Dynamic effective connectivity

Dysregulated brain dynamics in the visualmotor network in type 2 diabetes patients and their relationship with cognitive impairment

OBJECTIVE

Type 2 diabetes mellitus (T2DM) is a significant risk factor for mild cognitive impairment (MCI). Here, we identified a T2DM-specific effective connectivity (EC) network, the dynamic features of which could be used to distinguish T2DM patients with MCI from healthy controls (HC) and correlation with cognitive performance.

METHODS

Local and multicentered T2DM patients and matched HC who underwent functional magnetic resonance imaging were recruited. Their static and dynamic effective connectivity were compared. The relationships between connectome characteristics and cognitive performance were also evaluated.

RESULTS

The nodes of the T2DM-related static causality network included the anterior central gyrus, tail of the parahippocampal gyrus, posterior superior temporal sulcus, posterior central parietal lobe, posterior central gyrus and V5 region of the occipital lobe. The V5 region of the visual cortex was the core node. In the multicentered dataset, compared with the HC group, the T2DM with MCI group had significantly greater fractional window and mean dwell time. Fractional windows of the state, which was dominated by the interaction of the nodes from SomMot_Network, Limbic_Network, Default_Network, in the T2DM-specific network increased with poorer cognitive performance in T2DM with MCI patients.

CONCLUSION

Our findings provide insights into the neurobiological mechanisms of the cognitive impairment of T2DM patients from a dynamic network perspective, which may ultimately inform more targeted and effective strategies to prevent MCI.

Methods for Brain Connectivity Analysis with Applications to Rat Local Field Potential Recordings

Modeling the brain dependence network is central to understanding underlying neural mechanisms such as perception, action, and memory. In this study, we present a broad range of statistical methods for analyzing dependence in a brain network. Leveraging a combination of classical and cutting-edge approaches, we analyze multivariate hippocampal local field potential (LFP) time series data concentrating on the encoding of nonspatial olfactory information in rats. We present the strengths and limitations of each method in capturing neural dynamics and connectivity. Our analysis begins with exploratory techniques, including correlation, partial correlation, spectral matrices, and coherence, to establish foundational connectivity insights. We then investigate advanced methods such as Granger causality (GC), robust canonical coherence analysis, spectral transfer entropy (STE), and wavelet coherence to capture dynamic and nonlinear interactions. Additionally, we investigate the utility of topological data analysis (TDA) to extract multi-scale topological features and explore deep learning-based canonical correlation frameworks for connectivity modeling. This comprehensive approach offers an introduction to the state-of-the-art techniques for the analysis of dependence networks, emphasizing the unique strengths of various methodologies, addressing computational challenges, and paving the way for future research.

Knowledge concept recognition in the learning brain via fMRI classification

Knowledge concept recognition (KCR) aims to identify the concepts learned in the brain, which has been a longstanding area of interest for learning science and education. While many studies have investigated object recognition using brain fMRIs, there are limited research on identifying specific knowledge points within the classroom. In this paper, we propose to recognize the knowledge concepts in computer science by classifying the brain fMRIs taken when students are learning the concepts. More specifically, this study made attempts on two representation strategies, i.e., voxel and time difference. Based on the representations, we evaluated traditional classifiers and the combination of CNN and LSTM for KCR. Experiments are conducted on a public dataset collected from 25 students and teachers in a computer science course. The evaluations of classifying fMRI segments show that the used classifiers all can attain a good performance when using the time-difference representation, where the CNN-LSTM model reaches the highest accuracy. This research contributes to the understanding of human learning and supports the development of personalized learning.

Resting-state voxel-wise dynamic effective connectivity predicts risky decision-making in patients with bipolar disorder type I

Patients with Bipolar Disorder type I (BD-I) exhibit maladaptive risky decision-making, which is related to impulsivity, suicide attempts, and aggressive behavior. Currently, there is a lack of effective predictive methods for early intervention in risky behaviors for patients with BD-I. This study aimed to predict risky behavior in patients with BD-I using resting-state functional magnetic resonance imaging (rs-fMRI). We included 48 patients with BD-I and 124 healthy controls (HC) and constructed voxel-wise functional connectivity (FC), dynamic FC (dFC), effective connectivity (EC), and dynamic EC (dEC) for each subject. The Balloon Analogue Risk Task (BART) was employed to measure the risky decision-making of all participants. We applied connectome-based predictive modeling (CPM) with five regression algorithms to predict risky behaviors as well as Barratt Impulsivity Scale (BIS) scores. Results showed that the BD-I had significantly lower risky adjusted pump scores compared to HC. The dEC-based linear regression-CPM model exhibited significant predictive ability for the adjusted pump scores in BD-I, while no significant predictive power was observed in HC. Furthermore, this model successfully predicted non-planning impulsiveness, motor impulsiveness, and BIS total score, but failed for attentional impulsiveness in BD-I. These findings provide a foundation for future work in predicting risky behaviors of psychiatric patients by using voxel-wise dEC underlying resting state.

Dynamic brain entropy predicts risky decision-making across transdiagnostic dimensions of psychopathology

OBJECTIVES

Maladaptive risky decision-making is a common pathological behavior among patients with various psychiatric disorders. Brain entropy, which measures the complexity of brain time series signals, provides a novel approach to assessing brain health. Despite its potential, the dynamics of brain entropy have seldom been explored. This study aimed to construct a dynamic model of brain entropy and examine its predictive value for risky decision-making in patients with mental disorders, utilizing resting-state functional magnetic resonance imaging (rs-fMRI).

METHODS

This study analyzed the rs-fMRI data from a total of 198 subjects, including 48 patients with bipolar disorder (BD), 47 patients with schizophrenia (SZ), 40 patients with adult attention deficit hyperactivity disorder (ADHD), as well as 63 healthy controls (HC). Time series signals were extracted from 264 brain regions based on rs-fMRI. The traditional static entropy and dynamic entropy (coefficient of variation, CV; rate of change, Rate) were constructed, respectively. Support vector regression was employed to predict risky decision-making utilizing leave-one-out cross-validation within each group.

RESULTS

Our findings showed that CV achieved the best performances in HC and BD groups (r = -0.58, MAE = 6.43, R2 = 0.32; r = -0.78, MAE = 12.10, R2 = 0.61), while the Rate achieved the best in SZ and ADHD groups (r = -0.69, MAE = 10.20, R2 = 0.47; r = -0.78, MAE = 7.63, R2 = 0.60). For the dynamic entropy, the feature selection threshold rather than the time window length and overlapping ratio influenced predictive performance.

CONCLUSIONS

These results suggest that dynamic brain entropy could be a more effective predictor of risky decision-making than traditional static brain entropy. Our findings offer a novel perspective on exploring brain signal complexity and can serve as a reference for interventions targeting risky decision-making behaviors, particularly in individuals with psychiatric diagnoses.

Beyond neurons and spikes: cognon, the hierarchical dynamical unit of thought

From the dynamical point of view, most cognitive phenomena are hierarchical, transient and sequential. Such cognitive spatio-temporal processes can be represented by a set of sequential metastable dynamical states together with their associated transitions: The state is quasi-stationary close to one metastable state before a rapid transition to another state. Hence, we postulate that metastable states are the central players in cognitive information processing. Based on the analogy of quasiparticles as elementary units in physics, we introduce here the quantum of cognitive information dynamics, which we term "cognon". A cognon, or dynamical unit of thought, is represented by a robust finite chain of metastable neural states. Cognons can be organized at multiple hierarchical levels and coordinate complex cognitive information representations. Since a cognon is an abstract conceptualization, we link this abstraction to brain sequential dynamics that can be measured using common modalities and argue that cognons and brain rhythms form binding spatiotemporal complexes to keep simultaneous dynamical information which relate the 'what', 'where' and 'when'.

NHSMM-MAR-sdNC: A novel data-driven computational framework for state-dependent effective connectivity analysis

The brain exhibits intrinsic dynamics characterized by spontaneous spatiotemporal reorganization of neural activity or metastability, which is associated closely with functional integration and segregation. Compared to dynamic functional connectivity, state-dependent effective connectivity (i.e., dynamic effective connectivity) is more suitable for exploring the metastability as its ability to infer causalities between brain regions. However, methods for state-dependent effective connectivity are scarce and urgently needed. In this study, a novel data-driven computational framework, named NHSMM-MAR-sdNC integrating nonparametric hidden semi-Markov model combined with multivariate autoregressive model and state-dependent new causality, is proposed to investigate the state-dependent effective connectivity. The framework is not constrained by any biological assumptions. Furthermore, state number can be inferred from the observed data directly and the state duration distributions will be estimated explicitly rather than restricted by geometric form, which overcomes limitations of hidden Markov model. Experimental results of synthetic data show that the framework can identify the state number adaptively and the state-dependent causality networks accurately. The dynamics of state-related causality networks are also revealed by the new method on real-world resting-state fMRI data. Our method provides a new data-driven computational framework for identifying state-dependent effective connectivity, which will facilitate the identification and assessment of metastability and itinerant dynamics of the brain.

Brain state and dynamic transition patterns of motor imagery revealed by the bayes hidden markov model

Motor imagery (MI) is a high-level cognitive process that has been widely applied to brain-computer inference (BCI) and motor recovery. In practical applications, however, huge individual differences and unclear neural mechanisms have seriously hindered the application of MI and BCI systems. Thus, it is urgently needed to explore MI from a new perspective. Here, we applied a hidden Markov model (HMM) to explore the dynamic organization patterns of left- and right-hand MI tasks. Eleven distinct HMM states were identified based on MI-related EEG data. We found that these states can be divided into three metastates by clustering analysis, showing a highly organized structure. We also assessed the probability activation of each HMM state across time. The results showed that the state probability activation of task-evoked have similar trends to that of event-related desynchronization/synchronization (ERD/ERS). By comparing the differences in temporal features of HMM states between left- and right-hand MI, we found notable variations in fractional occupancy, mean life time, mean interval time, and transition probability matrix across stages and states. Interestingly, we found that HMM states activated in the left occipital lobe had higher occupancy during the left-hand MI task, and conversely, during the right-hand MI task, HMM states activated in the right occipital lobe had higher occupancy. Moreover, significant correlations were observed between BCI performance and features of HMM states. Taken together, our findings explored dynamic networks underlying the MI-related process and provided a complementary understanding of different MI tasks, which may contribute to improving the MI-BCI systems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11571-024-10099-9.

Thalamocortical dysconnectivity is associated with pain in patients with knee osteoarthritis

Previous studies have suggested that the morphology and function of the thalamus and cortex are abnormal in patients with knee osteoarthritis (KOA). However, whether the thalamocortical network is differentially affected in this disorder is unknown. In this study, we examined functional and effective connectivity between the thalamus and major divisions of the cortex in 27 healthy controls and 27 KOA patients using functional magnetic resonance imaging. We also explored the topological features of the brain via graph theory analysis. The results suggested that patients with KOA had significantly reduced resting-state functional connectivity (rsFC) of the thalamo-sensorimotor pathway; enhanced rsFC of the thalamo-medial/lateral frontal cortex (mFC/LFC), parietal, temporal and occipital pathways; reduced effective connectivity of the left sensorimotor-to-thalamus pathway; and enhanced effective connectivity of the right thalamus-to-sensorimotor pathway compared with healthy controls. The functional connectivity of the thalamo-sensorimotor and thalamo-mFC pathways was enhanced when patients performed the multisource interference task. Moreover, patients with KOA presented altered nodal properties associated with thalamocortical circuits, including the thalamus, amygdala, and regions in default mode networks, compared with healthy controls. The correlation analysis suggested a significant negative correlation between thalamo-mFC rsFC and pain intensity, between thalamo-sensorimotor task-related connectivity and disease duration/depression scores, and a positive correlation between right frontal nodal properties and pain intensity in KOA patients. Taken together, these findings establish abnormal and differential alterations in the thalamocortical network associated with pain characteristics in KOA patients, which extends our understanding of their role in the pathophysiology of KOA.

Dynamic effective connectivity in the cerebellar dorsal dentate nucleus and the cerebrum, cognitive impairment, and clinical correlates in patients with schizophrenia

BACKGROUND

Schizophrenia (SZ) is characterized by disconnected cerebral networks. Recent studies have shown that functional connectivity between the cerebellar dorsal dentate nucleus (dDN) and cerebrum is correlated with psychotic symptoms, and processing speed in SZ patients. Dynamic effective connectivity (dEC) is a reliable indicator of brain functional status. However, the dEC between the dDN and cerebrum in patients with SZ remains largely unknown.

METHODS

Resting-state functional MRI data, symptom severity, and cognitive performance were collected from 74 SZ patients and 53 healthy controls (HC). Granger causality analysis and sliding time window methods were used to calculate dDN-based dEC maps for all subjects, and k-means clustering was performed to obtain several dEC states. Finally, between-group differences in dynamic effective connectivity variability (dECV) and clinical correlations were obtained using two-sample t-tests and correlation analysis.

RESULTS

We detected four dEC states from the cerebrum to the right dDN (IN states) and three dEC states from the right dDN to the cerebrum (OUT states), with SZ group having fewer transitions in the OUT states. SZ group had increased dECV from the right dDN to the right middle frontal gyrus (MFG) and left lingual gyrus (LG). Correlations were found between the dECV from the right dDN to the right MFG and symptom severity and between the dECV from the right dDN to the left LG and working memory performance.

CONCLUSIONS

This study reveals a dynamic causal relationship between cerebellar dDN and the cerebrum in SZ and provides new evidence for the involvement of cerebellar neural circuits in neurocognitive functions in SZ.

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.

Dynamic Organization of Large-scale Functional Brain Networks Supports Interactions Between Emotion and Executive Control

Emotion and executive control are often conceptualized as two distinct modes of human brain functioning. Little, however, is known about how the dynamic organization of large-scale functional brain networks that support flexible emotion processing and executive control, especially their interactions. The amygdala and prefrontal systems have long been thought to play crucial roles in these processes. Recent advances in human neuroimaging studies have begun to delineate functional organization principles among the large-scale brain networks underlying emotion, executive control, and their interactions. Here, we propose a dynamic brain network model to account for interactive competition between emotion and executive control by reviewing recent resting-state and task-related neuroimaging studies using network-based approaches. In this model, dynamic interactions among the executive control network, the salience network, the default mode network, and sensorimotor networks enable dynamic processes of emotion and support flexible executive control of multiple processes; neural oscillations across multiple frequency bands and the locus coeruleus-norepinephrine pathway serve as communicational mechanisms underlying dynamic synergy among large-scale functional brain networks. This model has important implications for understanding how the dynamic organization of complex brain systems and networks empowers flexible cognitive and affective functions.

Seizure onset zone (SOZ) identification using effective brain connectivity of epileptogenic networks

Objective. To demonstrate the capability of utilizing graph feature-based supervised machine learning (ML) algorithm on intracranial electroencephalogram recordings for the identification of seizure onset zones (SOZs) in individuals with drug-resistant epilepsy.Approach. Utilizing three model-free measures of effective connectivity (EC)-directed information, mutual information-guided Granger causality index (MI-GCI), and frequency-domain convergent cross-mapping (FD-CCM) - directed graphs are generated. Graph centrality measures at different sparsity are used as the classifier's features.Main results. The centrality features achieve high accuracies exceeding 90% in distinguishing SOZ electrodes from non-SOZ electrodes. Notably, a sparse graph representation with just ten features and simple ML models effectively achieves such performance. The study identifies FD-CCM centrality measures as particularly significant, with a mean AUC of 0.93, outperforming prior literature. The FD-CCM-based graph modeling also highlights elevated centrality measures among SOZ electrodes, emphasizing heightened activity relative to non-SOZ electrodes during ictogenesis.Significance. This research not only underscores the efficacy of automated SOZ identification but also illuminates the potential of specific EC measures in enhancing discriminative power within the context of epilepsy research.

