Opening the black-box of artificial intelligence predictions on clinical decision support systems

Cardiovascular diseases are the leading global death cause. Their treatment and prevention rely on electrocardiogram interpretation, which is dependent on the physician’s variability. Subjectiveness is intrinsic to electrocardiogram interpretation and hence, prone to errors. To assist physicians in making precise and thoughtful decisions, artificial intelligence is being deployed to develop models that can interpret extent datasets and provide accurate decisions. However, the lack of interpretability of most machine learning models stands as one of the drawbacks of their deployment, particularly in the medical domain. Furthermore, most of the currently deployed explainable artificial intelligence methods assume independence between features, which means temporal independence when dealing with time series. The inherent characteristic of time series cannot be ignored as it carries importance for the human decision making process. This dissertation focuses on the explanation of heartbeat classification using several adaptations of state-of-the-art model-agnostic methods, to locally explain time series classification. To address the explanation of time series classifiers, a preliminary conceptual framework is proposed, and the use of the derivative is suggested as a complement to add temporal dependency between samples. The results were validated on an extent public dataset, through the 1-D Jaccard’s index, which consists of the comparison of the subsequences extracted from an interpretable model and the explanation methods used. Secondly, through the performance’s decrease, to evaluate whether the explanation fits the model’s behaviour. To assess models with distinct internal logic, the validation was conducted on a more transparent model and more opaque one in both binary and multiclass situation. The results show the promising use of including the signal’s derivative to introduce temporal dependency between samples in the explanations, for models with simpler internal logic.As doenças cardiovasculares são, a nível mundial, a principal causa de morte e o seu tratamento e prevenção baseiam-se na interpretação do electrocardiograma. A interpretação do electrocardiograma, feita por médicos, é intrinsecamente subjectiva e, portanto, sujeita a erros. De modo a apoiar a decisão dos médicos, a inteligência artificial está a ser usada para desenvolver modelos com a capacidade de interpretar extensos conjuntos de dados e fornecer decisões precisas. No entanto, a falta de interpretabilidade da maioria dos modelos de aprendizagem automática é uma das desvantagens do recurso à mesma, principalmente em contexto clínico. Adicionalmente, a maioria dos métodos inteligência artifical explicável assumem independência entre amostras, o que implica a assunção de independência temporal ao lidar com séries temporais. A característica inerente das séries temporais não pode ser ignorada, uma vez que apresenta importância para o processo de tomada de decisão humana. Esta dissertação baseia-se em inteligência artificial explicável para tornar inteligível a classificação de batimentos cardíacos, através da utilização de várias adaptações de métodos agnósticos do estado-da-arte. Para abordar a explicação dos classificadores de séries temporais, propõe-se uma taxonomia preliminar, e o uso da derivada como um complemento para adicionar dependência temporal entre as amostras. Os resultados foram validados para um conjunto extenso de dados públicos, por meio do índice de Jaccard em 1-D, com a comparação das subsequências extraídas de um modelo interpretável e os métodos inteligência artificial explicável utilizados, e a análise de qualidade, para avaliar se a explicação se adequa ao comportamento do modelo. De modo a avaliar modelos com lógicas internas distintas, a validação foi realizada usando, por um lado, um modelo mais transparente e, por outro, um mais opaco, tanto numa situação de classificação binária como numa situação de classificação multiclasse. Os resultados mostram o uso promissor da inclusão da derivada do sinal para introduzir dependência temporal entre as amostras nas explicações fornecidas, para modelos com lógica interna mais simples

