Learning Biosignals with Deep Learning

The healthcare system, which is ubiquitously recognized as one of the most influential system in society, is facing new challenges since the start of the decade.The myriad of physiological data generated by individuals, namely in the healthcare system, is generating a burden on physicians, losing effectiveness on the collection of patient data. Information systems and, in particular, novel deep learning (DL) algorithms have been prompting a way to take this problem. This thesis has the aim to have an impact in biosignal research and industry by presenting DL solutions that could empower this field. For this purpose an extensive study of how to incorporate and implement Convolutional Neural Networks (CNN), Recursive Neural Networks (RNN) and Fully Connected Networks in biosignal studies is discussed. Different architecture configurations were explored for signal processing and decision making and were implemented in three different scenarios: (1) Biosignal learning and synthesis; (2) Electrocardiogram (ECG) biometric systems, and; (3) Electrocardiogram (ECG) anomaly detection systems. In (1) a RNN-based architecture was able to replicate autonomously three types of biosignals with a high degree of confidence. As for (2) three CNN-based architectures, and a RNN-based architecture (same used in (1)) were used for both biometric identification, reaching values above 90% for electrode-base datasets (Fantasia, ECG-ID and MIT-BIH) and 75% for off-person dataset (CYBHi), and biometric authentication, achieving Equal Error Rates (EER) of near 0% for Fantasia and MIT-BIH and bellow 4% for CYBHi. As for (3) the abstraction of healthy clean the ECG signal and detection of its deviation was made and tested in two different scenarios: presence of noise using autoencoder and fully-connected network (reaching 99% accuracy for binary classification and 71% for multi-class), and; arrhythmia events by including a RNN to the previous architecture (57% accuracy and 61% sensitivity). In sum, these systems are shown to be capable of producing novel results. The incorporation of several AI systems into one could provide to be the next generation of preventive medicine, as the machines have access to different physiological and anatomical states, it could produce more informed solutions for the issues that one may face in the future increasing the performance of autonomous preventing systems that could be used in every-day life in remote places where the access to medicine is limited. These systems will also help the study of the signal behaviour and how they are made in real life context as explainable AI could trigger this perception and link the inner states of a network with the biological traits.O sistema de saúde, que é ubiquamente reconhecido como um dos sistemas mais influentes da sociedade, enfrenta novos desafios desde o ínicio da década. A miríade de dados fisiológicos gerados por indíviduos, nomeadamente no sistema de saúde, está a gerar um fardo para os médicos, perdendo a eficiência no conjunto dos dados do paciente. Os sistemas de informação e, mais espcificamente, da inovação de algoritmos de aprendizagem profunda (DL) têm sido usados na procura de uma solução para este problema. Esta tese tem o objetivo de ter um impacto na pesquisa e na indústria de biosinais, apresentando soluções de DL que poderiam melhorar esta área de investigação. Para esse fim, é discutido um extenso estudo de como incorporar e implementar redes neurais convolucionais (CNN), redes neurais recursivas (RNN) e redes totalmente conectadas para o estudo de biosinais. Diferentes arquiteturas foram exploradas para processamento e tomada de decisão de sinais e foram implementadas em três cenários diferentes: (1) Aprendizagem e síntese de biosinais; (2) sistemas biométricos com o uso de eletrocardiograma (ECG), e; (3) Sistema de detecção de anomalias no ECG. Em (1) uma arquitetura baseada na RNN foi capaz de replicar autonomamente três tipos de sinais biológicos com um alto grau de confiança. Quanto a (2) três arquiteturas baseadas em CNN e uma arquitetura baseada em RNN (a mesma usada em (1)) foram usadas para ambas as identificações, atingindo valores acima de 90 % para conjuntos de dados à base de eletrodos (Fantasia, ECG-ID e MIT -BIH) e 75 % para o conjunto de dados fora da pessoa (CYBHi) e autenticação, atingindo taxas de erro iguais (EER) de quase 0 % para Fantasia e MIT-BIH e abaixo de 4 % para CYBHi. Quanto a (3) a abstração de sinais limpos e assimptomáticos de ECG e a detecção do seu desvio foram feitas e testadas em dois cenários diferentes: na presença de ruído usando um autocodificador e uma rede totalmente conectada (atingindo 99 % de precisão na classificação binária e 71 % na multi-classe), e; eventos de arritmia incluindo um RNN na arquitetura anterior (57 % de precisão e 61 % de sensibilidade). Em suma, esses sistemas são mais uma vez demonstrados como capazes de produzir resultados inovadores. A incorporação de vários sistemas de inteligência artificial em um unico sistema pederá desencadear a próxima geração de medicina preventiva. Os algoritmos ao terem acesso a diferentes estados fisiológicos e anatómicos, podem produzir soluções mais informadas para os problemas que se possam enfrentar no futuro, aumentando o desempenho de sistemas autónomos de prevenção que poderiam ser usados na vida quotidiana, nomeadamente em locais remotos onde o acesso à medicinas é limitado. Estes sistemas também ajudarão o estudo do comportamento do sinal e como eles são feitos no contexto da vida real, pois a IA explicável pode desencadear essa percepção e vincular os estados internos de uma rede às características biológicas