The subcortical brain regions influence the cortical areas during resting-state: an fMRI study

Introduction

Numerous modes or patterns of neural activity can be seen in the brain of individuals during the resting state. However, those functions do not persist long, and they are continuously altering in the brain. We have hypothesized that the brain activations during the resting state should themselves be responsible for this alteration of the activities.

Methods

Using the resting-state fMRI data of 63 healthy young individuals, we estimated the causality effects of each resting-state activation map on all other networks. The resting-state networks were identified, their causality effects on the other components were extracted, the networks with the top 20% of the causality were chosen, and the networks which were under the influence of those causal networks were also identified.

Results

Our results showed that the influence of each activation component over other components is different. The brain areas which showed the highest causality coefficients were subcortical regions, such as the brain stem, thalamus, and amygdala. On the other hand, nearly all the areas which were mostly under the causal effects were cortical regions.

Discussion

In summary, our results suggest that subcortical brain areas exert a higher influence on cortical regions during the resting state, which could help in a better understanding the dynamic nature of brain functions.

Brain functional network changes in patients with juvenile myoclonic epilepsy: a study based on graph theory and Granger causality analysis

Many resting-state functional magnetic resonance imaging (rs-fMRI) studies have shown that the brain networks are disrupted in adolescent patients with juvenile myoclonic epilepsy (JME). However, previous studies have mainly focused on investigating brain connectivity disruptions from the perspective of static functional connections, overlooking the dynamic causal characteristics between brain network connections. In our study involving 37 JME patients and 35 Healthy Controls (HC), we utilized rs-fMRI to construct whole-brain functional connectivity network. By applying graph theory, we delved into the altered topological structures of the brain functional connectivity network in JME patients and identified abnormal regions as key regions of interest (ROIs). A novel aspect of our research was the application of a combined approach using the sliding window technique and Granger causality analysis (GCA). This method allowed us to delve into the dynamic causal relationships between these ROIs and uncover the intricate patterns of dynamic effective connectivity (DEC) that pervade various brain functional networks. Graph theory analysis revealed significant deviations in JME patients, characterized by abnormal increases or decreases in metrics such as nodal betweenness centrality, degree centrality, and efficiency. These findings underscore the presence of widespread disruptions in the topological features of the brain. Further, clustering analysis of the time series data from abnormal brain regions distinguished two distinct states indicative of DEC patterns: a state of strong connectivity at a lower frequency (State 1) and a state of weak connectivity at a higher frequency (State 2). Notably, both states were associated with connectivity abnormalities across different ROIs, suggesting the disruption of local properties within the brain functional connectivity network and the existence of widespread multi-functional brain functional networks damage in JME patients. Our findings elucidate significant disruptions in the local properties of whole-brain functional connectivity network in patients with JME, revealing causal impairments across multiple functional networks. These findings collectively suggest that JME is a generalized epilepsy with localized abnormalities. Such insights highlight the intricate network dysfunctions characteristic of JME, thereby enriching our understanding of its pathophysiological features.

Linking fast and slow: The case for generative models

A pervasive challenge in neuroscience is testing whether neuronal connectivity changes over time due to specific causes, such as stimuli, events, or clinical interventions. Recent hardware innovations and falling data storage costs enable longer, more naturalistic neuronal recordings. The implicit opportunity for understanding the self-organised brain calls for new analysis methods that link temporal scales: from the order of milliseconds over which neuronal dynamics evolve, to the order of minutes, days, or even years over which experimental observations unfold. This review article demonstrates how hierarchical generative models and Bayesian inference help to characterise neuronal activity across different time scales. Crucially, these methods go beyond describing statistical associations among observations and enable inference about underlying mechanisms. We offer an overview of fundamental concepts in state-space modeling and suggest a taxonomy for these methods. Additionally, we introduce key mathematical principles that underscore a separation of temporal scales, such as the slaving principle, and review Bayesian methods that are being used to test hypotheses about the brain with multiscale data. We hope that this review will serve as a useful primer for experimental and computational neuroscientists on the state of the art and current directions of travel in the complex systems modelling literature.

Spectral dynamic causal modeling: A didactic introduction and its relationship with functional connectivity

We present a didactic introduction to spectral dynamic causal modeling (DCM), a Bayesian state-space modeling approach used to infer effective connectivity from noninvasive neuroimaging data. Spectral DCM is currently the most widely applied DCM variant for resting-state functional MRI analysis. Our aim is to explain its technical foundations to an audience with limited expertise in state-space modeling and spectral data analysis. Particular attention will be paid to cross-spectral density, which is the most distinctive feature of spectral DCM and is closely related to functional connectivity, as measured by (zero-lag) Pearson correlations. In fact, the model parameters estimated by spectral DCM are those that best reproduce the cross-correlations between all measurements-at all time lags-including the zero-lag correlations that are usually interpreted as functional connectivity. We derive the functional connectivity matrix from the model equations and show how changing a single effective connectivity parameter can affect all pairwise correlations. To complicate matters, the pairs of brain regions showing the largest changes in functional connectivity do not necessarily coincide with those presenting the largest changes in effective connectivity. We discuss the implications and conclude with a comprehensive summary of the assumptions and limitations of spectral DCM.

Dementia classification using a graph neural network on imaging of effective brain connectivity

Alzheimer's disease (AD) and Parkinson's disease (PD) are two of the most common forms of neurodegenerative diseases. The literature suggests that effective brain connectivity (EBC) has the potential to track differences between AD, PD and healthy controls (HC). However, how to effectively use EBC estimations for the research of disease diagnosis remains an open problem. To deal with complex brain networks, graph neural network (GNN) has been increasingly popular in very recent years and the effectiveness of combining EBC and GNN techniques has been unexplored in the field of dementia diagnosis. In this study, a novel directed structure learning GNN (DSL-GNN) was developed and performed on the imaging of EBC estimations and power spectrum density (PSD) features. In comparison to the previous studies on GNN, our proposed approach enhanced the functionality for processing directional information, which builds the basis for more efficiently performing GNN on EBC. Another contribution of this study is the creation of a new framework for applying univariate and multivariate features simultaneously in a classification task. The proposed framework and DSL-GNN are validated in four discrimination tasks and our approach exhibited the best performance, against the existing methods, with the highest accuracy of 94.0% (AD vs. HC), 94.2% (PD vs. HC), 97.4% (AD vs. PD) and 93.0% (AD vs. PD vs. HC). In a word, this research provides a robust analytical framework to deal with complex brain networks containing causal directional information and implies promising potential in the diagnosis of two of the most common neurodegenerative conditions.

[Connectome in stroke patients]

Stroke is the main cause of disability among neurological diseases. There are questions of the accuracy of topical diagnosis and rehabilitation prognosis in clinical practice. Answers to these questions may be given by an approach to the study of the nervous system as a dynamic network consisting of a set of brain regions with anatomical and functional connections between them. Active study of the connectome in neurological patients in recent years became possible due to the availability of noninvasive neuroimaging methods. This review covers types of connectome and most accessible methods of obtaining research data for their construction in a neurological hospital. The review also describes resting-state networks that reflect basic brain activity in the absence of tasks. Resting-state connectivity can be used for the diagnosis of patients with severe neurological deficits. Also, changes in resting-state connectivity may indicate recovery after a stroke. The connectome analysis uses graph theory, representing the nervous system as a set of nodes and connections between them, and providing a mathematical framework allowing to study it, and methods of algebraic topology that expand the possibilities of analyzing neuroimaging data beyond graph theory. Attention is paid to the concept of self-organized criticality, which describes the brain as a system located near the critical point, where the transmission of information is most optimized. Also presented are data from studies of self-organized criticality in relation to the dynamics of recovery of patients after stroke.

