Machine learning approaches to model cardiac shape in large-scale imaging studies

Recent improvements in non-invasive imaging, together with the introduction of fully-automated segmentation algorithms and big data analytics, has paved the way for large-scale population-based imaging studies. These studies promise to increase our understanding of a large number of medical conditions, including cardiovascular diseases. However, analysis of cardiac shape in such studies is often limited to simple morphometric indices, ignoring large part of the information available in medical images. Discovery of new biomarkers by machine learning has recently gained traction, but often lacks interpretability. The research presented in this thesis aimed at developing novel explainable machine learning and computational methods capable of better summarizing shape variability, to better inform association and predictive clinical models in large-scale imaging studies. A powerful and flexible framework to model the relationship between three-dimensional (3D) cardiac atlases, encoding multiple phenotypic traits, and genetic variables is first presented. The proposed approach enables the detection of regional phenotype-genotype associations that would be otherwise neglected by conventional association analysis. Three learning-based systems based on deep generative models are then proposed. In the first model, I propose a classifier of cardiac shapes which exploits task-specific generative shape features, and it is designed to enable the visualisation of the anatomical effect these features encode in 3D, making the classification task transparent. The second approach models a database of anatomical shapes via a hierarchy of conditional latent variables and it is capable of detecting, quantifying and visualising onto a template shape the most discriminative anatomical features that characterize distinct clinical conditions. Finally, a preliminary analysis of a deep learning system capable of reconstructing 3D high-resolution cardiac segmentations from a sparse set of 2D views segmentations is reported. This thesis demonstrates that machine learning approaches can facilitate high-throughput analysis of normal and pathological anatomy and of its determinants without losing clinical interpretability.Open Acces

Apprentissage automatique pour simplifier l’utilisation de banques d’images cardiaques

The recent growth of data in cardiac databases has been phenomenal. Cleveruse of these databases could help find supporting evidence for better diagnosis and treatment planning. In addition to the challenges inherent to the large quantity of data, the databases are difficult to use in their current state. Data coming from multiple sources are often unstructured, the image content is variable and the metadata are not standardised. The objective of this thesis is therefore to simplify the use of large databases for cardiology specialists withautomated image processing, analysis and interpretation tools. The proposed tools are largely based on supervised machine learning techniques, i.e. algorithms which can learn from large quantities of cardiac images with groundtruth annotations and which automatically find the best representations. First, the inconsistent metadata are cleaned, interpretation and visualisation of images is improved by automatically recognising commonly used cardiac magnetic resonance imaging views from image content. The method is based on decision forests and convolutional neural networks trained on a large image dataset. Second, the thesis explores ways to use machine learning for extraction of relevant clinical measures (e.g. volumes and masses) from3D and 3D+t cardiac images. New spatio-temporal image features are designed andclassification forests are trained to learn how to automatically segment the main cardiac structures (left ventricle and left atrium) from voxel-wise label maps. Third, a web interface is designed to collect pairwise image comparisons and to learn how to describe the hearts with semantic attributes (e.g. dilation, kineticity). In the last part of the thesis, a forest-based machinelearning technique is used to map cardiac images to establish distances and neighborhoods between images. One application is retrieval of the most similar images.L'explosion récente de données d'imagerie cardiaque a été phénoménale. L'utilisation intelligente des grandes bases de données annotées pourrait constituer une aide précieuse au diagnostic et à la planification de thérapie. En plus des défis inhérents à la grande taille de ces banques de données, elles sont difficilement utilisables en l'état. Les données ne sont pas structurées, le contenu des images est variable et mal indexé, et les métadonnées ne sont pas standardisées. L'objectif de cette thèse est donc le traitement, l'analyse et l'interprétation automatique de ces bases de données afin de faciliter leur utilisation par les spécialistes de cardiologie. Dans ce but, la thèse explore les outils d'apprentissage automatique supervisé, ce qui aide à exploiter ces grandes quantités d'images cardiaques et trouver de meilleures représentations. Tout d'abord, la visualisation et l'interprétation d'images est améliorée en développant une méthode de reconnaissance automatique des plans d'acquisition couramment utilisés en imagerie cardiaque. La méthode se base sur l'apprentissage par forêts aléatoires et par réseaux de neurones à convolution, en utilisant des larges banques d'images, où des types de vues cardiaques sont préalablement établies. La thèse s'attache dans un deuxième temps au traitement automatique des images cardiaques, avec en perspective l'extraction d'indices cliniques pertinents. La segmentation des structures cardiaques est une étape clé de ce processus. A cet effet une méthode basée sur les forêts aléatoires qui exploite des attributs spatio-temporels originaux pour la segmentation automatique dans des images 3Det 3D+t est proposée. En troisième partie, l'apprentissage supervisé de sémantique cardiaque est enrichi grâce à une méthode de collecte en ligne d'annotations d'usagers. Enfin, la dernière partie utilise l'apprentissage automatique basé sur les forêts aléatoires pour cartographier des banques d'images cardiaques, tout en établissant les notions de distance et de voisinage d'images. Une application est proposée afin de retrouver dans une banque de données, les images les plus similaires à celle d'un nouveau patient

