Exploring variability in medical imaging

Although recent successes of deep learning and novel machine learning techniques improved the perfor- mance of classification and (anomaly) detection in computer vision problems, the application of these methods in medical imaging pipeline remains a very challenging task. One of the main reasons for this is the amount of variability that is encountered and encapsulated in human anatomy and subsequently reflected in medical images. This fundamental factor impacts most stages in modern medical imaging processing pipelines. Variability of human anatomy makes it virtually impossible to build large datasets for each disease with labels and annotation for fully supervised machine learning. An efficient way to cope with this is to try and learn only from normal samples. Such data is much easier to collect. A case study of such an automatic anomaly detection system based on normative learning is presented in this work. We present a framework for detecting fetal cardiac anomalies during ultrasound screening using generative models, which are trained only utilising normal/healthy subjects. However, despite the significant improvement in automatic abnormality detection systems, clinical routine continues to rely exclusively on the contribution of overburdened medical experts to diagnosis and localise abnormalities. Integrating human expert knowledge into the medical imaging processing pipeline entails uncertainty which is mainly correlated with inter-observer variability. From the per- spective of building an automated medical imaging system, it is still an open issue, to what extent this kind of variability and the resulting uncertainty are introduced during the training of a model and how it affects the final performance of the task. Consequently, it is very important to explore the effect of inter-observer variability both, on the reliable estimation of model’s uncertainty, as well as on the model’s performance in a specific machine learning task. A thorough investigation of this issue is presented in this work by leveraging automated estimates for machine learning model uncertainty, inter-observer variability and segmentation task performance in lung CT scan images. Finally, a presentation of an overview of the existing anomaly detection methods in medical imaging was attempted. This state-of-the-art survey includes both conventional pattern recognition methods and deep learning based methods. It is one of the first literature surveys attempted in the specific research area.Open Acces

Automatic analysis and classification of cardiac acoustic signals for long term monitoring