Macroscopic resting-state brain dynamics are best described by linear models

It is typically assumed that large networks of neurons exhibit a large repertoire of nonlinear behaviours. Here we challenge this assumption by leveraging mathematical models derived from measurements of local field potentials via intracranial electroencephalography and of whole-brain blood-oxygen-level-dependent brain activity via functional magnetic resonance imaging. We used state-of-the-art linear and nonlinear families of models to describe spontaneous resting-state activity of 700 participants in the Human Connectome Project and 122 participants in the Restoring Active Memory project. We found that linear autoregressive models provide the best fit across both data types and three performance metrics: predictive power, computational complexity and the extent of the residual dynamics unexplained by the model. To explain this observation, we show that microscopic nonlinear dynamics can be counteracted or masked by four factors associated with macroscopic dynamics: averaging over space and over time, which are inherent to aggregated macroscopic brain activity, and observation noise and limited data samples, which stem from technological limitations. We therefore argue that easier-to-interpret linear models can faithfully describe macroscopic brain dynamics during resting-state conditions.

A new causal centrality measure reveals the prominent role of subcortical structures in the causal architecture of the extended default mode network

Network representation has been an incredibly useful concept for understanding the behavior of complex systems in social sciences, biology, neuroscience, and beyond. Network science is mathematically founded on graph theory, where nodal importance is gauged using measures of centrality. Notably, recent work suggests that the topological centrality of a node should not be over-interpreted as its dynamical or causal importance in the network. Hence, identifying the influential nodes in dynamic causal models (DCM) remains an open question. This paper introduces causal centrality for DCM, a dynamics-sensitive and causally-founded centrality measure based on the notion of intervention in graphical models. Operationally, this measure simplifies to an identifiable expression using Bayesian model reduction. As a proof of concept, the average DCM of the extended default mode network (eDMN) was computed in 74 healthy subjects. Next, causal centralities of different regions were computed for this causal graph, and compared against several graph-theoretical centralities. The results showed that the subcortical structures of the eDMN were more causally central than the cortical regions, even though the graph-theoretical centralities unanimously favored the latter. Importantly, model comparison revealed that only the pattern of causal centrality was causally relevant. These results are consistent with the crucial role of the subcortical structures in the neuromodulatory systems of the brain, and highlight their contribution to the organization of large-scale networks. Potential applications of causal centrality-to study causal models of other neurotypical and pathological functional networks-are discussed, and some future lines of research are outlined.

Understanding the concept of a novel tool requires interaction of the dorsal and ventral streams

The left hemisphere tool-use network consists of the dorso-dorsal, ventro-dorsal, and ventral streams, each with distinct computational abilities. In the dual-loop model, the ventral pathway through the extreme capsule is associated with conceptual understanding. We performed a learning experiment with fMRI to investigate how these streams interact when confronted with novel tools. In session one, subjects observed pictures and video sequences in real world action of known and unknown tools and were asked whether they knew the tools and whether they understood their function. In session two, video sequences of unknown tools were presented again, followed again by the question of understanding their function. Different conditions were compared to each other and effective connectivity (EC) in the tool-use network was examined. During concept acquisition of an unknown tool, EC between dorsal and ventral streams was found posterior in fusiform gyrus and anterior in inferior frontal gyrus, with a functional interaction between BA44d and BA45. When previously unknown tools were presented for a second time, EC was prominent only between dorsal stream areas. Understanding the concept of a novel tool requires an interaction of the ventral stream with the dorsal streams. Once the concept is acquired, dorsal stream areas are sufficient.

Frequency specificity of aberrant triple networks in major depressive disorder: a resting-state effective connectivity study

Major depressive disorder (MDD) has been associated with aberrant effective connectivity (EC) among the default mode network (DMN), salience network (SN), and central executive network (CEN)-collectively referred to as triple networks. However, prior research has predominantly concentrated on broad frequency bands (0.01-0.08 Hz or 0.01-0.15 Hz), ignoring the influence of distinct rhythms on triple network causal dynamics. In the present study, we aim to investigate EC alterations within the triple networks across various frequency bands in patients with MDD. Utilizing a data-driven frequency decomposition approach and a multivariate Granger causality analysis, we characterized frequency-specific EC patterns of triple networks in 49 MDD patients and 54 healthy controls. A support vector machine classifier was subsequently employed to assess the discriminative capacity of the frequency-specific EC features. Our findings revealed that, compared to controls, patients exhibited not only enhanced mean EC within the CEN in the conventional frequency band (0.01-0.08 Hz), but also decreased mean EC from the SN to the DMN in a higher frequency band (0.12-0.18 Hz), and increased mean EC from the CEN to the SN in a sub-frequency band (0.04-0.08 Hz); the latter was significantly correlated with disease severity. Moreover, optimal classification performance for distinguishing patients from controls was attained by combining EC features across all three frequency bands, with the area under the curve (AUC) value of 0.8831 and the corresponding accuracy, sensitivity, and specificity of 89.97%, 92.63%, and 87.32%, respectively. These insights into EC changes within the triple networks across multiple frequency bands offer valuable perspectives on the neurobiological basis of MDD and could aid in developing frequency-specific EC features as potential biomarkers for disease diagnosis.

Amortized Bayesian inference on generative dynamical network models of epilepsy using deep neural density estimators

Whole-brain modeling of epilepsy combines personalized anatomical data with dynamical models of abnormal activities to generate spatio-temporal seizure patterns as observed in brain imaging data. Such a parametric simulator is equipped with a stochastic generative process, which itself provides the basis for inference and prediction of the local and global brain dynamics affected by disorders. However, the calculation of likelihood function at whole-brain scale is often intractable. Thus, likelihood-free algorithms are required to efficiently estimate the parameters pertaining to the hypothetical areas, ideally including the uncertainty. In this study, we introduce the simulation-based inference for the virtual epileptic patient model (SBI-VEP), enabling us to amortize the approximate posterior of the generative process from a low-dimensional representation of whole-brain epileptic patterns. The state-of-the-art deep learning algorithms for conditional density estimation are used to readily retrieve the statistical relationships between parameters and observations through a sequence of invertible transformations. We show that the SBI-VEP is able to efficiently estimate the posterior distribution of parameters linked to the extent of the epileptogenic and propagation zones from sparse intracranial electroencephalography recordings. The presented Bayesian methodology can deal with non-linear latent dynamics and parameter degeneracy, paving the way for fast and reliable inference on brain disorders from neuroimaging modalities.

Effective Connectivity Evaluation of Resting-State Brain Networks in Alzheimer's Disease, Amnestic Mild Cognitive Impairment, and Normal Aging: An Exploratory Study

(1) Background: Alzheimer's disease (AD) is a neurodegenerative disease with a high prevalence. Despite the cognitive tests to diagnose AD, there are pitfalls in early diagnosis. Brain deposition of pathological markers of AD can affect the direction and intensity of the signaling. The study of effective connectivity allows the evaluation of intensity flow and signaling pathways in functional regions, even in the early stage, known as amnestic mild cognitive impairment (aMCI). (2) Methods: 16 aMCI, 13 AD, and 14 normal subjects were scanned using resting-state fMRI and T1-weighted protocols. After data pre-processing, the signal of the predefined nodes was extracted, and spectral dynamic causal modeling analysis (spDCM) was constructed. Afterward, the mean and standard deviation of the Jacobin matrix of each subject describing effective connectivity was calculated and compared. (3) Results: The maps of effective connectivity in the brain networks of the three groups were different, and the direction and strength of the causal effect with the progression of the disease showed substantial changes. (4) Conclusions: Impaired information flow in the resting-state networks of the aMCI and AD groups was found versus normal groups. Effective connectivity can serve as a potential marker of Alzheimer's pathophysiology, even in the early stages of the disease.

Objective biomarkers of depression: A study of Granger causality and wavelet coherence in resting-state fMRI

BACKGROUND AND PURPOSE

The lack of a robust diagnostic biomarker makes understanding depression from a neurobiological standpoint an important goal, especially in the context of brain imaging.

METHODS

In this study, we aim to create novel image-based features for objective diagnosis of depression. Resting-state network time series are used to investigate neurodynamics with the help of wavelet coherence and Granger causality (G-causality). Three new features are introduced: total wavelet coherence, wavelet lead coherence, and wavelet coherence blob analysis. The fourth feature, pair-wise conditional G-causality, is used to establish the causality between resting-state networks. We use the proposed features to classify depression in adult subjects.

