Decoding brain states on the intrinsic manifold of human brain dynamics across wakefulness and sleep

Brain states as wave-like motifs

There is ample evidence of wave-like activity in the brain at multiple scales and levels. This emerging literature supports the broader adoption of a wave perspective of brain activity. Specifically, a brain state can be described as a set of recurring, sequential patterns of propagating brain activity, namely a wave. We examine a collective body of experimental work investigating wave-like properties. Based on these works, we consider brain states as waves using a scale-agnostic framework across time and space. Emphasis is placed on the sequentiality and periodicity associated with brain activity. We conclude by discussing the implications, prospects, and experimental opportunities of this framework.

Reproducible, data-driven characterization of sleep based on brain dynamics and transitions from whole-night fMRI

Understanding the function of sleep requires studying the dynamics of brain activity across whole-night sleep and their transitions. However, current gold standard polysomnography (PSG) has limited spatial resolution to track brain activity. Additionally, previous fMRI studies were too short to capture full sleep stages and their cycling. To study whole-brain dynamics and transitions across whole-night sleep, we used an unsupervised learning approach, the Hidden Markov model (HMM), on two-night, 16-hour fMRI recordings of 12 non-sleep-deprived participants who reached all PSG-based sleep stages. This method identified 21 recurring brain states and their transition probabilities, beyond PSG-defined sleep stages. The HMM trained on one night accurately predicted the other, demonstrating unprecedented reproducibility. We also found functionally relevant subdivisions within rapid eye movement (REM) and within non-REM 2 stages. This study provides new insights into brain dynamics and transitions during sleep, aiding our understanding of sleep disorders that impact sleep transitions.

Comparative analysis of sleep parameters and structures derived from wearable flexible electrode sleep patches and polysomnography in young adults

Polysomnography (PSG) is the gold standard for clinical sleep monitoring, but its cost, discomfort, and limited suitability for continuous use present challenges. The flexible electrode sleep patch (FESP) emerges as an economically viable and patient-friendly solution, offering lightweight, simple operation, and self-applicable. Nevertheless, its utilization in young individuals remains uncertain. The objective of this study was to compare sleep data obtained by FESP and PSG in healthy young individuals and analyze agreement for sleep parameters and structure classification. Overnight monitoring with FESP and PSG recordings in 48 participants (mean age: 23 yr) was done. Correlation analysis, Bland-Altman plots, and Cohen's kappa coefficient assessed consistency. Sensitivity, specificity, and predictive values compared classification against PSG. FESP showed strong correlation and consistency with PSG for sleep monitoring. Bland-Altman plots indicated small errors and high consistency. Kappa values (0.70-0.84) suggested substantial agreement for sleep stage classification. Pearson correlation coefficient values for sleep stages (0.75-0.88) and sleep parameters (0.80-0.96) confirm that FESP has a strong application. Intraclass correlation coefficient yielded values between 0.65 and 0.97. In addition, FESP demonstrated an impressive accuracy range of 84.12-93.47% for sleep stage classification. The FESP also features a wearable self-test program with an error rate of no more than 8% for both deep sleep and wake. In young adults, FESP demonstrated reliable monitoring capabilities comparable to PSG. With its low cost and user-friendly design, FESP is a potential alternative for portable sleep assessment in clinical and research applications. Further studies involving larger populations are needed to validate its diagnostic potential.NEW & NOTEWORTHY By comparison with PSG, this study confirmed the reliability of an efficient, objective, low-cost, and noninvasive portable automatic sleep-monitoring device FESP, which provides effective information for long-term family sleep disorder diagnosis and sleep quality monitoring.

Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex

Brain signal irreversibility has been shown to be a promising approach to study neural dynamics. Nevertheless, the relation with cortical hierarchy and the influence of different electrophysiological features is not completely understood. In this study, we recorded local field potentials (LFPs) during spontaneous behavior, including awake and sleep periods, using custom micro-electrocorticographic (μECoG) arrays implanted in ferrets. In contrast to humans, ferrets remain less time in each state across the sleep-wake cycle. We deployed a diverse set of metrics in order to measure the levels of complexity of the different behavioral states. In particular, brain irreversibility, which is a signature of non-equilibrium dynamics, captured by the arrow of time of the signal, revealed the hierarchical organization of the ferret's cortex. We found different signatures of irreversibility and functional hierarchy of large-scale dynamics in three different brain states (active awake, quiet awake, and deep sleep), showing a lower level of irreversibility in the deep sleep stage, compared to the other. Irreversibility also allowed us to disentangle the influence of different cortical areas and frequency bands in this process, showing a predominance of the parietal cortex and the theta band. Furthermore, when inspecting the embedded dynamic through a Hidden Markov Model, the deep sleep stage was revealed to have a lower switching rate and lower entropy production. These results suggest functional hierarchies in organization that can be revealed through thermodynamic features and information theory metrics.

Integration and segregation manifolds in the brain ensure cognitive flexibility during tasks and rest

Adapting to a constantly changing environment requires the human brain to flexibly switch among many demanding cognitive tasks, processing both specialized and integrated information associated with the activity in functional networks over time. In this study, we investigated the nature of the temporal alternation between segregated and integrated states in the brain during rest and six cognitive tasks using functional MRI. We employed a deep autoencoder to explore the 2D latent space associated with the segregated and integrated states. Our results show that the integrated state occupies less space in the latent space manifold compared to the segregated states. Moreover, the integrated state is characterized by lower entropy of occupancy than the segregated state, suggesting that integration plays a consolidating role, while segregation may serve as cognitive expertness. Comparing rest and the tasks, we found that rest exhibits higher entropy of occupancy, indicating a more random wandering of the mind compared to the expected focus during task performance. Our study demonstrates that both transient, short-lived integrated and segregated states are present during rest and task performance, flexibly switching between them, with integration serving as information compression and segregation related to information specialization.

Brain decoding of the Human Connectome Project tasks in a dense individual fMRI dataset

Brain decoding aims to infer cognitive states from patterns of brain activity. Substantial inter-individual variations in functional brain organization challenge accurate decoding performed at the group level. In this paper, we tested whether accurate brain decoding models can be trained entirely at the individual level. We trained several classifiers on a dense individual functional magnetic resonance imaging (fMRI) dataset for which six participants completed the entire Human Connectome Project (HCP) task battery >13 times over ten separate fMRI sessions. We evaluated nine decoding methods, from Support Vector Machines (SVM) and Multi-Layer Perceptron (MLP) to Graph Convolutional Neural Networks (GCN). All decoders were trained to classify single fMRI volumes into 21 experimental conditions simultaneously, using ∼7 h of fMRI data per participant. The best prediction accuracies were achieved with GCN and MLP models, whose performance (57-67 % accuracy) approached state-of-the-art accuracy (76 %) with models trained at the group level on >1 K hours of data from the original HCP sample. Our SVM model also performed very well (54-62 % accuracy). Feature importance maps derived from MLP -our best-performing model- revealed informative features in regions relevant to particular cognitive domains, notably in the motor cortex. We also observed that inter-subject classification achieved substantially lower accuracy than subject-specific models, indicating that our decoders learned individual-specific features. This work demonstrates that densely-sampled neuroimaging datasets can be used to train accurate brain decoding models at the individual level. We expect this work to become a useful benchmark for techniques that improve model generalization across multiple subjects and acquisition conditions.

Towards a dynamical understanding of microstate analysis of M/EEG data

One of the interesting aspects of EEG data is the presence of temporally stable and spatially coherent patterns of activity, known as microstates, which have been linked to various cognitive and clinical phenomena. However, there is still no general agreement on the interpretation of microstate analysis. Various clustering algorithms have been used for microstate computation, and multiple studies suggest that the microstate time series may provide insight into the neural activity of the brain in the resting state. This study addresses two gaps in the literature. Firstly, by applying several state-of-the-art microstate algorithms to a large dataset of EEG recordings, we aim to characterise and describe various microstate algorithms. We demonstrate and discuss why the three "classically" used algorithms ((T)AAHC and modified K-Means) yield virtually the same results, while HMM algorithm generates the most dissimilar results. Secondly, we aim to test the hypothesis that dynamical microstate properties might be, to a large extent, determined by the linear characteristics of the underlying EEG signal, in particular, by the cross-covariance and autocorrelation structure of the EEG data. To this end, we generated a Fourier transform surrogate of the EEG signal to compare microstate properties. Here, we found that these are largely similar, thus hinting that microstate properties depend to a very high degree on the linear covariance and autocorrelation structure of the underlying EEG data. Finally, we treated the EEG data as a vector autoregression process, estimated its parameters, and generated surrogate stationary and linear data from fitted VAR. We observed that such a linear model generates microstates highly comparable to those estimated from real EEG data, supporting the conclusion that a linear EEG model can help with the methodological and clinical interpretation of both static and dynamic human brain microstate properties.

