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Cette thèse explore la reconnaissance de gestes à partir de capteurs inertiels pour Smartphone. Ces gestes consistent en la réalisation d'un tracé dans l'espace présentant une valeur sémantique, avec l'appareil en main. Notre étude porte en particulier sur l'apprentissage de métrique entre signatures gestuelles grâce à l'architecture "Siamoise" (réseau de neurones siamois, SNN), qui a pour but de modéliser les relations sémantiques entre classes afin d'extraire des caractéristiques discriminantes. Cette architecture est appliquée au perceptron multicouche (MultiLayer Perceptron). Les stratégies classiques de formation d'ensembles d'apprentissage sont essentiellement basées sur des paires similaires et dissimilaires, ou des triplets formés d'une référence et de deux échantillons respectivement similaires et dissimilaires à cette référence. Ainsi, nous proposons une généralisation de ces approches dans un cadre de classification, où chaque ensemble d'apprentissage est composé d’une référence, un exemple positif, et un exemple négatif pour chaque classe dissimilaire. Par ailleurs, nous appliquons une régularisation sur les sorties du réseau au cours de l'apprentissage afin de limiter les variations de la norme moyenne des vecteurs caractéristiques obtenus. Enfin, nous proposons une redéfinition du problème angulaire par une adaptation de la notion de « sinus polaire », aboutissant à une analyse en composantes indépendantes non-linéaire supervisée. A l'aide de deux bases de données inertielles, la base MHAD (Multimodal Human Activity Dataset) ainsi que la base Orange, composée de gestes symboliques inertiels réalisés avec un Smartphone, les performances de chaque contribution sont caractérisées. Ainsi, des protocoles modélisant un monde ouvert, qui comprend des gestes inconnus par le système, mettent en évidence les meilleures capacités de détection et rejet de nouveauté du SNN. En résumé, le SNN proposé permet de réaliser un apprentissage supervisé de métrique de similarité non-linéaire, qui extrait des vecteurs caractéristiques discriminants, améliorant conjointement la classification et le rejet de gestes inertiels. / As consumer devices become more and more ubiquitous, new interaction solutions are required. In this thesis, we explore inertial-based gesture recognition on Smartphones, where gestures holding a semantic value are drawn in the air with the device in hand. In our research, speed and delay constraints required by an application are critical, leading us to the choice of neural-based models. Thus, our work focuses on metric learning between gesture sample signatures using the "Siamese" architecture (Siamese Neural Network, SNN), which aims at modelling semantic relations between classes to extract discriminative features, applied to the MultiLayer Perceptron. Contrary to some popular versions of this algorithm, we opt for a strategy that does not require additional parameter fine tuning, namely a set threshold on dissimilar outputs, during training. Indeed, after a preprocessing step where the data is filtered and normalised spatially and temporally, the SNN is trained from sets of samples, composed of similar and dissimilar examples, to compute a higher-level representation of the gesture, where features are collinear for similar gestures, and orthogonal for dissimilar ones. While the original model already works for classification, multiple mathematical problems which can impair its learning capabilities are identified. Consequently, as opposed to the classical similar or dissimilar pair; or reference, similar and dissimilar sample triplet input set selection strategies, we propose to include samples from every available dissimilar classes, resulting in a better structuring of the output space. Moreover, we apply a regularisation on the outputs to better determine the objective function. Furthermore, the notion of polar sine enables a redefinition of the angular problem by maximising a normalised volume induced by the outputs of the reference and dissimilar samples, which effectively results in a Supervised Non-Linear Independent Component Analysis. Finally, we assess the unexplored potential of the Siamese network and its higher-level representation for novelty and error detection and rejection. With the help of two real-world inertial datasets, the Multimodal Human Activity Dataset as well as the Orange Dataset, specifically gathered for the Smartphone inertial symbolic gesture interaction paradigm, we characterise the performance of each contribution, and prove the higher novelty detection and rejection rate of our model, with protocols aiming at modelling unknown gestures and open world configurations. To summarise, the proposed SNN allows for supervised non-linear similarity metric learning, which extracts discriminative features, improving both inertial gesture classification and rejection.

