Understanding the complex neural activity dynamics is crucial for the development of the field of neuroscience. Although current functional MRI classification approaches tend to be based on static functional connectivity or cannot capture spatio-temporal relationships comprehensively, we present a new framework that leverages dynamic graph creation and spatiotemporal attention mechanisms for Autism Spectrum Disorder(ASD) diagnosis. The approach used in this research dynamically infers functional brain connectivity in each time interval using transformer-based attention mechanisms, enabling the model to selectively focus on crucial brain regions and time segments. By constructing time-varying graphs that are then processed with Graph Convolutional Networks (GCNs) and transformers, our method successfully captures both localized interactions and global temporal dependencies. Evaluated on the subset of ABIDE dataset, our model achieves 63.2 accuracy and 60.0 AUC, outperforming static graph-based approaches (e.g., GCN:51.8). This validates the efficacy of joint modeling of dynamic connectivity and spatio-temporal context for fMRI classification. The core novelty arises from (1) attention-driven dynamic graph creation that learns temporal brain region interactions and (2) hierarchical spatio-temporal feature fusion through GCNtransformer fusion.

Functional brain networks are well described and estimated from data with Gaussian Graphical Models (GGMs), e.g.\ using sparse inverse covariance estimators. Comparing functional connectivity of subjects in two populations calls for comparing these estimated GGMs. Our goal is to identify differences in GGMs known to have similar structure. We characterize the uncertainty of differences with confidence intervals obtained using a parametric distribution on parameters of a sparse estimator. Sparse penalties enable statistical guarantees and interpretable models even in high-dimensional and low-sample settings. Characterizing the distributions of sparse models is inherently challenging as the penalties produce a biased estimator.

The goal of improving testing for differences between graphs is clearly relevant to neuroimaging and other application domains. While the specifics are somewhat incremental, I think this is a great idea, and reasonably well executed. Major issues: * Please explain specifically which gradients are used to get from (4) to (5). This derivation seems incorrect if one takes separate derivatives with respect to \beta_1 and \beta_2. How do you end up with a sum of terms (and not two separate terms)?

This study investigated the dynamic connectivity patterns between EEG and fMRI modalities, contributing to our understanding of brain network interactions. By employing a comprehensive approach that integrated static and dynamic analyses of EEG-fMRI data, we were able to uncover distinct connectivity states and characterize their temporal fluctuations. The results revealed modular organization within the intrinsic connectivity networks (ICNs) of the brain, highlighting the significant roles of sensory systems and the default mode network. The use of a sliding window technique allowed us to assess how functional connectivity varies over time, further elucidating the transient nature of brain connectivity. Additionally, our findings align with previous literature, reinforcing the notion that cognitive states can be effectively identified through short-duration data, specifically within the 30-60 second timeframe. The established relationships between connectivity strength and cognitive processes, particularly during different visual states, underscore the relevance of our approach for future research into brain dynamics. Overall, this study not only enhances our understanding of the interplay between EEG and fMRI signals but also paves the way for further exploration into the neural correlates of cognitive functions and their implications in clinical settings. Future research should focus on refining these methodologies and exploring their applications in various cognitive and clinical contexts.

Divergent brain connectivity is thought to underlie the behavioral and cognitive symptoms observed in many neurodevelopmental disorders. Quantifying divergence from neurotypical connectivity patterns offers a promising pathway to inform diagnosis and therapeutic interventions. While advanced neuroimaging techniques, such as diffusion MRI (dMRI), have facilitated the mapping of brain's structural connectome, the challenge lies in accurately modeling developmental trajectories within these complex networked structures to create robust neurodivergence markers. In this work, we present the Brain Representation via Individualized Deep Generative Embedding (BRIDGE) framework, which integrates normative modeling with a bio-inspired deep generative model to create a reference trajectory of connectivity transformation as part of neurotypical development. This will enable the assessment of neurodivergence by comparing individuals to the established neurotypical trajectory. BRIDGE provides a global neurodivergence score based on the difference between connectivity-based brain age and chronological age, along with region-wise neurodivergence maps that highlight localized connectivity differences. Application of BRIDGE to a large cohort of children with autism spectrum disorder demonstrates that the global neurodivergence score correlates with clinical assessments in autism, and the regional map offers insights into the heterogeneity at the individual level in neurodevelopmental disorders. Together, the neurodivergence score and map form powerful tools for quantifying developmental divergence in connectivity patterns, advancing the development of imaging markers for personalized diagnosis and intervention in various clinical contexts.

This paper addresses the problem of understanding brain connectivity (i.e. More generally, perhaps, the paper attempts to uncover causal structure and uses neuroscience insights to specifically apply the model to brain connectivity. The model can be seen as an extension of (linear) dynamic causal models (DCMs) and assumes that the observations are a linear combination of latent activities, which have a GP prior, plus Gaussian noise (Eq 11). Overall the paper is readable but more clarity in the details of how the posterior over the influence from i- j is actually computed (paragraph just below Eq 12). I write this review as a machine learning researcher (i.e.

