Computer-Aided Assessment of Tuberculosis with Radiological Imaging: From rule-based methods to Deep Learning

Mención Internacional en el título de doctorTuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb.) that produces pulmonary damage due to its airborne nature. This fact facilitates the disease fast-spreading, which, according to the World Health Organization (WHO), in 2021 caused 1.2 million deaths and 9.9 million new cases. Traditionally, TB has been considered a binary disease (latent/active) due to the limited specificity of the traditional diagnostic tests. Such a simple model causes difficulties in the longitudinal assessment of pulmonary affectation needed for the development of novel drugs and to control the spread of the disease. Fortunately, X-Ray Computed Tomography (CT) images enable capturing specific manifestations of TB that are undetectable using regular diagnostic tests, which suffer from limited specificity. In conventional workflows, expert radiologists inspect the CT images. However, this procedure is unfeasible to process the thousands of volume images belonging to the different TB animal models and humans required for a suitable (pre-)clinical trial. To achieve suitable results, automatization of different image analysis processes is a must to quantify TB. It is also advisable to measure the uncertainty associated with this process and model causal relationships between the specific mechanisms that characterize each animal model and its level of damage. Thus, in this thesis, we introduce a set of novel methods based on the state of the art Artificial Intelligence (AI) and Computer Vision (CV). Initially, we present an algorithm to assess Pathological Lung Segmentation (PLS) employing an unsupervised rule-based model which was traditionally considered a needed step before biomarker extraction. This procedure allows robust segmentation in a Mtb. infection model (Dice Similarity Coefficient, DSC, 94%±4%, Hausdorff Distance, HD, 8.64mm±7.36mm) of damaged lungs with lesions attached to the parenchyma and affected by respiratory movement artefacts. Next, a Gaussian Mixture Model ruled by an Expectation-Maximization (EM) algorithm is employed to automatically quantify the burden of Mtb.using biomarkers extracted from the segmented CT images. This approach achieves a strong correlation (R2 ≈ 0.8) between our automatic method and manual extraction. Consequently, Chapter 3 introduces a model to automate the identification of TB lesions and the characterization of disease progression. To this aim, the method employs the Statistical Region Merging algorithm to detect lesions subsequently characterized by texture features that feed a Random Forest (RF) estimator. The proposed procedure enables a selection of a simple but powerful model able to classify abnormal tissue. The latest works base their methodology on Deep Learning (DL). Chapter 4 extends the classification of TB lesions. Namely, we introduce a computational model to infer TB manifestations present in each lung lobe of CT scans by employing the associated radiologist reports as ground truth. We do so instead of using the classical manually delimited segmentation masks. The model adjusts the three-dimensional architecture, V-Net, to a multitask classification context in which loss function is weighted by homoscedastic uncertainty. Besides, the method employs Self-Normalizing Neural Networks (SNNs) for regularization. Our results are promising with a Root Mean Square Error of 1.14 in the number of nodules and F1-scores above 0.85 for the most prevalent TB lesions (i.e., conglomerations, cavitations, consolidations, trees in bud) when considering the whole lung. In Chapter 5, we present a DL model capable of extracting disentangled information from images of different animal models, as well as information of the mechanisms that generate the CT volumes. The method provides the segmentation mask of axial slices from three animal models of different species employing a single trained architecture. It also infers the level of TB damage and generates counterfactual images. So, with this methodology, we offer an alternative to promote generalization and explainable AI models. To sum up, the thesis presents a collection of valuable tools to automate the quantification of pathological lungs and moreover extend the methodology to provide more explainable results which are vital for drug development purposes. Chapter 6 elaborates on these conclusions.Programa de Doctorado en Multimedia y Comunicaciones por la Universidad Carlos III de Madrid y la Universidad Rey Juan CarlosPresidenta: María Jesús Ledesma Carbayo.- Secretario: David Expósito Singh.- Vocal: Clarisa Sánchez Gutiérre

Un estudi aproximatiu a l’imaginari social dels professionals que intervenen amb joves infractores a les Illes Balears

Aquest treball explora les percepcions, emocions i actituds dels diferents professionals que intervenen en diferents moments i àmbits amb les dones joves infractores a les Illes Balears. Així mateix, identi!ca necessitats i analitza dificultats o reptes futurs en el coneixement (en termes de recerca i intervenció) de la delinqüència juvenil femenina. El treball empíric descrit és eminentment qualitatiu, basat en grups de discussió i entrevistes en profunditat amb professionals d’intervenció directa (personal educador de reforma i de protecció de menors, treballadors socials, mestres i psicòlegs, entre d’altres) i indirecta (fiscals, policies, advocats, directors i sociòlegs, entre d’altres). Finalment, tot això s’ha complementat amb estudis i recerques actuals, que han enriquit significativament aquest treball.Este trabajo explora las percepciones, emociones y actitudes de los diferentes profesionales que intervienen en diferentes momentos y ámbitos con las mujeres jóvenes infractoras a las Islas Baleares. Asimismo, identifica necesidades y analiza dificultades o retos futuros en el conocimiento (en términos de búsqueda e intervención) de la delincuencia juvenil femenina. El trabajo empírico descrito es eminentemente cualitativo, basado en grupos de discusión y entrevistas en profundidad con profesionales de intervención directa (personal educador de reforma y de protección de menores, trabajadores sociales, maestras y psicólogos, entre otros) e indirecta (fiscales, policías, abogados, directores y sociólogos, entre otros). Finalmente, todo esto se ha complementado con estudios y búsquedas actuales, que han enriquecido significativamente este trabajo

Fair learning : une approche basée sur le transport optimale

L'objectif de cette thèse est double. D'une part, les méthodes de transport optimal sont étudiées pour l'inférence statistique. D'autre part, le récent problème de l'apprentissage équitable est considéré avec des contributions à travers le prisme de la théorie du transport optimal. L'utilisation généralisée des applications basées sur les modèles d'apprentissage automatique dans la vie quotidienne et le monde professionnel s'est accompagnée de préoccupations quant aux questions éthiques qui peuvent découler de l'adoption de ces technologies. Dans la première partie de cette thèse, nous motivons le problème de l'équité en présentant quelques résultats statistiques complets en étudiant le critère statistical parity par l'analyse de l'indice disparate impact sur l'ensemble de données réel Adult income. Il est important de noter que nous montrons qu'il peut être particulièrement difficile de créer des modèles d'apprentissage machine équitables, surtout lorsque les observations de formation contiennent des biais. Ensuite, une revue des mathématiques pour l'équité dans l'apprentissage machine est donné dans un cadre général, avec également quelques contributions nouvelles dans l'analyse du prix pour l'équité dans la régression et la classification. Dans cette dernière, nous terminons cette première partie en reformulant les liens entre l'équité et la prévisibilité en termes de mesures de probabilité. Nous analysons les méthodes de réparation basées sur le transport de distributions conditionnelles vers le barycentre de Wasserstein. Enfin, nous proposons le random repair qui permet de trouver un compromis entre une perte minimale d'information et un certain degré d'équité. La deuxième partie est dédiée à la théorie asymptotique du coût de transport empirique. Nous fournissons un Théorème de Limite Centrale pour la distance de Monge-Kantorovich entre deux distributions empiriques de tailles différentes n et m, Wp(Pn,Qm), p > = 1, avec observations sur R. Dans le cas de p > 1, nos hypothèses sont nettes en termes de moments et de régularité. Nous prouvons des résultats portant sur le choix des constantes de centrage. Nous fournissons une estimation consistente de la variance asymptotique qui permet de construire tests à deux échantillons et des intervalles de confiance pour certifier la similarité entre deux distributions. Ceux-ci sont ensuite utilisés pour évaluer un nouveau critère d'équité de l'ensemble des données dans la classification. En outre, nous fournissons un principe de déviations modérées pour le coût de transport empirique dans la dimension générale. Enfin, les barycentres de Wasserstein et le critère de variance en termes de la distance de Wasserstein sont utilisés dans de nombreux problèmes pour analyser l'homogénéité des ensembles de distributions et les relations structurelles entre les observations. Nous proposons l'estimation des quantiles du processus empirique de la variation de Wasserstein en utilisant une procédure bootstrap. Ensuite, nous utilisons ces résultats pour l'inférence statistique sur un modèle d'enregistrement de distribution avec des fonctions de déformation générale. Les tests sont basés sur la variance des distributions par rapport à leurs barycentres de Wasserstein pour lesquels nous prouvons les théorèmes de limite centrale, y compris les versions bootstrap.The aim of this thesis is two-fold. On the one hand, optimal transportation methods are studied for statistical inference purposes. On the other hand, the recent problem of fair learning is addressed through the prism of optimal transport theory. The generalization of applications based on machine learning models in the everyday life and the professional world has been accompanied by concerns about the ethical issues that may arise from the adoption of these technologies. In the first part of the thesis, we motivate the fairness problem by presenting some comprehensive results from the study of the statistical parity criterion through the analysis of the disparate impact index on the real and well-known Adult Income dataset. Importantly, we show that trying to make fair machine learning models may be a particularly challenging task, especially when the training observations contain bias. Then a review of Mathematics for fairness in machine learning is given in a general setting, with some novel contributions in the analysis of the price for fairness in regression and classification. In the latter, we finish this first part by recasting the links between fairness and predictability in terms of probability metrics. We analyze repair methods based on mapping conditional distributions to the Wasserstein barycenter. Finally, we propose a random repair which yields a tradeoff between minimal information loss and a certain amount of fairness. The second part is devoted to the asymptotic theory of the empirical transportation cost. We provide a Central Limit Theorem for the Monge-Kantorovich distance between two empirical distributions with different sizes n and m, Wp(Pn,Qm), p > = 1, for observations on R. In the case p > 1 our assumptions are sharp in terms of moments and smoothness. We prove results dealing with the choice of centering constants. We provide a consistent estimate of the asymptotic variance which enables to build two sample tests and confidence intervals to certify the similarity between two distributions. These are then used to assess a new criterion of data set fairness in classification. Additionally, we provide a moderate deviation principle for the empirical transportation cost in general dimension. Finally, Wasserstein barycenters and variance-like criterion using Wasserstein distance are used in many problems to analyze the homogeneity of collections of distributions and structural relationships between the observations. We propose the estimation of the quantiles of the empirical process of the Wasserstein's variation using a bootstrap procedure. Then we use these results for statistical inference on a distribution registration model for general deformation functions. The tests are based on the variance of the distributions with respect to their Wasserstein's barycenters for which we prove central limit theorems, including bootstrap versions

