Assessing the effectiveness of spatial PCA on SVM-based decoding of EEG data.

Principal component analysis (PCA) has been widely employed for dimensionality reduction prior to multivariate pattern classification (decoding) in EEG research. The goal of the present study was to provide an evaluation of the effectiveness of PCA on decoding accuracy (using support vector machines) across a broad range of experimental paradigms. We evaluated several different PCA variations, including group-based and subject-based component decomposition and the application of Varimax rotation or no rotation. We also varied the numbers of PCs that were retained for the decoding analysis. We evaluated the resulting decoding accuracy for seven common event-related potential components (N170, mismatch negativity, N2pc, P3b, N400, lateralized readiness potential, and error-related negativity). We also examined more challenging decoding tasks, including decoding of face identity, facial expression, stimulus location, and stimulus orientation. The datasets also varied in the number and density of electrode sites. Our findings indicated that none of the PCA approaches consistently improved decoding performance related to no PCA, and the application of PCA frequently reduced decoding performance. Researchers should therefore be cautious about using PCA prior to decoding EEG data from similar experimental paradigms, populations, and recording setups.

Removal of site effects and enhancement of signal using dual projection independent component analysis for pooling multi-site MRI data.

Combining magnetic resonance imaging (MRI) data from multi-site studies is a popular approach for constructing larger datasets to greatly enhance the reliability and reproducibility of neuroscience research. However, the scanner/site variability is a significant confound that complicates the interpretation of the results, so effective and complete removal of the scanner/site variability is necessary to realise the full advantages of pooling multi-site datasets. Independent component analysis (ICA) and general linear model (GLM) based harmonisation methods are the two primary methods used to eliminate scanner/site effects. Unfortunately, there are challenges with both ICA-based and GLM-based harmonisation methods to remove site effects completely when the signals of interest and scanner/site effects-related variables are correlated, which may occur in neuroscience studies. In this study, we propose an effective and powerful harmonisation strategy that implements dual projection (DP) theory based on ICA to remove the scanner/site effects more completely. This method can separate the signal effects correlated with site variables from the identified site effects for removal without losing signals of interest. Both simulations and vivo structural MRI datasets, including a dataset from Autism Brain Imaging Data Exchange II and a travelling subject dataset from the Strategic Research Program for Brain Sciences, were used to test the performance of a DP-based ICA harmonisation method. Results show that DP-based ICA harmonisation has superior performance for removing site effects and enhancing the sensitivity to detect signals of interest as compared with GLM-based and conventional ICA harmonisation methods.

Denoising brain networks using a fixed mathematical phase change in independent component analysis of magnitude-only fMRI data.

Brain networks extracted by independent component analysis (ICA) from magnitude-only fMRI data are usually denoised using various amplitude-based thresholds. By contrast, spatial source phase (SSP) or the phase information of ICA brain networks extracted from complex-valued fMRI data, has provided a simple yet effective way to perform the denoising using a fixed phase change. In this work, we extend the approach to magnitude-only fMRI data to avoid testing various amplitude thresholds for denoising magnitude maps extracted by ICA, as most studies do not save the complex-valued data. The main idea is to generate a mathematical SSP map for a magnitude map using a mapping framework, and the mapping framework is built using complex-valued fMRI data with a known SSP map. Here we leverage the fact that the phase map derived from phase fMRI data has similar phase information to the SSP map. After verifying the use of the magnitude data of complex-valued fMRI, this framework is generalized to work with magnitude-only data, allowing use of our approach even without the availability of the corresponding phase fMRI datasets. We test the proposed method using both simulated and experimental fMRI data including complex-valued data from University of New Mexico and magnitude-only data from Human Connectome Project. The results provide evidence that the mathematical SSP denoising with a fixed phase change is effective for denoising spatial maps from magnitude-only fMRI data in terms of retaining more BOLD-related activity and fewer unwanted voxels, compared with amplitude-based thresholding. The proposed method provides a unified and efficient SSP approach to denoise ICA brain networks in fMRI data.

[Automated detection of sleep-arousal using multi-scale convolution and self-attention mechanism].

In clinical, manually scoring by technician is the major method for sleep arousal detection. This method is time-consuming and subjective. This study aimed to achieve an end-to-end sleep-arousal events detection by constructing a convolutional neural network based on multi-scale convolutional layers and self-attention mechanism, and using 1 min single-channel electroencephalogram (EEG) signals as its input. Compared with the performance of the baseline model, the results of the proposed method showed that the mean area under the precision-recall curve and area under the receiver operating characteristic were both improved by 7%. Furthermore, we also compared the effects of single modality and multi-modality on the performance of the proposed model. The results revealed the power of single-channel EEG signals in automatic sleep arousal detection. However, the simple combination of multi-modality signals may be counterproductive to the improvement of model performance. Finally, we also explored the scalability of the proposed model and transferred the model into the automated sleep staging task in the same dataset. The average accuracy of 73% also suggested the power of the proposed method in task transferring. This study provides a potential solution for the development of portable sleep monitoring and paves a way for the automatic sleep data analysis using the transfer learning method.

Discovering hidden brain network responses to naturalistic stimuli via tensor component analysis of multi-subject fMRI data.

The study of brain network interactions during naturalistic stimuli facilitates a deeper understanding of human brain function. To estimate large-scale brain networks evoked with naturalistic stimuli, a tensor component analysis (TCA) based framework was used to characterize shared spatio-temporal patterns across subjects in a purely data-driven manner. In this framework, a third-order tensor is constructed from the timeseries extracted from all brain regions from a given parcellation, for all participants, with modes of the tensor corresponding to spatial distribution, time series and participants. TCA then reveals spatially and temporally shared components, i.e., evoked networks with the naturalistic stimuli, their time courses of activity and subject loadings of each component. To enhance the reproducibility of the estimation with the adaptive TCA algorithm, a novel spectral clustering method, tensor spectral clustering, was proposed and applied to evaluate the stability of the TCA algorithm. We demonstrated the effectiveness of the proposed framework via simulations and real fMRI data collected during a motor task with a traditional fMRI study design. We also applied the proposed framework to fMRI data collected during passive movie watching to illustrate how reproducible brain networks are evoked by naturalistic movie viewing.

An efficient functional magnetic resonance imaging data reduction strategy using neighborhood preserving embedding algorithm.

High dimensionality data have become common in neuroimaging fields, especially group-level functional magnetic resonance imaging (fMRI) datasets. fMRI connectivity analysis is a widely used, powerful technique for studying functional brain networks to probe underlying mechanisms of brain function and neuropsychological disorders. However, data-driven technique like independent components analysis (ICA), can yield unstable and inconsistent results, confounding the true effects of interest and hindering the understanding of brain functionality and connectivity. A key contributing factor to this instability is the information loss that occurs during fMRI data reduction. Data reduction of high dimensionality fMRI data in the temporal domain to identify the important information within group datasets is necessary for such analyses and is crucial to ensure the accuracy and stability of the outputs. In this study, we describe an fMRI data reduction strategy based on an adapted neighborhood preserving embedding (NPE) algorithm. Both simulated and real data results indicate that, compared with the widely used data reduction method, principal component analysis, the NPE-based data reduction method (a) shows superior performance on efficient data reduction, while enhancing group-level information, (b) develops a unique stratagem for selecting components based on an adjacency graph of eigenvectors, (c) generates more reliable and reproducible brain networks under different model orders when the outputs of NPE are used for ICA, (d) is more sensitive to revealing task-evoked activation for task fMRI, and (e) is extremely attractive and powerful for the increasingly popular fast fMRI and very large datasets.

Optimal Number of Clusters by Measuring Similarity Among Topographies for Spatio-Temporal ERP Analysis.

Averaging amplitudes over consecutive time samples (i.e., time window) is widely used to calculate the peak amplitude of event-related potentials (ERPs). Cluster analysis of the spatio-temporal ERP data is a promising tool to determine the time window of an ERP of interest. However, determining an appropriate number of clusters to optimally represent ERPs is still challenging. Here, we develop a new method to estimate the optimal number of clusters utilizing consensus clustering. Various polarity dependent clustering methods, namely, k-means, hierarchical clustering, fuzzy c-means, self-organizing map, spectral clustering, and Gaussian mixture model, are used to configure consensus clustering after assessing them individually. When a range of clusters is applied many times, the optimal number of clusters should correspond to the expectation, which is the average of the obtained mean inner-similarities of estimated time windows across all conditions and groups converge in the satisfactory thresholds. In order to assess our method, the proposed method has been applied to simulated data and prospective memory experiment ERP data aimed to qualify N2 and P3, and N300 and prospective positivity components, respectively. The results of determining the optimal number of clusters meet at six cluster maps for both ERP data. In addition, our results revealed that the proposed method could be reliably applied to ERP data to determine the appropriate time window for the ERP of interest when the measurement interval is not accurately defined.

