each collection as the result is domain dependent. A threshold value for a collection could be totally inappropriate for another, even though the same similarity function is applied. As a measure of quality of similarity functions for range queries, this thesis introduces discernability. This is a measure to quantify the ability of the similarity function in separating relevant and irrelevant elements. Comparing discernability and mean average precision, the rst one can capture variations that are not noticed by precision-based measures. This property shows that discernability presents better results for evaluating similarity functions for range queries. An extended experimental evaluation using real data shows the viability of both, the estimation method and the discernability measure, applied to range queries.

La present tesi està centrada en l'ús de la Teoria de Semblança Quàntica per a calcular descriptors moleculars. Aquests descriptors s'utilitzen com a paràmetres estructurals per a derivar correlacions entre l'estructura i la funció o activitat experimental per a un conjunt de compostos. Els estudis de Relacions Quantitatives Estructura-Activitat són d'especial interès per al disseny racional de molècules assistit per ordinador i, en particular, per al disseny de fàrmacs.
Aquesta memòria consta de quatre parts diferenciades. En els dos primers blocs es revisen els fonaments de la teoria de semblança quàntica, així com l'aproximació topològica basada en la teoria de grafs. Ambdues teories es fan servir per a calcular els descriptors moleculars. En el segon bloc, s'ha de remarcar la programació i implementació de programari per a calcular els anomenats índexs topològics de semblança quàntica. La tercera secció detalla les bases de les Relacions Quantitatives Estructura-Activitat i, finalment, el darrer apartat recull els resultats d'aplicació obtinguts per a diferents sistemes biològics.
The present thesis is centred in the use of the Quantum Similarity Theory to calculate molecular descriptors. These molecular descriptors are used as structural parameters to derive correlations between the structure and the function or experimental activity for a set of compounds. Quantitative Structure-Activity Relationship studies are of special interest for the rational Computer-Aided Molecular Design and, in particular, for Computer-Aided Drug Design.
The memory has been structured in four differenced parts. The two first blocks revise the foundations of quantum similarity theory, as well as the topological approximation, based in classical graph theory. These theories are used to calculate the molecular descriptors. In the second block, the programming and implementation of Topological Quantum Similarity Indices must be remarked. The third section details the basis for Quantitative Structure-Activity Relationships and, finally, the last section gathers the application results obtained for different biological systems.

A Wikipédia é uma enciclopédia pública composta por milhões de artigos editados diariamente por uma comunidade de autores de diferentes regiões do mundo. Os artigos que constituem a Wikipédia possuem um tipo de link chamado de Cross-language Link que relaciona artigos correspondentes em idiomas diferentes. O objetivo principal dessa estrutura é permitir a navegação dos usuários por diferentes versões de um mesmo artigo em busca da informação desejada. Além disso, por permitir a obtenção de corpora comparáveis, os Cross-language Links são extremamente importantes para aplicações que trabalham com tradução automática e recuperação de informações multilíngues. Visto que os Cross-language Links são inseridos manualmente pelos autores dos artigos, quando o autor não reconhece o seu correspondente em determinado idioma ocorre uma situação de Cross-language Links ausente. Sendo assim, é importante o desenvolvimento de uma abordagem que realize a descoberta de Cross-language Links entre artigos que são correspondentes, porém, não estão conectados por esse tipo link. Nesta dissertação, é apresentado o CLLFinder, uma abordagem para a descoberta de Cross-language Links ausentes. A nossa abordagem utiliza o relacionamento entre as categorias e a indexação e consulta do conteúdo dos artigos para realizar a seleção do conjunto de candidatos. Para a identificação do artigo correspondente, são utilizados atributos que exploram a transitividade de Cross-language Links entre outros idiomas bem como características textuais dos artigos. Os resultados demonstram a criação de um conjunto de candidatos com 84,3% de presença do artigo correspondente, superando o trabalho utilizado como baseline. A avaliação experimental com mais de dois milhões de pares de artigos aponta uma precisão de 99,2% e uma revocação geral de 78,9%, superando, também, o baseline. Uma inspeção manual dos resultados do CLLFinder aplicado em um cenário real indica que 73,6% dos novos Cross-language Links sugeridos pela nossa abordagem eram de fato correspondentes.
Wikipedia is a public encyclopedia composed of millions of articles written daily by volunteer authors from different regions of the world. The articles contain links called Cross-language Links which relate corresponding articles across different languages. This feature is extremely useful for applications that work with automatic translation and multilingual information retrieval as it allows the assembly of comparable corpora. Since these links are created manually, in many occasions, the authors fail to do so. Thus, it is important to have a mechanism that automatically creates such links. This has been motivating the development of techniques to identify missing cross-language links. In this work, we present CLLFinder, an approach for finding missing cross-language links. The approach makes use of the links between categories and an index of the content of the articles to select candidates. In order to identify corresponding articles, the method uses the transitivity between existing cross-language links in other languages as well as textual features extracted from the articles. Experiments on over two million pairs of articles from the English and Portuguese Wikipedias show that our approach has a recall of 78.9% and a precision of 99.2%, outperforming the baseline system.A manual inspection of the results of CLLFinder applied to a real situation indicates that our approach was able to identify the Cross-language Link correctly 73.6% of the time.

In two related studies with dating and married couples, the protective function of beliefs about personal value similarity was examined. Relational threat was measured when couple members' value similarity beliefs were disconfirmed or when couple members reported beliefs of value dissimilarity. Gender-specific compensatory mechanisms, reflective of relational self-construal, were examined in association with relational well being. Study 1 was a controlled laboratory experiment with dating couples that examined disconfirmation of perceived value similarity. Study 2 examined naturally occurring variance of married couples' beliefs about value similarity in the context of pregnancy and amniocentesis testing. Results revealed that dating and married couples did assume similarity about their personal values in moral contexts that reflected relational significance.
Results supported that assumptions about value similarity were protective for couple members. Beliefs about value similarity that were disconfirmed by experimentally controlled feedback as well as perceived value dissimilarity in a naturally occurring context both posed relational threat for dating couples and pregnant women, respectively. Gender-specific compensatory mechanisms were evoked and were associated with overall relational well being when romantic intimates considered personal value dissimilarity. Women demonstrated pro-relational behaviors, consistent with their relational self-construal, such that they shifted their personal values and brought their values in closer alignment with their partners' values while, additionally, increasing their ratings of partners' positive attributes. Dating men, consistent with their less relational self-construal, did not alter their personal values and instead increased their ratings of their partners' positive attributes, which accounted for increased relational satisfaction. Married men who considered value dissimilarity with their pregnant partners did not experience relational threat but demonstrated pro-relational behaviors such that they shifted their personal values and brought their values in closer alignment with their partners' values while increasing their ratings of partners' positive attributes. The studies provide expanded knowledge for the growing field of close relationship literature. Results were also discussed in the context of pregnancy, social support, and the utilization of amniocentesis tests.

ABSTRACT Beach and nearshore surveys are conducted in a variety of ways, the most commonly used being the level-and-transit method; because it is inexpensive, time conducive and highly accurate. Specifically, beach surveys are conducted to better understand cross-shore, long-shore sediment transport processes, as well as to quantify volume changes, which are used to evaluate beach performance. In this study, a section of the beach on Sand Key, FL was surveyed using rod-and-transit. In addition to the commonly used linear data analysis, a non-linear analysis was conducted using NURBS (Non-Uniform Rational B-Splines). Survey data was collected within a short time window to ensure minimal environmental changes associated with waves and anthropological factors. Beach profiles were surveyed using two spatial resolutions, including 1) a typical variable resolution determined by the rodman based on observed morphology changes, and 2) a uniform, high resolution of 25 centimeters per point. The results indicate that variable resolution survey with careful observation by the rodman provided adequate accuracy as compared to the very high-resolution survey. The goal of this study is to create a realistic surface between the beach profiles that are spaced relatively far apart. The commonly used contouring method (a linear method) may create mismatch among major morphology units, .e.g., bar crest, if they have different elevations alongshore. Here a non-linear method is developed by 1) identifying major morphological units, in this case dune top, berm crest, trough bottom, and bar crest 2) linking the units using a cubic spline, and 3) generating a surface using a NURBS sweep2 function. Bisector profiles are sliced from the surface generated using linear and non-linear methods, and compared with surveyed profiles at the same location. The profiles generated using the non-linear method matched more closely to the measured profile than that from the linear method. The non-linear NURBS surface resulted in a consistently greater beach volume between the surveyed profiles than the linear method of volume calculation.

The process of protein structure prediction is a crucial part of understanding the function of the building blocks of life. It is based on the approximation of a protein free energy that is used to guide the search through the space of protein structures towards the thermodynamic equilibrium of the native state. A function that gives a good approximation of the protein free energy should be able to estimate the structural distance of the evaluated candidate structure to the protein native state. This correlation between the energy and the similarity to the native is the key to high quality predictions. State-of-the-art protein structure prediction methods use very simple techniques to design such energy functions. The individual components of the energy functions are created by human experts with the use of statistical analysis of common structural patterns that occurs in the known native structures. The energy function itself is then defined as a simple weighted sum of these components. Exact values of the weights are set in the process of maximisation of the correlation between the energy and the similarity to the native measured by a root mean square deviation between coordinates of the protein backbone. In this dissertation I argue that this process is oversimplified and could be improved on at least two levels. Firstly, a more complex functional combination of the energy components might be able to reflect the similarity more accurately and thus improve the prediction quality. Secondly, a more robust similarity measure that combines different notions of the protein structural similarity might provide a much more realistic baseline for the energy function optimisation. To test these two hypotheses I have proposed a novel approach to the design of energy functions for protein structure prediction using a genetic programming algorithm to evolve the energy functions and a structural similarity consensus to provide a reference similarity measure. The best evolved energy functions were found to reflect the similarity to the native better than the optimised weighted sum of terms, and therefore opening a new interesting area of research for the machine learning techniques.

Recent work in microbial ecology has focused on elucidating controls over biogeographic patterns and connecting microbial community composition to ecosystem function. My objective was to investigate the relative influences of landscape legacies and contemporary environmental factors on the distribution of soil microbial communities and their contribution to ecosystem processes across a glacial till sequence in Taylor Valley, Antarctica. Within each till unit, I sampled from dry areas and areas with visible evidence of recent surface water movement generated by seasonal melting of ephemeral snow packs and hillslope ground ice. Using T-RFLP 16S rRNA gene profiles of microbial communities, I analyzed the contribution of till and environmental factors to community similarity, and assessed the functional potential of the microbial community using extracellular enzyme activity assays. Microbial communities were influenced by geochemical differences among both tills and local environments, but especially organized by variables associated with water availability as the first axis of an NMDS ordination was strongly related to shifts in soil moisture content. CCA revealed that tills explained only 3.4% of the variability in community similarity among sites, while geochemical variables explained 18.5%. Extracellular enzyme activity was correlated with relevant geochemical variables reflecting the influence of nutrient limitation on microbial activity. In addition, enzyme activity was related to changes in community similarity, particularly in wet environments with a partial Mantel correlation of 0.32. These results demonstrate how landscape history and environmental conditions can shape the functional potential of a microbial community mediated through shifts in microbial community composition.
Master of Science

One of the problems associated with automatic thesaurus construction is with determining the semantic relationship between word pairs. Quasi-synonyms provide a type of equivalence relationship: words are similar only for purposes of information retrieval. Determining such relationships in a thesaurus is hard to achieve automatically. The term vector space model and an inverse term frequency similarity function can provide a way to automatically determine the similarity between words in thesaurus. A thesaurus constructed using this method can also improve precision and recall in information retrieval, when the thesaurus is constructed in conjunction with fuzzy rough set algorithms and used with tight upper approximation query expansion. This dissertation presents a method that combines fuzzy rough sets and a word weighting and inverse term frequency similarity function as a technique for automatic thesaurus construction.

Os mecanismos tradicionais de consulta a bases de dados, que utilizam o critério de igualdade, têm se tornado ineficazes quando os dados armazenados possuem variações tanto ortográficas quanto de formato. Nesses casos, torna-se necessário o uso de funções de similaridade ao invés dos operadores booleanos. Os mecanismos de consulta por similaridade retornam um ranking de elementos ordenados pelo seu valor de similaridade em relação ao objeto consultado. Para delimitar os elementos desse ranking que efetivamente fazem parte do resultado pode-se utilizar um limiar de similaridade. Entretanto, a definição do limiar de similaridade adequado é complexa, visto que este valor varia de acordo com a função de similaridade usada e a semântica dos dados consultados. Uma das formas de auxiliar na definição do limiar adequado é avaliar a qualidade do resultado de consultas que utilizam funções de similaridade para diferentes limiares sobre uma amostra da coleção de dados. Este trabalho apresenta um método automático de estimativa da qualidade de funções de similaridade através de medidas de revocação e precisão computadas para diferentes limiares. Os resultados obtidos a partir da aplicação desse método podem ser utilizados como metadados e, a partir dos requisitos de uma aplicação específica, auxiliar na definição do limiar mais adequado. Este processo automático utiliza métodos de agrupamento por similaridade, bem como medidas para validar os grupos formados por esses métodos, para eliminar a intervenção humana durante a estimativa de valores de revocação e precisão.
Traditional database query mechanisms, which use the equality criterion, have become inefficient when the stored data have spelling and format variations. In such cases, it's necessary to use similarity functions instead of boolean operators. Query mechanisms that use similarity functions return a ranking of elements ordered by their score in relation to the query object. To define the relevant elements that must be returned in this ranking, a threshold value can be used. However, the definition of the appropriated threshold value is complex, because it depends on the similarity function used and the semantics of the queried data. One way to help to choose an appropriate threshold is to evaluate the quality of similarity functions results using different thresholds values on a database sample. This work presents an automatic method to estimate the quality of similarity functions through recall and precision measures computed for different thresholds. The results obtained by this method can be used as metadata and, through the requirements of an specific application, assist in setting the appropriated threshold value. This process uses clustering methods and cluster validity measures to eliminate human intervention during the process of estimating recall and precision.

Dans ce travail, nous présentons des techniques de réduction de données et de sécurité conçues pour économiser de l’énergie dans les réseaux de capteurs sans fil. Premièrement, nous proposons un modèle d’agrégation de données basé sur la fonction de similarité servant à éliminer les données redondantes. En plus, nous avons travaillé sur l’envoi, le moins possible, de caractéristiques de données en se basant sur des fonctions d’ajustement qui expriment ces caractéristiques. Deuxièmement, nous nous sommes intéressés à l’hétérogénéité des données tout en étudiant la corrélation entre ces caractéristiques multi variantes après avoir éliminé les mesures identiques durant la phase d’agrégation. Finalement, nous donnons un cadre de sécurité rigoureux, conçu à partir de la cryptographie, qui satisfait le niveau d’exigence atteint normalement dans les réseaux de capteurs sans fil arborescents. Il empêche les pirates d’obtenir des informations à propos des données détectées en assurant une certaine confidentialité de bout-en-bout entre les nœuds du capteur et le puits. Afin de valider nos techniques proposées, nous avons implémenté les simulations de la première technique sur des données collectées en temps réel à partir du réseau Sensor Scope déployé à Grand-St-Bernard. Les simulations de la deuxième et de la troisième technique sont réalisées sur des données collectées en temps réel à partir de 54 capteurs déployés au laboratoire de recherche Intel Berkeley. L’efficacité de nos techniques est évaluée selon le taux de réduction de données, la consommation de l’énergie, la précision des données et la complexité de temps
In this thesis, we present energy-efficient data reduction and security techniques dedicated for wireless sensor networks. First, we propose a data aggregation model based on the similarity function that helps in removing the redundant data. In addition, based on the fitting functions we worked on sending less data features, accompanied with the fitting function that expresses all features. Second, we focus on heterogeneity of the data while studying the correlation among these multivariate features in order to enhance the data prediction technique that is based on the polynomial function, all after removing the similar measures in the aggregation phase using the Euclidean distance. Finally, we provide a rigorous security framework inherited from cryptography satisfies the level of exigence usually attained in tree-based WSNs. It prevents attackers from gaining any information about sensed data, by ensuring an end-to-end privacy between sensor nodes and the sink. In order to validate our proposed techniques, we implemented the simulations of the first technique on real readings collected from a small Sensor Scope network which is deployed at the Grand-St-Bernard, while the simulations of the second and the third techniques are conducted on real data collected from 54 sensors deployed in the Intel Berkeley Research Lab. The performance of our techniques is evaluated according to data reduction rate, energy consumption, data accuracy and time complexity

This dissertation contributes to two fundamental problems of digital image formation: the modeling and estimation of the blur introduced by an optical digital camera and the fast generation of realistic synthetic images. The accurate estimation of the camera's intrinsic blur is a longstanding problem in image processing. Recent technological advances have significantly impacted on image quality. Thus improving the accuracy of calibration procedures is imperative to further push this development. The first part of this thesis presents a mathematical theory that models the physical acquisition of digital cameras. Based on this modeling, two fully automatic algorithms to estimate the intrinsic camera blur are introduced. For the first one, the estimation is performed from a photograph of a specially designed calibration pattern. One of the main contributions of this dissertation is the proof that a pattern with white noise characteristics is near optimal for the estimation purpose. The second algorithm circumvents the tedious process of using a calibration pattern. Indeed, we prove that two photographs of a textured planar scene, taken at two different distances with the same camera configuration, are enough to produce an accurate estimation. In the second part of this thesis, we propose an algorithm to accelerate realistic image synthesis. Several hours or even days may be necessary to produce high-quality images. In a typical renderer, image pixels are formed by averaging the contribution of stochastic rays cast from a virtual camera. The simple yet powerful acceleration principle consists of detecting similar pixels by comparing their ray histograms and letting them share their rays. Results show a significant acceleration while preserving image quality.

Notre compréhension de la physique de la source sismique, qui donne naissance à des séismes de toute magnitude, requiert l’observation d’une large population d’événements. Les méthodes d’analyse systématique de la sismicité mondiale remplissent ce rôle et permettent d’extraire les propriétés des séismes puis de les confronter aux modèles de rupture sismique. La méthode SCARDEC fait partie de ces méthodes et retrouve les fonctions source d’événements sur une large gamme de magnitudes (Mw > 5.7). La fonction source, puisqu’elle décrit l’évolution tem porelle du taux de moment, est un observable privilégié pour l’analyse des propriétés transitoires de la rupture. L’objectif de notre étude est d’observer le développement de la rupture lors de ces séismes afin de plus précisément contraindre les modèles cinématiques et dynamiques de la source. La première partie de notre travail s’intéresse au développement des séismes à partir du catalogue SCARDEC. La phase menant au pic de la fonction source (“phase de dévelop pement”) est extraite pour caractériser son évolution. À partir du calcul des accélérations de moment pour des taux de moment donnés, nous observons que l’évolution du taux de moment pendant la phase de développement est indépendante de la magnitude finale. Une analyse quantitative de l’augmentation du taux de moment en fonction du temps indique que cette phase ne respecte pas la dépendance en t 2 de la loi auto-similaire, suggérant une variation transitoire de la vitesse de rupture et/ou de la chute de contrainte. Ces observations sont dans un deuxième temps confrontées aux modèles cinématiques de la source. Un modèle de crack avec des variations radiales de la vitesse de rupture, associées à une faible chute de contrainte, met en évidence que la corrélation entre vitesse de rupture et vitesse de glissement est un ingrédient nécessaire au comportement transitoire de la phase de développement vu dans les observations. Nous générons ensuite à partir du modèle composite fractal RIK des catalogues synthétiques de fonctions source. Ces derniers montrent également que la corrélation entre la vitesse de rupture et la vitesse de glissement, ainsi que la durée du temps de montée, ont une influence sur les valeurs de l’accélération de moment. Nous développons finalement des modèles dynamiques hétérogènes qui prennent en compte la physique de la rupture. Les dis tributions hétérogènes du paramètre de friction Dc et de la contrainte initiale τ0 sur la faille participent à générer des scénarios de rupture particulièrement réalistes. La propagation de la rupture est en particulier influencée par ces deux paramètres dynamiques qui entraînent une direction de propagation préférentielle couplée à une variabilité plus locale de la vitesse de rupture. La corrélation entre vitesse de rupture et vitesse de glissement, mise en lumière dans les modèles cinématiques précédents, est retrouvée et permet la reproduction des observations SCARDEC. Ces résultats devraient fournir des contraintes additionnelles pour la constitution de scenarios réalistes de la dynamique de la rupture
Our knowledge of earthquake source physics, giving rise to events of very different magnitudes, requires observations of a large population of earthquakes. The development of systematic analysis tools for the global seismicity meets these expectations, and allows us to extract the generic properties of earthquakes, which can then be integrated into models of the rupture process. Following this approach, the SCARDEC method is able to retrieve source time func tions of events on a large range of magnitude (Mw > 5.7). The source time function (which describes the temporal evolution of the moment rate) is suitable for the analysis of transient rupture properties which provide insights into the generation of earthquakes of various sizes. The purpose of our study is to observe the rupture development of such earthquakes in order to add better constraints on kinematic and dynamic source models. The first part of our work focuses on the development of earthquakes through the analysis of the SCARDEC catalog. The phase leading to the peak of the source time function (“development phase”) is extracted to characterize its evolution. From the computation of moment accelerations at prescribed mo ment rates, we observe that the evolution of the moment rate during the developement phase is independent of the final magnitude. A quantitative analysis of the moment rate increase as a function of time further indicates that this phase does not respect the steady t 2 self-similar growth, suggesting a transient variation of rupture velocity and/or stress drop. In a second part, these observations are compared with kinematic source models. A crack model with ra dial variations of the rupture velocity combined with low stress drop highlights that correlation between rupture velocity and slip velocity is a key feature for the transient behavior of the development phase previously observed. We then generate, using the composite fractal RIK model, synthetic catalogs of source time functions. This also supports that the correlation bet ween rupture velocity and slip velocity, as well as the duration of the rise-time, have a strong effect on moment acceleration values. We finally develop heterogeneous dynamic models which take into consideration rupture physics. Heterogeneous distributions of the friction parameter Dc and the initial stress τ0 contribute to generate highly realistic rupture scenarios. Rupture propagation is strongly influenced by these two dynamic parameters which induce a clear pre ferential direction of propagation together with a local variability of the rupture velocity. The correlation between rupture velocity and slip velocity highlighted by the previous kinematic models is retrieved and allows to reproduce the SCARDEC observations. These findings are expected to put further constraints on future realistic dynamic rupture scenarios

