nCREANN: Nonlinear Causal Relationship Estimation by Artificial Neural Network; Applied for Autism Connectivity Study

MCAN: Multimodal Causal Adversarial Networks for Dynamic Effective Connectivity Learning From fMRI and EEG Data

Dynamic effective connectivity (DEC) is the accumulation of effective connectivity in the time dimension, which can describe the continuous neural activities in the brain. Recently, learning DEC from functional magnetic resonance imaging (fMRI) and electroencephalography (EEG) data has attracted the attention of neuroinformatics researchers. However, the current methods fail to consider the gap between the fMRI and EEG modality, which can not precisely learn the DEC network from multimodal data. In this paper, we propose a multimodal causal adversarial network for DEC learning, named MCAN. The MCAN contains two modules: multimodal causal generator and multimodal causal discriminator. First, MCAN employs a multimodal causal generator with an attention-guided layer to produce a posterior signal and output a set of DEC networks. Then, the proposed method uses a multimodal causal discriminator to unsupervised calculate the joint gradient, which directs the update of the whole network. The experimental results on simulated data sets show that MCAN is superior to other state-of-the-art methods in learning the network structure of DEC and can effectively estimate the brain states. The experimental results on real data sets show that MCAN can better reveal abnormal patterns of brain activity and has good application potential in brain network analysis.

Neural connectivity patterns explain why adolescents perceive the world as moving slow

That younger individuals perceive the world as moving slower than adults is a familiar phenomenon. Yet, it remains an open question why that is. Using event segmentation theory, electroencephalogram (EEG) beamforming and nonlinear causal relationship estimation using artificial neural network methods, we studied neural activity while adolescent and adult participants segmented a movie. We show when participants were instructed to segment a movie into meaningful units, adolescents partitioned incoming information into fewer encapsulated segments or episodes of longer duration than adults. Importantly, directed communication between medial frontal and lower-level perceptual areas and between occipito-temporal regions in specific neural oscillation spectrums explained behavioral differences between groups. Overall, the study reveals that a different organization of directed communication between brain regions and inefficient transmission of information between brain regions are key to understand why younger people perceive the world as moving slow.

Event segmentation in ADHD: neglect of social information and deviant theta activity point to a mechanism underlying ADHD

Background

Attention-deficit/hyperactivity disorder (ADHD) is one of the most frequently diagnosed psychiatric conditions in children and adolescents. Although the symptoms appear to be well described, no coherent conceptual mechanistic framework integrates their occurrence and variance and the associated problems that people with ADHD face.

Aims

The current study proposes that altered event segmentation processes provide a novel mechanistic framework for understanding deficits in ADHD.

Methods

Adolescents with ADHD and neurotypically developing (NT) peers watched a short movie and were then asked to indicate the boundaries between meaningful segments of the movie. Concomitantly recorded electroencephalography (EEG) data were analysed for differences in frequency band activity and effective connectivity between brain areas.

Results

Compared with their NT peers, the ADHD group showed less dependence of their segmentation behaviour on social information, indicating that they did not consider social information to the same extent as their unaffected peers. This divergence was accompanied by differences in EEG theta band activity and a different effective connectivity network architecture at the source level. Specifically, NT adolescents primarily showed error signalling in and between the left and right fusiform gyri related to social information processing, which was not the case in the ADHD group. For the ADHD group, the inferior frontal cortex associated with attentional sampling served as a hub instead, indicating problems in the deployment of attentional control.

Conclusions

This study shows that adolescents with ADHD perceive events differently from their NT peers, in association with a different brain network architecture that reflects less adaptation to the situation and problems in attentional sampling of environmental information. The results call for a novel conceptual view of ADHD, based on event segmentation theory.

Neurophysiological effective network connectivity supports a threshold-dependent management of dynamic working memory gating

To facilitate goal-directed actions, effective management of working memory (WM) is crucial, involving a hypothesized WM "gating mechanism." We investigate the underlying neural basis through behavioral modeling and connectivity assessments between neuroanatomical regions linked to theta, alpha, and beta frequency bands. We found opposing, threshold-dependent mechanisms governing WM gate opening and closing. Directed beta band connectivity in the parieto-frontal and parahippocampal-occipital networks was crucial for threshold-dependent WM gating dynamics. Fronto-parahippocampal connectivity in the theta band was also notable for both gating processes, although weaker than that in the beta band. Distinct roles for theta, beta, and alpha bands emerge in maintaining information in WM and shielding against interference, whereby alpha band activity likely acts as a "gatekeeper" supporting processes reflected by beta and theta band activity. The study shows that the decision criterion for WM gate opening/closing relies on concerted interplay within neuroanatomical networks defined by beta and theta band activities.

