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
The sleep diary is a widely used clinical tool for understanding and treating sleep disorders in Behavioral Sleep Medicine (BSM); however, low patient compliance and limited capture of contextual information constrain its effectiveness and leave specialists with an incomplete picture of patients' sleep-related behaviors. In this work, we explore conversational agents (CAs) as an alternative to traditional diary methods by designing a voice-based sleep diary and a specialist-facing analytics tool, and using them as design probes to understand how CAs might support BSM more broadly. Our multi-stage study with specialists comprised: (1) interviews to identify shortcomings of current text-based diaries, (2) iterative co-design of the conversational diary and analytics tool, and (3) focus groups to examine broader opportunities for CAs in BSM. This work offers empirical insights into how specialists envision CAs in clinical care and outlines design implications for integrating them into existing self-report practices and behavioral interventions.
The American Academy of Sleep Medicine (AASM) Manual is the clinical standard for polysomnography (PSG) scoring, but its narrative rules can admit multiple reasonable interpretations, contributing to inter-scorer variability and implementation differences across studies and software systems. We present a formal framework for translating sleep-scoring rules into Rational Ensemble Logic (QEL), a dense-time (i.e., a continuous, rational-valued timeline rather than discrete steps) formalism that combines first-order quantification with metric temporal operators. Using an extraction-and-compilation procedure, we identified 18 unique atomic propositions and derived 12 final specifications corresponding to clinically scoreable AASM events. Back-translation of QEL specifications into clinician-facing language retained high semantic fidelity to the original scoring narratives (embedding cosine similarity: 79.3, 95% CI: 79.0--79.7) despite low lexical overlap (ROUGE-L: 18.3, 95 CI: 17.6--18.9). Formalization also clarifies latent ambiguities, including implicit physiological latencies and overlapping exclusions. This framework yields executable, rigorous rule specifications for computational
Polysomnography (PSG), the gold standard test for sleep analysis, generates vast amounts of multimodal clinical data, presenting an opportunity to leverage self-supervised representation learning (SSRL) for pre-training foundation models to enhance sleep analysis. However, progress in sleep foundation models is hindered by two key limitations: (1) the lack of a shared dataset and benchmark with diverse tasks for training and evaluation, and (2) the absence of a systematic evaluation of SSRL approaches across sleep-related tasks. To address these gaps, we introduce Stanford Sleep Bench, a large-scale PSG dataset comprising 17,467 recordings totaling over 163,000 hours from a major sleep clinic, including 13 clinical disease prediction tasks alongside canonical sleep-related tasks such as sleep staging, apnea diagnosis, and age estimation. We systematically evaluate SSRL pre-training methods on Stanford Sleep Bench, assessing downstream performance across four tasks: sleep staging, apnea diagnosis, age estimation, and disease and mortality prediction. Our results show that multiple pretraining methods achieve comparable performance for sleep staging, apnea diagnosis, and age estimati
Sleep foundation models have recently demonstrated strong performance on in-domain polysomnography tasks, including sleep staging, apnea detection, and disease risk prediction. In this work, we investigate whether sleep biosignals can serve as an effective pretraining distribution for learning representations that transfer beyond sleep to adjacent domains. Following sleep foundation models, we perform sleep-only multimodal contrastive pretraining (with a leave-one-out objective) and evaluate transfer to non-sleep EEG and ECG, two well-benchmarked biosignal modalities with heterogeneous datasets and clinically meaningful downstream tasks. Across eight downstream tasks spanning multiple EEG and ECG datasets, sleep pretraining consistently improves performance relative to training from scratch. Moreover, on several tasks, we achieve performance competitive with or surpassing prior specialized state-of-the-art and foundation models.