Nacionalinių mokinių pasiekimų tyrimo metodologija yra nuolat plėtojama. Pasitarus su Švietimo plėtotės centro tyrimo skyriaus darbuotojais, buvo nuspręsta įsigilinti į klasterinės ir diskriminantinės analizės metodus, jų pritaikomumą nacionalinių tyrimų rezultatų analizei. Tai įtakojo šio darbo pasirinkimą ir tikslą - susipažinti su Klasterinės ir Diskriminantinės analizės metodais, pateikti ir aptarti jų taikymo pavyzdžius. Darbe išnagrinėti du daugiamačiai statistiniai metodai: klasterinė ir diskriminantinė analizė. Yra aptarti šių metodų teoriniai aspektai bei pateikti originalūs šių metodų pritaikymo mokinių pasiekimų tyrimams pavyzdžiai. Padarytos išvados apie šių metodų pritaikomumą nacionalinių mokinių pasiekimų tyrimo analizei atlikti.
National research of student marches are continually evolving. With Educational evolve center’s help I decided to analyse Cluster and Disckriminant analysis methods and how they can be used in National research analysis. This was a reason of my work purpose - to have a look at Cluster and Disckriminant analysis methods, to offer examples of practical use. There are two statistical multidimensional methods discussed in this work (Cluster and Disckriminant analysis). There are discussed theoretical side of these methods, also you can find original examples of practical use. In conclusion I discuss about practical use of these methods in national research of student marches.

This dissertation investigates how cognates are organized in the bilingual mental lexicon and examines whether orthography in one language, via phonological representations, influences the processing of cognates and false friends in the other language. In light of the framework of two well-known models of bilingual visual word recognition, the Bilingual Interactive Activation (BIA) and the Bilingual Interactive Activation Plus (BIA+), the premise is that there is activation from orthography to phonology across a bilingual’s two languages and that this activation is modulated by the degree of orthographic and phonological code overlap. Two objective metrics were used to assess crosslinguistic similarity of Portuguese-English cognates and false friends that were selected for a cross-language lexical decision task with masked priming. Dynamic time warping (DTW), an algorithm that was originally conceived to compare different speech patterns in automatic speech recognition and to measure acoustic similarity between two time-dependent sequences, was used to compute crosslinguistic phonological similarity. The Normalized Levenshtein Distance (NLD), an algorithm that calculates the minimum number of single-character insertions, deletions or substitutions required to change one word into another and normalizes the result by their lengths, was used to compute crosslinguistic orthographic similarity. Portuguese-English bilinguals who acquired their second language after reaching puberty, and English functional monolinguals who grew up speaking primarily English were recruited to participate in the experimental task. Based on collected reaction time and accuracy data, mixed-effects models analyses are used to estimate the individual effects of crosslinguistic orthographic, phonological and semantic similarity and the role each of them, along with English proficiency, word frequency and length play in the organization of the Portuguese-English bilingual mental lexicon.

Esta dissertação trata do Princípio da similaridade para as soluções das equações da forma L\'OMEGA\' = A(z) ·\'OMEGA\' + B(z) · \'BARRA\' \'omega\' , sendo L um campo vetorial complexo não singular e A,B \'PERTENCE\' \'C POT. sigma\' (\'R POT. 2\'), com 0 < \'sigma\' < 1. Aqui são apresentados resultados para o campo vetorial elítico L = \'PARTIAL SUP\' \'\'PARTIAL\' z e para classes de campos vetoriais elíticos degenerados
This dissertation deals with the Similarity principle for solutions of equations of the form L \'omega\' = A(z) · \'omega\' + B(z) · \' BARRA\' \'omega\' where L is a nonsingular complex vector field and A,B \'IT BELONGS\' \'C POT. sigma \' (\'R POT. 2\'), with 0 < \'sigma\' < 1. Here are presented results for elliptic vector field and for classes of degenerate elliptic vector fields

It is of great importance to find an analytical copula that will represent the empirical lower tail dependence. In this study, the pairwise empirical copula are estimated using data of the S&P 500 stocks during the period 2007-2010.Different optimization methods and measures of dependence have been used to fit Gaussian, t and Clayton copula to the empirical copulas, in order to represent the empirical lower tail dependence. These different measures of dependence and optimization methods with their restrictions, point at different analytical copulas being optimal. In this study the t copula with 5 degrees of freedom is giving the most fulfilling result, when it comes to representing lower tail dependence. The t copula with 5 degrees of freedom gives the best representation of empirical lower tail dependence, whether one uses the 'Empirical maximum likelihood estimator', or 'Equal Ƭ' as an approach.

