Electroencephalography (EEG) allows monitoring of brain activity, providing insights into the functional dynamics of various brain regions and their roles in cognitive processes. EEG is a cornerstone in sleep research, serving as the primary modality of polysomnography, the gold standard in the field. However, EEG signals are prone to artifacts caused by both internal (device-specific) factors and external (environmental) interferences. As sleep studies are becoming larger, most rely on automatic sleep staging, a process highly susceptible to artifacts, leading to erroneous sleep scores. This paper addresses this challenge by introducing eegFloss, an open-source Python package to utilize eegUsability, a novel machine learning (ML) model designed to detect segments with artifacts in sleep EEG recordings. eegUsability has been trained and evaluated on manually artifact-labeled EEG data collected from 15 participants over 127 nights using the Zmax headband. It demonstrates solid overall classification performance (F1-score is approximately 0.85, Cohens kappa is 0.78), achieving a high recall rate of approximately 94% in identifying channel-wise usable EEG data, and extends beyond Zmax. Additionally, eegFloss offers features such as automatic time-in-bed detection using another ML model named eegMobility, filtering out certain artifacts, and generating hypnograms and sleep statistics. By addressing a fundamental challenge faced by most sleep studies, eegFloss can enhance the precision and rigor of their analysis as well as the accuracy and reliability of their outcomes.
Despite advances in deep learning for automatic sleep staging, clinical adoption remains limited due to challenges in fair model evaluation, generalization across diverse datasets, model bias, and variability in human annotations. We present SLEEPYLAND, an open-source sleep staging evaluation framework designed to address these barriers. It includes more than 220'000 hours in-domain (ID) sleep recordings, and more than 84'000 hours out-of-domain (OOD) sleep recordings, spanning a broad range of ages, sleep-wake disorders, and hardware setups. We release pre-trained models based on high-performing SoA architectures and evaluate them under standardized conditions across single- and multi-channel EEG/EOG configurations. We introduce SOMNUS, an ensemble combining models across architectures and channel setups via soft voting. SOMNUS achieves robust performance across twenty-four different datasets, with macro-F1 scores between 68.7% and 87.2%, outperforming individual models in 94.9% of cases. Notably, SOMNUS surpasses previous SoA methods, even including cases where compared models were trained ID while SOMNUS treated the same data as OOD. Using a subset of the BSWR (N=6'633), we quantify model biases linked to age, gender, AHI, and PLMI, showing that while ensemble improves robustness, no model architecture consistently minimizes bias in performance and clinical markers estimation. In evaluations on OOD multi-annotated datasets (DOD-H, DOD-O), SOMNUS exceeds the best human scorer, i.e., MF1 85.2% vs 80.8% on DOD-H, and 80.2% vs 75.9% on DOD-O, better reproducing the scorer consensus than any individual expert (k = 0.89/0.85 and ACS = 0.95/0.94 for healthy/OSA cohorts). Finally, we introduce ensemble disagreement metrics - entropy and inter-model divergence based - predicting regions of scorer disagreement with ROC AUCs up to 0.828, offering a data-driven proxy for human uncertainty.
Automation of sleep analysis, including both macrostructural (sleep stages) and microstructural (e.g., sleep spindles) elements, promises to enable large-scale sleep studies and to reduce variance due to inter-rater incongruencies. While individual steps, such as sleep staging and spindle detection, have been studied separately, the feasibility of automating multi-step sleep analysis remains unclear. Here, we evaluate whether a fully automated analysis using state-of-the-art machine learning models for sleep staging (RobustSleepNet) and subsequent spindle detection (SUMOv2) can replicate findings from an expert-based study of bipolar disorder. The automated analysis qualitatively reproduced key findings from the expert-based study, including significant differences in fast spindle densities between bipolar patients and healthy controls, accomplishing in minutes what previously took months to complete manually. While the results of the automated analysis differed quantitatively from the expert-based study, possibly due to biases between expert raters or between raters and the models, the models individually performed at or above inter-rater agreement for both sleep staging and spindle detection. Our results demonstrate that fully automated approaches have the potential to facilitate large-scale sleep research. We are providing public access to the tools used in our automated analysis by sharing our code and introducing SomnoBot, a privacy-preserving sleep analysis platform.
