Deep Learning in Cardiology

The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table

Towards adversarial robustness with 01 lossmodels, and novel convolutional neural netsystems for ultrasound images

This dissertation investigates adversarial robustness with 01 loss models and a novel convolutional neural net systems for vascular ultrasound images. In the first part, the dissertation presents stochastic coordinate descent for 01 loss and its sensitivity to adversarial attacks. The study here suggests that 01 loss may be more resilient to adversarial attacks than the hinge loss and further work is required. In the second part, this dissertation proposes sign activation network with a novel gradient-free stochastic coordinate descent algorithm and its ensembling model. The study here finds that the ensembling model gives a high minimum distortion (as measured by HopSkipJump) compared to full precision, binary, and convolutional neural networks, and explains this phenomenon by measuring the transferability between networks in an ensemble. In the last part, this dissertation tackles three important segmentation problems for vascular ultrasound images with novel convolutional neural networks. More specifically, these three problems are: (1) vessel segmentation in the internal carotid artery, (2) vessel segmentation in the entire carotid system, and (3) vessel and plaque segmentation in the entire carotid system. The study here represents a first successful step towards the automated segmentation of vessel and plaque in carotid artery ultrasound images and is an important step in creating a system that can independently evaluate carotid ultrasounds

Automatic Segmentation of Brachial Artery based on Fuzzy C-Means Pixel Clustering from Ultrasound Images

Automatic extraction of brachial artery and measuring associated indices such as flow-mediated dilatation and Intima-media thickness are important for early detection of cardiovascular disease and other vascular endothelial malfunctions. In this paper, we propose the basic but important component of such decision-assisting medical software development – noise tolerant fully automatic segmentation of brachial artery from ultrasound images. Pixel clustering with Fuzzy C-Means algorithm in the quantization process is the key component of that segmentation with various image processing algorithms involved. This algorithm could be an alternative choice of segmentation process that can replace speckle noise-suffering edge detection procedures in this application domain

Basic Science to Clinical Research: Segmentation of Ultrasound and Modelling in Clinical Informatics

The world of basic science is a world of minutia; it boils down to improving even a fraction of a percent over the baseline standard. It is a domain of peer reviewed fractions of seconds and the world of squeezing every last ounce of efficiency from a processor, a storage medium, or an algorithm. The field of health data is based on extracting knowledge from segments of data that may improve some clinical process or practice guideline to improve the time and quality of care. Clinical informatics and knowledge translation provide this information in order to reveal insights to the world of improving patient treatments, regimens, and overall outcomes. In my world of minutia, or basic science, the movement of blood served an integral role. The novel detection of sound reverberations map out the landscape for my research. I have applied my algorithms to the various anatomical structures of the heart and artery system. This serves as a basis for segmentation, active contouring, and shape priors. The algorithms presented, leverage novel applications in segmentation by using anatomical features of the heart for shape priors and the integration of optical flow models to improve tracking. The presented techniques show improvements over traditional methods in the estimation of left ventricular size and function, along with plaque estimation in the carotid artery. In my clinical world of data understanding, I have endeavoured to decipher trends in Alzheimer’s disease, Sepsis of hospital patients, and the burden of Melanoma using mathematical modelling methods. The use of decision trees, Markov models, and various clustering techniques provide insights into data sets that are otherwise hidden. Finally, I demonstrate how efficient data capture from providers can achieve rapid results and actionable information on patient medical records. This culminated in generating studies on the burden of illness and their associated costs. A selection of published works from my research in the world of basic sciences to clinical informatics has been included in this thesis to detail my transition. This is my journey from one contented realm to a turbulent one

Classification approach for diagnosis of arteriosclerosis using B-mode ultrasound carotid images

Tese de mestrado. Engenharia Biomédica. Faculdade de Engenharia. Universidade do Porto. 201

Bimodal automated carotid ultrasound segmentation using geometrically constrained deep neural networks

For asymptomatic patients suffering from carotid stenosis, the assessment of plaque morphology is an important clinical task which allows monitoring of the risk of plaque rupture and future incidents of stroke. Ultrasound Imaging provides a safe and non-invasive modality for this, and the segmentation of media-adventitia boundaries and lumen-intima boundaries of the Carotid artery form an essential part in this monitoring process. In this paper, we propose a novel Deep Neural Network as a fully automated segmentation tool, and its application in delineating both the media-adventitia boundary and the lumen-intima boundary. We develop a new geometrically constrained objective function as part of the Network's Stochastic Gradient Descent optimisation, thus tuning it to the problem at hand. Furthermore, we also apply a bimodal fusion of amplitude and phase congruency data proposed by us in previous work, as an input to the network, as the latter provides an intensity-invariant data source to the network. We finally report the segmentation performance of the network on transverse sections of the carotid. Tests are carried out on an augmented dataset of 81,000 images, and the results are compared to other studies by reporting the DICE coefficient of similarity, modified Hausdorff Distance, sensitivity and specificity. Our proposed modification is shown to yield improved results on the standard network over this larger dataset, with the advantage of it being fully automated. We conclude that Deep Neural Networks provide a reliable trained manner in which carotid ultrasound images may be automatically segmented, using amplitude data and intensity invariant phase congruency maps as a data source