Objective: Cardiovascular diseases are the leading cause of death worldwide resulting in over 17.9 million deaths each year. Most of these diseases are preventable and treatable, but their progression and outcomes are significantly more positive with early-stage diagnosis and proper disease management. Among the approaches available to assist with the task of early-stage diagnosis and management of cardiac conditions, automatic analysis of auscultatory recordings is one of the most promising ones, since it could be particularly suitable for ambulatory/wearable monitoring. Thus, proper investigation of abnormalities present in cardiac acoustic signals can provide vital clinical information to assist long term monitoring. Cardiac acoustic signals, however, are very susceptible to noise and artifacts, and their characteristics vary largely with the recording conditions which makes the analysis challenging. Additionally, there are challenges in the steps used for automatic analysis and classification of cardiac acoustic signals. Broadly, these steps are the segmentation, feature extraction and subsequent classification of recorded signals using selected features. This thesis presents approaches using novel features with the aim to assist the automatic early-stage detection of cardiovascular diseases with improved performance, using cardiac acoustic signals collected in real-world conditions. Methods: Cardiac auscultatory recordings were studied to identify potential features to help in the classification of recordings from subjects with and without cardiac diseases. The diseases considered in this study for the identification of the symptoms and characteristics are the valvular heart diseases due to stenosis and regurgitation, atrial fibrillation, and splitting of fundamental heart sounds leading to additional lub/dub sounds in the systole or diastole interval of a cardiac cycle. The localisation of cardiac sounds of interest was performed using an adaptive wavelet-based filtering in combination with the Shannon energy envelope and prior information of fundamental heart sounds. This is a prerequisite step for the feature extraction and subsequent classification of recordings, leading to a more precise diagnosis. Localised segments of S1 and S2 sounds, and artifacts, were used to extract a set of perceptual and statistical features using wavelet transform, homomorphic filtering, Hilbert transform and mel-scale filtering, which were then fed to train an ensemble classifier to interpret S1 and S2 sounds. Once sound peaks of interest were identified, features extracted from these peaks, together with the features used for the identification of S1 and S2 sounds, were used to develop an algorithm to classify recorded signals. Overall, 99 features were extracted and statistically analysed using neighborhood component analysis (NCA) to identify the features which showed the greatest ability in classifying recordings. Selected features were then fed to train an ensemble classifier to classify abnormal recordings, and hyperparameters were optimized to evaluate the performance of the trained classifier. Thus, a machine learning-based approach for the automatic identification and classification of S1 and S2, and normal and abnormal recordings, in real-world noisy recordings using a novel feature set is presented. The validity of the proposed algorithm was tested using acoustic signals recorded in real-world, non-controlled environments at four auscultation sites (aortic valve, tricuspid valve, mitral valve, and pulmonary valve), from the subjects with and without cardiac diseases; together with recordings from the three large public databases. The performance metrics of the methodology in relation to classification accuracy (CA), sensitivity (SE), precision (P+), and F1 score, were evaluated. Results: This thesis proposes four different algorithms to automatically classify fundamental heart sounds – S1 and S2; normal fundamental sounds and abnormal additional lub/dub sounds recordings; normal and abnormal recordings; and recordings with heart valve disorders, namely the mitral stenosis (MS), mitral regurgitation (MR), mitral valve prolapse (MVP), aortic stenosis (AS) and murmurs, using cardiac acoustic signals. The results obtained from these algorithms were as follows: • The algorithm to classify S1 and S2 sounds achieved an average SE of 91.59% and 89.78%, and F1 score of 90.65% and 89.42%, in classifying S1 and S2, respectively. 87 features were extracted and statistically studied to identify the top 14 features which showed the best capabilities in classifying S1 and S2, and artifacts. The analysis showed that the most relevant features were those extracted using Maximum Overlap Discrete Wavelet Transform (MODWT) and Hilbert transform. • The algorithm to classify normal fundamental heart sounds and abnormal additional lub/dub sounds in the systole or diastole intervals of a cardiac cycle, achieved an average SE of 89.15%, P+ of 89.71%, F1 of 89.41%, and CA of 95.11% using the test dataset from the PASCAL database. The top 10 features that achieved the highest weights in classifying these recordings were also identified. • Normal and abnormal classification of recordings using the proposed algorithm achieved a mean CA of 94.172%, and SE of 92.38%, in classifying recordings from the different databases. Among the top 10 acoustic features identified, the deterministic energy of the sound peaks of interest and the instantaneous frequency extracted using the Hilbert Huang-transform, achieved the highest weights. • The machine learning-based approach proposed to classify recordings of heart valve disorders (AS, MS, MR, and MVP) achieved an average CA of 98.26% and SE of 95.83%. 99 acoustic features were extracted and their abilities to differentiate these abnormalities were examined using weights obtained from the neighborhood component analysis (NCA). The top 10 features which showed the greatest abilities in classifying these abnormalities using recordings from the different databases were also identified. The achieved results demonstrate the ability of the algorithms to automatically identify and classify cardiac sounds. This work provides the basis for measurements of many useful clinical attributes of cardiac acoustic signals and can potentially help in monitoring the overall cardiac health for longer duration. The work presented in this thesis is the first-of-its-kind to validate the results using both, normal and pathological cardiac acoustic signals, recorded for a long continuous duration of 5 minutes at four different auscultation sites in non-controlled real-world conditions.Open Acces

A Comprehensive Survey on Heart Sound Analysis in the Deep Learning Era

Heart sound auscultation has been demonstrated to be beneficial in clinical usage for early screening of cardiovascular diseases. Due to the high requirement of well-trained professionals for auscultation, automatic auscultation benefiting from signal processing and machine learning can help auxiliary diagnosis and reduce the burdens of training professional clinicians. Nevertheless, classic machine learning is limited to performance improvement in the era of big data. Deep learning has achieved better performance than classic machine learning in many research fields, as it employs more complex model architectures with stronger capability of extracting effective representations. Deep learning has been successfully applied to heart sound analysis in the past years. As most review works about heart sound analysis were given before 2017, the present survey is the first to work on a comprehensive overview to summarise papers on heart sound analysis with deep learning in the past six years 2017--2022. We introduce both classic machine learning and deep learning for comparison, and further offer insights about the advances and future research directions in deep learning for heart sound analysis