Tremendous recent literature show that associations between different brain regions, i.e., brain connectivity, provide early symptoms of neurological disorders. Despite significant efforts made for graph neural network (GNN) techniques, their focus on graph nodes makes the state-of-the-art GNN methods not suitable for classifying brain connectivity as graphs where the objective is to characterize disease-relevant network dysfunction patterns on graph links. To address this issue, we propose Multi-resolution Edge Network (MENET) to detect disease-specific connectomic benchmarks with high discrimination power across diagnostic categories. The core of MENET is a novel graph edge-wise transform that we propose, which allows us to capture multi-resolution ``connectomic'' features. Using a rich set of the connectomic features, we devise a graph learning framework to jointly select discriminative edges and assign diagnostic labels for graphs. Experiments on two real datasets show that MENET accurately predicts diagnostic labels and identify brain connectivities highly associated with neurological disorders such as Alzheimer's Disease and Attention-Deficit/Hyperactivity Disorder.

We evaluate the effectiveness of combining brain connectivity metrics with signal statistics for early stage Parkinson's Disease (PD) classification using electroencephalogram data (EEG). The data is from 5 arousal states - wakeful and four sleep stages (N1, N2, N3 and REM). Our pipeline uses an Ada Boost model for classification on a challenging early stage PD classification task with with only 30 participants (11 PD , 19 Healthy Control). Evaluating 9 brain connectivity metrics we find the best connectivity metric to be different for each arousal state with Phase Lag Index achieving the highest individual classification accuracy of 86\% on N1 data. Further to this our pipeline using regional signal statistics achieves an accuracy of 78\%, using brain connectivity only achieves an accuracy of 86\% whereas combining the two achieves a best accuracy of 91\%. This best performance is achieved on N1 data using Phase Lag Index (PLI) combined with statistics derived from the frequency characteristics of the EEG signal. This model also achieves a recall of 80 \% and precision of 96\%. Furthermore we find that on data from each arousal state, combining PLI with regional signal statistics improves classification accuracy versus using signal statistics or brain connectivity alone. Thus we conclude that combining brain connectivity statistics with regional EEG statistics is optimal for classifier performance on early stage Parkinson's. Additionally, we find outperformance of N1 EEG for classification of Parkinson's and expect this could be due to disrupted N1 sleep in PD. This should be explored in future work.

Building comprehensive brain connectomes has proved of fundamental importance in resting-state fMRI (rs-fMRI) analysis. Based on the foundation of brain network, spatial-temporal-based graph convolutional networks have dramatically improved the performance of deep learning methods in rs-fMRI time series classification. However, existing works either pre-define the brain network as the correlation matrix derived from the raw time series or jointly learn the connectome and model parameters without any topology constraint. These methods could suffer from degraded classification performance caused by the deviation from the intrinsic brain connectivity and lack biological interpretability of demonstrating the causal structure (i.e., effective connectivity) among brain regions. Moreover, most existing methods for effective connectivity learning are unaware of the downstream classification task and cannot sufficiently exploit useful rs-fMRI label information. To address these issues in an end-to-end manner, we model the brain network as a directed acyclic graph (DAG) to discover direct causal connections between brain regions and propose Spatial-Temporal DAG Convolutional Network (ST-DAGCN) to jointly infer effective connectivity and classify rs-fMRI time series by learning brain representations based on nonlinear structural equation model. The optimization problem is formulated into a continuous program and solved with score-based learning method via gradient descent. We evaluate ST-DAGCN on two public rs-fMRI databases. Experiments show that ST-DAGCN outperforms existing models by evident margins in rs-fMRI classification and simultaneously learns meaningful edges of effective connectivity that help understand brain activity patterns and pathological mechanisms in brain disease.

Early brain development is characterized by the formation of a highly organized structural connectome. The interconnected nature of this connectome underlies the brain's cognitive abilities and influences its response to diseases and environmental factors. Hence, quantitative assessment of structural connectivity in the perinatal stage is useful for studying normal and abnormal neurodevelopment. However, estimation of the connectome from diffusion MRI data involves complex computations. For the perinatal period, these computations are further challenged by the rapid brain development and imaging difficulties. Combined with high inter-subject variability, these factors make it difficult to chart the normal development of the structural connectome. As a result, there is a lack of reliable normative baselines of structural connectivity metrics at this critical stage in brain development. In this study, we developed a computational framework, based on spatio-temporal averaging, for determining such baselines. We used this framework to analyze the structural connectivity between 33 and 44 postmenstrual weeks using data from 166 subjects. Our results unveiled clear and strong trends in the development of structural connectivity in perinatal stage. Connection weighting based on fractional anisotropy and neurite density produced the most consistent results. We observed increases in global and local efficiency, a decrease in characteristic path length, and widespread strengthening of the connections within and across brain lobes and hemispheres. We also observed asymmetry patterns that were consistent between different connection weighting approaches. The new computational method and results are useful for assessing normal and abnormal development of the structural connectome early in life.