Accurately and preoperatively predicting survival for high-grade gliomas (HGGs) is important for optimizing treatment strategies. Increasing evidence suggests that brain structural and functional connectivity networks derived from advanced magnetic resonance imaging (MRI) are promising predictors for HGG survival. However, advanced MRIs (e.g., diffusion MRI and functional MRI) are generally clinically inaccessible for HGG patients before initiating therapy. To compensate for lack of advanced MRI modalities in brain network studies, in this paper we evaluate the feasibility and performance of predicting HGG survival using exclusively preoperative multi-modal basic structural MRI (sMRI, e.g., T1- and T2-weighted MRI) based brain regional radiomics similarity networks (R2SNs). To this end, we propose a new cooperative multiplex graph neural network (GNN) based multi-modal R2SN integration framework for preoperative HGG survival prediction. First, multi-modal R2SNs are represented by a multiplex network, where each modality-specific R2SN forms one multiplex layer and nodes (i.e., brain regions of interest (ROIs)) are coupled to their replicas across multiplex layers. This facilitates flexible inter-ROI communications both within and between R2SNs. Second, a cooperative GNN is applied to capture intra-modal node feature propagations within each multiplex layer, followed by attention mechanisms used to capture inter-modal node feature interactions across multiplex layers. Finally, a tailored tumor-aware graph pooling is developed to assemble features from the tumor-intersecting ROIs for survival prediction. Extensive experiments on a collected HGG database with three basic sMRI modalities demonstrate the superiority of our method over state-of-the-art baselines in survival stratification. The code is available at https://github.com/ZiLaoTou/TCM-GNN.

Functional connectivity networks (FCNs), as graph-structured data derived from functional magnetic resonance imaging (fMRI), are essential for understanding how brain functions coordinate with behavior and cognition. However, the utility of these FCNs is often limited by the brain atlas, since the predefined regions of interest by the atlas represent nodes in FCNs. To address these limitations and enhance the comparability of functional connectivity analyses across different atlases, we introduce the Spatio-Temporal Mapping Generative Adversarial Network (STMap-GAN) based on generative modeling. Convolutional networks and long short-term memory modules are used in the generator to improve the spatio and temporal consistency of generated fMRI time series for target brain atlases. The transformer module in the discriminator can effectively capture different features in fMRI time series, thus accurately distinguishing the generated time series from ground truth. This study demonstrates the ability of STMap-GAN to maintain high fidelity in FCN mapping across various atlases, ensuring consistency and replicability in neuroscience research.

Resting-state functional connectivity networks (rs-FCNs) have been most frequently used for brain network analysis in neuroscience. However, a body of evidence indicates that task-state FCNs (ts-FCNs) are better associated with individual differences in behavior than rs-FCN. Until now there have been no studies of ascertaining to what extent rs-FCNs can account for ts-FCNs. In this paper, we propose a Multiple Graph Autoencoder based Generative Adversarial Network (MGAE-GAN) model to enable the inference of ts-FCNs from rs-FCNs. The generator of MGAE-GAN is built upon several graph autoencoders to learn and adaptively combine multiple implicit relationships between rs-FCNs and ts-FCNs. To ensure the authenticity of the predicted ts-FCNs, we design the discriminator of MGAE-GAN based on graph metric learning. Additionally, we incorporate a correlation loss and a subject-similarity-preserving loss to maintain overall correlation and between-subject similarities before and after the generator, respectively. Experimental results on the Human Connectome Project (HCP) S1200 demonstrate the effectiveness of our MGAE-GAN for predicting ts-FCNs from rs-FCNs.

Polygenic risk scores (PRS) are widely used to assess genetic susceptibility in Alzheimer's disease (AD) research. However, the rapid expansion of PRS studies has led to dataset-specific biases-stemming from factors like population makeup, genotyping methods, and analysis pipelines-that result in inconsistent variant prioritization and limit generalizability and reproducibility. To address these challenges, we propose a transductive learning framework that integrates multiple PRS datasets for more robust risk variant prioritization, incorporating genome-wide association study (GWAS) priority scores as biologically informed priors. Additionally, we introduce BrainGeneBot, an AI-driven tool leveraging generative pretrained transformers with retrieval-augmented generation technology to streamline genomic analyses in AD, including the STRING for protein interaction analysis, Enrichr for gene set enrichment, ClinVar for genetic variant interpretation, and Biopython for conducting literature searches. We apply our approach to publicly available AD datasets from the PGS Catalog and conduct further analyses to validate its efficacy. In parallel, we perform conventional unsupervised rank aggregation as a baseline. The transductive learning approach not only verifies high-risk variants identified by traditional methods but also reveals unique insights that better correlate with GWAS signals. Our framework streamlines data retrieval and interpretation, effectively prioritizing genetic variants in multiple PRS studies. Moreover, BrainGeneBot facilitates the discovery of biologically meaningful insights to enhance PRS interpretability and applicability in AD research, supporting the development of precise AD interventions and treatments. Our approach provides a robust framework for AD genetic research, improving data accessibility, accelerating discoveries, and refining genetic insights.