Large language models (LLMs) exhibit remarkable capabilities in visual inspection of medical time-series data, achieving proficiency comparable to human clinicians. However, their broad scope limits domain-specific precision, and proprietary weights hinder fine-tuning for specialized datasets. In contrast, small specialized models (SSMs) excel in targeted tasks but lack the contextual reasoning required for complex clinical decision-making. To address these challenges, we propose ConMIL (Conformalized Multiple Instance Learning), a decision-support SSM that integrates seamlessly with LLMs. By using Multiple Instance Learning (MIL) to identify clinically significant signal segments and conformal prediction for calibrated set-valued outputs, ConMIL enhances LLMs' interpretative capabilities for medical time-series analysis. Experimental results demonstrate that ConMIL significantly improves the performance of state-of-the-art LLMs, such as ChatGPT4.0 and Qwen2-VL-7B. Specifically, \ConMIL{}-supported Qwen2-VL-7B achieves 94.92% and 96.82% precision for confident samples in arrhythmia detection and sleep staging, compared to standalone LLM accuracy of 46.13% and 13.16%. These findings highlight the potential of ConMIL to bridge task-specific precision and broader contextual reasoning, enabling more reliable and interpretable AI-driven clinical decision support.
Sleep staging is a challenging task, typically manually performed by sleep technologists based on electroencephalogram and other biosignals of patients taken during overnight sleep studies. Recent work aims to leverage automated algorithms to perform sleep staging not based on electroencephalogram signals, but rather based on the airflow signals of subjects. Prior work uses ideas from topological data analysis (TDA), specifically Hermite function expansions of persistence curves (HEPC) to featurize airflow signals. However, finite order HEPC captures only partial information. In this work, we propose Fourier approximations of persistence curves (FAPC), and use this technique to perform sleep staging based on airflow signals. We analyze performance using an XGBoost model on 1155 pediatric sleep studies taken from the Nationwide Children's Hospital Sleep DataBank (NCHSDB), and find that FAPC methods provide complimentary information to HEPC methods alone, leading to a 4.9% increase in performance over baseline methods.
Sleep staging is critical to assess sleep quality and diagnose disorders. Despite advancements in artificial intelligence enabling automated sleep staging, significant challenges remain: (1) Simultaneously extracting prominent temporal and spatial sleep features from multi-channel raw signals, including characteristic sleep waveforms and salient spatial brain networks. (2) Capturing the spatial-temporal coupling patterns essential for accurate sleep staging. To address these challenges, we propose a novel framework named ST-USleepNet, comprising a spatial-temporal graph construction module (ST) and a U-shaped sleep network (USleepNet). The ST module converts raw signals into a spatial-temporal graph based on signal similarity, temporal, and spatial relationships to model spatial-temporal coupling patterns. The USleepNet employs a U-shaped structure for both the temporal and spatial streams, mirroring its original use in image segmentation to isolate significant targets. Applied to raw sleep signals and graph data from the ST module, USleepNet effectively segments these inputs, simultaneously extracting prominent temporal and spatial sleep features. Testing on three datasets demonstrates that ST-USleepNet outperforms existing baselines, and model visualizations confirm its efficacy in extracting prominent sleep features and temporal-spatial coupling patterns across various sleep stages. The code is available at https://github.com/Majy-Yuji/ST-USleepNet.
Traditional sleep staging categorizes sleep and wakefulness into five coarse-grained classes, overlooking subtle variations within each stage. It provides limited information about the duration of arousal and may hinder research on sleep fragmentation and relevant sleep disorders. To address this issue, we propose a deep learning method for automatic and scalable annotation of continuous sleep depth index (SDI) using existing discrete sleep staging labels. Our approach was validated using polysomnography from over 10,000 recordings across four large-scale cohorts. The results showcased a strong correlation between the decrease in sleep depth index and the increase in duration of arousal. Specific case studies indicated that the sleep depth index captured more nuanced sleep structures than conventional sleep staging. Gaussian mixture models based on the digital biomarkers extracted from the sleep depth index identified two subtypes of sleep, where participants in the disturbed sleep group had a higher prevalence of sleep apnea, insomnia, poor subjective sleep quality, hypertension, and cardiovascular disease. The disturbed subtype was associated with a 42% (hazard ratio 1.42, 95% CI 1.24-1.62) increased risk of mortality and a 29% (hazard ratio 1.29, 95% CI 1.00-1.67) increased risk of fatal cardiovascular disease. Our study underscores the utility of the proposed method for continuous sleep depth annotation, which could reveal more detailed information about the sleep structure and yield novel digital biomarkers for routine clinical use in sleep medicine.