Description length guided nonlinear unified Granger causality analysis

Most Granger causality analysis (GCA) methods still remain a two-stage scheme guided by different mathematical theories; both can actually be viewed as the same generalized model selection issues. Adhering to Occam's razor, we present a unified GCA (uGCA) based on the minimum description length principle. In this research, considering the common existence of nonlinearity in functional brain networks, we incorporated the nonlinear modeling procedure into the proposed uGCA method, in which an approximate representation of Taylor's expansion was adopted. Through synthetic data experiments, we revealed that nonlinear uGCA was obviously superior to its linear representation and the conventional GCA. Meanwhile, the nonlinear characteristics of high-order terms and cross-terms would be successively drowned out as noise levels increased. Then, in real fMRI data involving mental arithmetic tasks, we further illustrated that these nonlinear characteristics in fMRI data may indeed be drowned out at a high noise level, and hence a linear causal analysis procedure may be sufficient. Next, involving autism spectrum disorder patients data, compared with conventional GCA, the network property of causal connections obtained by uGCA methods appeared to be more consistent with clinical symptoms.

Amortization Transformer for Brain Effective Connectivity Estimation from fMRI Data

Using machine learning methods to estimate brain effective connectivity networks from functional magnetic resonance imaging (fMRI) data has garnered significant attention in the fields of neuroinformatics and bioinformatics. However, existing methods usually require retraining the model for each subject, which ignores the knowledge shared across subjects. In this paper, we propose a novel framework for estimating effective connectivity based on an amortization transformer, named AT-EC. In detail, AT-EC first employs an amortization transformer to model the dynamics of fMRI time series and infer brain effective connectivity across different subjects, which can train an amortized model that leverages the shared knowledge from different subjects. Then, an assisted learning mechanism based on functional connectivity is designed to assist the estimation of the brain effective connectivity network. Experimental results on both simulated and real-world data demonstrate the efficacy of our method.

Altered default mode network causal connectivity patterns in autism spectrum disorder revealed by Liang information flow analysis

Autism spectrum disorder (ASD) is a pervasive developmental disorder with severe cognitive impairment in social communication and interaction. Previous studies have reported that abnormal functional connectivity patterns within the default mode network (DMN) were associated with social dysfunction in ASD. However, how the altered causal connectivity pattern within the DMN affects the social functioning in ASD remains largely unclear. Here, we introduced the Liang information flow method, widely applied to climate science and quantum mechanics, to uncover the brain causal network patterns in ASD. Compared with the healthy controls (HC), we observed that the interactions among the dorsal medial prefrontal cortex (dMPFC), ventral medial prefrontal cortex (vMPFC), hippocampal formation, and temporo-parietal junction showed more inter-regional causal connectivity differences in ASD. For the topological property analysis, we also found the clustering coefficient of DMN and the In-Out degree of anterior medial prefrontal cortex were significantly decreased in ASD. Furthermore, we found that the causal connectivity from dMPFC to vMPFC was correlated with the clinical symptoms of ASD. These altered causal connectivity patterns indicated that the DMN inter-regions information processing was perturbed in ASD. In particular, we found that the dMPFC acts as a causal source in the DMN in HC, whereas it plays a causal target in ASD. Overall, our findings indicated that the Liang information flow method could serve as an important way to explore the DMN causal connectivity patterns, and it also can provide novel insights into the nueromechanisms underlying DMN dysfunction in ASD.