RESULTS

We obtained an accuracy of 86% in the wavelet lead coherence, 80% in Granger causality, and 86% in wavelet coherence blob analysis. Subjects with depression showed hyperconnectivity between the dorsal attention network and the auditory network as well as between the posterior default mode network and the dorsal attention network. Hypoconnectivity was found between the anterior default mode network and the auditory network as well as the right frontoparietal network and the lateral visual network. An abnormal co-activation pattern was found between cerebellum and the lateral motor network according to the wavelet coherence blob analysis.

CONCLUSION

Based on abnormal functional dynamics between brain networks, we were able to identify subjects with depression with high accuracy. The findings of this study contribute to the understanding of the impaired emotional and attention processing associated with depression, as well as decreased motor activity.

Dynamic Effective Connectivity using Physiologically informed Dynamic Causal Model with Recurrent Units: A functional Magnetic Resonance Imaging simulation study

Functional MRI (fMRI) is an indirect reflection of neuronal activity. Using generative biophysical model of fMRI data such as Dynamic Causal Model (DCM), the underlying neuronal activities of different brain areas and their causal interactions (i.e., effective connectivity) can be calculated. Most DCM studies typically consider the effective connectivity to be static for a cognitive task within an experimental run. However, changes in experimental conditions during complex tasks such as movie-watching might result in temporal variations in the connectivity strengths. In this fMRI simulation study, we leverage state-of-the-art Physiologically informed DCM (P-DCM) along with a recurrent window approach and discretization of the equations to infer the underlying neuronal dynamics and concurrently the dynamic (time-varying) effective connectivities between various brain regions for task-based fMRI. Results from simulation studies on 3- and 10-region models showed that functional magnetic resonance imaging (fMRI) blood oxygenation level-dependent (BOLD) responses and effective connectivity time-courses can be accurately predicted and distinguished from faulty graphical connectivity models representing cognitive hypotheses. In summary, we propose and validate a novel approach to determine dynamic effective connectivity between brain areas during complex cognitive tasks by combining P-DCM with recurrent units.

Diagnosis of late-life depression using structural equation modeling and dynamic effective connectivity during resting fMRI

BACKGROUND

Late-life depression (LLD) is characterized by cognitive and social impairments. Determining neurobiological alterations in connectivity in LLD by means of fMRI may lead to a better understanding of the neural basis underlying this disorder and more precise diagnostic markers. The primary objective of this paper is to identify a structural model that best explains the dynamic effective connectivity (EC) of the default mode network (DMN) in LLD patients compared to controls.

METHODS

Twenty-seven patients and 29 healthy controls underwent resting-state fMRI during a period of eight minutes. In both groups, jackknife correlation matrices were generated with six ROIs of the DMN that constitute the posterior DMN (pDMN). The different correlation matrices were used as input to estimate each structural equation model (SEM) for each subject in both groups incorporating dynamic effects.

RESULTS

The results show that the proposed LLD diagnosis algorithm achieves perfect accuracy in classifying LLD patients and controls. This differentiation is based on three aspects: the importance of ROIs 4 and 6, which seem to be the most distinctive among the subnetworks; the shape that the specific connections adopt in their networks, or in other words, the directed connections that are established among the ROIs in the pDMN for each group; and the number of dynamic effects that seem to be greater throughout the six ROIs studied [t = 54.346; df = 54; p < .001; 95 % CI difference = 5.486-5.906].

LIMITATIONS

The sample size was moderate, and the participants continued their current medications.

CONCLUSIONS

The network models that we developed describe a pattern of dynamic activation in the pDMN that may be considered a possible biomarker for LLD, which may allow early diagnosis of this disorder.

Automatic autism spectrum disorder detection using artificial intelligence methods with MRI neuroimaging: A review

Autism spectrum disorder (ASD) is a brain condition characterized by diverse signs and symptoms that appear in early childhood. ASD is also associated with communication deficits and repetitive behavior in affected individuals. Various ASD detection methods have been developed, including neuroimaging modalities and psychological tests. Among these methods, magnetic resonance imaging (MRI) imaging modalities are of paramount importance to physicians. Clinicians rely on MRI modalities to diagnose ASD accurately. The MRI modalities are non-invasive methods that include functional (fMRI) and structural (sMRI) neuroimaging methods. However, diagnosing ASD with fMRI and sMRI for specialists is often laborious and time-consuming; therefore, several computer-aided design systems (CADS) based on artificial intelligence (AI) have been developed to assist specialist physicians. Conventional machine learning (ML) and deep learning (DL) are the most popular schemes of AI used for diagnosing ASD. This study aims to review the automated detection of ASD using AI. We review several CADS that have been developed using ML techniques for the automated diagnosis of ASD using MRI modalities. There has been very limited work on the use of DL techniques to develop automated diagnostic models for ASD. A summary of the studies developed using DL is provided in the Supplementary Appendix. Then, the challenges encountered during the automated diagnosis of ASD using MRI and AI techniques are described in detail. Additionally, a graphical comparison of studies using ML and DL to diagnose ASD automatically is discussed. We suggest future approaches to detecting ASDs using AI techniques and MRI neuroimaging.

The Problem of Meaning: The Free Energy Principle and Artificial Agency

Biological agents can act in ways that express a sensitivity to context-dependent relevance. So far it has proven difficult to engineer this capacity for context-dependent sensitivity to relevance in artificial agents. We give this problem the label the "problem of meaning". The problem of meaning could be circumvented if artificial intelligence researchers were to design agents based on the assumption of the continuity of life and mind. In this paper, we focus on the proposal made by enactive cognitive scientists to design artificial agents that possess sensorimotor autonomy-stable, self-sustaining patterns of sensorimotor interaction that can ground values, norms and goals necessary for encountering a meaningful environment. More specifically, we consider whether the Free Energy Principle (FEP) can provide formal tools for modeling sensorimotor autonomy. There is currently no consensus on how to understand the relationship between enactive cognitive science and the FEP. However, a number of recent papers have argued that the two frameworks are fundamentally incompatible. Some argue that biological systems exhibit historical path-dependent learning that is absent from systems that minimize free energy. Others have argued that a free energy minimizing system would fail to satisfy a key condition for sensorimotor agency referred to as "interactional asymmetry". These critics question the claim we defend in this paper that the FEP can be used to formally model autonomy and adaptivity. We will argue it is too soon to conclude that the two frameworks are incompatible. There are undeniable conceptual differences between the two frameworks but in our view each has something important and necessary to offer. The FEP needs enactive cognitive science for the solution it provides to the problem of meaning. Enactive cognitive science needs the FEP to formally model the properties it argues to be constitutive of agency. Our conclusion will be that active inference models based on the FEP provides a way by which scientists can think about how to address the problems of engineering autonomy and adaptivity in artificial agents in formal terms. In the end engaging more closely with this formalism and its further developments will benefit those working within the enactive framework.

Dynamical differential covariance recovers directional network structure in multiscale neural systems

Investigating neural interactions is essential to understanding the neural basis of behavior. Many statistical methods have been used for analyzing neural activity, but estimating the direction of network interactions correctly and efficiently remains a difficult problem. Here, we derive dynamical differential covariance (DDC), a method based on dynamical network models that detects directional interactions with low bias and high noise tolerance under nonstationarity conditions. Moreover, DDC scales well with the number of recording sites and the computation required is comparable to that needed for covariance. DDC was validated and compared favorably with other methods on networks with false positive motifs and multiscale neural simulations where the ground-truth connectivity was known. When applied to recordings of resting-state functional magnetic resonance imaging (rs-fMRI), DDC consistently detected regional interactions with strong structural connectivity in over 1,000 individual subjects obtained by diffusion MRI (dMRI). DDC is a promising family of methods for estimating connectivity that can be generalized to a wide range of dynamical models and recording techniques and to other applications where system identification is needed.

