Massive online data annotation, crowdsourcing to generate high quality sleep spindle annotations from EEG data

Unveil sleep spindles with concentration of frequency and time (ConceFT)

Objective.Sleep spindles contain crucial brain dynamics information. We introduce the novel non-linear time-frequency (TF) analysis tool 'Concentration of Frequency and Time' (ConceFT) to create an interpretable automated algorithm for sleep spindle annotation in EEG data and to measure spindle instantaneous frequencies (IFs).Approach.ConceFT effectively reduces stochastic EEG influence, enhancing spindle visibility in the TF representation. Our automated spindle detection algorithm, ConceFT-Spindle (ConceFT-S), is compared to A7 (non-deep learning) and SUMO (deep learning) using Dream and Montreal Archive of Sleep Studies (MASS) benchmark databases. We also quantify spindle IF dynamics.Main results.ConceFT-S achieves F1 scores of 0.765 in Dream and 0.791 in MASS, which surpass A7 and SUMO. We reveal that spindle IF is generally nonlinear.Significance.ConceFT offers an accurate, interpretable EEG-based sleep spindle detection algorithm and enables spindle IF quantification.

A personalized semi-automatic sleep spindle detection (PSASD) framework

BACKGROUND

Sleep spindles are distinct electroencephalogram (EEG) patterns of brain activity that have been posited to play a critical role in development, learning, and neurological disorders. Manual scoring for sleep spindles is labor-intensive and tedious but could supplement automated algorithms to resolve challenges posed with either approaches alone.

NEW METHODS

A Personalized Semi-Automatic Sleep Spindle Detection (PSASD) framework was developed to combine the strength of automated detection algorithms and visual expertise of human scorers. The underlying model in the PSASD framework assumes a generative model for EEG sleep spindles as oscillatory components, optimized to EEG amplitude, with remaining signals distributed into transient and low-frequency components.

RESULTS

A single graphical user interface (GUI) allows both manual scoring of sleep spindles (model training data) and verification of automatically detected spindles. A grid search approach allows optimization of parameters to balance tradeoffs between precision and recall measures.

COMPARISON WITH EXISTING METHODS

PSASD outperformed DETOKS in F1-score by 19% and 4% on the DREAMS and P-DROWS-E datasets, respectively. It also outperformed YASA in F1-score by 25% in the P-DROWS-E dataset. Further benchmarking analysis showed that PSASD outperformed four additional widely used sleep spindle detectors in F1-score in the P-DROWS-E dataset. Titration analysis revealed that four 30-second epochs are sufficient to fine-tune the model parameters of PSASD. Associations of frequency, duration, and amplitude of detected sleep spindles matched those previously reported with automated approaches.

CONCLUSIONS

Overall, PSASD improves detection of sleep spindles in EEG data acquired from both younger healthy and older adult patient populations.

Two-Stage Atomic Decomposition of Multichannel EEG and the Previously Undetectable Sleep Spindles

We propose a two-step procedure for atomic decomposition of multichannel EEGs, based upon multivariate matching pursuit and dipolar inverse solution, from which atoms representing relevant EEG structures are selected according to prior knowledge. We detect sleep spindles in 147 polysomnographic recordings from the Montreal Archive of Sleep Studies. Detection is compared with human scorers and two state-of-the-art algorithms, which find only about a third of the structures conforming to the definition of sleep spindles and detected by the proposed method. We provide arguments supporting the thesis that the previously undetectable sleep spindles share the same properties as those marked by human experts and previously applied methods, and were previously omitted only because of unfavorable local signal-to-noise ratios, obscuring their visibility to both human experts and algorithms replicating their markings. All detected EEG structures are automatically parametrized by their time and frequency centers, width duration, phase, and spatial location of an equivalent dipolar source within the brain. It allowed us, for the first time, to estimate the spatial gradient of sleep spindles frequencies, which not only confirmed quantitatively the well-known prevalence of higher frequencies in posterior regions, but also revealed a significant gradient in the sagittal plane. The software used in this study is freely available.

A robust deep learning detector for sleep spindles and K-complexes: towards population norms

Sleep spindles (SSs) and K-complexes (KCs) are brain patterns involved in cognitive functions that appear during sleep. Large-scale sleep studies would benefit from precise and robust automatic sleep event detectors, capable of adapting the variability in both electroencephalography (EEG) signals and expert annotation rules. We introduce the Sleep EEG Event Detector (SEED), a deep learning system that outperforms existing approaches in SS and KC detection, reaching an F1-score of 80.5% and 83.7%, respectively, on the MASS2 dataset. SEED transfers well and requires minimal fine-tuning for new datasets and annotation styles. Remarkably, SEED substantially reduces the required amount of annotated data by using a novel pretraining approach that leverages the rule-based detector A7. An analysis of 11,224 subjects revealed that SEED's detections provide better estimates of SS population statistics than existing approaches. SEED is a powerful resource for obtaining sleep-event statistics that could be useful for establishing population norms.