Cross-Subject Emotion Recognition Using Fused Entropy Features of EEG.

Emotion recognition based on electroencephalography (EEG) has attracted high interest in fields such as health care, user experience evaluation, and human-computer interaction (HCI), as it plays an important role in human daily life. Although various approaches have been proposed to detect emotion states in previous studies, there is still a need to further study the dynamic changes of EEG in different emotions to detect emotion states accurately. Entropy-based features have been proved to be effective in mining the complexity information in EEG in many areas. However, different entropy features vary in revealing the implicit information of EEG. To improve system reliability, in this paper, we propose a framework for EEG-based cross-subject emotion recognition using fused entropy features and a Bidirectional Long Short-term Memory (BiLSTM) network. Features including approximate entropy (AE), fuzzy entropy (FE), Rényi entropy (RE), differential entropy (DE), and multi-scale entropy (MSE) are first calculated to study dynamic emotional information. Then, we train a BiLSTM classifier with the inputs of entropy features to identify different emotions. Our results show that MSE of EEG is more efficient than other single-entropy features in recognizing emotions. The performance of BiLSTM is further improved with an accuracy of 70.05% using fused entropy features compared with that of single-type feature.

Discovering dynamic task-modulated functional networks with specific spectral modes using MEG.

Efficient neuronal communication between brain regions through oscillatory synchronization at certain frequencies is necessary for cognition. Such synchronized networks are transient and dynamic, established on the timescale of milliseconds in order to support ongoing cognitive operations. However, few studies characterizing dynamic electrophysiological brain networks have simultaneously accounted for temporal non-stationarity, spectral structure, and spatial properties. Here, we propose an analysis framework for characterizing the large-scale phase-coupling network dynamics during task performance using magnetoencephalography (MEG). We exploit the high spatiotemporal resolution of MEG to measure time-frequency dynamics of connectivity between parcellated brain regions, yielding data in tensor format. We then use a tensor component analysis (TCA)-based procedure to identify the spatio-temporal-spectral modes of covariation among separate regions in the human brain. We validate our pipeline using MEG data recorded during a hand movement task, extracting a transient motor network with beta-dominant spectral mode, which is significantly modulated by the movement task. Next, we apply the proposed pipeline to explore brain networks that support cognitive operations during a working memory task. The derived results demonstrate the temporal formation and dissolution of multiple phase-coupled networks with specific spectral modes, which are associated with face recognition, vision, and movement. The proposed pipeline can characterize the spectro-temporal dynamics of functional connectivity in the brain on the subsecond timescale, commensurate with that of cognitive performance.

Sustaining Attention for a Prolonged Duration Affects Dynamic Organizations of Frequency-Specific Functional Connectivity.

Sustained attention encompasses a cascade of fundamental functions. The human ability to implement a sustained attention task is supported by brain networks that dynamically formed and dissolved through oscillatory synchronization. The decrement of vigilance induced by prolonged task engagement affects sustained attention. However, little is known about which stage or combinations are affected by vigilance decrement. Here, we applied an analysis framework composed of weighted phase lag index (wPLI) and tensor component analysis (TCA) to an EEG dataset collected during 80 min sustained attention task to examine the electrophysiological basis of such effect. We aimed to characterize the phase-coupling networks to untangle different phases involved in sustained attention and study how they are modulated by vigilance decrement. We computed the time-frequency domain wPLI from each block and subject and constructed a fourth-order tensor, containing the time, frequency, functional connectivity (FC), and blocks × subjects. This tensor was subjected to the TCA to identify the interacted and low-dimensional components representing the frequency-specific dynamic FC (fdFC). We extracted four types of neuromakers during a sustained attention task, namely the pre-stimulus alpha right-lateralized parieto-occipital FC, the post-stimulus theta fronto-parieto-occipital FC, delta fronto-parieto-occipital FC, and beta right/left sensorimotor FCs. All these fdFCs were impaired by vigilance decrement. These fdFCs, except for the beta left sensorimotor network, were restored by rewards, although the restoration by reward in the beta right sensorimotor network was transient. These findings provide implications for dissociable effects of vigilance decrement on sustained attention by utilizing the tensor-based framework.