Obstructive sleep apnea (OSA) is a sleep disorder that affects nearly one billion people globally and significantly elevates cardiovascular risk. Traditional diagnosis through polysomnography is resource-intensive and limits widespread access, creating a critical need for accurate and efficient alternatives. In this paper, we introduce KindSleep, a deep learning framework that integrates clinical knowledge with single-channel patient-specific oximetry signals and clinical data for precise OSA diagnosis. KindSleep first learns to identify clinically interpretable concepts, such as desaturation indices and respiratory disturbance events, directly from raw oximetry signals. It then fuses these AI-derived concepts with multimodal clinical data to estimate the Apnea-Hypopnea Index (AHI). We evaluate KindSleep on three large, independent datasets from the National Sleep Research Resource (SHHS, CFS, MrOS; total n = 9,815). KindSleep demonstrates excellent performance in estimating AHI scores (R2 = 0.917, ICC = 0.957) and consistently outperforms existing approaches in classifying OSA severity, achieving weighted F1-scores from 0.827 to 0.941 across diverse populations. By grounding its p
Efficiently identifying sleep stages is crucial for unraveling the intricacies of sleep in both preclinical and clinical research. The labor-intensive nature of manual sleep scoring, demanding substantial expertise, has prompted a surge of interest in automated alternatives. Sleep studies in mice play a significant role in understanding sleep patterns and disorders and underscore the need for robust scoring methodologies. In response, this study introduces LG-Sleep, a novel subject-independent deep neural network architecture designed for mice sleep scoring through electroencephalogram (EEG) signals. LG-Sleep extracts local and global temporal transitions within EEG signals to categorize sleep data into three stages: wake, rapid eye movement (REM) sleep, and non-rapid eye movement (NREM) sleep. The model leverages local and global temporal information by employing time-distributed convolutional neural networks to discern local temporal transitions in EEG data. Subsequently, features derived from the convolutional filters traverse long short-term memory blocks, capturing global transitions over extended periods. Crucially, the model is optimized in an autoencoder-decoder fashion, fa
Automatic sleep staging is a critical role in sleep disorder diagnosis, sleep quality assessment, and long-term health monitoring; however, existing approaches suffer poor performance on ambiguous and transition-related sleep stages, caused by inadequate modeling of fine-grained intra-epoch structures and complex cross-region spectral dependencies. Traditional epoch-level encoders commonly fail to extract subtle temporal microstructures and intra-epoch cross-region interactions, resulting in unsatisfactory recognition accuracy for hard categories such as the N1 stage. To tackle these drawbacks, we propose SwinSleepNet, a hierarchical context-aware dual-stream framework that separately optimizes intra-epoch representation learning and inter-epoch contextual modeling. Concretely, we characterize each sleep epoch from two complementary perspectives: raw time-domain EEG signal and its time-frequency transformation. The time-domain branch adopts convolutional encoders to capture fine waveform temporal details, and the time-frequency branch uses Swin Transformer to extract local spectro-temporal features, hierarchical multi-scale information and long-range spatial dependencies. The multi
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
SleepioTM is a digital mobile phone and web platform that uses techniques from cognitive behavioural therapy (CBT) to improve sleep in people with sleep difficulty. As part of this process, Sleepio captures data about the sleep behaviour of the users that have consented to such data being processed. For neural networks, the scale of the data is an opportunity to train meaningful models translatable to actual clinical practice. In collaboration with Big Health, the therapeutics company that created and utilizes Sleepio, we have analysed data from a random sample of 401,174 sleep diaries and built a neural network to model sleep behaviour and sleep quality of each individual in a personalised manner. We demonstrate that this neural network is more accurate than standard statistical methods in predicting the sleep quality of an individual based on his/her behaviour from the last 10 days. We compare model performance in a wide range of hyperparameter settings representing various scenarios. We further show that the neural network can be used to produce personalised recommendations of what sleep habits users should follow to maximise sleep quality, and show that these recommendations ar