MPCNN: A Novel Matrix Profile Approach for CNN-based Sleep Apnea Classification

Sleep apnea (SA) is a significant respiratory condition that poses a major global health challenge. Previous studies have investigated several machine and deep learning models for electrocardiogram (ECG)-based SA diagnoses. Despite these advancements, conventional feature extractions derived from ECG signals, such as R-peaks and RR intervals, may fail to capture crucial information encompassed within the complete PQRST segments. In this study, we propose an innovative approach to address this diagnostic gap by delving deeper into the comprehensive segments of the ECG signal. The proposed methodology draws inspiration from Matrix Profile algorithms, which generate an Euclidean distance profile from fixed-length signal subsequences. From this, we derived the Min Distance Profile (MinDP), Max Distance Profile (MaxDP), and Mean Distance Profile (MeanDP) based on the minimum, maximum, and mean of the profile distances, respectively. To validate the effectiveness of our approach, we use the modified LeNet-5 architecture as the primary CNN model, along with two existing lightweight models, BAFNet and SE-MSCNN, for ECG classification tasks. Our extensive experimental results on the PhysioNet Apnea-ECG dataset revealed that with the new feature extraction method, we achieved a per-segment accuracy up to 92.11 \% and a per-recording accuracy of 100\%. Moreover, it yielded the highest correlation compared to state-of-the-art methods, with a correlation coefficient of 0.989. By introducing a new feature extraction method based on distance relationships, we enhanced the performance of certain lightweight models, showing potential for home sleep apnea test (HSAT) and SA detection in IoT devices. The source code for this work is made publicly available in GitHub: https://github.com/vinuni-vishc/MPCNN-Sleep-Apnea

Individual identification via electrocardiogram analysis

Background: During last decade the use of ECG recordings in biometric recognition studies has increased. ECG characteristics made it suitable for subject identification: it is unique, present in all living individuals, and hard to forge. However, in spite of the great number of approaches found in literature, no agreement exists on the most appropriate methodology. This study aimed at providing a survey of the techniques used so far in ECG-based human identification. Specifically, a pattern recognition perspective is here proposed providing a unifying framework to appreciate previous studies and, hopefully, guide future research. Methods: We searched for papers on the subject from the earliest available date using relevant electronic databases (Medline, IEEEXplore, Scopus, and Web of Knowledge). The following terms were used in different combinations: electrocardiogram, ECG, human identification, biometric, authentication and individual variability. The electronic sources were last searched on 1st March 2015. In our selection we included published research on peer-reviewed journals, books chapters and conferences proceedings. The search was performed for English language documents. Results: 100 pertinent papers were found. Number of subjects involved in the journal studies ranges from 10 to 502, age from 16 to 86, male and female subjects are generally present. Number of analysed leads varies as well as the recording conditions. Identification performance differs widely as well as verification rate. Many studies refer to publicly available databases (Physionet ECG databases repository) while others rely on proprietary recordings making difficult them to compare. As a measure of overall accuracy we computed a weighted average of the identification rate and equal error rate in authentication scenarios. Identification rate resulted equal to 94.95 % while the equal error rate equal to 0.92 %. Conclusions: Biometric recognition is a mature field of research. Nevertheless, the use of physiological signals features, such as the ECG traits, needs further improvements. ECG features have the potential to be used in daily activities such as access control and patient handling as well as in wearable electronics applications. However, some barriers still limit its growth. Further analysis should be addressed on the use of single lead recordings and the study of features which are not dependent on the recording sites (e.g. fingers, hand palms). Moreover, it is expected that new techniques will be developed using fiducials and non-fiducial based features in order to catch the best of both approaches. ECG recognition in pathological subjects is also worth of additional investigations

Causality-Inspired Taxonomy for Explainable Artificial Intelligence

As two sides of the same coin, causality and explainable artificial intelligence (xAI) were initially proposed and developed with different goals. However, the latter can only be complete when seen through the lens of the causality framework. As such, we propose a novel causality-inspired framework for xAI that creates an environment for the development of xAI approaches. To show its applicability, biometrics was used as case study. For this, we have analysed 81 research papers on a myriad of biometric modalities and different tasks. We have categorised each of these methods according to our novel xAI Ladder and discussed the future directions of the field

Towards a continuous biometric system based on ECG signals acquired on the steering wheel

Electrocardiogram signals acquired through a steering wheel could be the key to seamless, highly comfortable, and continuous human recognition in driving settings. This paper focuses on the enhancement of the unprecedented lesser quality of such signals, through the combination of Savitzky-Golay and moving average filters, followed by outlier detection and removal based on normalised cross-correlation and clustering, which was able to render ensemble heartbeats of significantly higher quality. Discrete Cosine Transform (DCT) and Haar transform features were extracted and fed to decision methods based on Support Vector Machines (SVM), k-Nearest Neighbours (kNN), Multilayer Perceptrons (MLP), and Gaussian Mixture Models – Universal Background Models (GMM-UBM) classifiers, for both identification and authentication tasks. Additional techniques of user-tuned authentication and past score weighting were also studied. The method’s performance was comparable to some of the best recent state-of-the-art methods (94.9% identification rate (IDR) and 2.66% authentication equal error rate (EER)), despite lesser results with scarce train data (70.9% IDR and 11.8% EER). It was concluded that the method was suitable for biometric recognition with driving electrocardiogram signals, and could, with future developments, be used on a continuous system in seamless and highly noisy settings.info:eu-repo/semantics/publishedVersio