Sleep quality directly impacts human health and quality of life, so accurate sleep staging is essential for assessing sleep quality. However, most traditional methods are inefficient and time-consuming due to segmenting different sleep cycles by manual labeling. In contrast, automated sleep staging technology not only directly assesses sleep quality but also helps sleep specialists analyze sleep status, significantly improving efficiency and reducing the cost of sleep monitoring, especially for continuous sleep monitoring. Most of the existing models, however, are deficient in computational efficiency, lightweight design, and model interpretability. In this paper, we propose a neural network architecture based on the prior knowledge of sleep experts. Specifically, 1) Propose an end-to-end model named DetectsleepNet that uses single-channel EEG signals without additional data processing, which has achieved an impressive 80.9% accuracy on the SHHS dataset and an outstanding 88.0% accuracy on the Physio2018 dataset. 2) Constructure an efficient lightweight sleep staging model named DetectsleepNet-tiny based on DetectsleepNet, which has just 6% of the parameter numbers of existing models, but its accuracy exceeds 99% of state-of-the-art models, 3) Introducing a specific inference header to assess the attention given to a specific EEG segment in each sleep frame, enhancing the transparency in the decisions of models. Our model comprises fewer parameters compared to existing ones and ulteriorly explores the interpretability of the model to facilitate its application in healthcare. The code is available at https://github.com/komdec/DetectSleepNet.git.
The progression of deep learning and the widespread adoption of sensors have facilitated automatic multi-view fusion (MVF) about the cardiovascular system (CVS) signals. However, prevalent MVF model architecture often amalgamates CVS signals from the same temporal step but different views into a unified representation, disregarding the asynchronous nature of cardiovascular events and the inherent heterogeneity across views, leading to catastrophic view confusion. Efficient training strategies specifically tailored for MVF models to attain comprehensive representations need simultaneous consideration. Crucially, real-world data frequently arrives with incomplete views, an aspect rarely noticed by researchers. Thus, the View-Centric Transformer (VCT) and Multitask Masked Autoencoder (M2AE) are specifically designed to emphasize the centrality of each view and harness unlabeled data to achieve superior fused representations. Additionally, we systematically define the missing-view problem for the first time and introduce prompt techniques to aid pretrained MVF models in flexibly adapting to various missing-view scenarios. Rigorous experiments involving atrial fibrillation detection, blood pressure estimation, and sleep staging-typical health monitoring tasks-demonstrate the remarkable advantage of our method in MVF compared to prevailing methodologies. Notably, the prompt technique requires finetuning less than 3% of the entire model's data, substantially fortifying the model's resilience to view missing while circumventing the need for complete retraining. The results demonstrate the effectiveness of our approaches, highlighting their potential for practical applications in cardiovascular health monitoring. Codes and models are released at URL.
Analyzing electroencephalographic (EEG) time series can be challenging, especially with deep neural networks, due to the large variability among human subjects and often small datasets. To address these challenges, various strategies, such as self-supervised learning, have been suggested, but they typically rely on extensive empirical datasets. Inspired by recent advances in computer vision, we propose a pretraining task termed "frequency pretraining" to pretrain a neural network for sleep staging by predicting the frequency content of randomly generated synthetic time series. Our experiments demonstrate that our method surpasses fully supervised learning in scenarios with limited data and few subjects, and matches its performance in regimes with many subjects. Furthermore, our results underline the relevance of frequency information for sleep stage scoring, while also demonstrating that deep neural networks utilize information beyond frequencies to enhance sleep staging performance, which is consistent with previous research. We anticipate that our approach will be advantageous across a broad spectrum of applications where EEG data is limited or derived from a small number of subjects, including the domain of brain-computer interfaces.
Automatic sleep staging is essential for sleep assessment and disorder diagnosis. Most existing methods depend on one specific dataset and are limited to be generalized to other unseen datasets, for which the training data and testing data are from the same dataset. In this paper, we introduce domain generalization into automatic sleep staging and propose the task of generalizable sleep staging which aims to improve the model generalization ability to unseen datasets. Inspired by existing domain generalization methods, we adopt the feature alignment idea and propose a framework called SleepDG to solve it. Considering both of local salient features and sequential features are important for sleep staging, we propose a Multi-level Feature Alignment combining epoch-level and sequence-level feature alignment to learn domain-invariant feature representations. Specifically, we design an Epoch-level Feature Alignment to align the feature distribution of each single sleep epoch among different domains, and a Sequence-level Feature Alignment to minimize the discrepancy of sequential features among different domains. SleepDG is validated on five public datasets, achieving the state-of-the-art performance.
