Scalable automatic sleep staging in the era of Big Data

Numerous automatic sleep staging approacheshave been proposed to provide an eHealth alternative to thecurrent gold-standard – hypnogram scoring by human experts.However, a majority of such studies exploit data of limited scale,which compromises both the validation and the reproducibilityand transferability of such automatic sleep staging systemsin the real clinical settings. In addition, the computationalissues and physical meaningfulness of the analysis are typicallyneglected, yet affordable computation is a key criterion inBig Data analytics. To this end, we establish a comprehensiveanalysis framework to rigorously evaluate the feasibility ofautomatic sleep staging from multiple perspectives, includingrobustness with respect to the number of training subjects,model complexity, and different classifiers. This is achievedfor a large collection of publicly accessible polysomnography(PSG) data, recorded over 515 subjects. The trade-off betweenaffordable computation and satisfactory accuracy is shown tobe fulfilled by an extreme learning machine (ELM) classifier,which in conjunction with the physically meaningful hiddenMarkov model (HMM) of the transition between the differentsleep stages (smoothing model) is shown to achieve both fastcomputation and highest average Cohen’s kappa value ofκ=0.73(Substantial Agreement). Finally, it is shown thatfor accurate and robust automatic sleep staging, a combinationof structural complexity (multi-scale entropy) and frequency-domain (spectral edge frequency) features is both computation-ally affordable and physically meaningful

Rise of big data – issues and challenges

The recent rapid rise in the availability of big data due to Internet-based technologies such as social media platforms and mobile devices has left many market leaders unprepared for handling very large, random and high velocity data. Conventionally, technologies are initially developed and tested in labs and appear to the public through media such as press releases and advertisements. These technologies are then adopted by the general public. In the case of big data technology, fast development and ready acceptance of big data by the user community has left little time to be scrutinized by the academic community. Although many books and electronic media articles are published by professionals and authors for their work on big data, there is still a lack of fundamental work in academic literature. Through survey methods, this paper discusses challenges in different aspects of big data, such as data sources, content format, data staging, data processing, and prevalent data stores. Issues and challenges related to big data, specifically privacy attacks and counter-techniques such as k-anonymity, t-closeness, l-diversity and differential privacy are discussed. Tools and techniques adopted by various organizations to store different types of big data are also highlighted. This study identifies different research areas to address such as a lack of anonymization techniques for unstructured big data, data traffic pattern determination for developing scalable data storage solutions and controlling mechanisms for high velocity data

Digital phenotyping through multimodal, unobtrusive sensing

The growing adoption of multimodal wearable and mobile devices, such as smartphones and wrist-worn watches has generated an increase in the collection of physiological and behavioural data at scale. This digital phenotyping data enables researchers to make inferences regarding users’ physical and mental health at scale, for the first time. However, translating this data into actionable insights requires computational approaches that turn unlabelled, multimodal time-series sensor data into validated measures that can be interpreted at scale. This thesis describes the derivation of novel computational methods that leverage digital phenotyping data from wearable devices in large-scale populations to infer physical behaviours. These methods combine insights from signal processing, data mining and machine learning alongside domain knowledge in physical activity and sleep epidemiology. First, the inference of sleeping windows in free-living conditions through a heart rate sensing approach is explored. This algorithm is particularly valuable in the absence of ground truth or sleep diaries given its simplicity, adaptability and capacity for personalization. I then explore multistage sleep classification through combined movement and cardiac wearable sensing and machine learning. Further, I demonstrate that postural changes detected through wrist accelerometers can inform habitual behaviours and are valuable complements to traditional, intensity-based physical activity metrics. I then leverage the concomitant responses of heart rate to physical activity that can be captured through multimodal wearable sensors through a self-supervised training task. The resulting embeddings from this task are shown to be useful for the downstream classification of demographic factors, BMI, energy expenditure and cardiorespiratory fitness. Finally, I describe a deep learning model for the adaptive inference of cardiorespiratory fitness (VO2max) using wearable data in free living conditions. I demonstrate the robustness of the model in a large UK population and show the models’ adaptability by evaluating its performance in a subset of the population with repeated measures ~6 years after the original recordings. Together, this work increases the potential of multimodal wearable and mobile sensors for physical activity and behavioural inferences in population studies. In particular, this thesis showcases the potential of using wearable devices to make valuable physical activity, sleep and fitness inferences in large cohort studies. Given the nature of the data collected and the fact that most of this data is currently generated by commercial providers and not research institutes, laying the foundations for responsible data governance and ethical use of these technologies will be critical to building trust and enabling the development of the field of digital phenotyping.I was funded by GlaxoSmithKline and the Engineering and Physical Sciences Research Council. I was also supported by the Alan Turing Institute through their Enrichment Scheme

Review and perspective on sleep-disordered breathing research and translation to clinics

Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.Sleep-disordered breathing, ranging from habitual snoring to severe obstructive sleep apnea, is a prevalent public health issue. Despite rising interest in sleep and awareness of sleep disorders, sleep research and diagnostic practices still rely on outdated metrics and laborious methods reducing the diagnostic capacity and preventing timely diagnosis and treatment. Consequently, a significant portion of individuals affected by sleep-disordered breathing remain undiagnosed or are misdiagnosed. Taking advantage of state-of-the-art scientific, technological, and computational advances could be an effective way to optimize the diagnostic and treatment pathways. We discuss state-of-the-art multidisciplinary research, review the shortcomings in the current practices of SDB diagnosis and management in adult populations, and provide possible future directions. We critically review the opportunities for modern data analysis methods and machine learning to combine multimodal information, provide a perspective on the pitfalls of big data analysis, and discuss approaches for developing analysis strategies that overcome current limitations. We argue that large-scale and multidisciplinary collaborative efforts based on clinical, scientific, and technical knowledge and rigorous clinical validation and implementation of the outcomes in practice are needed to move the research of sleep-disordered breathing forward, thus increasing the quality of diagnostics and treatment.Peer reviewe

