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

Uncovering the structure of clinical EEG signals with self-supervised learning

Objective. Supervised learning paradigms are often limited by the amount of labeled data that is available. This phenomenon is particularly problematic in clinically-relevant data, such as electroencephalography (EEG), where labeling can be costly in terms of specialized expertise and human processing time. Consequently, deep learning architectures designed to learn on EEG data have yielded relatively shallow models and performances at best similar to those of traditional feature-based approaches. However, in most situations, unlabeled data is available in abundance. By extracting information from this unlabeled data, it might be possible to reach competitive performance with deep neural networks despite limited access to labels. Approach. We investigated self-supervised learning (SSL), a promising technique for discovering structure in unlabeled data, to learn representations of EEG signals. Specifically, we explored two tasks based on temporal context prediction as well as contrastive predictive coding on two clinically-relevant problems: EEG-based sleep staging and pathology detection. We conducted experiments on two large public datasets with thousands of recordings and performed baseline comparisons with purely supervised and hand-engineered approaches. Main results. Linear classifiers trained on SSL-learned features consistently outperformed purely supervised deep neural networks in low-labeled data regimes while reaching competitive performance when all labels were available. Additionally, the embeddings learned with each method revealed clear latent structures related to physiological and clinical phenomena, such as age effects. Significance. We demonstrate the benefit of SSL approaches on EEG data. Our results suggest that self-supervision may pave the way to a wider use of deep learning models on EEG data.Peer reviewe

Self-adjustable domain adaptation in personalized ECG monitoring integrated with IR-UWB radar

To enhance electrocardiogram (ECG) monitoring systems in personalized detections, deep neural networks (DNNs) are applied to overcome individual differences by periodical retraining. As introduced previously [4], DNNs relieve individual differences by fusing ECG with impulse radio ultra-wide band (IR-UWB) radar. However, such DNN-based ECG monitoring system tends to overfit into personal small datasets and is difficult to generalize to newly collected unlabeled data. This paper proposes a self-adjustable domain adaptation (SADA) strategy to prevent from overfitting and exploit unlabeled data. Firstly, this paper enlarges the database of ECG and radar data with actual records acquired from 28 testers and expanded by the data augmentation. Secondly, to utilize unlabeled data, SADA combines self organizing maps with the transfer learning in predicting labels. Thirdly, SADA integrates the one-class classification with domain adaptation algorithms to reduce overfitting. Based on our enlarged database and standard databases, a large dataset of 73200 records and a small one of 1849 records are built up to verify our proposal. Results show SADA\u27s effectiveness in predicting labels and increments in the sensitivity of DNNs by 14.4% compared with existing domain adaptation algorithms

ManyDG: Many-domain Generalization for Healthcare Applications

The vast amount of health data has been continuously collected for each patient, providing opportunities to support diverse healthcare predictive tasks such as seizure detection and hospitalization prediction. Existing models are mostly trained on other patients data and evaluated on new patients. Many of them might suffer from poor generalizability. One key reason can be overfitting due to the unique information related to patient identities and their data collection environments, referred to as patient covariates in the paper. These patient covariates usually do not contribute to predicting the targets but are often difficult to remove. As a result, they can bias the model training process and impede generalization. In healthcare applications, most existing domain generalization methods assume a small number of domains. In this paper, considering the diversity of patient covariates, we propose a new setting by treating each patient as a separate domain (leading to many domains). We develop a new domain generalization method ManyDG, that can scale to such many-domain problems. Our method identifies the patient domain covariates by mutual reconstruction and removes them via an orthogonal projection step. Extensive experiments show that ManyDG can boost the generalization performance on multiple real-world healthcare tasks (e.g., 3.7% Jaccard improvements on MIMIC drug recommendation) and support realistic but challenging settings such as insufficient data and continuous learning.Comment: The paper has been accepted by ICLR 2023, refer to https://openreview.net/forum?id=lcSfirnflpW. We will release the data and source codes here https://github.com/ycq091044/ManyD

Low-complexity algorithms for automatic detection of sleep stages and events for use in wearable EEG systems

Objective: Diagnosis of sleep disorders is an expensive procedure that requires performing a sleep study, known as polysomnography (PSG), in a controlled environment. This study monitors the neural, eye and muscle activity of a patient using electroencephalogram (EEG), electrooculogram (EOG) and electromyogram (EMG) signals which are then scored in to different sleep stages. Home PSG is often cited as an alternative of clinical PSG to make it more accessible, however it still requires patients to use a cumbersome system with multiple recording channels that need to be precisely placed. This thesis proposes a wearable sleep staging system using a single channel of EEG. For realisation of such a system, this thesis presents novel features for REM sleep detection from EEG (normally detected using EMG/EOG), a low-complexity automatic sleep staging algorithm using a single EEG channel and its complete integrated circuit implementation. Methods: The difference between Spectral Edge Frequencies (SEF) at 95% and 50% in the 8-16 Hz frequency band is shown to have high discriminatory ability for detecting REM sleep stages. This feature, together with other spectral features from single-channel EEG are used with a set of decision trees controlled by a state machine for classification. The hardware for the complete algorithm is designed using low-power techniques and implemented on chip using 0.18μm process node technology. Results: The use of SEF features from one channel of EEG resulted in 83% of REM sleep epochs being correctly detected. The automatic sleep staging algorithm, based on contextually aware decision trees, resulted in an accuracy of up to 79% on a large dataset. Its hardware implementation, which is also the very first complete circuit level implementation of any sleep staging algorithm, resulted in an accuracy of 98.7% with great potential for use in fully wearable sleep systems.Open Acces