Sleep staging has become a critical task in diagnosing and treating sleep disorders to prevent sleep related diseases. With growing large scale sleep databases, significant progress has been made toward automatic sleep staging. However, previous studies face critical problems in sleep studies; the heterogeneity of subjects' physiological signals, the inability to extract meaningful information from unlabeled data to improve predictive performances, the difficulty in modeling correlations between sleep stages, and the lack of an effective mechanism to quantify predictive uncertainty. In this study, we propose a neural network based sleep staging model, DREAM, to learn domain generalized representations from physiological signals and models sleep dynamics. DREAM learns sleep related and subject invariant representations from diverse subjects' sleep signals and models sleep dynamics by capturing interactions between sequential signal segments and between sleep stages. We conducted a comprehensive empirical study to demonstrate the superiority of DREAM, including sleep stage prediction experiments, a case study, the usage of unlabeled data, and uncertainty. Notably, the case study validates DREAM's ability to learn generalized decision function for new subjects, especially in case there are differences between testing and training subjects. Uncertainty quantification shows that DREAM provides prediction uncertainty, making the model reliable and helping sleep experts in real world applications.
Scoring sleep stages in polysomnography recordings is a time-consuming task plagued by significant inter-rater variability. Therefore, it stands to benefit from the application of machine learning algorithms. While many algorithms have been proposed for this purpose, certain critical architectural decisions have not received systematic exploration. In this study, we meticulously investigate these design choices within the broad category of encoder-predictor architectures. We identify robust architectures applicable to both time series and spectrogram input representations. These architectures incorporate structured state space models as integral components and achieve statistically significant performance improvements compared to state-of-the-art approaches on the extensive Sleep Heart Health Study dataset. We anticipate that the architectural insights gained from this study along with the refined methodology for architecture search demonstrated herein will not only prove valuable for future research in sleep staging but also hold relevance for other time series annotation tasks.
In recent years, Transformer-based auto-attention mechanisms have been successfully applied to the analysis of a variety of context-reliant data types, from texts to images and beyond, including data from non-Euclidean geometries. In this paper, we present such a mechanism, designed to classify sequences of Symmetric Positive Definite matrices while preserving their Riemannian geometry throughout the analysis. We apply our method to automatic sleep staging on timeseries of EEG-derived covariance matrices from a standard dataset, obtaining high levels of stage-wise performance.
In recent years, multitudes of researches have applied deep learning to automatic sleep stage classification. Whereas actually, these works have paid less attention to the issue of cross-subject in sleep staging. At the same time, emerging neuroscience theories on inter-subject correlations can provide new insights for cross-subject analysis. This paper presents the MViTime model that have been used in sleep staging study. And we implement the inter-subject correlation theory through contrastive learning, providing a feasible solution to address the cross-subject problem in sleep stage classification. Finally, experimental results and conclusions are presented, demonstrating that the developed method has achieved state-of-the-art performance on sleep staging. The results of the ablation experiment also demonstrate the effectiveness of the cross-subject approach based on contrastive learning.
Human sleep is cyclical with a period of approximately 90 minutes, implying long temporal dependency in the sleep data. Yet, exploring this long-term dependency when developing sleep staging models has remained untouched. In this work, we show that while encoding the logic of a whole sleep cycle is crucial to improve sleep staging performance, the sequential modelling approach in existing state-of-the-art deep learning models are inefficient for that purpose. We thus introduce a method for efficient long sequence modelling and propose a new deep learning model, L-SeqSleepNet, which takes into account whole-cycle sleep information for sleep staging. Evaluating L-SeqSleepNet on four distinct databases of various sizes, we demonstrate state-of-the-art performance obtained by the model over three different EEG setups, including scalp EEG in conventional Polysomnography (PSG), in-ear EEG, and around-the-ear EEG (cEEGrid), even with a single EEG channel input. Our analyses also show that L-SeqSleepNet is able to alleviate the predominance of N2 sleep (the major class in terms of classification) to bring down errors in other sleep stages. Moreover the network becomes much more robust, meaning that for all subjects where the baseline method had exceptionally poor performance, their performance are improved significantly. Finally, the computation time only grows at a sub-linear rate when the sequence length increases.