MENTORING DEEP LEARNING MODELS FOR MASS SCREENING WITH LIMITED DATA

Deep Learning (DL) has an extensively rich state-of-the-art literature in medical imaging analysis. However, it requires large amount of data to begin training. This limits its usage in tackling future epidemics, as one might need to wait for months and even years to collect fully annotated data, raising a fundamental question: is it possible to deploy AI-driven tool earlier in epidemics to mass screen the infected cases? For such a context, human/Expert in the loop Machine Learning (ML), or Active Learning (AL), becomes imperative enabling machines to commence learning from the first day with minimum available labeled dataset. In an unsupervised learning, we develop pretrained DL models that autonomously refine themselves through iterative learning, with human experts intervening only when the model misclassifies and for a limited amount of data. We introduce a new terminology for this process, calling it mentoring. We validated this concept in the context of Covid-19 in three distinct datasets: Chest X-rays, Computed Tomography (CT) scans, and cough sounds, each consisting of 1364, 4714, and 10,000 images, respectively. The framework classifies the deep features of the data into two clusters (0/1: Covid-19/non-Covid-19). Our main goal is to strongly emphasize the potential use of AL in predicting diseases during future epidemics. With this framework, we achieved the AUC scores of 0.76, 0.99, and 0.94 on cough sound, Chest X-rays, and CT scans dataset using only 40%, 33%, and 30% of the annotated dataset, respectively. For reproducibility, the link of implementation is provided: https://github.com/2ailab/Active-Learning

Analysis and Development of an End-to-End Convolutional Neural Network for Sounds Classification Through Deep Learning Techniques

El presente trabajo estudia el análisis y desarrollo continuo de un modelo de inteligencia artificial orientado a la clasificación de audio. El capítulo 1 presenta antecedentes sobre las diferentes tareas relacionadas a audio que la comunidad de investigación ha seguido a lo largo de los últimos años, también establece la hipótesis central de este trabajo y define objetivos generales y específicos para contribuir a la mejora del rendimiento sobre un generador de embeddings de audio de tipo end-to-end. El capítulo 2 presenta los métodos de vanguardia y trabajos publicados que se enfocan principalmente al desarrollo de la clasificación de audio y el aprendizaje profundo como disciplinas que aún tienen un gran potencial. El capítulo 3 presenta el marco conceptual en el que se basa esta tesis, dividido en dos secciones principales: preprocesamiento de audio y técnicas de aprendizaje profundo. Cada una de estas secciones se divide en varias subsecciones para representar el proceso de clasificación de audio a través de redes neuronales profundas. El capítulo 4 brinda una explicación profunda del generador de embeddings de audio llamado AemNet y sus componentes, utilizado como objeto de estudio, donde se detalla en las siguientes subsecciones. Se realizó una experimentación inicial sobre este enfoque y se presentaron resultados experimentales que sugirieron un mejor rendimiento mediante la modificación de las etapas de arquitectura de la red neuronal. El capítulo 5 es la primera aplicación objetivo de nuestra adaptación de AemNet que se presentó al desafío DCASE 2021. Los detalles sobre el desafío y los resultados se describen en las secciones de este capítulo, así como la metodología seguida para presentar nuestra propuesta. El capítulo 6 es la segunda aplicación objetivo y el primero en apuntar a los sonidos respiratorios. El desafío de ICBHI se explica en las secciones de este capítulo, así como la metodología y los experimentos realizados para llegar a un clasificador robusto que distingue cuatro anomalías de tos diferentes. Se creó un artículo a partir de la solución propuesta y se presentó en el IEEE LA-CCI 2021. El capítulo 7 aprovecha los diversos resultados anteriores para cumplir con un enfoque moderno como lo es la detección de COVID-19, cuya recopilación y experimentación de fuentes de datos se describen profundamente y los resultados experimentales sugieren que una adaptación de red residual denominada AemResNet, puede cumplir la función de distinguir a los pacientes con COVID-19 a partir de tos y sonidos respiratorios. Finalmente, las conclusiones de toda esta investigación y los resultados evaluados en cada una de las aplicaciones objetivo se discuten en el capítulo 8.ITESO, A. C

Deep Learning in Medical Image Analysis

The accelerating power of deep learning in diagnosing diseases will empower physicians and speed up decision making in clinical environments. Applications of modern medical instruments and digitalization of medical care have generated enormous amounts of medical images in recent years. In this big data arena, new deep learning methods and computational models for efficient data processing, analysis, and modeling of the generated data are crucially important for clinical applications and understanding the underlying biological process. This book presents and highlights novel algorithms, architectures, techniques, and applications of deep learning for medical image analysis