May the 4C's be with you: an overview of complexity-inspired frameworks for analysing resting-state neuroimaging data

Competing and complementary models of resting-state brain dynamics contribute to our phenomenological and mechanistic understanding of whole-brain coordination and communication, and provide potential evidence for differential brain functioning associated with normal and pathological behaviour. These neuroscientific theories stem from the perspectives of physics, engineering, mathematics and psychology and create a complicated landscape of domain-specific terminology and meaning, which, when used outside of that domain, may lead to incorrect assumptions and conclusions within the neuroscience community. Here, we review and clarify the key concepts of connectivity, computation, criticality and coherence-the 4C's-and outline a potential role for metastability as a common denominator across these propositions. We analyse and synthesize whole-brain neuroimaging research, examined through functional magnetic imaging, to demonstrate that complexity science offers a principled and integrated approach to describe, and potentially understand, macroscale spontaneous brain functioning.

Towards an efficient validation of dynamical whole-brain models

Simulating the resting-state brain dynamics via mathematical whole-brain models requires an optimal selection of parameters, which determine the model’s capability to replicate empirical data. Since the parameter optimization via a grid search (GS) becomes unfeasible for high-dimensional models, we evaluate several alternative approaches to maximize the correspondence between simulated and empirical functional connectivity. A dense GS serves as a benchmark to assess the performance of four optimization schemes: Nelder-Mead Algorithm (NMA), Particle Swarm Optimization (PSO), Covariance Matrix Adaptation Evolution Strategy (CMAES) and Bayesian Optimization (BO). To compare them, we employ an ensemble of coupled phase oscillators built upon individual empirical structural connectivity of 105 healthy subjects. We determine optimal model parameters from two- and three-dimensional parameter spaces and show that the overall fitting quality of the tested methods can compete with the GS. There are, however, marked differences in the required computational resources and stability properties, which we also investigate before proposing CMAES and BO as efficient alternatives to a high-dimensional GS. For the three-dimensional case, these methods generated similar results as the GS, but within less than 6% of the computation time. Our results contribute to an efficient validation of models for personalized simulations of brain dynamics.

Altered static and dynamic voxel-mirrored homotopic connectivity in patients with frontal glioma

Contralateral regions play critical role in functional compensation in glioma patients. Voxel-mirrored homotopic connectivity (VMHC) characterizes the intrinsic functional connectivity (FC) of the brain, considered to have a regional functional basis. We aimed to investigate the alterations of brain regional function and VMHC in patients with frontal glioma, and further investigated the correlation between these alterations and cognition. We enrolled patients with frontal glioma and matched healthy controls (HC). We chose degree centrality (DC), regional homogeneity (ReHo), and VMHC to investigate the alterations of regional function and intrinsic FC in patients. Furthermore, partial correlation analyses were conducted to explore the relationship between imaging functional indicators and cognitions. Compared with HC, patients showed decreased static VMHC within right and left middle frontal gyrus (MFG.R, MFG.L), left superior frontal gyrus (SFG.L), right precuneus (PCUN.R), and left precuneus (PCUN.L), decreased static DC within left cingulate gyrus (CG.L), right superior frontal gyrus (SFG.R), and right postcentral gyrus (POCG.R), decreased static ReHo within CG.L, decreased dynamic ReHo within right inferior parietal lobule (IPL.R), but increased dynamic VMHC (dVMHC) within PCUN.R and PCUN.L. Furthermore, values of decreased VMHC within MFG.R, decreased DC within CG.L, decreased ReHo within CG.L, and increased dVMHC within PCUN.R were significantly positively correlated with cognitive functions. We preliminarily confirmed glioma causes regional dysfunction and disturbs long-distance FC, and long-distance FC showed strong instability in patients with frontal glioma. Meanwhile, the correlation analyses indicated directions for cognitive protection in patients with frontal glioma.

Functional connectivity of fMRI using differential covariance predicts structural connectivity and behavioral reaction times

Recordings from resting state functional Magnetic Resonance Imaging (rs-fMRI) reflect the influence of pathways between brain areas. A wide range of methods have been proposed to measure this functional connectivity (FC), but the lack of “ground truth” has made it difficult to systematically validate them. Most measures of FC produce connectivity estimates that are symmetrical between brain areas. Differential covariance (dCov) is an algorithm for analyzing FC with directed graph edges. When we applied dCov to rs-fMRI recordings from the human connectome project (HCP) and anesthetized mice, dCov-FC accurately identified strong cortical connections from diffusion Magnetic Resonance Imaging (dMRI) in individual humans and viral tract tracing in mice. In addition, those HCP subjects whose dCov-FCs were more integrated, as assessed by a graph-theoretic measure, tended to have shorter reaction times in several behavioral tests. Thus, dCov-FC was able to identify anatomically verified connectivity that yielded measures of brain integration significantly correlated with behavior.

On the Importance of Being Flexible: Dynamic Brain Networks and Their Potential Functional Significances

In this theoretical review, we begin by discussing brains and minds from a dynamical systems perspective, and then go on to describe methods for characterizing the flexibility of dynamic networks. We discuss how varying degrees and kinds of flexibility may be adaptive (or maladaptive) in different contexts, specifically focusing on measures related to either more disjoint or cohesive dynamics. While disjointed flexibility may be useful for assessing neural entropy, cohesive flexibility may potentially serve as a proxy for self-organized criticality as a fundamental property enabling adaptive behavior in complex systems. Particular attention is given to recent studies in which flexibility methods have been used to investigate neurological and cognitive maturation, as well as the breakdown of conscious processing under varying levels of anesthesia. We further discuss how these findings and methods might be contextualized within the Free Energy Principle with respect to the fundamentals of brain organization and biological functioning more generally, and describe potential methodological advances from this paradigm. Finally, with relevance to computational psychiatry, we propose a research program for obtaining a better understanding of ways that dynamic networks may relate to different forms of psychological flexibility, which may be the single most important factor for ensuring human flourishing.

Abnormal Static and Dynamic Functional Connectivity in Left and Right Temporal Lobe Epilepsy

Objective

Temporal lobe epilepsy (TLE) can be conceptualized as a network disease. However, the network characteristics in lateralization remain controversial.

Methods

In this study, resting-state functional MRI scans were acquired from 53 TLE patients [22 with left-side TLE (LTLE) and 31 with right-side TLE (RTLE)] and 37 matched healthy controls. We focused on the characteristics of static and dynamic functional connectivity, including static connectivity patterns and topological properties, as well as temporal properties of the dynamic connectivity state and the variability of the dynamic connectivity and network topological organization. Correlation analyses were conducted between abnormal static and dynamic properties and cognitive performances.

Results

The static functional connectivity analysis presented a significantly decreased cortical-cortical connectivity pattern and increased subcortical-cortical connectivity pattern in RTLE. The global-level network in RTLE showed a significant decrease in global efficiency. The dynamic functional connectivity analysis revealed that RTLE patients exhibited aberrant connectivity states, as well as increased variability in the subcortical-cortical connectivity. The global-level network in RTLE revealed increased variance in global efficiency and local efficiency. The static or dynamic functional connectivity in LTLE did not show any significant abnormalities. The altered dynamic properties were associated with worsening cognitive performance in language and conceptual thinking by the TLE patients.

Conclusion

Our findings demonstrated the presence of abnormalities in the static and dynamic functional connectivity of TLE patients. RTLE patients exhibited more pronounced aberrant connectivity patterns and topological properties, which might represent a mechanism for reconfiguration of brain networks in RTLE patients. These observations extended our understanding of the pathophysiological network mechanisms of TLE.

Atypically high influence of subcortical activity on primary sensory regions in autism

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The age-dependent decrease of subcortico-cortical connectivity is attenuated in ASD.

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Primary sensory regions remain less segregated from subcortical activity in ASD.

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This could underlie an excessive amount of sensory input relayed to the cortex.