Esta pesquisa descreve um modelo para descobrir e pontuar competências acadêmicas de pesquisadores, baseado na combinação de indicadores quantitativos que permitem mensurar a produção acadêmica dos cientistas. Um diferencial do modelo é a inclusão de indicadores quantitativos relacionados com a importância da produção bibliográfica dos pesquisadores. Estes indicadores possibilitam uma avaliação da produção considerando aspectos como repercussão na comunidade acadêmica e nível dos veículos de publicação. A pesquisa também contribui com a especificação de uma arquitetura flexível e extensível fundamentada em técnicas de extração de dados na Web e casamento aproximado de dados (através de funções de similaridade). A arquitetura foi implementada em um sistema Web cuja principal característica é a integração de diversas tecnologias open source. O sistema desenvolvido permite que qualquer pesquisador avalie quantitativamente sua produção científica, automatizando diversos aspectos relacionados à tarefa de avaliação, como a obtenção dos indicadores e a integração das diferentes bases de informações.
The present research describes a model that aims finding out and scoring academic researchers skills or competences based on the combination of quantitative indicators that make it possible to measure the production of academic scientists. A special feature concerning our model is the inclusion of quantitative indicators related to the importance of the researchers’ bibliographic production. These indicators allow the evaluation of the production considering both the outcome it has had in the academic community, and the quality level of the place it was published. The study also presents a flexible and extensible architecture specification based on techniques of web data extraction, and on approximate data matching (which is carried out through similarity functions). The architecture has been implemented in a web system whose main feature relies on the integration of several open-source technologies. The developed system allows any researcher to evaluate his/her own scientific production in quantitative terms, automating as well the so many aspects regarding the evaluation task, by making it easier to obtain the indicators and to integrate the different information databases, for instance.

A better understanding of the exchange processes taking place over the oceans is of great importance since the oceans cover about 70 % of the Earth’s surface. With better knowledge the turbulent fluxes can be more accurate parameterized, which is essential in order to improve the weather- and climate models. In this study, the non-dimensional gradient functions for water vapor (Φq) and carbon dioxide (Φc) in the marine boundary layer have principally been studied. The quality of the instrumentation used in the study has also been evaluated. The study is mainly based on tower measurements of turbulent fluxes and vertical profiles of water vapor and carbon dioxide, taken from the Östergarnsholm Island located in the Baltic Sea. The measurements have been shown to represent open-sea conditions for most situations when the winds are coming from the east-south sector, even though the measurements are obtained over land. It was found that the best fitting non-dimensional gradient functions for water vapor during unstable conditions were Φq = 2(1–18z/L)–1/2 and Φq = 1.2(1–14z/L) –1/2 at the 10 and 26 m level on the tower, respectively. No unique relationship could be established for Φq during stable conditions. Φq showed a dependence with wind direction and could for winds coming from the sector 80°– 160° be described with the relationship Φq = 1.2 + 10.7z/L during stable conditions. For the wind sector 50°– 80° the relationship for Φq was found to be Φq = 1.8 + 7.1z/L during stable conditions. A high degree of scatter was apparent in the calculated values of Φc during both stable and unstable conditions and did not seem to show any Monin-Obukhov similarity behaviour. The results indicate that there might be measurement problems with the instruments measuring the turbulent fluxes of carbon dioxide, but further studies are needed in order to draw a firm conclusion about the quality of the instruments. The profile measurements of water vapor seem to work fine, but more studies of carbon dioxide are needed before a statement can be made regarding the quality of the profile measurements of carbon dioxide.
Skiktet närmast marken kallas det atmosfäriska gränsskiktet och karaktäriseras av turbulens, dvs. oregelbundna virvelrörelser av olika storlekar som uppstår av vindens friktion mot jordytan (land eller hav) eller av luftens uppvärmning av jordytan. Genom turbulens kan utbyte av värme, vattenånga, momentum, koldioxid och andra gaser ske mellan jordytan och atmosfären. Turbulenta utbytesprocesser i det atmosfäriska gränsskiktet är viktiga att studera för att kunna beräkna ett turbulent flöde från en yta i väder- och klimatmodeller. Genom en ökad förståelse av flödena kan dessa bli mer noggrant parametriserade (dvs. en fysikalisk process som sker på en mindre skala eller är för komplex för att kunna beskrivas i en modell förenklas genom att beskriva processen med hjälp av ett antal kända parametrar som kan upplösas i modellen), vilket är grundläggande för att kunna förbättra modellerna. Flödena beräknas med hjälp av de s.k. dimensionslösa gradientfunktionerna, vilka relaterar flödet av en viss turbulent kvantitet, t.ex. värme, momentum, vattenånga, koldioxid etc., till dess vertikala gradient. Enligt Monin-Obukhovs similaritetsteori ska funktionerna vara universella och endast bero på den atmosfäriska stabiliteten. I denna studie har de dimensionslösa gradientfunktionerna för vattenånga (Φq) och koldioxid (Φc) i det marina gränsskiktet huvudsakligen analyserats. Kvaliteten på de instrument som har använts i studien har också utvärderats. I studien har främst data av turbulenta flöden och vertikala profiler av vattenånga och koldioxid använts som erhållits från ett torn på ön Östergarnsholm i Östersjön. Även om mätningarna sker över land har det visat sig att de för de flesta situationer när vinden blåser från sektorn ost-syd representerar likvärdiga förhållanden som gäller över öppet hav. Resultaten visade på att uttrycken Φq = 2(1–18z/L)–1/2 respektive Φq = 1.2(1–14z/L)–1/2 bäst beskriver de dimensionslösa gradientfunktionerna för vattenånga under instabila förhållanden på mäthöjderna 10 respektive 26 m. Något unikt uttryck för Φq under stabila förhållanden kunde inte fastställas. Φq visade ett beroende av vindriktning och kunde under stabila förhållanden beskrivas med uttrycket Φq = 1.2 + 10.7z/L för vindsektorn 80°– 160°. För vindar i sektorn 50°– 80° kunde Φq beskrivas enligt Φq = 1.8 + 7.1z/L under stabila förhållanden. En stor spridning syntes i de beräknade värdena av Φc under både stabila och instabila förhållanden och verkade inte följa Monin-Obukhov’s similaritetsteori. Resultatet tyder på att det kan vara mätproblem med de instrument som mäter de turbulenta flödena av koldioxid, men fler studier behövs för att kunna dra en definitiv slutsats om instrumentens kvalitet. Profilmätningarna av vattenånga verkar fungera bra, men fler studier om koldioxid måste utföras innan ett uttalande angående kvaliteten på profilmätningarna av koldioxid kan göras.