Wearable in-ear pulse oximetry: theory and applications

Wearable health technology, most commonly in the form of the smart watch, is employed by millions of users worldwide. These devices generally exploit photoplethysmography (PPG), the non-invasive use of light to measure blood volume, in order to track physiological metrics such as pulse and respiration. Moreover, PPG is commonly used in hospitals in the form of pulse oximetry, which measures light absorbance by the blood at different wavelengths of light to estimate blood oxygen levels (SpO2). This thesis aims to demonstrate that despite its widespread usage over many decades, this sensor still possesses a wealth of untapped value. Through a combination of advanced signal processing and harnessing the ear as a location for wearable sensing, this thesis introduces several novel high impact applications of in-ear pulse oximetry and photoplethysmography. The aims of this thesis are accomplished through a three pronged approach: rapid detection of hypoxia, tracking of cognitive workload and fatigue, and detection of respiratory disease. By means of the simultaneous recording of in-ear and finger pulse oximetry at rest and during breath hold tests, it was found that in-ear SpO2 responds on average 12.4 seconds faster than the finger SpO2. This is likely due in part to the ear being in close proximity to the brain, making it a priority for oxygenation and thus making wearable in-ear SpO2 a good proxy for core blood oxygen. Next, the low latency of in-ear SpO2 was further exploited in the novel application of classifying cognitive workload. It was found that in-ear pulse oximetry was able to robustly detect tiny decreases in blood oxygen during increased cognitive workload, likely caused by increased brain metabolism. This thesis demonstrates that in-ear SpO2 can be used to accurately distinguish between different levels of an N-back memory task, representing different levels of mental effort. This concept was further validated through its application to gaming and then extended to the detection of driver related fatigue. It was found that features derived from SpO2 and PPG were predictive of absolute steering wheel angle, which acts as a proxy for fatigue. The strength of in-ear PPG for the monitoring of respiration was investigated with respect to the finger, with the conclusion that in-ear PPG exhibits far stronger respiration induced intensity variations and pulse amplitude variations than the finger. All three respiratory modes were harnessed through multivariate empirical mode decomposition (MEMD) to produce spirometry-like respiratory waveforms from PPG. It was discovered that these PPG derived respiratory waveforms can be used to detect obstruction to breathing, both through a novel apparatus for the simulation of breathing disorders and through the classification of chronic obstructive pulmonary disease (COPD) in the real world. This thesis establishes in-ear pulse oximetry as a wearable technology with the potential for immense societal impact, with applications from the classification of cognitive workload and the prediction of driver fatigue, through to the detection of chronic obstructive pulmonary disease. The experiments and analysis in this thesis conclusively demonstrate that widely used pulse oximetry and photoplethysmography possess a wealth of untapped value, in essence teaching the old PPG sensor new tricks.Open Acces

Bioinformatics and Medicine in the Era of Deep Learning

Many of the current scientific advances in the life sciences have their origin in the intensive use of data for knowledge discovery. In no area this is so clear as in bioinformatics, led by technological breakthroughs in data acquisition technologies. It has been argued that bioinformatics could quickly become the field of research generating the largest data repositories, beating other data-intensive areas such as high-energy physics or astroinformatics. Over the last decade, deep learning has become a disruptive advance in machine learning, giving new live to the long-standing connectionist paradigm in artificial intelligence. Deep learning methods are ideally suited to large-scale data and, therefore, they should be ideally suited to knowledge discovery in bioinformatics and biomedicine at large. In this brief paper, we review key aspects of the application of deep learning in bioinformatics and medicine, drawing from the themes covered by the contributions to an ESANN 2018 special session devoted to this topic

Bipolar disorder in the digital age: new tools for the same illness

“Nothing is more difficult than to ascertain the length of time that a maniacal patient can exist without sleep.”—Dr. Sutherland (Br J Psychiatry 7(37):1–19, 1861). Dr. Sutherland’s patient was suffering from an acute manic episode, which today is called bipolar illness. 150 years later, we continue to struggle with the same challenges in ascertaining accurate symptoms from patients. In era of new digital tools, the quantified self-movement, and precision medicine, we can ask the question: Can we advance understanding and treatment for bipolar illness beyond asking the same questions as in 1861

Towards fog-driven IoT eHealth:Promises and challenges of IoT in medicine and healthcare

Internet of Things (IoT) offers a seamless platform to connect people and objects to one another for enriching and making our lives easier. This vision carries us from compute-based centralized schemes to a more distributed environment offering a vast amount of applications such as smart wearables, smart home, smart mobility, and smart cities. In this paper we discuss applicability of IoT in healthcare and medicine by presenting a holistic architecture of IoT eHealth ecosystem. Healthcare is becoming increasingly difficult to manage due to insufficient and less effective healthcare services to meet the increasing demands of rising aging population with chronic diseases. We propose that this requires a transition from the clinic-centric treatment to patient-centric healthcare where each agent such as hospital, patient, and services are seamlessly connected to each other. This patient-centric IoT eHealth ecosystem needs a multi-layer architecture: (1) device, (2) fog computing and (3) cloud to empower handling of complex data in terms of its variety, speed, and latency. This fog-driven IoT architecture is followed by various case examples of services and applications that are implemented on those layers. Those examples range from mobile health, assisted living, e-medicine, implants, early warning systems, to population monitoring in smart cities. We then finally address the challenges of IoT eHealth such as data management, scalability, regulations, interoperability, device–network–human interfaces, security, and privacy