Background

Hypersensitivity, stereotyped behaviors and attentional problems in autism spectrum disorder (ASD) are compatible with inefficient filtering of undesired or irrelevant sensory information at early stages of neural processing. This could stem from the persistent overconnectivity between primary sensory regions and deep brain nuclei in both children and adults with ASD – as reported by several previous studies – which could reflect a decreased or arrested maturation of brain connectivity. However, it has not yet been investigated whether this overconnectivity can be modelled as an excessive directional influence of subcortical brain activity on primary sensory cortical regions in ASD, with respect to age-matched typically developing (TD) individuals.

Methods

To this aim, we used dynamic causal modelling to estimate (1) the directional influence of subcortical activity on cortical processing and (2) the functional segregation of primary sensory cortical regions from subcortical activity in 166 participants with ASD and 193 TD participants from the Autism Brain Imaging Data Exchange (ABIDE). We then specifically tested the hypothesis that the age-related changes of these indicators of brain connectivity would differ between the two groups.

Results

We found that in TD participants age was significantly associated with decreased influence of subcortical activity on cortical processing, paralleled by an increased functional segregation of cortical sensory processing from subcortical activity. Instead these effects were highly reduced and mostly absent in ASD participants, suggesting a delayed or arrested development of the segregation between subcortical and cortical sensory processing in ASD.

Conclusion

This atypical configuration of subcortico-cortical connectivity in ASD can result in an excessive amount of unprocessed sensory input relayed to the cortex, which is likely to impact cognitive functioning in everyday situations where it is beneficial to limit the influence of basic sensory information on cognitive processing, such as activities requiring focused attention or social interactions.

Cognition Without Neural Representation: Dynamics of a Complex System

This paper proposes an account of neurocognitive activity without leveraging the notion of neural representation. Neural representation is a concept that results from assuming that the properties of the models used in computational cognitive neuroscience (e.g., information, representation, etc.) must literally exist the system being modelled (e.g., the brain). Computational models are important tools to test a theory about how the collected data (e.g., behavioural or neuroimaging) has been generated. While the usefulness of computational models is unquestionable, it does not follow that neurocognitive activity should literally entail the properties construed in the model (e.g., information, representation). While this is an assumption present in computationalist accounts, it is not held across the board in neuroscience. In the last section, the paper offers a dynamical account of neurocognitive activity with Dynamical Causal Modelling (DCM) that combines dynamical systems theory (DST) mathematical formalisms with the theoretical contextualisation provided by Embodied and Enactive Cognitive Science (EECS).

Altered dynamic functional architecture in type 2 diabetes mellitus

INTRODUCTION

Type 2 diabetes mellitus (T2DM) can accelerate cognitive decline and even dementia so that the underlying mechanism deserves further exploration. In the resting state, brain function is still changing dynamically. At present, it is still unknown whether the dynamic functional connectivity (dFC) between various brain regions is in a stable state. It is necessary to interpret brain changes from a new perspective, that is, the stability of brain architecture.

METHODS

In this study, we used a fixed dynamic time scale to explore the stability of dynamic functional architecture in T2DM, then the dynamic effective connectivity (dEC) was used to further explain how information flows through dynamically fluctuating brain architecture in T2DM.

RESULT

Two brain regions with decreased stability were found including the right supra-marginal gyrus (SMG) and the right median cingulate gyrus (MCG) in T2DM subjects. The dEC variation has increased between the left inferior frontal gyrus (IFG) and the right MCG. The direction of causal flow is from the right MCG to the left IFG.

CONCLUSION

The combination of stability and dEC can not only show the stability of dynamic functional architecture in brain but also reflect the fluidity of brain information, which is an innovative and interesting attempt in the field of neuroimaging. The changes of dynamic architecture in T2DM patients may present an innovative perspective and explanation for their cognitive decline.

The Predictive Dynamics of Happiness and Well-Being

We offer an account of mental health and well-being using the predictive processing framework (PPF). According to this framework, the difference between mental health and psychopathology can be located in the goodness of the predictive model as a regulator of action. What is crucial for avoiding the rigid patterns of thinking, feeling and acting associated with psychopathology is the regulation of action based on the valence of affective states. In PPF, valence is modelled as error dynamics—the change in prediction errors over time . Our aim in this paper is to show how error dynamics can account for both momentary happiness and longer term well-being. What will emerge is a new neurocomputational framework for making sense of human flourishing.

Broken detailed balance and entropy production in the human brain

To perform biological functions, living systems must break detailed balance by consuming energy and producing entropy. At microscopic scales, broken detailed balance enables a suite of molecular and cellular functions, including computations, kinetic proofreading, sensing, adaptation, and transportation. But do macroscopic violations of detailed balance enable higher-order biological functions, such as cognition and movement? To answer this question, we adapt tools from nonequilibrium statistical mechanics to quantify broken detailed balance in complex living systems. Analyzing neural recordings from hundreds of human subjects, we find that the brain violates detailed balance at large scales and that these violations increase with physical and cognitive exertion. Generally, we provide a flexible framework for investigating broken detailed balance at large scales in complex systems.

Living systems break detailed balance at small scales, consuming energy and producing entropy in the environment to perform molecular and cellular functions. However, it remains unclear how broken detailed balance manifests at macroscopic scales and how such dynamics support higher-order biological functions. Here we present a framework to quantify broken detailed balance by measuring entropy production in macroscopic systems. We apply our method to the human brain, an organ whose immense metabolic consumption drives a diverse range of cognitive functions. Using whole-brain imaging data, we demonstrate that the brain nearly obeys detailed balance when at rest, but strongly breaks detailed balance when performing physically and cognitively demanding tasks. Using a dynamic Ising model, we show that these large-scale violations of detailed balance can emerge from fine-scale asymmetries in the interactions between elements, a known feature of neural systems. Together, these results suggest that violations of detailed balance are vital for cognition and provide a general tool for quantifying entropy production in macroscopic systems.

State-Dependent Effective Connectivity in Resting-State fMRI

The human brain at rest exhibits intrinsic dynamics transitioning among the multiple metastable states of the inter-regional functional connectivity. Accordingly, the demand for exploring the state-specific functional connectivity increases for a deeper understanding of mental diseases. Functional connectivity, however, lacks information about the directed causal influences among the brain regions, called effective connectivity. This study presents the dynamic causal modeling (DCM) framework to explore the state-dependent effective connectivity using spectral DCM for the resting-state functional MRI (rsfMRI). We established the sequence of brain states using the hidden Markov model with the multivariate autoregressive coefficients of rsfMRI, summarizing the functional connectivity. We decomposed the state-dependent effective connectivity using a parametric empirical Bayes scheme that models the effective connectivity of consecutive windows with the time course of the discrete states as regressors. We showed the plausibility of the state-dependent effective connectivity analysis in a simulation setting. To test the clinical applicability, we applied the proposed method to characterize the state- and subtype-dependent effective connectivity of the default mode network in children with combined-type attention deficit hyperactivity disorder (ADHD-C) compared with age-matched, typically developed children (TDC). All 88 children were subtyped according to the occupation times (i.e., dwell times) of the three dominant functional connectivity states, independently of clinical diagnosis. The state-dependent effective connectivity differences between ADHD-C and TDC according to the subtypes and those between the subtypes of ADHD-C were expressed mainly in self-inhibition, magnifying the importance of excitation inhibition balance in the subtyping. These findings provide a clear motivation for decomposing the state-dependent dynamic effective connectivity and state-dependent analysis of the directed coupling in exploring mental diseases.

Pathologically reduced neural flexibility recovers during psychotherapy of OCD patients

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Psychiatric impairment is associated with decreased neural flexibility.

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Psychotherapy was able to increase the neural flexibility of the patients.

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Psychotherapy should increase adaptivity of cognitive-emotional-behavioral patterns.

