Non-linear dynamical analysis of biosignals

Biosignals are physiological signals that are recorded from various parts of the body. Some of the major biosignals are electromyograms (EMG), electroencephalograms (EEG) and electrocardiograms (ECG). These signals are of great clinical and diagnostic importance, and are analysed to understand their behaviour and to extract maximum information from them. However, they tend to be random and unpredictable in nature (non-linear). Conventional linear methods of analysis are insufficient. Hence, analysis using non-linear and dynamical system theory, chaos theory and fractal dimensions, is proving to be very beneficial. In this project, ECG signals are of interest. Changes in the normal rhythm of a human heart may result in different cardiac arrhythmias, which may be fatal or cause irreparable damage to the heart when sustained over long periods of time. Hence the ability to identify arrhythmias from ECG recordings is of importance for clinical diagnosis and treatment and also for understanding the electrophysiological mechanism of arrhythmias. To achieve this aim, algorithms were developed with the help of MATLAB® software. The classical logic of correlation was used in the development of algorithms to place signals into the various categories of cardiac arrhythmias. A sample set of 35 known ECG signals were obtained from the Physionet website for testing purposes. Later, 5 unknown ECG signals were used to determine the efficiency of the algorithms. A peak detection algorithm was written to detect the QRS complex. This complex is the most prominent waveform within an ECG signal and its shape, duration and time of occurrence provides valuable information about the current state of the heart. The peak detection algorithm gave excellent results with very good accuracy for all the downloaded ECG signals, and was developed using classical linear techniques. Later, a peak detection algorithm using the discrete wavelet transform (DWT) was implemented. This code was developed using nonlinear techniques and was amenable for implementation. Also, the time required for execution was reduced, making this code ideal for real-time processing. Finally, algorithms were developed to calculate the Kolmogorov complexity and Lyapunov exponent, which are nonlinear descriptors and enable the randomness and chaotic nature of ECG signals to be estimated. These measures of randomness and chaotic nature enable us to apply correct interrogative methods to the signal to extract maximum information. The codes developed gave fair results. It was possible to differentiate between normal ECGs and ECGs with ventricular fibrillation. The results show that the Kolmogorov complexity measure increases with an increase in pathology, approximately 12.90 for normal ECGs and increasing to 13.87 to 14.39 for ECGs with ventricular fibrillation and ventricular tachycardia. Similar results were obtained for Lyapunov exponent measures with a notable difference between normal ECG (0 – 0.0095) and ECG with ventricular fibrillation (0.1114 – 0.1799). However, it was difficult to differentiate between different types of arrhythmias.Biosignals are physiological signals that are recorded from various parts of the body. Some of the major biosignals are electromyograms (EMG), electroencephalograms (EEG) and electrocardiograms (ECG). These signals are of great clinical and diagnostic importance, and are analysed to understand their behaviour and to extract maximum information from them. However, they tend to be random and unpredictable in nature (non-linear). Conventional linear methods of analysis are insufficient. Hence, analysis using non-linear and dynamical system theory, chaos theory and fractal dimensions, is proving to be very beneficial. In this project, ECG signals are of interest. Changes in the normal rhythm of a human heart may result in different cardiac arrhythmias, which may be fatal or cause irreparable damage to the heart when sustained over long periods of time. Hence the ability to identify arrhythmias from ECG recordings is of importance for clinical diagnosis and treatment and also for understanding the electrophysiological mechanism of arrhythmias. To achieve this aim, algorithms were developed with the help of MATLAB® software. The classical logic of correlation was used in the development of algorithms to place signals into the various categories of cardiac arrhythmias. A sample set of 35 known ECG signals were obtained from the Physionet website for testing purposes. Later, 5 unknown ECG signals were used to determine the efficiency of the algorithms. A peak detection algorithm was written to detect the QRS complex. This complex is the most prominent waveform within an ECG signal and its shape, duration and time of occurrence provides valuable information about the current state of the heart. The peak detection algorithm gave excellent results with very good accuracy for all the downloaded ECG signals, and was developed using classical linear techniques. Later, a peak detection algorithm using the discrete wavelet transform (DWT) was implemented. This code was developed using nonlinear techniques and was amenable for implementation. Also, the time required for execution was reduced, making this code ideal for real-time processing. Finally, algorithms were developed to calculate the Kolmogorov complexity and Lyapunov exponent, which are nonlinear descriptors and enable the randomness and chaotic nature of ECG signals to be estimated. These measures of randomness and chaotic nature enable us to apply correct interrogative methods to the signal to extract maximum information. The codes developed gave fair results. It was possible to differentiate between normal ECGs and ECGs with ventricular fibrillation. The results show that the Kolmogorov complexity measure increases with an increase in pathology, approximately 12.90 for normal ECGs and increasing to 13.87 to 14.39 for ECGs with ventricular fibrillation and ventricular tachycardia. Similar results were obtained for Lyapunov exponent measures with a notable difference between normal ECG (0 – 0.0095) and ECG with ventricular fibrillation (0.1114 – 0.1799). However, it was difficult to differentiate between different types of arrhythmias

Permutation entropy and its main biomedical and econophysics applications: a review

Entropy is a powerful tool for the analysis of time series, as it allows describing the probability distributions of the possible state of a system, and therefore the information encoded in it. Nevertheless, important information may be codified also in the temporal dynamics, an aspect which is not usually taken into account. The idea of calculating entropy based on permutation patterns (that is, permutations defined by the order relations among values of a time series) has received a lot of attention in the last years, especially for the understanding of complex and chaotic systems. Permutation entropy directly accounts for the temporal information contained in the time series; furthermore, it has the quality of simplicity, robustness and very low computational cost. To celebrate the tenth anniversary of the original work, here we analyze the theoretical foundations of the permutation entropy, as well as the main recent applications to the analysis of economical markets and to the understanding of biomedical systems.Facultad de Ingenierí