Sleep has a profound influence on the physiology of body systems and biological processes. Molecular studies have shown circadian-regulated shifts in protein expression patterns across human tissues, further emphasizing the unique functional, behavioral and pharmacokinetic landscape of sleep. Thus, many pathological processes are also expected to exhibit sleep-specific manifestations. Nevertheless, sleep is seldom utilized for the study, detection and treatment of non-sleep-specific pathologies. Modern advances in biosensor technologies have enabled remote, non-invasive recording of a growing number of physiologic parameters and biomarkers. Sleep is an ideal time frame for the collection of long and clean physiological time series data which can then be analyzed using data-driven algorithms such as deep learning. In this perspective paper, we aim to highlight the potential of sleep as an auspicious time for diagnosis, management and therapy of nonsleep-specific pathologies. We introduce key clinical studies in selected medical fields, which leveraged novel technologies and the advantageous period of sleep to diagnose, monitor and treat pathologies. We then discuss possible opportun
Although deep learning algorithms have proven their efficiency in automatic sleep staging, the widespread skepticism about their "black-box" nature has limited its clinical acceptance. In this study, we propose WaveSleepNet, an interpretable neural network for sleep staging that reasons in a similar way to sleep experts. In this network, we utilize the latent space representations generated during training to identify characteristic wave prototypes corresponding to different sleep stages. The feature representation of an input signal is segmented into patches within the latent space, each of which is compared against the learned wave prototypes. The proximity between these patches and the wave prototypes is quantified through scores, indicating the prototypes' presence and relative proportion within the signal. The scores are served as the decision-making criteria for final sleep staging. During training, an ensemble of loss functions is employed for the prototypes' diversity and robustness. Furthermore, the learned wave prototypes are visualized by analysing occlusion sensitivity. The efficacy of WaveSleepNet is validated across three public datasets, achieving sleep staging perfo
Study Objectives: Fetal sleep is a vital yet underexplored aspect of prenatal neurodevelopment. Its cyclic organization reflects the maturation of central neural circuits, and disturbances in these patterns may offer some of the earliest detectable signs of neurological compromise. This is the first review to integrate more than seven decades of research into a unified, cross-species synthesis of fetal sleep. We examine: (i) Physiology and Ontogeny-comparing human fetuses with animal models; and (ii) Methodological Evolution-transitioning from invasive neurophysiology to non-invasive monitoring and deep learning frameworks. Methods: A structured narrative synthesis was guided by a systematic literature search across four databases (PubMed, Scopus, IEEE Xplore, and Google Scholar). From 2,925 identified records, 171 studies involving fetal sleep-related physiology, sleep-state classification, or signal-based monitoring were included in this review. Results: Across the 171 studies, fetal sleep states become clearly observable as the brain matures. In fetal sheep and baboons, organized cycling between active and quiet sleep emerges at approximately 80%-90% gestation. In humans, this d
State-of-the-art automatic sleep staging methods have already demonstrated comparable reliability and superior time efficiency to manual sleep staging. However, fully automatic black-box solutions are difficult to adapt into clinical workflow and the interaction between explainable automatic methods and the work of sleep technologists remains underexplored and inadequately conceptualized. Thus, we propose a human-in-the-loop concept for sleep analysis, presenting an automatic sleep staging model (aSAGA), that performs effectively with both clinical polysomnographic recordings and home sleep studies. To validate the model, extensive testing was conducted, employing a preclinical validation approach with three retrospective datasets; open-access, clinical, and research-driven. Furthermore, we validate the utilization of uncertainty mapping to identify ambiguous regions, conceptualized as gray areas, in automatic sleep analysis that warrants manual re-evaluation. The results demonstrate that the automatic sleep analysis achieved a comparable level of agreement with manual analysis across different sleep recording types. Moreover, validation of the gray area concept revealed its potent
We introduce new quantitative approaches to study sleep-stage transitions with the goal of addressing the two following questions: (i) Can the new approaches provide more information on the structure of sleep-stage transitions? (ii) How does sleep fragmentation in patients with sleep apnea affect the structure of sleep-stage transitions? Our new results show that the distribution of sleep and wake duration have different functional forms, indicating fundamental differences in the dynamics between sleep and wake control. The difference remains even in the fragmented sleep of sleep apnea. The fragmentation of sleep in sleep apnea results in a shorter wake duration and interrupts the structure of sleep-stage transitions of sleep apnea subjects, causing the loss of certain particular transition paths.