Exploring Frequency-Dependent Brain Networks from Ongoing EEG Using Spatial ICA During Music Listening.

Recently, exploring brain activity based on functional networks during naturalistic stimuli especially music and video represents an attractive challenge because of the low signal-to-noise ratio in collected brain data. Although most efforts focusing on exploring the listening brain have been made through functional magnetic resonance imaging (fMRI), sensor-level electro- or magnetoencephalography (EEG/MEG) technique, little is known about how neural rhythms are involved in the brain network activity under naturalistic stimuli. This study exploited cortical oscillations through analysis of ongoing EEG and musical feature during freely listening to music. We used a data-driven method that combined music information retrieval with spatial Fourier Independent Components Analysis (spatial Fourier-ICA) to probe the interplay between the spatial profiles and the spectral patterns of the brain network emerging from music listening. Correlation analysis was performed between time courses of brain networks extracted from EEG data and musical feature time series extracted from music stimuli to derive the musical feature related oscillatory patterns in the listening brain. We found brain networks of musical feature processing were frequency-dependent. Musical feature time series, especially fluctuation centroid and key feature, were associated with an increased beta activation in the bilateral superior temporal gyrus. An increased alpha oscillation in the bilateral occipital cortex emerged during music listening, which was consistent with alpha functional suppression hypothesis in task-irrelevant regions. We also observed an increased delta-beta oscillatory activity in the prefrontal cortex associated with musical feature processing. In addition to these findings, the proposed method seems valuable for characterizing the large-scale frequency-dependent brain activity engaged in musical feature processing.

Multi-domain Features of the Non-phase-locked Component of Interest Extracted from ERP Data by Tensor Decomposition.

The waveform in the time domain, spectrum in the frequency domain, and topography in the space domain of component(s) of interest are the fundamental indices in neuroscience research. Despite the application of time-frequency analysis (TFA) to extract the temporal and spectral characteristics of non-phase-locked component (NPLC) of interest simultaneously, the statistical results are not always expectedly satisfying, in that the spatial information is not considered. Complex Morlet wavelet transform is widely applied to TFA of event-related-potential (ERP) data, and mother wavelet (which should be firstly defined by center frequency and bandwidth (CFBW) before using the method to TFA of ERP data) influences the time-frequency results. In this study, an optimal set of CFBW was firstly selected from the number sets of CFBW, to further analyze for TFA of the ERP data in a cognitive experiment paradigm of emotion (Anger and Neutral) and task (Go and Nogo). Then tensor decomposition algorithm was introduced to investigate the NPLC of interest from the fourth-order tensor. Compared with the TFA results which only revealed a significant difference between Go and Nogo task condition, the tensor-based analysis showed significant interaction effect between emotion and task. Moreover, significant differences were found in both emotion and task conditions through tensor decomposition. In addition, the statistical results of TFA would be affected by the selected region of interest (ROI), whereas those of the proposed method were not subject to ROI. Hence, this study demonstrated that tensor decomposition method was effective in extracting NPLC, by considering spatial information simultaneously as the potential to explore the brain mechanisms related to experimental design.

Assessment of nonnegative matrix factorization algorithms for electroencephalography spectral analysis.

BACKGROUND: Nonnegative matrix factorization (NMF) has been successfully used for electroencephalography (EEG) spectral analysis. Since NMF was proposed in the 1990s, many adaptive algorithms have been developed. However, the performance of their use in EEG data analysis has not been fully compared. Here, we provide a comparison of four NMF algorithms in terms of accuracy of estimation, stability (repeatability of the results) and time complexity of algorithms with simulated data. In the practical application of NMF algorithms, stability plays an important role, which was an emphasis in the comparison. A Hierarchical clustering algorithm was implemented to evaluate the stability of NMF algorithms. RESULTS: In simulation-based comprehensive analysis of fit, stability, accuracy of estimation and time complexity, hierarchical alternating least squares (HALS) low-rank NMF algorithm (lraNMF_HALS) outperformed the other three NMF algorithms. In the application of lraNMF_HALS for real resting-state EEG data analysis, stable and interpretable features were extracted. CONCLUSION: Based on the results of assessment, our recommendation is to use lraNMF_HALS, providing the most accurate and robust estimation.