A Machine Learning Model for the Prognosis of Pulseless Electrical Activity during Out-of-Hospital Cardiac Arrest

Pulseless electrical activity (PEA) is characterized by the disassociation of the mechanical and electrical activity of the heart and appears as the initial rhythm in 20–30% of out-of-hospital cardiac arrest (OHCA) cases. Predicting whether a patient in PEA will convert to return of spontaneous circulation (ROSC) is important because different therapeutic strategies are needed depending on the type of PEA. The aim of this study was to develop a machine learning model to differentiate PEA with unfavorable (unPEA) and favorable (faPEA) evolution to ROSC. An OHCA dataset of 1921 5s PEA signal segments from defibrillator files was used, 703 faPEA segments from 107 patients with ROSC and 1218 unPEA segments from 153 patients with no ROSC. The solution consisted of a signal-processing stage of the ECG and the thoracic impedance (TI) and the extraction of the TI circulation component (ICC), which is associated with ventricular wall movement. Then, a set of 17 features was obtained from the ECG and ICC signals, and a random forest classifier was used to differentiate faPEA from unPEA. All models were trained and tested using patientwise and stratified 10-fold cross-validation partitions. The best model showed a median (interquartile range) area under the curve (AUC) of 85.7(9.8)% and a balance accuracy of 78.8(9.8)% , improving the previously available solutions at more than four points in the AUC and three points in balanced accuracy. It was demonstrated that the evolution of PEA can be predicted using the ECG and TI signals, opening the possibility of targeted PEA treatment in OHCA.This work was supported by the Spanish Ministerio de Ciencia, Innovacion y Universidades through Grant RTI2018-101475-BI00, jointly with the Fondo Europeo de Desarrollo Regional (FEDER), by the Basque Government through Grant IT1229-19 and Grant PRE2020_1_0177, and by the university of the Basque Country (UPV/EHU) under Grant COLAB20/01

Machine learning and signal processing contributions to identify circulation states during out-of-hospital cardiac arrest

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Advanced Signal Processing in Wearable Sensors for Health Monitoring