Remote measurements of heart valve sounds for health assessment and biometric identification

Heart failure will contribute to the death of one in three people who read this thesis; and one in three of those who don't. Although in order to diagnose patients’ heart condition cardiologists have access to electrocardiograms, chest X-rays, ultrasound imaging, MRI, Doppler techniques, angiography, and transesophageal echocardiography, these diagnostic techniques require a cardiologist’s visit, are expensive, the examination time is long and so are the waiting lists. Furthermore abnormal events might be sporadic and thus constant monitoring would be needed to avoid fatalities. Therefore in this thesis we propose a cost effective device which can constantly monitor the heart condition based on the principles of phonocardiography, which is a cost-effective method which records heart sounds. Manual auscultation is not widely used to diagnose because it requires considerable training, it relies on the hearing abilities of the clinician and specificity and sensitivity for manual auscultation are low since results are qualitative and not reproducible. However we propose a cheap laser-based device which is contactless and can constantly monitor patients’ heart sounds with a better SNR than the digital stethoscope. We also propose a Machine Learning (ML) aided software trained on data acquired with our device which can classify healthy from unhealthy heart sounds and can perform biometric authentication. This device might allow development of gadgets for remote monitoring of cardiovascular health in different settings

Special Topics in Cardiac Surgery

This book considers mainly the current perioperative care, as well as progresses in new cardiac surgery technologies. Perioperative strategies and new technologies in the field of cardiac surgery will continue to contribute to improvements in postoperative outcomes and enable the cardiac surgical society to optimize surgical procedures. This book should prove to be a useful reference for trainees, senior surgeons and nurses in cardiac surgery, as well as anesthesiologists, perfusionists, and all the related health care workers who are involved in taking care of patients with heart disease which require surgical therapy. I hope these internationally cumulative and diligent efforts will provide patients undergoing cardiac surgery with meticulous perioperative care methods

New Technologies for the Treatment of Coronary and Structural Heart Diseases

There has been significant progress in the field of interventional cardiology, from the development of newer devices to newer applications of technology, resulting in improved cardiovascular outcomes. The goal of this Special Issue is to update practicing clinicians and provide a comprehensive collection of original articles, reviews, and editorials. To this end, we invited state-of-the-art reviews, including reviews of new technology and therapeutics, as well as original research in this area to be considered for inclusion in this issue. Examples include the history and evolution of interventional techniques, reviews of specific devices and technologies for coronary artery disease (i.e., stent technology, atherectomy devices, coronary physiology, intracoronary imaging, and robotics), structural heart diseases (i.e., ASD: atrial septal defect; LAAC: left atrial appendage closure; MC: MitraClip; PFO: patent foramen ovale; TAVI: transcatheter aortic valve implantation), advances in the management of challenging coronary anatomy, new biomarkers of cardiovascular disease (noncoding RNAs, etc.), and interventional techniques in the management of heart failure, peripheral arterial diseases, and pulmonary embolism. This Special Issue presents the most recent advances in the field of coronary and structural heart diseases as well as their implications for future patient care

Combining multiple dynamic models and deep learning architectures for tracking the left ventricle endocardium in ultrasound data

We present a new statistical pattern recognition approach for the problem of left ventricle endocardium tracking in ultrasound data. The problem is formulated as a sequential importance resampling algorithm such that the expected segmentation of the current time step is estimated based on the appearance, shape, and motion models that take into account all previous and current images and previous segmentation contours produced by the method. The new appearance and shape models decouple the affine and nonrigid segmentations of the left ventricle to reduce the running time complexity. The proposed motion model combines the systole and diastole motion patterns and an observation distribution built by a deep neural network. The functionality of our approach is evaluated using a dataset of diseased cases containing 16 sequences and another dataset of normal cases comprised of four sequences, where both sets present long axis views of the left ventricle. Using a training set comprised of diseased and healthy cases, we show that our approach produces more accurate results than current state-of-the-art endocardium tracking methods in two test sequences from healthy subjects. Using three test sequences containing different types of cardiopathies, we show that our method correlates well with interuser statistics produced by four cardiologists.Gustavo Carneiro and Jacinto C. Nasciment