Objective Extraction of Evoked Event-Related Oscillation from Time-Frequency Representation of Event-Related Potentials.

Evoked event-related oscillations (EROs) have been widely used to explore the mechanisms of brain activities for both normal people and neuropsychiatric disease patients. In most previous studies, the calculation of the regions of evoked EROs of interest is commonly based on a predefined time window and a frequency range given by the experimenter, which tends to be subjective. Additionally, evoked EROs sometimes cannot be fully extracted using the conventional time-frequency analysis (TFA) because they may be overlapped with each other or with artifacts in time, frequency, and space domains. To further investigate the related neuronal processes, a novel approach was proposed including three steps: (1) extract the temporal and spatial components of interest simultaneously by temporal principal component analysis (PCA) and Promax rotation and project them to the electrode fields for correcting their variance and polarity indeterminacies, (2) calculate the time-frequency representations (TFRs) of the back-projected components, and (3) compute the regions of evoked EROs of interest on TFRs objectively using the edge detection algorithm. We performed this novel approach, conventional TFA, and TFA-PCA to analyse both the synthetic datasets with different levels of SNR and an actual ERP dataset in a two-factor paradigm of waiting time (short/long) and feedback (loss/gain) separately. Synthetic datasets results indicated that N2-theta and P3-delta oscillations can be stably detected from different SNR-simulated datasets using the proposed approach, but, by comparison, only one oscillation was obtained via the last two approaches. Furthermore, regarding the actual dataset, the statistical results for the proposed approach revealed that P3-delta was sensitive to the waiting time but not for that of the other approaches. This study manifested that the proposed approach could objectively extract evoked EROs of interest, which allows a better understanding of the modulations of the oscillatory responses.

Rapid Yeast Cell Viability Analysis by Using a Portable Microscope Based on the Fiber Optic Array and Simple Image Processing.

A fiber optic array (FOA) can be used as an alternative or a supplement to the lens in a microscope due to its large magnification, high coupling efficiency and extremely low distortion. Based on our previous research, this paper first demonstrated the resolution and field-of-view (FOV) of the microscope based on the FOA. To further validate the FOA microscope's imaging capability, yeast activity and concentration were investigated by simple image processing. The results showed that the percentages of live and dead yeast cells correctly identified were 92.1% and 84.8%, except for the clusters, which agreed well with the manual counting methods. Then, the performances of the portable microscopes based on the FOA and lens were compared and the factors that affect the FOA microscope imaging performance were analyzed.

Decoding Analysis of Alpha Oscillation Networks on Maintaining Driver Alertness.

The countermeasure of driver fatigue is valuable for reducing the risk of accidents caused by vigilance failure during prolonged driving. Listening to the radio (RADIO) has been proven to be a relatively effective "in-car" countermeasure. However, the connectivity analysis, which can be used to investigate its alerting effect, is subject to the issue of signal mixing. In this study, we propose a novel framework based on clustering and entropy to improve the performance of the connectivity analysis to reveal the effect of RADIO to maintain driver alertness. Regardless of reducing signal mixing, we introduce clustering algorithm to classify the functional connections with their nodes into different categories to mine the effective information of the alerting effect. Differential entropy (DE) is employed to measure the information content in different brain regions after clustering. Compared with the Louvain-based community detection method, the proposed method shows more superior ability to present RADIO effectin confused functional connection matrices. Our experimental results reveal that the active connection clusters distinguished by the proposed method gradually move from frontal region to parieto-occipital regionwith the progress of fatigue, consistent with the alpha energy changes in these two brain areas. The active class of the clusters in parieto-occipital region significantly decreases and the most active clusters remain in the frontal region when RADIO is taken. The estimation results of DE confirm the significant change (p < 0.05) of information content due to the cluster movements. Hence, preventing the movement of the active clusters from frontal region to parieto-occipital region may correlate with maintaining driver alertness. The revelation of alerting effect is helpful for the targeted upgrade of fatigue countermeasures.