Investigating the discrimination of linear and nonlinear effective connectivity patterns of EEG signals in children with Attention-Deficit/Hyperactivity Disorder and Typically Developing children

BACKGROUND

Analysis of effective connectivity among brain regions is an important key to decipher the mechanisms underlying neural disorders such as Attention Deficit Hyperactivity Disorder (ADHD). We previously introduced a new method, called nCREANN (nonlinear Causal Relationship Estimation by Artificial Neural Network), for estimating linear and nonlinear components of effective connectivity, and provided novel findings about effective connectivity of EEG signals of children with autism. Using the nCREANN method in the present study, we assessed effective connectivity patterns of ADHD children based on their EEG signals recorded during a visual attention task, and compared them with the aged-matched Typically Developing (TD) subjects.

METHOD

In addition to the nCREANN method for estimating linear and nonlinear aspects of effective connectivity, the direct Directed Transfer Function (dDTF) was utilized to extract the spectral information of connectivity patterns.

RESULTS

The dDTF results did not suggest a specific frequency band for distinguishing between the two groups, and different patterns of effective connectivity were observed in all bands. Both nCREANN and dDTF methods showed decreased connectivity between temporal/frontal and temporal/occipital regions, and increased connection between frontal/parietal regions in ADHDs than TDs. Furthermore, the nCREANN results showed more left-lateralized connections in ADHDs compared to the symmetric bilateral inter-hemispheric interactions in TDs. In addition, by fusion of linear and nonlinear connectivity measures of nCREANN method, we achieved an accuracy of 99% in classification of the two groups.

CONCLUSION

These findings emphasize the capability of nCREANN method to investigate the brain functioning of neural disorders and its strength in preciously distinguish between healthy and disordered subjects.

Granger causality test with nonlinear neural-network-based methods: Python package and simulation study

BACKGROUND AND OBJECTIVE

Causality defined by Granger in 1969 is a widely used concept, particularly in neuroscience and economics. As there is an increasing interest in nonlinear causality research, a Python package with a neural-network-based causality analysis approach was created. It allows performing causality tests using neural networks based on Long Short-Term Memory (LSTM), Gated Recurrent Unit (GRU), or Multilayer Perceptron (MLP). The aim of this paper is to present the nonlinear method for causality analysis and the created Python package.

METHODS

The created functions with the autoregressive (AR) and Generalized Radial Basis Functions (GRBF) neural network models were tested on simulated signals in two cases: with nonlinear dependency and with absence of causality from Y to X signal. The train-test split (70/30) was used. Errors obtained on the test set were compared using the Wilcoxon signed-rank test to determine the presence of the causality. For the chosen model, the proposed method of study the change of causality over time was presented.

RESULTS

In the case when X was a polynomial of Y, nonlinear methods were able to detect the causality, while the AR model did not manage to indicate it. The best results (in terms of the prediction accuracy) were obtained for the MLP for the lag of 150 (MSE equal to 0.011, compared to 0.041 and 0.036 for AR and GRBF, respectively). When there was no causality between the signals, none of the proposed and AR models did indicate false causality, while it was detected by GRBF models in one case. Only the proposed models gave the expected results in each of the tested scenarios.

CONCLUSIONS

The proposed method appeared to be superior to the compared methods. They were able to detect non-linear causality, make accurate forecasting and not indicate false causality. The created package enables easy usage of neural networks to study the causal relationship between signals. The neural-networks-based approach is a suitable method that allows the detection of a nonlinear causal relationship, which cannot be detected by the classical Granger method. Unlike other similar tools, the package allows for the study of changes in causality over time.

Estimating Effective Connectivity by Recurrent Generative Adversarial Networks

Estimating effective connectivity from functional magnetic resonance imaging (fMRI) time series data has become a very hot topic in neuroinformatics and brain informatics. However, it is hard for the current methods to accurately estimate the effective connectivity due to the high noise and small sample size of fMRI data. In this paper, we propose a novel framework for estimating effective connectivity based on recurrent generative adversarial networks, called EC-RGAN. The proposed framework employs the generator that consists of a set of effective connectivity generators based on recurrent neural networks to generate the fMRI time series of each brain region, and uses the discriminator to distinguish between the joint distributions of the real and generated fMRI time series. When the model is well-trained and generated fMRI data is similar to real fMRI data, EC-RGAN outputs the effective connectivity by means of the causal parameters of the effective connectivity generators. Experimental results on both simulated and real-world fMRI time series data demonstrate the efficacy of our proposed framework.