Manifold learning for fMRI time-varying functional connectivity

Whole-brain functional connectivity (FC) measured with functional MRI (fMRI) evolves over time in meaningful ways at temporal scales going from years (e.g., development) to seconds [e.g., within-scan time-varying FC (tvFC)]. Yet, our ability to explore tvFC is severely constrained by its large dimensionality (several thousands). To overcome this difficulty, researchers often seek to generate low dimensional representations (e.g., 2D and 3D scatter plots) hoping those will retain important aspects of the data (e.g., relationships to behavior and disease progression). Limited prior empirical work suggests that manifold learning techniques (MLTs)-namely those seeking to infer a low dimensional non-linear surface (i.e., the manifold) where most of the data lies-are good candidates for accomplishing this task. Here we explore this possibility in detail. First, we discuss why one should expect tvFC data to lie on a low dimensional manifold. Second, we estimate what is the intrinsic dimension (ID; i.e., minimum number of latent dimensions) of tvFC data manifolds. Third, we describe the inner workings of three state-of-the-art MLTs: Laplacian Eigenmaps (LEs), T-distributed Stochastic Neighbor Embedding (T-SNE), and Uniform Manifold Approximation and Projection (UMAP). For each method, we empirically evaluate its ability to generate neuro-biologically meaningful representations of tvFC data, as well as their robustness against hyper-parameter selection. Our results show that tvFC data has an ID that ranges between 4 and 26, and that ID varies significantly between rest and task states. We also show how all three methods can effectively capture subject identity and task being performed: UMAP and T-SNE can capture these two levels of detail concurrently, but LE could only capture one at a time. We observed substantial variability in embedding quality across MLTs, and within-MLT as a function of hyper-parameter selection. To help alleviate this issue, we provide heuristics that can inform future studies. Finally, we also demonstrate the importance of feature normalization when combining data across subjects and the role that temporal autocorrelation plays in the application of MLTs to tvFC data. Overall, we conclude that while MLTs can be useful to generate summary views of labeled tvFC data, their application to unlabeled data such as resting-state remains challenging.

Atypical functional connectivity hierarchy in Rolandic epilepsy

Functional connectivity hierarchy is an important principle in the process of brain functional organization and an important feature reflecting brain development. However, atypical brain network hierarchy organization in Rolandic epilepsy have not been systematically investigated. We examined connectivity alteration with age and its relation to epileptic incidence, cognition, or underlying genetic factors in 162 cases of Rolandic epilepsy and 117 typically developing children, by measuring fMRI multi-axis functional connectivity gradients. Rolandic epilepsy is characterized by contracting and slowing expansion of the functional connectivity gradients, highlighting the atypical age-related change of the connectivity hierarchy in segregation properties. The gradient alterations are relevant to seizure incidence, cognition, and connectivity deficit, and development-associated genetic basis. Collectively, our approach provides converging evidence for atypical connectivity hierarchy as a system-level substrate of Rolandic epilepsy, suggesting this is a disorder of information processing across multiple functional domains, and established a framework for large-scale brain hierarchical research.

Low-dimensional organization of global brain states of reduced consciousness

Brain states are frequently represented using a unidimensional scale measuring the richness of subjective experience (level of consciousness). This description assumes a mapping between the high-dimensional space of whole-brain configurations and the trajectories of brain states associated with changes in consciousness, yet this mapping and its properties remain unclear. We combine whole-brain modeling, data augmentation, and deep learning for dimensionality reduction to determine a mapping representing states of consciousness in a low-dimensional space, where distances parallel similarities between states. An orderly trajectory from wakefulness to patients with brain injury is revealed in a latent space whose coordinates represent metrics related to functional modularity and structure-function coupling, increasing alongside loss of consciousness. Finally, we investigate the effects of model perturbations, providing geometrical interpretation for the stability and reversibility of states. We conclude that conscious awareness depends on functional patterns encoded as a low-dimensional trajectory within the vast space of brain configurations.

Repairing Artifacts in Neural Activity Recordings Using Low-Rank Matrix Estimation

Electrophysiology recordings are frequently affected by artifacts (e.g., subject motion or eye movements), which reduces the number of available trials and affects the statistical power. When artifacts are unavoidable and data are scarce, signal reconstruction algorithms that allow for the retention of sufficient trials become crucial. Here, we present one such algorithm that makes use of large spatiotemporal correlations in neural signals and solves the low-rank matrix completion problem, to fix artifactual entries. The method uses a gradient descent algorithm in lower dimensions to learn the missing entries and provide faithful reconstruction of signals. We carried out numerical simulations to benchmark the method and estimate optimal hyperparameters for actual EEG data. The fidelity of reconstruction was assessed by detecting event-related potentials (ERP) from a highly artifacted EEG time series from human infants. The proposed method significantly improved the standardized error of the mean in ERP group analysis and a between-trial variability analysis compared to a state-of-the-art interpolation technique. This improvement increased the statistical power and revealed significant effects that would have been deemed insignificant without reconstruction. The method can be applied to any time-continuous neural signal where artifacts are sparse and spread out across epochs and channels, increasing data retention and statistical power.