Spatial source phase: A new feature for identifying spatial differences based on complex-valued resting-state fMRI data.

Spatial source phase, the phase information of spatial maps extracted from functional magnetic resonance imaging (fMRI) data by data-driven methods such as independent component analysis (ICA), has rarely been studied. While the observed phase has been shown to convey unique brain information, the role of spatial source phase in representing the intrinsic activity of the brain is yet not clear. This study explores the spatial source phase for identifying spatial differences between patients with schizophrenia (SZs) and healthy controls (HCs) using complex-valued resting-state fMRI data from 82 individuals. ICA is first applied to preprocess fMRI data, and post-ICA phase de-ambiguity and denoising are then performed. The ability of spatial source phase to characterize spatial differences is examined by the homogeneity of variance test (voxel-wise F-test) with false discovery rate correction. Resampling techniques are performed to ensure that the observations are significant and reliable. We focus on two components of interest widely used in analyzing SZs, including the default mode network (DMN) and auditory cortex. Results show that the spatial source phase exhibits more significant variance changes and higher sensitivity to the spatial differences between SZs and HCs in the anterior areas of DMN and the left auditory cortex, compared to the magnitude of spatial activations. Our findings show that the spatial source phase can potentially serve as a new brain imaging biomarker and provide a novel perspective on differences in SZs compared to HCs, consistent with but extending previous work showing increased variability in patient data.

Embodiment Effect on the Comprehension of Mandarin Manual Action Language: An ERP Study.

Embodiment theories argue that language comprehension involves activating specific sensory-motor systems in the brain. Previous research performed in English and other Indo-European languages suggests that, when compared to compatible sentences referring to the same actions performed sequentially (e.g. 'After cleaning the wound he unrolled the bandage'), incompatible sentences describing two manual actions performed simultaneously by an agent (e.g. 'While cleaning the wound he unrolled the bandage') were worse understood and increased the event-related potentials (ERPs) component N400. The present ERP research aims to further investigate brain response to motor compatibility in native Mandarin speakers. The Chinese experimental sentences described two manual actions either in incongruent conditions marked by the Chinese parallel structure … … ('yibian…yibian…'/'while… while…') or congruent conditions marked by the sequential structure … … ('xian…ranhou…'/'firstly… then…'). The last action clause elicited larger fronto-central N400 in the incongruent condition, which reveals that there are semantic embodiment effects on the comprehension of Mandarin manual action language.

Network Entropy for the Sequence Analysis of Functional Connectivity Graphs of the Brain.

Dynamic representation of functional brain networks involved in the sequence analysis of functional connectivity graphs of the brain (FCGB) gains advances in uncovering evolved interaction mechanisms. However, most of the networks, even the event-related ones, are highly heterogeneous due to spurious interactions, which bring challenges to revealing the change patterns of interactive information in the complex dynamic process. In this paper, we propose a network entropy (NE) method to measure connectivity uncertainty of FCGB sequences to alleviate the spurious interaction problem in dynamic network analysis to realize associations with different events during a complex cognitive task. The proposed dynamic analysis approach calculated the adjacency matrices from ongoing electroencephalpgram (EEG) in a sliding time-window to form the FCGB sequences. The probability distribution of Shannon entropy was replaced by the connection sequence distribution to measure the uncertainty of FCGB constituting NE. Without averaging, we used time frequency transform of the NE of FCGB sequences to analyze the event-related changes in oscillatory activity in the single-trial traces during the complex cognitive process of driving. Finally, the results of a verification experiment showed that the NE of the FCGB sequences has a certain time-locked performance for different events related to driver fatigue in a prolonged driving task. The time errors between the extracted time of high-power NE and the recorded time of event occurrence were distributed within the range [-30 s, 30 s] and 90.1% of the time errors were distributed within the range [-10 s, 10 s]. The high correlation (r = 0.99997, p < 0.001) between the timing characteristics of the two types of signals indicates that the NE can reflect the actual dynamic interaction states of brain. Thus, the method may have potential implications for cognitive studies and for the detection of physiological states.