Dans cette thèse, nous proposons des techniques de gestion de données pour économiser l’énergie dans les réseaux de capteurs périodiques basés sur l’architecture de clustering. Premièrement, nous proposons d’adapter le taux d’échantillonnage du capteur à la dynamique de la condition surveillée en utilisant le modèle de one-way ANOVA et des tests statistiques (Fisher, Tukey et Bartlett), tout en prenant en compte l’énergie résiduelle du capteur. Le deuxième objectif est d’éliminer les données redondantes générées dans chaque cluster. Au niveau du capteur, chaque capteur cherche la similarité entre les données collectées à chaque période et entre des périodes successives, en utilisant des fonctions de similarité. Au niveau du CH, nous utilisons des fonctions de distance pour permettre CH d’éliminer les ensembles de données redondantes générées par les nœuds voisins. Enfin, nous proposons deux stratégies actif/inactif pour ordonnancer les capteurs dans chaque cluster, après avoir cherché la corrélation spatio-temporelle entre les capteurs. La première stratégie est basée sur le problème de couverture des ensembles tandis que la seconde prend avantages du degré de corrélation et les énergies résiduelles de capteurs pour ordonnancer les nœuds dans chaque cluster. Pour évaluer la performance des techniques proposées, des simulations sur des données de capteurs réelles ont été menées. La performance a été analysée selon la consommation d’énergie, la latence et l’exactitude des données, et la couverture, tout en montrant comment nos techniques peuvent améliorer considérablement les performances des réseaux de capteurs
In this thesis, we propose energy-efficient data management techniques dedicated to periodic sensor networks based on clustering architecture. First, we propose to adapt sensor sampling rate to the changing dynamics of the monitored condition using one-way ANOVA model and statistical tests (Fisher, Tukey and Bartlett), while taking into account the residual energy of sensor. The second objective is to eliminate redundant data generated in each cluster. At the sensor level, each sensor searches the similarity between readings collected at each period and among successive periods, based on the sets similarity functions. At the CH level, we use distance functions to allow CH to eliminate redundant data sets generated by neighboring nodes. Finally, we propose two sleep/active strategies for scheduling sensors in each cluster, after searching the spatio-temporal correlation between sensor nodes. The first strategy uses the set covering problem while the second one takes advantages from the correlation degree and the sensors residual energies for scheduling nodes in the cluster. To evaluate the performance of the proposed techniques, simulations on real sensor data have been conducted. We have analyzed their performances according to energy consumption, data latency and accuracy, and area coverage, and we show how our techniques can significantly improve the performance of sensor networks