The gut microbiota has emerged as a fundamental regulator of sleep physiology, influencing neural, endocrine, and immune pathways through the gut-microbiota-brain axis (GMBA). This bidirectional communication system modulates neurotransmitter production, circadian rhythms, and metabolic homeostasis, while disruptions in microbial composition have been linked to sleep disorders, neuroinflammation, and systemic immune dysfunction. Recent findings suggest that gut dysbiosis contributes to sleep disturbances by altering serotonin, GABA, and short-chain fatty acid (SCFA) metabolism, with implications for neurodegenerative diseases, metabolic syndromes, and mood disorders. Additionally, the gut microbiota interacts with the endocrine and immune systems, shaping inflammatory responses and stress adaptation mechanisms. This review explores the intricate connections between sleep and the gut microbiota, integrating emerging research on microbiota-targeted therapies, such as probiotics, fecal microbiota transplantation (FMT), and chrononutrition, as potential interventions to restore sleep homeostasis and improve health outcomes
Model Medicine is the science of understanding, diagnosing, treating, and preventing disorders in AI models, grounded in the principle that AI models -- like biological organisms -- have internal structures, dynamic processes, heritable traits, observable symptoms, classifiable conditions, and treatable states. This paper introduces Model Medicine as a research program, bridging the gap between current AI interpretability research (anatomical observation) and the systematic clinical practice that complex AI systems increasingly require. We present five contributions: (1) a discipline taxonomy organizing 15 subdisciplines across four divisions -- Basic Model Sciences, Clinical Model Sciences, Model Public Health, and Model Architectural Medicine; (2) the Four Shell Model (v3.3), a behavioral genetics framework empirically grounded in 720 agents and 24,923 decisions from the Agora-12 program, explaining how model behavior emerges from Core--Shell interaction; (3) Neural MRI (Model Resonance Imaging), a working open-source diagnostic tool mapping five medical neuroimaging modalities to AI interpretability techniques, validated through four clinical cases demonstrating imaging, compari
Time irreversibility (TIR) refers to the manifestation of nonequilibrium brain activity influenced by various physiological conditions; however, the influence of sleep on electroencephalogram (EEG) TIR has not been sufficiently investigated. In this paper, a comprehensive study on permutation TIR (pTIR) of EEG data under different sleep stages is conducted. Two basic ordinal patterns (i.e., the original and amplitude permutations) are distinguished to simplify sleep EEGs, and then the influences of equal values and forbidden permutation on pTIR are elucidated. To detect pTIR of brain electric signals, 5 groups of EEGs in the awake, stages I, II, III, and rapid eye movement (REM) stages are collected from the public Polysomnographic Database in PhysioNet. Test results suggested that the pTIR of sleep EEGs significantly decreases as the sleep stage increases (p<0.001), with the awake and REM EEGs, demonstrating greater differences than others. Comparative analysis and numerical simulations support the importance of equal values. Distribution of equal states, a simple quantification of amplitude fluctuations, significantly increases with the sleep stage (p<0.001). If these equal
Alzheimer's Disease (AD) is the most common form of dementia in the United States. Sleep is one of the lifestyle-related factors that has been shown critical for optimal cognitive function in old age. However, there is a lack of research studying the association between sleep and AD incidence. A major bottleneck for conducting such research is that the traditional way to acquire sleep information is time-consuming, inefficient, non-scalable, and limited to patients' subjective experience. A gold standard dataset is created from manual annotation of 570 randomly sampled clinical note documents from the adSLEEP, a corpus of 192,000 de-identified clinical notes of 7,266 AD patients retrieved from the University of Pittsburgh Medical Center (UPMC). We developed a rule-based Natural Language Processing (NLP) algorithm, machine learning models, and Large Language Model(LLM)-based NLP algorithms to automate the extraction of sleep-related concepts, including snoring, napping, sleep problem, bad sleep quality, daytime sleepiness, night wakings, and sleep duration, from the gold standard dataset. Rule-based NLP algorithm achieved the best performance of F1 across all sleep-related concepts.
Despite being crucial to health and quality of life, sleep -- especially pediatric sleep -- is not yet well understood. This is exacerbated by lack of access to sufficient pediatric sleep data with clinical annotation. In order to accelerate research on pediatric sleep and its connection to health, we create the Nationwide Children's Hospital (NCH) Sleep DataBank and publish it at Physionet and the National Sleep Research Resource (NSRR), which is a large sleep data common with physiological data, clinical data, and tools for analyses. The NCH Sleep DataBank consists of 3,984 polysomnography studies and over 5.6 million clinical observations on 3,673 unique patients between 2017 and 2019 at NCH. The novelties of this dataset include: 1) large-scale sleep dataset suitable for discovering new insights via data mining, 2) explicit focus on pediatric patients, 3) gathered in a real-world clinical setting, and 4) the accompanying rich set of clinical data. The NCH Sleep DataBank is a valuable resource for advancing automatic sleep scoring and real-time sleep disorder prediction, among many other potential scientific discoveries.