Apuntes, voces y reflexiones en mujeres jóvenes en espacios de vida institucionales

Aquest article selecciona apunts, veus i reflexions sobre el tema de les dones joves en els espais de vida institucionals. Després d’una breu contextualització i justificació de l’estudi, i a partir de factors, contextos i processos socials descoberts en aquesta investigació, s’analitza, es descriu i es proposen claus a considerar per a estudis i intervencions futures. A més de reivindicar la necessitat de crear un debat seriós sobre el rol de les joves en el sistema de justícia juvenil.This article selects notes, voices and thoughts on the issue of young women in the areas of institutional life. AfteAbstract: This article selects notes, voices and thoughts on the issue of young women in areas of institutional life. After a brief contextualization and justification of the study, based on the factors, contexts and social processes discovered in this research, this document analyses, describes and suggests key issues to consider for future studies and interventions; in addition to claiming the need for a serious debate concerning the role of youth within the juvenile justice system

A general trimming approach to robust Cluster Analysis

We introduce a new method for performing clustering with the aim of fitting clusters with different scatters and weights. It is designed by allowing to handle a proportion $\alpha$ of contaminating data to guarantee the robustness of the method. As a characteristic feature, restrictions on the ratio between the maximum and the minimum eigenvalues of the groups scatter matrices are introduced. This makes the problem to be well defined and guarantees the consistency of the sample solutions to the population ones. The method covers a wide range of clustering approaches depending on the strength of the chosen restrictions. Our proposal includes an algorithm for approximately solving the sample problem.Comment: Published in at http://dx.doi.org/10.1214/07-AOS515 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org