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

Extracting ECG-based cardiac information from the upper arm

Cardiovascular disease (CVD) is the global number one cause of death. Therefore, there is an acute need for constantly monitoring cardiac conditions and/or cardiac monitoring for extended periods. The current clinical Electrocardiogram (ECG) recording systems require precise placement of electrodes on the patient’s body, often performed by trained medical professionals. These systems also have long wires that require repeated disinfection and can be easily tangled and interfered with clothing and garment. These limitations have severely restricted the possible application scenarios of ECG systems. To overcome these limitations, there is a need for wearable ECG devices with minimal wires to detect possible cardiac abnormalities with minimal intervention from healthcare professionals. Previous research on this topic has focused on extracting cardiac information from the body surface by investigating various electrode placements and developing ECG processing algorithms. Building on these studies, it is possible to develop devices and algorithms that can extract ECG-related information without the need for precise electrode placements on the body's surface. The present thesis aims to extract ECG-based cardiac information using signals recorded from the upper arm. Far-field ECG is prone to contamination by artifacts such as Electromyogram (EMG), which greatly reduces its clinical value. The current study examines how various state-of-the-art heartbeat detection algorithms perform in four levels of simulated EMG artifacts. The simulated EMG was added to Lead II from two different datasets: the MIT-BIH arrhythmia dataset (Dataset 1) and data we collected from 20 healthy participants (Dataset 2). Results show that Stationary Wavelet Transform (SWT) provided the most robust features against EMG intensity level increment among various algorithms. The next step involved recording bio-potential signals using a high-density bio-potential amplification system attached to the upper arm. The system used three high-density electrodes, each with 64 channels, in addition to the standard Lead II. Twenty participants, reported healthy, were asked to perform two tasks: Rest and Elbow Flexion (EF): holding three weights (C1: 1.2 kg, C2: 2.2 kg, and C3: 3.6 kg). The tasks were repeated 2 and 3 times, respectively. Firstly, I identified optimal electrode locations on the upper arm for each task. I then generated a synthesized ECG using the selected electrodes with generalized weights over subjects and trials. Considering the robustness of SWT to EMG intensity level increment, I next focused on optimizing SWT by addressing two of its drawbacks: introducing phase shift and the requirement of a pre-defined mother wavelet. Regarding the first drawback, zero-phase wavelet (Zephlet) was implemented to replace SWT filters with zero-phase filters for the matter of feature extraction from the synthesized ECG. Next, I incorporated the synchronized extracted features with a Multiagent Detection Scheme (MDS) for the means of heartbeat detection. The F1-score for the heartbeat detection was 0.94 ± 0.16, 0.86 ± 0.22, 0.79 ± 0.26, and 0.67 ± 0.31 for Rest and EF with three different levels of muscle contraction (C1 to C3), respectively. Changing the acceptable distance between the detected and actual heartbeats from 50 ms to 20 ms, the F1-score changed to 0.81 ± 0.20, 0.66 ± 0.26, 0.57 ± 0.26, and 0.44 ± 0.26 for Rest and C1 to C3, respectively. Regarding the second drawback, Lattice parametrization was used to optimize the mother wavelet for the means of PQRST delineation. The mother wavelet was generalized over subjects, trials, and tasks. The Pearson’s Correlation Coefficient (CC) between the averaged delineated PQRST from analyzing feature and the averaged PQRST from Lead II using this generalized mother wavelet was 0.88 ± 0.05, 0.85 ± 0.08, 0.83± 0.11, and 0.81 ± 0.12 for Rest and C1-C3, respectively. This thesis makes several contributions to the current literature. It introduces locations on the upper arm that can be used to place sensors in a wearable to capture cardiac activity with robustness across intra-subject, inter-subject and inter-contraction variabilities. It also identifies a robust method against noise increment for heartbeat detection. Zephlet was implemented for the first time that can replace SWT in many applications in which there is a need for synchrony with respect to the original signal or among components. And finally, this thesis introduces a generalized mother wavelet that can be used to extract PQRST and enhance SNR in many applications, such as ECG waveform extraction, arrhythmia detection, and denoising