Sleep apnea diagnosis via polysomnography remains resource intensive and relies on time consuming manual data analysis and scoring. Recent work has demonstrated that central nervous system effects of sleep apnea events can be detected through electroencephalogram (EEG) signals. However, most work uses a single feature type on various datasets combined with different classification algorithms. In this work, we present a comprehensive comparison of deep learning architectures and feature representations for automated sleep apnea detection from multichannel EEG on a single dataset of pediatric subjects. We evaluate Vision Transformers and Graph Attention Networks across distinct signal representations: raw temporal signals, short-time Fourier transform spectrograms, coherence based graphs, and two topological data analysis (TDA) derived features. Using age and sex matching of our train and test sets, we train on 2410 pediatric subjects and test on 575 pediatric subjects. We achieve a best test AUC of 0.750 using a vision transformer based model trained on TDA features. Stratified analysis across patient demographics (age, sex, AHI severity) and sleep stages (N1, N2, N3, REM) reveals significant performance variation. Our results demonstrate the feasibility of EEG based automated OSA screening while highlighting essential challenges for clinical deployment.
Sleep physiology arises from the coordinated dynamics of the central nervous system (CNS) and autonomic nervous system (ANS), as reflected by multimodal polysomnography signals including EEG, EOG, EMG, ECG, and respiration. However, existing sleep foundation models often fuse heterogeneous biosignals in a topology-agnostic manner, overlooking their physiological organization. We introduce Omni-Sleep, a sleep foundation model that uses the CNS/ANS partition as a physiological prior for topology-constrained representation learning. Omni-Sleep learns structured representations through three objectives: intra-system consistency, which captures shared subsystem-level factors within neural and cardio-respiratory signals; inter-system synchronization, which aligns subsystem trajectories to model brain--body dynamics; and latent-space masked temporal modeling, which captures long-horizon sleep dynamics. Pre-trained on over 100,000 hours of multi-center multimodal PSG data, Omni-Sleep is evaluated on sleep staging and multi-disease classification. Across datasets and modality-ablation settings, Omni-Sleep outperforms strong foundation-model baselines, showing improved label efficiency, cross-dataset generalization, and robustness to missing modalities. These results highlight the value of physiological hierarchy for generalizable sleep representation learning. Code is available at https://github.com/AutoBrain-sleep/OmniSleep.
Saba A. Farahani, Elahe Khatibi, Manoj Vishwanath +2cs.LG eess.SP stat.AP
Objective sleep assessment relies on polysomnography (PSG), yet clinical impact is often better reflected in patient-reported outcomes (PROs) such as sleepiness and fatigue. Existing summary indices, including the Apnea-Hypopnea Index (AHI), provide limited insight into the multidomain physiology underlying functional recovery. We propose an interpretable, causal-discovery-guided framework for deriving a hierarchical Sleep Recovery Score (SRS) from multimodal PSG. Using two large population cohorts (MESA: \(n=1{,}540\); MrOS: \(n=825\)), we apply directed acyclic graph (DAG) learning to identify candidate physiological drivers spanning respiratory burden, hypoxic burden, sleep fragmentation, sleep architecture, and autonomic regulation. Although derived from clinical PSG, these domains map naturally to sensing streams increasingly available in connected health technologies, including wearable ECG, oximetry, and sleep-stage estimation devices. To preserve mechanistic plausibility, we introduce a two-stage screening process that combines physiology-based constraints with constrained LLM-assisted auditing to identify and remove structural confounders and construct-overlapping variables. Across cohorts, these five domains emerge as recurrent physiological domains associated with recovery, and the resulting SRS shows up to \(3.4\times\) stronger alignment with perceived recovery than AHI. By linking multimodal sleep physiology to patient-centered outcomes through an interpretable, bias-aware, and domain-structured framework, this work provides a practical foundation for recovery modeling across both clinical sleep studies and emerging smart and connected health settings.
Foundation models offer a promising route to compress multi-modal physiological signals into compact representations of human health, with broad applications across sleep medicine, cardiology, neurology and other healthcare domains. Existing models have typically been trained with masked-reconstruction or contrastive objectives. However, masked reconstruction may be poorly suited to the stochastic nature of these signals, while contrastive approaches rely on positive-pair definitions despite the semantic invariances of physiological signals being poorly understood. In this work, we show that next-token prediction is a simple and scalable alternative. We develop Hypnos, a multi-modal sleep foundation model trained using eight different sensing modalities (e.g. EEG, ECG, respiratory signals) drawn from over 20,000 overnight polysomnography recordings. We tokenize each modality into streams of discrete tokens using residual vector quantization, then train a large auto-regressive RQ-Transformer to jointly predict the next token across all modalities in parallel. After training, Hypnos can be applied to continuous streams of sensor data from any subset of supported modalities, generating embeddings for downstream tasks. Across a range of benchmarks, Hypnos significantly outperforms existing foundation models. In sleep stage classification, we match the performance of strong supervised baselines on held-out test sets whilst using \(100\times\) less labelled data. Hypnos even generalises to daytime physiology, surpassing a dedicated ECG foundation model at detecting atrial fibrillation. Our results demonstrate that next-token prediction is a strong self-supervised objective for representation learning from multi-modal physiological signals.
Automated sleep stage classification typically employs a single population-agnostic model, disregarding established demographic variations in sleep architecture. Sleep patterns, however, differ substantially across gender, age, and obstructive sleep apnea (OSA) severity, indicating that a onesize-fits all approach may be suboptimal for diverse clinical populations. In this paper, we propose a two stage training strategy based on demographic stratification and transfer learning framework. We first pretrains a convolutional recurrent model on the full population and then fine tunes it independently for demographic subgroups defined by gender, age, and Apnea-Hypopnea Index (AHI) severity according to the AASM clinical standard. Using the DREAMT dataset comprising 100 clinical subjects and 7 PSG channels, we evaluate 37 fine-tuned configurations across single-axis and two-way demographic combinations. Results demonstrate that 35 of the 37 fine-tuned models outperform the baseline, with Cohen's kappa improvements ranging from 0.9 to 12.9%. These findings indicate that stratified fine tuning tailored to specific patient demographics yields substantially more accurate sleep staging than a single generalized model, offering a practical and clinically grounded paradigm for personalized sleep assessment.