Multimodal neuroimaging data modeling has become a widely used approach but confronts considerable challenges due to their heterogeneity, which encompasses variability in data types, scales, and formats across modalities. This variability necessitates the deployment of advanced computational methods to integrate and interpret diverse datasets within a cohesive analytical framework. In our research, we combine functional magnetic resonance imaging (fMRI), diffusion tensor imaging (DTI), and structural MRI (sMRI) for joint analysis. This integration capitalizes on the unique strengths of each modality and their inherent interconnections, aiming for a comprehensive understanding of the brain's connectivity and anatomical characteristics. Utilizing the Glasser atlas for parcellation, we integrate imaging-derived features from multiple modalities-functional connectivity from fMRI, structural connectivity from DTI, and anatomical features from sMRI-within consistent regions. Our approach incorporates a masking strategy to differentially weight neural connections, thereby facilitating an amalgamation of multimodal imaging data. This technique enhances interpretability at the connectivity level, transcending traditional analyses centered on singular regional attributes. The model is applied to the Human Connectome Project's Development study to elucidate the associations between multimodal imaging and cognitive functions throughout youth. The analysis demonstrates improved prediction accuracy and uncovers crucial anatomical features and neural connections, deepening our understanding of brain structure and function. This study not only advances multimodal neuroimaging analytics by offering a novel method for integrative analysis of diverse imaging modalities but also improves the understanding of intricate relationships between brain's structural and functional networks and cognitive development.

Graph convolutional deep learning has emerged as a promising method to explore the functional organization of the human brain in neuroscience research. This paper presents a novel framework that utilizes the gated graph transformer (GGT) model to predict individuals' cognitive ability based on functional connectivity (FC) derived from fMRI. Our framework incorporates prior spatial knowledge and uses a random-walk diffusion strategy that captures the intricate structural and functional relationships between different brain regions. Specifically, our approach employs learnable structural and positional encodings (LSPE) in conjunction with a gating mechanism to efficiently disentangle the learning of positional encoding (PE) and graph embeddings. Additionally, we utilize the attention mechanism to derive multi-view node feature embeddings and dynamically distribute propagation weights between each node and its neighbors, which facilitates the identification of significant biomarkers from functional brain networks and thus enhances the interpretability of the findings. To evaluate our proposed model in cognitive ability prediction, we conduct experiments on two large-scale brain imaging datasets: the Philadelphia Neurodevelopmental Cohort (PNC) and the Human Connectome Project (HCP). The results show that our approach not only outperforms existing methods in prediction accuracy but also provides superior explainability, which can be used to identify important FCs underlying cognitive behaviors.

The hypergraph structure has been utilized to characterize the brain functional connectome (FC) by capturing the high order relationships among multiple brain regions of interest (ROIs) compared with a simple graph. Accordingly, hypergraph neural network (HGNN) models have emerged and provided efficient tools for hypergraph embedding learning. However, most existing HGNN models can only be applied to pre-constructed hypergraphs with a static structure during model training, which might not be a sufficient representation of the complex brain networks. In this study, we propose a dynamic weighted hypergraph convolutional network (dwHGCN) framework to consider a dynamic hypergraph with learnable hyperedge weights. Specifically, we generate hyperedges based on sparse representation and calculate the hyper similarity as node features. The hypergraph and node features are fed into a neural network model, where the hyperedge weights are updated adaptively during training. The dwHGCN facilitates the learning of brain FC features by assigning larger weights to hyperedges with higher discriminative power. The weighting strategy also improves the interpretability of the model by identifying the highly active interactions among ROIs shared by a common hyperedge. We validate the performance of the proposed model on two classification tasks with three paradigms functional magnetic resonance imaging (fMRI) data from Philadelphia Neurodevelopmental Cohort. Experimental results demonstrate the superiority of our proposed method over existing hypergraph neural networks. We believe our model can be applied to other applications in neuroimaging for its strength in representation learning and interpretation.

The combination of multimodal imaging and genomics provides a more comprehensive way for the study of mental illnesses and brain functions. Deep network-based data fusion models have been developed to capture their complex associations, resulting in improved diagnosis of diseases. However, deep learning models are often difficult to interpret, bringing about challenges for uncovering biological mechanisms using these models. In this work, we develop an interpretable multimodal fusion model to perform automated diagnosis and result interpretation simultaneously. We name it Grad-CAM guided convolutional collaborative learning (gCAM-CCL), which is achieved by combining intermediate feature maps with gradient-based weights. The gCAM-CCL model can generate interpretable activation maps to quantify pixel-level contributions of the input features. Moreover, the estimated activation maps are class-specific, which can therefore facilitate the identification of biomarkers underlying different groups. We validate the gCAM-CCL model on a brain imaging-genetic study, and demonstrate its applications to both the classification of cognitive function groups and the discovery of underlying biological mechanisms. Specifically, our analysis results suggest that during task-fMRI scans, several object recognition related regions of interests (ROIs) are activated followed by several downstream encoding ROIs. In addition, the high cognitive group may have stronger neurotransmission signaling while the low cognitive group may have problems in brain/neuron development due to genetic variations.