An examination of sleep spindle metrics in the Sleep Heart Health Study: superiority of automated spindle detection over total sigma power in assessing age-related spindle decline

BACKGROUND

Sleep spindle activity is commonly estimated by measuring sigma power during stage 2 non-rapid eye movement (NREM2) sleep. However, spindles account for little of the total NREM2 interval and therefore sigma power over the entire interval may be misleading. This study compares derived spindle measures from direct automated spindle detection with those from gross power spectral analyses for the purposes of clinical trial design.

METHODS

We estimated spindle activity in a set of 8,440 overnight electroencephalogram (EEG) recordings from 5,793 patients from the Sleep Heart Health Study using both sigma power and direct automated spindle detection. Performance of the two methods was evaluated by determining the sample size required to detect decline in age-related spindle coherence with each method in a simulated clinical trial.

RESULTS

In a simulated clinical trial, sigma power required a sample size of 115 to achieve 95% power to identify age-related changes in sigma coherence, while automated spindle detection required a sample size of only 60.

CONCLUSIONS

Measurements of spindle activity utilizing automated spindle detection outperformed conventional sigma power analysis by a wide margin, suggesting that many studies would benefit from incorporation of automated spindle detection. These results further suggest that some previous studies which have failed to detect changes in sigma power or coherence may have failed simply because they were underpowered.

Sleep spindles, stress and PTSD: The state of the science and future directions

Sleep spindles are a signature feature of non-REM (NREM) sleep, with demonstrated relationships to sleep maintenance and learning and memory. Because PTSD is characterized by disturbances in sleep maintenance and in stress learning and memory, there is now a growing interest in examining the role of sleep spindles in the neurobiology of PTSD. This review provides an overview of methods for measuring and detecting sleep spindles as they pertain to human PTSD and stress research, presents a critical review of early findings examining sleep spindles in PTSD and stress neurobiology, and proposes several directions for future research. In doing so, this review underscores the extensive heterogeneity in sleep spindle measurement and detection methods, the wide range of spindle features that may be and have been examined, the many persisting unknowns about the clinical and functional relevance of those features, and the problems considering PTSD as a homogeneous group in between-group comparisons. This review also highlights the progress that has been made in this field and underscores the strong rationale for ongoing work in this area.

Overcoming the Domain Gap in Neural Action Representations

Relating behavior to brain activity in animals is a fundamental goal in neuroscience, with practical applications in building robust brain-machine interfaces. However, the domain gap between individuals is a major issue that prevents the training of general models that work on unlabeled subjects. Since 3D pose data can now be reliably extracted from multi-view video sequences without manual intervention, we propose to use it to guide the encoding of neural action representations together with a set of neural and behavioral augmentations exploiting the properties of microscopy imaging. To test our method, we collect a large dataset that features flies and their neural activity. To reduce the domain gap, during training, we mix features of neural and behavioral data across flies that seem to be performing similar actions. To show our method can generalize further neural modalities and other downstream tasks, we test our method on a human neural Electrocorticography dataset, and another RGB video data of human activities from different viewpoints. We believe our work will enable more robust neural decoding algorithms to be used in future brain-machine interfaces.

The Portiloop: A deep learning-based open science tool for closed-loop brain stimulation

Closed-loop brain stimulation refers to capturing neurophysiological measures such as electroencephalography (EEG), quickly identifying neural events of interest, and producing auditory, magnetic or electrical stimulation so as to interact with brain processes precisely. It is a promising new method for fundamental neuroscience and perhaps for clinical applications such as restoring degraded memory function; however, existing tools are expensive, cumbersome, and offer limited experimental flexibility. In this article, we propose the Portiloop, a deep learning-based, portable and low-cost closed-loop stimulation system able to target specific brain oscillations. We first document open-hardware implementations that can be constructed from commercially available components. We also provide a fast, lightweight neural network model and an exploration algorithm that automatically optimizes the model hyperparameters to the desired brain oscillation. Finally, we validate the technology on a challenging test case of real-time sleep spindle detection, with results comparable to off-line expert performance on the Massive Online Data Annotation spindle dataset (MODA; group consensus). Software and plans are available to the community as an open science initiative to encourage further development and advance closed-loop neuroscience research [https://github.com/Portiloop].