Smart, wearables devices on a miniature scale are becoming increasingly widely available, typically in the form of smart watches and other connected devices. Consequently, devices to assist in measurements such as electroencephalography (EEG), electrocardiogram (ECG), electromyography (EMG), blood pressure (BP), photoplethysmography (PPG), heart rhythm, respiration rate, apnoea, and motion detection are becoming more available, and play a significant role in healthcare monitoring. The industry is placing great emphasis on making these devices and technologies available on smart devices such as phones and watches. Such measurements are clinically and scientifically useful for real-time monitoring, long-term care, and diagnosis and therapeutic techniques. However, a pertaining issue is that recorded data are usually noisy, contain many artefacts, and are affected by external factors such as movements and physical conditions. In order to obtain accurate and meaningful indicators, the signal has to be processed and conditioned such that the measurements are accurate and free from noise and disturbances. In this context, many researchers have utilized recent technological advances in wearable sensors and signal processing to develop smart and accurate wearable devices for clinical applications. The processing and analysis of physiological signals is a key issue for these smart wearable devices. Consequently, ongoing work in this field of study includes research on filtration, quality checking, signal transformation and decomposition, feature extraction and, most recently, machine learning-based methods

Noninvasive Dynamic Characterization of Swallowing Kinematics and Impairments in High Resolution Cervical Auscultation via Deep Learning

Swallowing is a complex sensorimotor activity by which food and liquids are transferred from the oral cavity to the stomach. Swallowing requires the coordination between multiple subsystems which makes it subject to impairment secondary to a variety of medical or surgically related conditions. Dysphagia refers to any swallowing disorder and is common in patients with head and neck cancer and neurological conditions such as stroke. Dysphagia affects nearly 9 million adults and causes death for more than 60,000 yearly in the US. In this research, we utilize advanced signal processing techniques with sensor technology and deep learning methods to develop a noninvasive and widely available tool for the evaluation and diagnosis of swallowing problems. We investigate the use of modern spectral estimation methods in addition to convolutional recurrent neural networks to demarcate and localize the important swallowing physiological events that contribute to airway protection solely based on signals collected from non-invasive sensors attached to the anterior neck. These events include the full swallowing activity, upper esophageal sphincter opening duration and maximal opening diameter, and aspiration. We believe that combining sensor technology and state of the art deep learning architectures specialized in time series analysis, will help achieve great advances for dysphagia detection and management in terms of non-invasiveness, portability, and availability. Like never before, such advances will enable patients to get continuous feedback about their swallowing out of standard clinical care setting which will extremely facilitate their daily activities and enhance the quality of their lives

Probabilistic Estimation of Chirp Instantaneous Frequency Using Gaussian Processes

We present a probabilistic approach for estimating chirp signal and its instantaneous frequency function when the true forms of the chirp and instantaneous frequency are unknown. To do so, we represent them by joint cascading Gaussian processes governed by a non-linear stochastic differential equation, and estimate their posterior distribution by using stochastic filters and smoothers. The model parameters are determined via maximum likelihood estimation. Theoretical results show that the estimation method has a bounded mean squared error. Experiments show that the method outperforms a number of baseline methods on a synthetic model, and we also apply the method to analyse a gravitational wave data.Comment: Submitted to IEEE Transactions on Signal Processin

Kalman-based Spectro-Temporal ECG Analysis using Deep Convolutional Networks for Atrial Fibrillation Detection

In this article, we propose a novel ECG classification framework for atrial fibrillation (AF) detection using spectro-temporal representation (i.e., time varying spectrum) and deep convolutional networks. In the first step we use a Bayesian spectro-temporal representation based on the estimation of time-varying coefficients of Fourier series using Kalman filter and smoother. Next, we derive an alternative model based on a stochastic oscillator differential equation to accelerate the estimation of the spectro-temporal representation in lengthy signals. Finally, after comparative evaluations of different convolutional architectures, we propose an efficient deep convolutional neural network to classify the 2D spectro-temporal ECG data. The ECG spectro-temporal data are classified into four different classes: AF, non-AF normal rhythm (Normal), non-AF abnormal rhythm (Other), and noisy segments (Noisy). The performance of the proposed methods is evaluated and scored with the PhysioNet/Computing in Cardiology (CinC) 2017 dataset. The experimental results show that the proposed method achieves the overall F1 score of 80.2%, which is in line with the state-of-the-art algorithms.Peer reviewe