A Comprehensive Review of Techniques for Processing and Analyzing Fetal Heart Rate Signals

The availability of standardized guidelines regarding the use of electronic fetal monitoring (EFM) in clinical practice has not effectively helped to solve the main drawbacks of fetal heart rate (FHR) surveillance methodology, which still presents inter- and intra-observer variability as well as uncertainty in the classification of unreassuring or risky FHR recordings. Given the clinical relevance of the interpretation of FHR traces as well as the role of FHR as a marker of fetal wellbeing autonomous nervous system development, many different approaches for computerized processing and analysis of FHR patterns have been proposed in the literature. The objective of this review is to describe the techniques, methodologies, and algorithms proposed in this field so far, reporting their main achievements and discussing the value they brought to the scientific and clinical community. The review explores the following two main approaches to the processing and analysis of FHR signals: traditional (or linear) methodologies, namely, time and frequency domain analysis, and less conventional (or nonlinear) techniques. In this scenario, the emerging role and the opportunities offered by Artificial Intelligence tools, representing the future direction of EFM, are also discussed with a specific focus on the use of Artificial Neural Networks, whose application to the analysis of accelerations in FHR signals is also examined in a case study conducted by the authors

Automated Classification for Electrophysiological Data: Machine Learning Approaches for Disease Detection and Emotion Recognition

Smart healthcare is a health service system that utilizes technologies, e.g., artificial intelligence and big data, to alleviate the pressures on healthcare systems. Much recent research has focused on the automatic disease diagnosis and recognition and, typically, our research pays attention on automatic classifications for electrophysiological signals, which are measurements of the electrical activity. Specifically, for electrocardiogram (ECG) and electroencephalogram (EEG) data, we develop a series of algorithms for automatic cardiovascular disease (CVD) classification, emotion recognition and seizure detection. With the ECG signals obtained from wearable devices, the candidate developed novel signal processing and machine learning method for continuous monitoring of heart conditions. Compared to the traditional methods based on the devices at clinical settings, the developed method in this thesis is much more convenient to use. To identify arrhythmia patterns from the noisy ECG signals obtained through the wearable devices, CNN and LSTM are used, and a wavelet-based CNN is proposed to enhance the performance. An emotion recognition method with a single channel ECG is developed, where a novel exploitative and explorative GWO-SVM algorithm is proposed to achieve high performance emotion classification. The attractive part is that the proposed algorithm has the capability to learn the SVM hyperparameters automatically, and it can prevent the algorithm from falling into local solutions, thereby achieving better performance than existing algorithms. A novel EEG-signal based seizure detector is developed, where the EEG signals are transformed to the spectral-temporal domain, so that the dimension of the input features to the CNN can be significantly reduced, while the detector can still achieve superior detection performance

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

Signal processing and analytics of multimodal biosignals

Ph. D. ThesisBiosignals have been extensively studied by researchers for applications in diagnosis, therapy, and monitoring. As these signals are complex, they have to be crafted as features for machine learning to work. This begs the question of how to extract features that are relevant and yet invariant to uncontrolled extraneous factors. In the last decade or so, deep learning has been used to extract features from the raw signals automatically. Furthermore, with the proliferation of sensors, more raw signals are now available, making it possible to use multi-view learning to improve on the predictive performance of deep learning. The purpose of this work is to develop an effective deep learning model of the biosignals and make use of the multi-view information in the sequential data. This thesis describes two proposed methods, namely: (1) The use of a deep temporal convolution network to provide the temporal context of the signals to the deeper layers of a deep belief net. (2) The use of multi-view spectral embedding to blend the complementary data in an ensemble. This work uses several annotated biosignal data sets that are available in the open domain. They are non-stationary, noisy and non-linear signals. Using these signals in their raw form without feature engineering will yield poor results with the traditional machine learning techniques. By passing abstractions that are more useful through the deep belief net and blending the complementary data in an ensemble, there will be improvement in performance in terms of accuracy and variance, as shown by the results of 10-fold validations.Nanyang Polytechni

Techniques of EMG signal analysis: detection, processing, classification and applications

Electromyography (EMG) signals can be used for clinical/biomedical applications, Evolvable Hardware Chip (EHW) development, and modern human computer interaction. EMG signals acquired from muscles require advanced methods for detection, decomposition, processing, and classification. The purpose of this paper is to illustrate the various methodologies and algorithms for EMG signal analysis to provide efficient and effective ways of understanding the signal and its nature. We further point up some of the hardware implementations using EMG focusing on applications related to prosthetic hand control, grasp recognition, and human computer interaction. A comparison study is also given to show performance of various EMG signal analysis methods. This paper provides researchers a good understanding of EMG signal and its analysis procedures. This knowledge will help them develop more powerful, flexible, and efficient applications

Intelligent Biosignal Analysis Methods

This book describes recent efforts in improving intelligent systems for automatic biosignal analysis. It focuses on machine learning and deep learning methods used for classification of different organism states and disorders based on biomedical signals such as EEG, ECG, HRV, and others

Brain electrical activity discriminant analysis using Reproducing Kernel Hilbert spaces

A deep an adequate understanding of the human brain functions has been an objective for interdisciplinar teams of scientists. Different types of technological acquisition methodologies, allow to capture some particular data that is related with brain activity. Commonly, the more used strategies are related with the brain electrical activity, where reflected neuronal interactions are reflected in the scalp and obtained via electrode arrays as time series. The processing of this type of brain electrical activity (BEA) data, poses some challenges that should be addressed carefully due their intrinsic properties. BEA in known to have a nonstationaty behavior and a high degree of variability dependenig of the stimulus or responses that are being adressed..