La radiothérapie est une des méthodes principales utilisée dans le traitement thérapeutique des tumeurs malignes. Pour améliorer son efficacité, deux problèmes essentiels doivent être soigneusement traités : la prédication fiable des résultats thérapeutiques et la segmentation précise des volumes tumoraux. La tomographie d’émission de positrons au traceur Fluoro- 18-déoxy-glucose (FDG-TEP) peut fournir de manière non invasive des informations significatives sur les activités fonctionnelles des cellules tumorales. Les objectifs de cette thèse sont de proposer: 1) des systèmes fiables pour prédire les résultats du traitement contre le cancer en utilisant principalement des caractéristiques extraites des images FDG-TEP; 2) des algorithmes automatiques pour la segmentation de tumeurs de manière précise en TEP et TEP-TDM. La théorie des fonctions de croyance est choisie dans notre étude pour modéliser et raisonner des connaissances incertaines et imprécises pour des images TEP qui sont bruitées et floues. Dans le cadre des fonctions de croyance, nous proposons une méthode de sélection de caractéristiques de manière parcimonieuse et une méthode d’apprentissage de métriques permettant de rendre les classes bien séparées dans l’espace caractéristique afin d’améliorer la précision de classification du classificateur EK-NN. Basées sur ces deux études théoriques, un système robuste de prédiction est proposé, dans lequel le problème d’apprentissage pour des données de petite taille et déséquilibrées est traité de manière efficace. Pour segmenter automatiquement les tumeurs en TEP, une méthode 3-D non supervisée basée sur le regroupement évidentiel (evidential clustering) et l’information spatiale est proposée. Cette méthode de segmentation mono-modalité est ensuite étendue à la co-segmentation dans des images TEP-TDM, en considérant que ces deux modalités distinctes contiennent des informations complémentaires pour améliorer la précision. Toutes les méthodes proposées ont été testées sur des données cliniques, montrant leurs meilleures performances par rapport aux méthodes de l’état de l’art. / Radiation therapy is one of the most principal options used in the treatment of malignant tumors. To enhance its effectiveness, two critical issues should be carefully dealt with, i.e., reliably predicting therapy outcomes to adapt undergoing treatment planning for individual patients, and accurately segmenting tumor volumes to maximize radiation delivery in tumor tissues while minimize side effects in adjacent organs at risk. Positron emission tomography with radioactive tracer fluorine-18 fluorodeoxyglucose (FDG-PET) can noninvasively provide significant information of the functional activities of tumor cells. In this thesis, the goal of our study consists of two parts: 1) to propose reliable therapy outcome prediction system using primarily features extracted from FDG-PET images; 2) to propose automatic and accurate algorithms for tumor segmentation in PET and PET-CT images. The theory of belief functions is adopted in our study to model and reason with uncertain and imprecise knowledge quantified from noisy and blurring PET images. In the framework of belief functions, a sparse feature selection method and a low-rank metric learning method are proposed to improve the classification accuracy of the evidential K-nearest neighbor classifier learnt by high-dimensional data that contain unreliable features. Based on the above two theoretical studies, a robust prediction system is then proposed, in which the small-sized and imbalanced nature of clinical data is effectively tackled. To automatically delineate tumors in PET images, an unsupervised 3-D segmentation based on evidential clustering using the theory of belief functions and spatial information is proposed. This mono-modality segmentation method is then extended to co-segment tumor in PET-CT images, considering that these two distinct modalities contain complementary information to further improve the accuracy. All proposed methods have been performed on clinical data, giving better results comparing to the state of the art ones.

Stem cells differentiate through an organized hierarchy of intermediate cell types to terminally differentiated cell types. This process is largely guided by master transcriptional regulators, but it also depends on the expression of many other types of genes. The discrete cell types in the differentiation hierarchy are often identified based on the expression or non-expression of certain marker genes. Historically, these have often been various cell-surface proteins, which are fairly easy to assay biochemically but are not necessarily causative of the cell type, in the sense of being master transcriptional regulators. This raises important questions about how gene expression across the whole genome controls or reflects cell state, and in particular, differentiation hierarchies. Traditional approaches to understanding gene expression patterns across multiple conditions, such as principal components analysis or K-means clustering, can group cell types based on gene expression, but they do so without knowledge of the differentiation hierarchy. Hierarchical clustering and maximization of parsimony can organize the cell types into a tree, but in general this tree is different from the differentiation hierarchy. Using hematopoietic differentiation as an example, we demonstrate how many genes other than marker genes are able to discriminate between different branches of the differentiation tree by proposing two models for detecting genes that are up-regulated or down-regulated in distinct lineages. We then propose a novel approach to solving the following problem: Given the differentiation hierarchy and gene expression data at each node, construct a weighted Euclidean distance metric such that the minimum spanning tree with respect to that metric is precisely the given differentiation hierarchy. We provide a set of linear constraints that are provably sufficient for the desired construction and a linear programming framework to identify sparse sets of weights, effectively identifying genes that are most relevant for discriminating different parts of the tree. We apply our method to microarray gene expression data describing 38 cell types in the hematopoiesis hierarchy, constructing a sparse weighted Euclidean metric that uses just 175 genes. These 175 genes are different than the marker genes that were used to identify the 38 cell types, hence offering a novel alternative way of discriminating different branches of the tree. A DAVID functional annotation analysis shows that the 175 genes reflect major processes and pathways active in different parts of the tree. However, we find that there are many alternative sets of weights that satisfy the linear constraints. Thus, in the style of random-forest training, we also construct metrics based on random subsets of the genes and compare them to the metric of 175 genes. Our results show that the 175 genes frequently appear in the random metrics, implicating their significance from an empirical point of view as well. Finally, we show how our linear programming method is able to identify columns that were selected to build minimum spanning trees on the nodes of random variable-size matrices.