Flexibility is a key feature of psychological health, allowing the individual to dynamically adapt to changing environmental demands, which is impaired in many psychiatric disorders like obsessive–compulsive disorder (OCD). Adequately responding to varying demands requires the brain to switch between different patterns of neural activity, which are represented by different brain network configurations (functional connectivity patterns). Here, we operationalize neural flexibility as the dissimilarity between consecutive connectivity matrices of brain regions (jump length). In total, 132 fMRI scans were obtained from 17 patients that were scanned four to five times during inpatient psychotherapy, and from 17 controls that were scanned at comparable time intervals. Significant negative correlations were found between the jump lengths and the symptom severity scores of OCD, depression, anxiety, and stress, suggesting that high symptom severity corresponds to inflexible brain functioning. Further analyses revealed that impaired reconfiguration (pattern stability) of the brain seems to be more related to general psychiatric impairment rather than to specific symptoms, e.g., of OCD or depression. Importantly, the group × time interaction of a repeated measures ANOVA was significant, as well as the post-hoc paired t-tests of the patients (first vs. last scan). The results suggest that psychotherapy is able to significantly increase the neural flexibility of patients. We conclude that psychiatric symptoms like anxiety, stress, depression, and OCD are associated with an impaired adaptivity of the brain. In general, our results add to the growing evidence that dynamic functional connectivity captures meaningful properties of brain functioning.

Inference of brain networks with approximate Bayesian computation - assessing face validity with an example application in Parkinsonism

This paper describes and validates a novel framework using the Approximate Bayesian Computation (ABC) algorithm for parameter estimation and model selection in models of mesoscale brain network activity. We provide a proof of principle, first pass validation of this framework using a set of neural mass models of the cortico-basal ganglia thalamic circuit inverted upon spectral features from experimental, in vivo recordings. This optimization scheme relaxes an assumption of fixed-form posteriors (i.e. the Laplace approximation) taken in previous approaches to inverse modelling of spectral features. This enables the exploration of model dynamics beyond that approximated from local linearity assumptions and so fit to explicit, numerical solutions of the underlying non-linear system of equations. In this first paper, we establish a face validation of the optimization procedures in terms of: (i) the ability to approximate posterior densities over parameters that are plausible given the known causes of the data; (ii) the ability of the model comparison procedures to yield posterior model probabilities that can identify the model structure known to generate the data; and (iii) the robustness of these procedures to local minima in the face of different starting conditions. Finally, as an illustrative application we show (iv) that model comparison can yield plausible conclusions given the known neurobiology of the cortico-basal ganglia-thalamic circuit in Parkinsonism. These results lay the groundwork for future studies utilizing highly nonlinear or brittle models that can explain time dependant dynamics, such as oscillatory bursts, in terms of the underlying neural circuits.

Biological constraints on neural network models of cognitive function

Neural network models are potential tools for improving our understanding of complex brain functions. To address this goal, these models need to be neurobiologically realistic. However, although neural networks have advanced dramatically in recent years and even achieve human-like performance on complex perceptual and cognitive tasks, their similarity to aspects of brain anatomy and physiology is imperfect. Here, we discuss different types of neural models, including localist, auto-associative, hetero-associative, deep and whole-brain networks, and identify aspects under which their biological plausibility can be improved. These aspects range from the choice of model neurons and of mechanisms of synaptic plasticity and learning to implementation of inhibition and control, along with neuroanatomical properties including areal structure and local and long-range connectivity. We highlight recent advances in developing biologically grounded cognitive theories and in mechanistically explaining, on the basis of these brain-constrained neural models, hitherto unaddressed issues regarding the nature, localization and ontogenetic and phylogenetic development of higher brain functions. In closing, we point to possible future clinical applications of brain-constrained modelling.

Frequency specific co-activation pattern analysis via sparse nonnegative tensor decomposition

BACKGROUND

Traditionally, the diagnosis of Parkinson's disease (PD) has been made based on symptoms. Extensive studies have demonstrated that PD may lead to variation of brain activity in different frequency bands. However, frequency specific dynamic alterations of PD have not yet been explored.

NEW METHOD

In order to address this gap, a novel sparse nonnegative tensor decomposition (SNTD) method was used to estimate frequency specific co-activation patterns (CAP). The difference between PD and healthy controls (HC) are investigated with the proposed framework.

RESULT

The difference between PD and HC mainly exists at frequency band 0.04-0.1 Hz in basal ganglia. We also found that the average intensity of PD in this frequency band is significantly correlated with the Hoehn and Yahr scale.

COMPARISON WITH EXISTING METHODS

Compared with conventional CAP approach, SNTD estimates frequency specific CAPs that show alterations in PD patients.

CONCLUSION

SNTD provides an alternative to K-means clustering used in conventional CAP analysis. With the proposed framework, frequency specific CAPs are extracted, and alterations in PD patients are also successfully discovered.

Brain Entropy During Aging Through a Free Energy Principle Approach

Neural complexity and brain entropy (BEN) have gained greater interest in recent years. The dynamics of neural signals and their relations with information processing continue to be investigated through different measures in a variety of noteworthy studies. The BEN of spontaneous neural activity decreases during states of reduced consciousness. This evidence has been showed in primary consciousness states, such as psychedelic states, under the name of "the entropic brain hypothesis." In this manuscript we propose an extension of this hypothesis to physiological and pathological aging. We review this particular facet of the complexity of the brain, mentioning studies that have investigated BEN in primary consciousness states, and extending this view to the field of neuroaging with a focus on resting-state functional Magnetic Resonance Imaging. We first introduce historic and conceptual ideas about entropy and neural complexity, treating the mindbrain as a complex nonlinear dynamic adaptive system, in light of the free energy principle. Then, we review the studies in this field, analyzing the idea that the aim of the neurocognitive system is to maintain a dynamic state of balance between order and chaos, both in terms of dynamics of neural signals and functional connectivity. In our exploration we will review studies both on acute psychedelic states and more chronic psychotic states and traits, such as those in schizophrenia, in order to show the increase of entropy in those states. Then we extend our exploration to physiological and pathological aging, where BEN is reduced. Finally, we propose an interpretation of these results, defining a general trend of BEN in primary states and cognitive aging.

Dual stream neural networks for brain signal classification

Objective. The primary objective of this work is to develop a neural nework classifier for arbitrary collections of functional neuroimaging signals to be used in brain–computer interfaces (BCIs). Approach. We propose a dual stream neural network (DSNN) for the classification problem. The first stream is an end-to-end classifier taking raw time-dependent signals as input and generating feature identification signatures from them. The second stream enhances the identified features from the first stream by adjoining a dynamic functional connectivity matrix aimed at incorporating nuanced multi-channel information during specified BCI tasks. Main results. The proposed DSNN classifier is benchmarked against three publicly available datasets, where the classifier demonstrates performance comparable to, or better than the state-of-art in each instance. An information theoretic examination of the trained network is also performed, utilizing various tools, to demonstrate how to glean interpretive insight into how the hidden layers of the network parse the underlying biological signals. Significance . The resulting DSNN is a subject-independent classifier that works for any collection of 1D functional neuroimaging signals, with the option of integrating domain specific information in the design.

Altered dynamic effective connectivity of the default mode network in newly diagnosed drug-naïve juvenile myoclonic epilepsy

Juvenile myoclonic epilepsy (JME) has been repeatedly revealed to be associated with brain dysconnectivity in the default mode network (DMN). However, the implicit assumption of stationary and nondirectional functional connectivity (FC) in most previous resting-state fMRI studies raises an open question of JME-related aberrations in dynamic causal properties of FC. Here, we introduces an empirical method incorporating sliding-window approach and a multivariate Granger causality analysis to investigate, for the first time, the reorganization of dynamic effective connectivity (DEC) in DMN for patients with JME. DEC was obtained from resting-state fMRI of 34 patients with newly diagnosed and drug-naïve JME and 34 matched controls. Through clustering analysis, we found two distinct states that characterize the DEC patterns (i.e., a less frequent, strongly connected state (State 1) and a more frequent, weakly connected state (State 2)). Patients showed altered ECs within DMN subnetworks in the State 2, whereas abnormal ECs between DMN subnetworks were found in the State 1. Furthermore, we observed that the causal influence flows of the medial prefrontal cortex and angular gyrus were altered in a manner of state specificity, and associated with disease severity of patients. Overall, our findings extend the dysconnectivity hypothesis in JME from static to dynamic causal FC and demonstrate that aberrant DEC may underlie abnormal brain function in JME at early phase of illness.