Resting-state functional magnetic resonance imaging (rsfMRI) is a powerful tool for investigating the relationship between brain function and cognitive processes as it allows for the functional organization of the brain to be captured without relying on a specific task or stimuli. In this paper, we present a novel modeling architecture called BrainRGIN for predicting intelligence (fluid, crystallized and total intelligence) using graph neural networks on rsfMRI derived static functional network connectivity matrices. Extending from the existing graph convolution networks, our approach incorporates a clustering-based embedding and graph isomorphism network in the graph convolutional layer to reflect the nature of the brain sub-network organization and efficient network expression, in combination with TopK pooling and attention-based readout functions. We evaluated our proposed architecture on a large dataset, specifically the Adolescent Brain Cognitive Development Dataset, and demonstrated its effectiveness in predicting individual differences in intelligence. Our model achieved lower mean squared errors and higher correlation scores than existing relevant graph architectures and other traditional machine learning models for all of the intelligence prediction tasks. The middle frontal gyrus exhibited a significant contribution to both fluid and crystallized intelligence, suggesting their pivotal role in these cognitive processes. Total composite scores identified a diverse set of brain regions to be relevant which underscores the complex nature of total intelligence. Our GitHub implementation is publicly available on https://github.com/bishalth01/BrainRGIN/.

Resting-state functional magnetic resonance imaging (rs-fMRI) is a noninvasive technique pivotal for understanding human neural mechanisms of intricate cognitive processes. Most rs-fMRI studies compute a single static functional connectivity matrix across brain regions of interest, or dynamic functional connectivity matrices with a sliding window approach. These approaches are at risk of oversimplifying brain dynamics and lack proper consideration of the goal at hand. While deep learning has gained substantial popularity for modeling complex relational data, its application to uncovering the spatiotemporal dynamics of the brain is still limited. In this study we propose a novel interpretable deep learning framework that learns goal-specific functional connectivity matrix directly from time series and employs a specialized graph neural network for the final classification. Our model, DSAM , leverages temporal causal convolutional networks to capture the temporal dynamics in both low- and high-level feature representations, a temporal attention unit to identify important time points, a self-attention unit to construct the goal-specific connectivity matrix, and a novel variant of graph neural network to capture the spatial dynamics for downstream classification. To validate our approach, we conducted experiments on the Human Connectome Project dataset with 1075 samples to build and interpret the model for the classification of sex group, and the Adolescent Brain Cognitive Development Dataset with 8520 samples for independent testing. Compared our proposed framework with other state-of-art models, results suggested this novel approach goes beyond the assumption of a fixed connectivity matrix, and provides evidence of goal-specific brain connectivity patterns, which opens up potential to gain deeper insights into how the human brain adapts its functional connectivity specific to the task at hand. Our implementation can be found on https://github.com/bishalth01/DSAM . • Multilevel Temporal Feature Extraction: • Utilizes a novel multilevel Temporal Convolutional Network (TCN) adaptation to directly extract temporal features from raw brain activity data. • Shared Temporal Attention for Key Time Points: • Implements shared temporal attention mechanisms to selectively focus on the most informative time points, enhancing model efficiency. • Node-Node Self-Attention for Dynamic Brain Connectivity: • Leverages self-attention mechanisms to dynamically construct a goal-specific brain connectivity matrix, capturing complex inter-node interactions. • ROI-Aware Graph Neural Networks (GNNs): • Introduces ROI-aware GNNs to model spatial brain dynamics, ensuring region-specific contextual learning and improving interpretability.

Alzheimer's disease (AD) is a neurodegenerative process characterized by the accumulation of amyloid-beta plaques and neurofibrillary tangles and is the most common cause of dementia. Studies have been striving to analyze the disease using available physiological and behavioral data. Functional/structural neuroimaging and genomics are complementary modalities for exploring the mechanisms subserving the development of AD. In this paper, we present a deep multimodal generative data fusion framework for integrating these sources in a classification task involving AD patients and healthy controls from the ADNI database. Biological data fusion has the potential to improve the final prediction, but at the same time, it is particularly challenging due to the unavailability of all sources of input for the entire cohort of subjects. