Sleep Stage Classification: A Deep Learning Approach

Sleep occupies significant part of human life. The diagnoses of sleep related disorders are of great importance. To record specific physical and electrical activities of the brain and body, a multi-parameter test, called polysomnography (PSG), is normally used. The visual process of sleep stage classification is time consuming, subjective and costly. To improve the accuracy and efficiency of the sleep stage classification, automatic classification algorithms were developed. In this research work, we focused on pre-processing (filtering boundaries and de-noising algorithms) and classification steps of automatic sleep stage classification. The main motivation for this work was to develop a pre-processing and classification framework to clean the input EEG signal without manipulating the original data thus enhancing the learning stage of deep learning classifiers. For pre-processing EEG signals, a lossless adaptive artefact removal method was proposed. Rather than other works that used artificial noise, we used real EEG data contaminated with EOG and EMG for evaluating the proposed method. The proposed adaptive algorithm led to a significant enhancement in the overall classification accuracy. In the classification area, we evaluated the performance of the most common sleep stage classifiers using a comprehensive set of features extracted from PSG signals. Considering the challenges and limitations of conventional methods, we proposed two deep learning-based methods for classification of sleep stages based on Stacked Sparse AutoEncoder (SSAE) and Convolutional Neural Network (CNN). The proposed methods performed more efficiently by eliminating the need for conventional feature selection and feature extraction steps respectively. Moreover, although our systems were trained with lower number of samples compared to the similar studies, they were able to achieve state of art accuracy and higher overall sensitivity

Automated Sleep Scoring, Deep Learning and Physician Supervision

Sleep plays a crucial role in human well-being. Polysomnography is used in sleep medicine as a diagnostic tool, so as to objectively analyze the quality of sleep. Sleep scoring is the procedure of extracting sleep cycle information from the whole-night electrophysiological signals. The scoring is done worldwide by the sleep physicians according to the official American Academy of Sleep Medicine (AASM) scoring manual. In the last decades, a wide variety of deep learning based algorithms have been proposed to automatise the sleep scoring task. In this thesis we study the reasons why these algorithms fail to be introduced in the daily clinical routine, with the perspective of bridging the existing gap between the automatic sleep scoring models and the sleep physicians. In this light, the primary step is the design of a simplified sleep scoring architecture, also providing an estimate of the model uncertainty. Beside achieving results on par with most up-to-date scoring systems, we demonstrate the efficiency of ensemble learning based algorithms, together with label smoothing techniques, in both enhancing the performance and calibrating the simplified scoring model. We introduced an uncertainty estimate procedure, so as to identify the most challenging sleep stage predictions, and to quantify the disagreement between the predictions given by the model and the annotation given by the physicians. In this thesis we also propose a novel method to integrate the inter-scorer variability into the training procedure of a sleep scoring model. We clearly show that a deep learning model is able to encode this variability, so as to better adapt to the consensus of a group of scorers-physicians. We finally address the generalization ability of a deep learning based sleep scoring system, further studying its resilience to the sleep complexity and to the AASM scoring rules. We can state that there is no need to train the algorithm strictly following the AASM guidelines. Most importantly, using data from multiple data centers results in a better performing model compared with training on a single data cohort. The variability among different scorers and data centers needs to be taken into account, more than the variability among sleep disorders

Feature Extraction and Selection in Automatic Sleep Stage Classification

Sleep stage classification is vital for diagnosing many sleep related disorders and Polysomnography (PSG) is an important tool in this regard. The visual process of sleep stage classification is time consuming, subjective and costly. To improve the accuracy and efficiency of the sleep stage classification, researchers have been trying to develop automatic classification algorithms. The automatic sleep stage classification mainly consists of three steps: pre-processing, feature extraction and classification. In this research work, we focused on feature extraction and selection steps. The main goal of this thesis was identifying a robust and reliable feature set that can lead to efficient classification of sleep stages. For achieving this goal, three types of contributions were introduced in feature selection, feature extraction and feature vector quality enhancement. Several feature ranking and rank aggregation methods were evaluated and compared for finding the best feature set. Evaluation results indicated that the decision on the precise feature selection method depends on the system design requirements such as low computational complexity, high stability or high classification accuracy. In addition to conventional feature ranking methods, in this thesis, novel methods such as Stacked Sparse AutoEncoder (SSAE) was used for dimensionality reduction. In feature extration area, new and effective features such as distancebased features were utilized for the first time in sleep stage classification. The results showed that these features contribute positively to the classification performance. For signal quality enhancement, a loss-less EEG artefact removal algorithm was proposed. The proposed adaptive algorithm led to a significant enhancement in the overall classification accuracy

U-Sleep's resilience to AASM guidelines

AASM guidelines are the result of decades of efforts aiming at standardizing sleep scoring procedure, with the final goal of sharing a worldwide common methodology. The guidelines cover several aspects from the technical/digital specifications,e.g., recommended EEG derivations, to detailed sleep scoring rules accordingly to age. Automated sleep scoring systems have always largely exploited the standards as fundamental guidelines. In this context, deep learning has demonstrated better performance compared to classical machine learning. Our present work shows that a deep learning based sleep scoring algorithm may not need to fully exploit the clinical knowledge or to strictly adhere to the AASM guidelines. Specifically, we demonstrate that U-Sleep, a state-of-the-art sleep scoring algorithm, can be strong enough to solve the scoring task even using clinically non-recommended or non-conventional derivations, and with no need to exploit information about the chronological age of the subjects. We finally strengthen a well-known finding that using data from multiple data centers always results in a better performing model compared with training on a single cohort. Indeed, we show that this latter statement is still valid even by increasing the size and the heterogeneity of the single data cohort. In all our experiments we used 28528 polysomnography studies from 13 different clinical studies

Learning Better Clinical Risk Models.

Risk models are used to estimate a patient’s risk of suffering particular outcomes throughout clinical practice. These models are important for matching patients to the appropriate level of treatment, for effective allocation of resources, and for fairly evaluating the performance of healthcare providers. The application and development of methods from the field of machine learning has the potential to improve patient outcomes and reduce healthcare spending with more accurate estimates of patient risk. This dissertation addresses several limitations of currently used clinical risk models, through the identification of novel risk factors and through the training of more effective models. As wearable monitors become more effective and less costly, the previously untapped predictive information in a patient’s physiology over time has the potential to greatly improve clinical practice. However translating these technological advances into real-world clinical impacts will require computational methods to identify high-risk structure in the data. This dissertation presents several approaches to learning risk factors from physiological recordings, through the discovery of latent states using topic models, and through the identification of predictive features using convolutional neural networks. We evaluate these approaches on patients from a large clinical trial and find that these methods not only outperform prior approaches to leveraging heart rate for cardiac risk stratification, but that they improve overall prediction of cardiac death when considered alongside standard clinical risk factors. We also demonstrate the utility of this work for learning a richer description of sleep recordings. Additionally, we consider the development of risk models in the presence of missing data, which is ubiquitous in real-world medical settings. We present a novel method for jointly learning risk and imputation models in the presence of missing data, and find significant improvements relative to standard approaches when evaluated on a large national registry of trauma patients.PhDComputer Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113326/1/alexve_1.pd

A Review of Physical Human Activity Recognition Chain Using Sensors

In the era of Internet of Medical Things (IoMT), healthcare monitoring has gained a vital role nowadays. Moreover, improving lifestyle, encouraging healthy behaviours, and decreasing the chronic diseases are urgently required. However, tracking and monitoring critical cases/conditions of elderly and patients is a great challenge. Healthcare services for those people are crucial in order to achieve high safety consideration. Physical human activity recognition using wearable devices is used to monitor and recognize human activities for elderly and patient. The main aim of this review study is to highlight the human activity recognition chain, which includes, sensing technologies, preprocessing and segmentation, feature extractions methods, and classification techniques. Challenges and future trends are also highlighted.

DeepSleepNet-Lite: A Simplified Automatic Sleep Stage Scoring Model with Uncertainty Estimates

Deep learning is widely used in the most recent automatic sleep scoring algorithms. Its popularity stems from its excellent performance and from its ability to process raw signals and to learn feature directly from the data. Most of the existing scoring algorithms exploit very computationally demanding architectures, due to their high number of training parameters, and process lengthy time sequences in input (up to 12 minutes). Only few of these architectures provide an estimate of the model uncertainty. In this study we propose DeepSleepNet-Lite, a simplified and lightweight scoring architecture, processing only 90-seconds EEG input sequences. We exploit, for the first time in sleep scoring, the Monte Carlo dropout technique to enhance the performance of the architecture and to also detect the uncertain instances. The evaluation is performed on a single-channel EEG Fpz-Cz from the open source Sleep-EDF expanded database. DeepSleepNet-Lite achieves slightly lower performance, if not on par, compared to the existing state-of-the-art architectures, in overall accuracy, macro F1-score and Cohen’s kappa (on Sleep-EDF v1-2013 ±30mins: 84.0%, 78.0%, 0.78; on Sleep-EDF v2-2018 ±30mins: 80.3%, 75.2%, 0.73). Monte Carlo dropout enables the estimate of the uncertain predictions. By rejecting the uncertain instances, the model achieves higher performance on both versions of the database (on Sleep-EDF v1-2013 ±30mins: 86.1.0%, 79.6%, 0.81; on Sleep-EDF v2-2018 ±30mins: 82.3%, 76.7%, 0.76). Our lighter sleep scoring approach paves the way to the application of scoring algorithms for sleep analysis in realtime

Deep Learning in EEG: Advance of the Last Ten-Year Critical Period

Deep learning has achieved excellent performance in a wide range of domains, especially in speech recognition and computer vision. Relatively less work has been done for EEG, but there is still significant progress attained in the last decade. Due to the lack of a comprehensive and topic widely covered survey for deep learning in EEG, we attempt to summarize recent progress to provide an overview, as well as perspectives for future developments. We first briefly mention the artifacts removal for EEG signal and then introduce deep learning models that have been utilized in EEG processing and classification. Subsequently, the applications of deep learning in EEG are reviewed by categorizing them into groups such as brain-computer interface, disease detection, and emotion recognition. They are followed by the discussion, in which the pros and cons of deep learning are presented and future directions and challenges for deep learning in EEG are proposed. We hope that this paper could serve as a summary of past work for deep learning in EEG and the beginning of further developments and achievements of EEG studies based on deep learning