Validation of a wearable forehead sleep recorder against polysomnography in sleep staging and desaturation events in a clinical sample

STUDY OBJECTIVES

Wearable sleep recording devices may be a helpful alternative method for polysomnography (PSG) due to their higher accessibility and comfort as well as lower cost, but their validities need to be examined. The aim of this study was to evaluate the accuracy of a novel single-channel, electroencephalography-based wearable forehead sleep recorder (UMindSleep) to assess sleep staging and oxygen desaturation.

METHODS

Two hundred and three Chinese adults recruited from a sleep medicine center underwent an overnight study wearing UMindSleep and PSG simultaneously. Sleep parameters including sleep staging and oxygen desaturation index were compared between UMindSleep and PSG.

RESULTS

A total of 195,349 valid epochs from 197 participants (171 with obstructive sleep apnea, 86.8%) were included in analyses of sleep staging. Sensitivities of UMindSleep compared to PSG were 79.7% for wake, 85.8% for light sleep, 79.4% for deep sleep, and 82.7% for rapid eye movement sleep. Specificities were 95.3% for wake, 83.4% for light sleep, 97.0% for deep sleep, and 96.8% for rapid eye movement sleep. Furthermore, the kappa agreements of 0.69-0.79 were indicative of a substantial agreement for sleep staging between UMindSleep and PSG. Sensitivity and specificity regarding oxygen desaturation index were 93.4% and 88.9%, yielding a kappa coefficient of 0.82.

CONCLUSIONS

Our findings suggest that UMindSleep may serve as a feasible, accurate, and dependable device for screening of sleep disorders (eg, obstructive sleep apnea) and assessing sleep structure.

CITATION

Chen X, Jin X, Zhang J, Ho KW, Wei Y, Cheng H. Validation of a wearable forehead sleep recorder against polysomnography in sleep staging and desaturation events in a clinical sample. J Clin Sleep Med. 2023;19(4):711-718.

Manifold Learning for fMRI time-varying FC

Whole-brain functional connectivity ( FC ) measured with functional MRI (fMRI) evolve over time in meaningful ways at temporal scales going from years (e.g., development) to seconds (e.g., within-scan time-varying FC ( tvFC )). Yet, our ability to explore tvFC is severely constrained by its large dimensionality (several thousands). To overcome this difficulty, researchers seek to generate low dimensional representations (e.g., 2D and 3D scatter plots) expected to retain its most informative aspects (e.g., relationships to behavior, disease progression). Limited prior empirical work suggests that manifold learning techniques ( MLTs )-namely those seeking to infer a low dimensional non-linear surface (i.e., the manifold) where most of the data lies-are good candidates for accomplishing this task. Here we explore this possibility in detail. First, we discuss why one should expect tv FC data to lie on a low dimensional manifold. Second, we estimate what is the intrinsic dimension (i.e., minimum number of latent dimensions; ID ) of tvFC data manifolds. Third, we describe the inner workings of three state-of-the-art MLTs : Laplacian Eigenmaps ( LE ), T-distributed Stochastic Neighbor Embedding ( T-SNE ), and Uniform Manifold Approximation and Projection ( UMAP ). For each method, we empirically evaluate its ability to generate neuro-biologically meaningful representations of tvFC data, as well as their robustness against hyper-parameter selection. Our results show that tvFC data has an ID that ranges between 4 and 26, and that ID varies significantly between rest and task states. We also show how all three methods can effectively capture subject identity and task being performed: UMAP and T-SNE can capture these two levels of detail concurrently, but L E could only capture one at a time. We observed substantial variability in embedding quality across MLTs , and within- MLT as a function of hyper-parameter selection. To help alleviate this issue, we provide heuristics that can inform future studies. Finally, we also demonstrate the importance of feature normalization when combining data across subjects and the role that temporal autocorrelation plays in the application of MLTs to tvFC data. Overall, we conclude that while MLTs can be useful to generate summary views of labeled tvFC data, their application to unlabeled data such as resting-state remains challenging.

Functional networks in prolonged disorders of consciousness

Prolonged disorders of consciousness (DoC) are characterized by extended disruptions of brain activities that sustain wakefulness and awareness and are caused by various etiologies. During the past decades, neuroimaging has been a practical method of investigation in basic and clinical research to identify how brain properties interact in different levels of consciousness. Resting-state functional connectivity within and between canonical cortical networks correlates with consciousness by a calculation of the associated temporal blood oxygen level-dependent (BOLD) signal process during functional MRI (fMRI) and reveals the brain function of patients with prolonged DoC. There are certain brain networks including the default mode, dorsal attention, executive control, salience, auditory, visual, and sensorimotor networks that have been reported to be altered in low-level states of consciousness under either pathological or physiological states. Analysis of brain network connections based on functional imaging contributes to more accurate judgments of consciousness level and prognosis at the brain level. In this review, neurobehavioral evaluation of prolonged DoC and the functional connectivity within brain networks based on resting-state fMRI were reviewed to provide reference values for clinical diagnosis and prognostic evaluation.

Modes of cognition: Evidence from metastable brain dynamics

Managing cognitive load depends on adequate resource allocation by the human brain through the engagement of metastable substates, which are large-scale functional networks that change over time. We employed a novel analysis method, deep autoencoder dynamical analysis (DADA), with 100 healthy adults selected from the Human Connectome Project (HCP) data set in rest and six cognitive tasks. The deep autoencoder of DADA described seven recurrent stochastic metastable substates from the functional connectome of BOLD phase coherence matrices. These substates were significantly differentiated in terms of their probability of appearance, time duration, and spatial attributes. We found that during different cognitive tasks, there was a higher probability of having more connected substates dominated by a high degree of connectivity in the thalamus. In addition, compared with those during tasks, resting brain dynamics have a lower level of predictability, indicating a more uniform distribution of metastability between substates, quantified by higher entropy. These novel findings provide empirical evidence for the philosophically motivated cognitive theory, suggesting on-line and off-line as two fundamentally distinct modes of cognition. On-line cognition refers to task-dependent engagement with the sensory input, while off-line cognition is a slower, environmentally detached mode engaged with decision and planning. Overall, the DADA framework provides a bridge between neuroscience and cognitive theory that can be further explored in the future.

Dynamic primitives of brain network interaction Special Issue "Advances in Mapping the Connectome"

What dynamic processes underly functional brain networks? Functional connectivity (FC) and functional connectivity dynamics (FCD) are used to represent the patterns and dynamics of functional brain networks. FC(D) is related to the synchrony of brain activity: when brain areas oscillate in a coordinated manner this yields a high correlation between their signal time series. To explain the processes underlying FC(D) we review how synchronized oscillations emerge from coupled neural populations in brain network models (BNMs). From detailed spiking networks to more abstract population models, there is strong support for the idea that the brain operates near critical instabilities that give rise to multistable or metastable dynamics that in turn lead to the intermittently synchronized slow oscillations underlying FC(D). We explore further consequences from these fundamental mechanisms and how they fit with reality. We conclude by highlighting the need for integrative brain models that connect separate mechanisms across levels of description and spatiotemporal scales and link them with cognitive function.

The connectome spectrum as a canonical basis for a sparse representation of fast brain activity

The functional organization of neural processes is constrained by the brain's intrinsic structural connectivity, i.e., the connectome. Here, we explore how structural connectivity can improve the representation of brain activity signals and their dynamics. Using a multi-modal imaging dataset (electroencephalography, structural MRI, and diffusion MRI), we represent electrical brain activity at the cortical surface as a time-varying composition of harmonic modes of structural connectivity. These harmonic modes are known as connectome harmonics. Here we describe brain activity signal as a time-varying combination of connectome harmonics. We term this description as the connectome spectrum of the signal. We found that: first, the brain activity signal is represented more compactly by the connectome spectrum than by the traditional area-based representation; second, the connectome spectrum characterizes fast brain dynamics in terms of signal broadcasting profile, revealing different temporal regimes of integration and segregation that are consistent across participants. And last, the connectome spectrum characterizes fast brain dynamics with fewer degrees of freedom than area-based signal representations. Specifically, we show that a smaller number of dimensions capture the differences between low-level and high-level visual processing in the connectome spectrum. Also, we demonstrate that connectome harmonics capture more sensitively the topological properties of brain activity. In summary, this work provides statistical, functional, and topological evidence indicating that the description of brain activity in terms of structural connectivity fosters a more comprehensive understanding of large-scale dynamic neural functioning.