Learning neural decoders without labels using multiple data streams

OBJECTIVE

Recent advances in neural decoding have accelerated the development of brain-computer interfaces aimed at assisting users with everyday tasks such as speaking, walking, and manipulating objects. However, current approaches for training neural decoders commonly require large quantities of labeled data, which can be laborious or infeasible to obtain in real-world settings. Alternatively, self-supervised models that share self-generated pseudo-labels between two data streams have shown exceptional performance on unlabeled audio and video data, but it remains unclear how well they extend to neural decoding.

APPROACH

We learn neural decoders without labels by leveraging multiple simultaneously recorded data streams, including neural, kinematic, and physiological signals. Specifically, we apply cross-modal, self-supervised deep clustering to train decoders that can classify movements from brain recordings. After training, we then isolate the decoders for each input data stream and compare the accuracy of decoders trained using cross-modal deep clustering against supervised and unimodal, self-supervised models.

MAIN RESULTS

We find that sharing pseudo-labels between two data streams during training substantially increases decoding performance compared to unimodal, self-supervised models, with accuracies approaching those of supervised decoders trained on labeled data. Next, we extend cross-modal decoder training to three or more modalities, achieving state-of-the-art neural decoding accuracy that matches or slightly exceeds the performance of supervised models. Significance: We demonstrate that cross-modal, self-supervised decoding can be applied to train neural decoders when few or no labels are available and extend the cross-modal framework to share information among three or more data streams, further improving self-supervised training.

[Sleep spindles-Function, detection and use as biomarker for diagnostics in psychiatry]

BACKGROUND

The sleep spindle is a graphoelement of an electroencephalogram (EEG), which can be observed in light and deep sleep. Alterations in spindle activity have been described for a range of psychiatric disorders. Due to their relatively constant properties, sleep spindles may therefore be potential biomarkers in psychiatric diagnostics.

METHOD

This article presents an overview of the state of the science on the characteristics and functions of the sleep spindle as well as known alterations of spindle activity in psychiatric disorders. Various methodological approaches and developments of spindle detection are explained with respect to their potential for application in psychiatric diagnostics.

RESULTS AND CONCLUSION

Although alterations in spindle activity in psychiatric disorders are known and have been described in detail, their exact potential for psychiatric diagnostics has yet to be fully determined. In this respect, the acquisition of knowledge in research is currently constrained by manual and automated methods for spindle detection, which require high levels of resources and are error prone. Newer approaches to spindle detection based on deep-learning procedures could overcome the difficulties of previous detection methods, and thus open up new possibilities for the practical application of sleep spindles as biomarkers in the psychiatric practice.

Advanced sleep spindle identification with neural networks

Sleep spindles are neurophysiological phenomena that appear to be linked to memory formation and other functions of the central nervous system, and that can be observed in electroencephalographic recordings (EEG) during sleep. Manually identified spindle annotations in EEG recordings suffer from substantial intra- and inter-rater variability, even if raters have been highly trained, which reduces the reliability of spindle measures as a research and diagnostic tool. The Massive Online Data Annotation (MODA) project has recently addressed this problem by forming a consensus from multiple such rating experts, thus providing a corpus of spindle annotations of enhanced quality. Based on this dataset, we present a U-Net-type deep neural network model to automatically detect sleep spindles. Our model’s performance exceeds that of the state-of-the-art detector and of most experts in the MODA dataset. We observed improved detection accuracy in subjects of all ages, including older individuals whose spindles are particularly challenging to detect reliably. Our results underline the potential of automated methods to do repetitive cumbersome tasks with super-human performance.

Cross-Frequency Slow Oscillation–Spindle Coupling in a Biophysically Realistic Thalamocortical Neural Mass Model