An electroencephalogram (EEG) signal is currently accepted as a standard for automatic sleep staging. Lately, Near-human accuracy in automated sleep staging has been achievable by Deep Learning (DL) based approaches, enabling multi-fold progress in this area. However, An extensive and expensive clinical setup is required for EEG based sleep staging. Additionally, the EEG setup being obtrusive in nature and requiring an expert for setup adds to the inconvenience of the subject under study, making it adverse in the point of care setting. An unobtrusive and more suitable alternative to EEG is Electrocardiogram (ECG). Unsurprisingly, compared to EEG in sleep staging, its performance remains sub-par. In order to take advantage of both the modalities, transferring knowledge from EEG to ECG is a reasonable approach, ultimately boosting the performance of ECG based sleep staging. Knowledge Distillation (KD) is a promising notion in DL that shares knowledge from a superior performing but usually more complex teacher model to an inferior but compact student model. Building upon this concept, a cross-modality KD framework assisting features learned through models trained on EEG to improve ECG-based sleep staging performance is proposed. Additionally, to better understand the distillation approach, extensive experimentation on the independent modules of the proposed model was conducted. Montreal Archive of Sleep Studies (MASS) dataset consisting of 200 subjects was utilized for this study. The results from the proposed model for weighted-F1-score in 3-class and 4-class sleep staging showed a 13.40 \% and 14.30 \% improvement, respectively. This study demonstrates the feasibility of KD for single-channel ECG based sleep staging's performance enhancement in 3-class (W-R-N) and 4-class (W-R-L-D) classification.
Multivariate biosignals are prevalent in many medical domains, such as electroencephalography, polysomnography, and electrocardiography. Modeling spatiotemporal dependencies in multivariate biosignals is challenging due to (1) long-range temporal dependencies and (2) complex spatial correlations between the electrodes. To address these challenges, we propose representing multivariate biosignals as time-dependent graphs and introduce GraphS4mer, a general graph neural network (GNN) architecture that improves performance on biosignal classification tasks by modeling spatiotemporal dependencies in biosignals. Specifically, (1) we leverage the Structured State Space architecture, a state-of-the-art deep sequence model, to capture long-range temporal dependencies in biosignals and (2) we propose a graph structure learning layer in GraphS4mer to learn dynamically evolving graph structures in the data. We evaluate our proposed model on three distinct biosignal classification tasks and show that GraphS4mer consistently improves over existing models, including (1) seizure detection from electroencephalographic signals, outperforming a previous GNN with self-supervised pre-training by 3.1 points in AUROC; (2) sleep staging from polysomnographic signals, a 4.1 points improvement in macro-F1 score compared to existing sleep staging models; and (3) 12-lead electrocardiogram classification, outperforming previous state-of-the-art models by 2.7 points in macro-F1 score.
Sleep plays a crucial role in the well-being of human lives. Traditional sleep studies using Polysomnography are associated with discomfort and often lower sleep quality caused by the acquisition setup. Previous works have focused on developing less obtrusive methods to conduct high-quality sleep studies, and ear-EEG is among popular alternatives. However, the performance of sleep staging based on ear-EEG is still inferior to scalp-EEG based sleep staging. In order to address the performance gap between scalp-EEG and ear-EEG based sleep staging, we propose a cross-modal knowledge distillation strategy, which is a domain adaptation approach. Our experiments and analysis validate the effectiveness of the proposed approach with existing architectures, where it enhances the accuracy of the ear-EEG based sleep staging by 3.46% and Cohen's kappa coefficient by a margin of 0.038.
Accurate sleep stage classification is significant for sleep health assessment. In recent years, several machine-learning based sleep staging algorithms have been developed , and in particular, deep-learning based algorithms have achieved performance on par with human annotation. Despite improved performance, a limitation of most deep-learning based algorithms is their black-box behavior, which have limited their use in clinical settings. Here, we propose a cross-modal transformer, which is a transformer-based method for sleep stage classification. The proposed cross-modal transformer consists of a novel cross-modal transformer encoder architecture along with a multi-scale one-dimensional convolutional neural network for automatic representation learning. Our method outperforms the state-of-the-art methods and eliminates the black-box behavior of deep-learning models by utilizing the interpretability aspect of the attention modules. Furthermore, our method provides considerable reductions in the number of parameters and training time compared to the state-of-the-art methods. Our code is available at https://github.com/Jathurshan0330/Cross-Modal-Transformer. A demo of our work can be found at https://bit.ly/Cross_modal_transformer_demo.