SemPSG: A Semantic Channel-Aware Foundation Model for Polysomnography Analysis

Automatic sleep staging from polysomnography (PSG) is a well-studied task, but PSG itself is expensive, clinic-based, and burdensome to manually score, which limits its use for long-term or at-home monitoring. Most existing sleep-staging foundation models are evaluated using the full PSG montage. We instead ask how much of that montage is actually necessary. We evaluate six sleep staging models on the Multi-Ethnic Study of Atherosclerosis (MESA) PSG dataset across three signal conditions: electroencephalography (EEG), electrocardiography (ECG), and their combination (EEG+ECG). This is motivated by edge-cloud deployment, where EEG requires a clinic-grade scalp electrode, whereas ECG is already captured by consumer wearables. We test state-of-the-art foundation models such as SleepFM with an encoder trained from scratch on MESA, alongside BIOT, MOMENT, LaBraM, a base-scale Vision Transformer (ViT-B) reimplementation of SensorLM trained from scratch, and YASA, spanning EEG-pretrained, general-time-series, from-scratch, and classical non-learned approaches. No model architecture is modified from its original form; SensorLM's encoder is reimplemented only in PyTorch. For EEG-only staging, BIOT achieves the best result with a macroF1 of 0.7237, followed by LaBraM (0.6835) and SleepFM from scratch (0.6582). Across the five models capable of ECG-only staging, switching from EEG to ECG costs between 0.2798 (MOMENT) and 0.4151 (BIOT) macroF1, averaging 0.3531, while cutting the raw channel data rate to a third. Adding ECG to EEG provides no gain for most models. These results show that EEG carries most of the sleep-staging signal, quantify the consistent accuracy cost of the wearable-compatible alternative, and demonstrate that sleep-relevant pretraining transfers well to MESA.

Polysomnography (PSG) provides the gold standard for sleep assessment but suffers from substantial heterogeneity across recording devices and cohorts. There have been growing efforts to build general-purpose foundation models (FMs) for sleep physiology, but lack an in-depth understanding of the pre-training process and scaling patterns that lead to more generalizable sleep FMs. To fill this gap, we curate a massive corpus of 166,500 hours of sleep recordings from nine public sources and establish SleepBench, a comprehensive, fully open-source benchmark. Leveraging SleepBench, we systematically evaluate four families of self-supervised pre-training objectives and uncover three critical findings: (1) existing FMs fail to generalize to missing channels at inference; (2) channel-invariant feature learning is essential for pre-training; and (3) scaling sample size, model capacity, and multi-source data mixture consistently improves downstream performance.With an enhanced pre-training and scaling recipe, we introduce OSF, a family of sleep FMs that achieves state-of-the-art performance across nine datasets on diverse sleep and disease prediction tasks. Further analysis of OSF also reveals intriguing properties in sample efficiency, hierarchical aggregation, and cross-dataset scaling.

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.