Sleep manifests itself by the spontaneous emergence of characteristic oscillatory rhythms, which often time-lock and are implicated in memory formation. Here, we analyze a neural mass model of the thalamocortical loop in which the cortical node can generate slow oscillations (approximately 1 Hz) while its thalamic component can generate fast sleep spindles of σ-band activity (12–15 Hz). We study the dynamics for different coupling strengths between the thalamic and cortical nodes, for different conductance values of the thalamic node's potassium leak and hyperpolarization-activated cation-nonselective currents, and for different parameter regimes of the cortical node. The latter are listed as follows: (1) a low activity (DOWN) state with noise-induced, transient excursions into a high activity (UP) state, (2) an adaptation induced slow oscillation limit cycle with alternating UP and DOWN states, and (3) a high activity (UP) state with noise-induced, transient excursions into the low activity (DOWN) state. During UP states, thalamic spindling is abolished or reduced. During DOWN states, the thalamic node generates sleep spindles, which in turn can cause DOWN to UP transitions in the cortical node. Consequently, this leads to spindle-induced UP state transitions in parameter regime (1), thalamic spindles induced in some but not all DOWN states in regime (2), and thalamic spindles following UP to DOWN transitions in regime (3). The spindle-induced σ-band activity in the cortical node, however, is typically the strongest during the UP state, which follows a DOWN state “window of opportunity” for spindling. When the cortical node is parametrized in regime (3), the model well explains the interactions between slow oscillations and sleep spindles observed experimentally during Non-Rapid Eye Movement sleep. The model is computationally efficient and can be integrated into large-scale modeling frameworks to study spatial aspects like sleep wave propagation.

Naturalistic viewing conditions can increase task engagement and aesthetic preference but have only minimal impact on EEG quality

Free gaze and moving images are typically avoided in EEG experiments due to the expected generation of artifacts and noise. Yet for a growing number of research questions, loosening these rigorous restrictions would be beneficial. Among these is research on visual aesthetic experiences, which often involve open-ended exploration of highly variable stimuli. Here we systematically compare the effect of conservative vs. more liberal experimental settings on various measures of behavior, brain activity and physiology in an aesthetic rating task. Our primary aim was to assess EEG signal quality. 43 participants either maintained fixation or were allowed to gaze freely, and viewed either static images or dynamic (video) stimuli consisting of dance performances or nature scenes. A passive auditory background task (auditory steady-state response; ASSR) was added as a proxy measure for overall EEG recording quality. We recorded EEG, ECG and eyetracking data, and participants rated their aesthetic preference and state of boredom on each trial. Whereas both behavioral ratings and gaze behavior were affected by task and stimulus manipulations, EEG SNR was barely affected and generally robust across all conditions, despite only minimal preprocessing and no trial rejection. In particular, we show that using video stimuli does not necessarily result in lower EEG quality and can, on the contrary, significantly reduce eye movements while increasing both the participants' aesthetic response and general task engagement. We see these as encouraging results indicating that - at least in the lab - more liberal experimental conditions can be adopted without significant loss of signal quality.

Optimal spindle detection parameters for predicting cognitive performance

STUDY OBJECTIVES

Alterations in sleep spindles have been linked to cognitive impairment. This finding has contributed to a growing interest in identifying sleep-based biomarkers of cognition and neurodegeneration, including sleep spindles. However, flexibility surrounding spindle definitions and algorithm parameter settings present a methodological challenge. The aim of this study was to characterize how spindle detection parameter settings influence the association between spindle features and cognition and to identify parameters with the strongest association with cognition.

METHODS

Adult patients (n = 167, 49 ± 18 years) completed the NIH Toolbox Cognition Battery after undergoing overnight diagnostic polysomnography recordings for suspected sleep disorders. We explored 1000 combinations across seven parameters in Luna, an open-source spindle detector, and used four features of detected spindles (amplitude, density, duration, and peak frequency) to fit linear multiple regression models to predict cognitive scores.

RESULTS

Spindle features (amplitude, density, duration, and mean frequency) were associated with the ability to predict raw fluid cognition scores (r = 0.503) and age-adjusted fluid cognition scores (r = 0.315) with the best spindle parameters. Fast spindle features generally showed better performance relative to slow spindle features. Spindle features weakly predicted total cognition and poorly predicted crystallized cognition regardless of parameter settings.

CONCLUSIONS

Our exploration of spindle detection parameters identified optimal parameters for studies of fluid cognition and revealed the role of parameter interactions for both slow and fast spindles. Our findings support sleep spindles as a sleep-based biomarker of fluid cognition.