A Review of Deep Learning Methods for Photoplethysmography Data

Photoplethysmography (PPG) is a highly promising device due to its advantages in portability, user-friendly operation, and non-invasive capabilities to measure a wide range of physiological information. Recent advancements in deep learning have demonstrated remarkable outcomes by leveraging PPG signals for tasks related to personal health management and other multifaceted applications. In this review, we systematically reviewed papers that applied deep learning models to process PPG data between January 1st of 2017 and July 31st of 2023 from Google Scholar, PubMed and Dimensions. Each paper is analyzed from three key perspectives: tasks, models, and data. We finally extracted 193 papers where different deep learning frameworks were used to process PPG signals. Based on the tasks addressed in these papers, we categorized them into two major groups: medical-related, and non-medical-related. The medical-related tasks were further divided into seven subgroups, including blood pressure analysis, cardiovascular monitoring and diagnosis, sleep health, mental health, respiratory monitoring and analysis, blood glucose analysis, as well as others. The non-medical-related tasks were divided into four subgroups, which encompass signal processing, biometric identification, electrocardiogram reconstruction, and human activity recognition. In conclusion, significant progress has been made in the field of using deep learning methods to process PPG data recently. This allows for a more thorough exploration and utilization of the information contained in PPG signals. However, challenges remain, such as limited quantity and quality of publicly available databases, a lack of effective validation in real-world scenarios, and concerns about the interpretability, scalability, and complexity of deep learning models. Moreover, there are still emerging research areas that require further investigation

Deep learning for automated sleep monitoring

Wearable electroencephalography (EEG) is a technology that is revolutionising the longitudinal monitoring of neurological and mental disorders, improving the quality of life of patients and accelerating the relevant research. As sleep disorders and other conditions related to sleep quality affect a large part of the population, monitoring sleep at home, over extended periods of time could have significant impact on the quality of life of people who suffer from these conditions. Annotating the sleep architecture of patients, known as sleep stage scoring, is an expensive and time-consuming process that cannot scale to a large number of people. Using wearable EEG and automating sleep stage scoring is a potential solution to this problem. In this thesis, we propose and evaluate two deep learning algorithms for automated sleep stage scoring using a single channel of EEG. In our first method, we use time-frequency analysis for extracting features that closely follow the guidelines that human experts follow, combined with an ensemble of stacked sparse autoencoders as our classification algorithm. In our second method, we propose a convolutional neural network (CNN) architecture for automatically learning filters that are specific to the problem of sleep stage scoring. We achieved state-of-the-art results (mean F1-score 84%; range 82-86%) with our first method and comparably good results with the second (mean F1-score 81%; range 79-83%). Both our methods effectively account for the skewed performance that is usually found in the literature due to sleep stage duration imbalance. We propose a filter analysis and visualisation methodology for CNNs to understand the filters that CNNs learn. Our results indicate that our CNN was able to robustly learn filters that closely follow the sleep scoring guidelines.Open Acces

Automated sleep classification using the new sleep stage standards

Sleep is fundamental for physical health and good quality of life, and clinicians and researchers have long debated how best to understand it. Manual approaches to sleep classification have been in use for over 40 years, and in 2007, the American Academy of Sleep Medicine (AASM) published a new sleep scoring manual. Over the years, many attempts have been made to introduce and validate machine learning and automated classification techniques in the sleep research field, with the goals of improving consistency and reliability. This thesis explored and assessed the use of automated classification systems with the updated sleep stage definitions and scoring rules using neuro-fuzzy system (NFS) and support vector machine (SVM) methodology. For both the NFS and SVM classification techniques, the overall percent correct was approximately 65%, with sensitivity and specificity rates around 80% and 95%, respectively. The overall Kappa scores, one means for evaluating system reliability, were approximately 0.57 for both the NFS and SVM, indicating moderate agreement that is not accidental. Stage 3 sleep was detected with an 87-89% success rate. The results presented in this thesis show that the use of NFS and SVM methods for classifying sleep stages is possible using the new AASM guidelines. While the current work supports and confirms the use of these classification techniques within the research community, the results did not indicate a significant difference in the accuracy of either approach-nor a difference in one over the other. The results suggest that the important clinical stage 3 (slow wave sleep) can be accurately scored with these classifiers; however, the techniques used here would need more investigation and optimization prior to serious use in clinical applications

Automated scoring of pre-REM sleep in mice with deep learning

Reliable automation of the labor-intensive manual task of scoring animal sleep can facilitate the analysis of long-term sleep studies. In recent years, deep-learning-based systems, which learn optimal features from the data, increased scoring accuracies for the classical sleep stages of Wake, REM, and Non-REM. Meanwhile, it has been recognized that the statistics of transitional stages such as pre-REM, found between Non-REM and REM, may hold additional insight into the physiology of sleep and are now under vivid investigation. We propose a classification system based on a simple neural network architecture that scores the classical stages as well as pre-REM sleep in mice. When restricted to the classical stages, the optimized network showed state-of-the-art classification performance with an out-of-sample F1 score of 0.95 in male C57BL/6J mice. When unrestricted, the network showed lower F1 scores on pre-REM (0.5) compared to the classical stages. The result is comparable to previous attempts to score transitional stages in other species such as transition sleep in rats or N1 sleep in humans. Nevertheless, we observed that the sequence of predictions including pre-REM typically transitioned from Non-REM to REM reflecting sleep dynamics observed by human scorers. Our findings provide further evidence for the difficulty of scoring transitional sleep stages, likely because such stages of sleep are under-represented in typical data sets or show large inter-scorer variability. We further provide our source code and an online platform to run predictions with our trained network.Comment: 14 pages, 5 figure