New and Emerging Approaches to Better Define Sleep Disruption and Its Consequences

Current approaches to quantify and diagnose sleep disorders and circadian rhythm disruption are imprecise, laborious, and often do not relate well to key clinical and health outcomes. Newer emerging approaches that aim to overcome the practical and technical constraints of current sleep metrics have considerable potential to better explain sleep disorder pathophysiology and thus to more precisely align diagnostic, treatment and management approaches to underlying pathology. These include more fine-grained and continuous EEG signal feature detection and novel oxygenation metrics to better encapsulate hypoxia duration, frequency, and magnitude readily possible via more advanced data acquisition and scoring algorithm approaches. Recent technological advances may also soon facilitate simple assessment of circadian rhythm physiology at home to enable sleep disorder diagnostics even for “non-circadian rhythm” sleep disorders, such as chronic insomnia and sleep apnea, which in many cases also include a circadian disruption component. Bringing these novel approaches into the clinic and the home settings should be a priority for the field. Modern sleep tracking technology can also further facilitate the transition of sleep diagnostics from the laboratory to the home, where environmental factors such as noise and light could usefully inform clinical decision-making. The “endpoint” of these new and emerging assessments will be better targeted therapies that directly address underlying sleep disorder pathophysiology via an individualized, precision medicine approach. This review outlines the current state-of-the-art in sleep and circadian monitoring and diagnostics and covers several new and emerging approaches to better define sleep disruption and its consequences.

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.

Crowdsourcing in Cognitive and Systems Neuroscience

Behavioral research in cognitive and human systems neuroscience has been largely carried out in-person in laboratory settings. Underpowering and lack of reproducibility due to small sample sizes have weakened conclusions of these investigations. In other disciplines, such as neuroeconomics and social sciences, crowdsourcing has been extensively utilized as a data collection tool, and a means to increase sample sizes. Recent methodological advances allow scientists, for the first time, to test online more complex cognitive, perceptual, and motor tasks. Here we review the nascent literature on the use of online crowdsourcing in cognitive and human systems neuroscience. These investigations take advantage of the ability to reliably track the activity of a participant's computer keyboard, mouse, and eye gaze in the context of large-scale studies online that involve diverse research participant pools. Crowdsourcing allows for testing the generalizability of behavioral hypotheses in real-life environments that are less accessible to lab-designed investigations. Crowdsourcing is further useful when in-laboratory studies are limited, for example during the current COVID-19 pandemic. We also discuss current limitations of crowdsourcing research, and suggest pathways to address them. We conclude that online crowdsourcing is likely to widen the scope and strengthen conclusions of cognitive and human systems neuroscience investigations.

The effect of zolpidem on memory consolidation over a night of sleep

STUDY OBJECTIVES

Nonrapid eye movement sleep boosts hippocampus-dependent, long-term memory formation more so than wake. Studies have pointed to several electrophysiological events that likely play a role in this process, including thalamocortical sleep spindles (12-15 Hz). However, interventional studies that directly probe the causal role of spindles in consolidation are scarce. Previous studies have used zolpidem, a GABA-A agonist, to increase sleep spindles during a daytime nap and promote hippocampal-dependent episodic memory. The current study investigated the effect of zolpidem on nighttime sleep and overnight improvement of episodic memories.

METHODS

We used a double-blind, placebo-controlled within-subject design to test the a priori hypothesis that zolpidem would lead to increased memory performance on a word-paired associates task by boosting spindle activity. We also explored the impact of zolpidem across a range of other spectral sleep features, including slow oscillations (0-1 Hz), delta (1-4 Hz), theta (4-8 Hz), sigma (12-15 Hz), as well as spindle-SO coupling.

RESULTS

We showed greater memory improvement after a night of sleep with zolpidem, compared to placebo, replicating a prior nap study. Additionally, zolpidem increased sigma power, decreased theta and delta power, and altered the phase angle of spindle-SO coupling, compared to placebo. Spindle density, theta power, and spindle-SO coupling were associated with next-day memory performance.

CONCLUSIONS

These results are consistent with the hypothesis that sleep, specifically the timing and amount of sleep spindles, plays a causal role in the long-term formation of episodic memories. Furthermore, our results emphasize the role of nonrapid eye movement theta activity in human memory consolidation.

Sleep spindle abnormalities related to Alzheimer's disease: a systematic mini-review

Accumulating evidence supports a bidirectional relationship between sleep disruption and Alzheimer's disease (AD) pathology. Among various sleep electroencephalography activities, the sleep spindle is one specific electroencephalographic rhythm that has potential to be a biomarker for AD. This review explores the association between sleep spindles and AD-related dementia from a neuropsychological perspective by a systematic re-examining of recent findings. In general, sleep spindles, characterized by density, amplitude, duration, and frequency, are disrupted in AD. Moreover, its functional coupling with slow oscillation also suffers in AD. While preliminary, our observations and comparisons suggest that spindle density rather than frequency and fast spindles rather than slow spindles could be more sensitive to AD-related dementia, and spindle plasticity provides possibilities for targeted interference. In conclusion, quantitative and qualitative features of sleep spindles represent potential non-invasive and cost-effective biomarkers for AD and provide both therapeutic and public health implications.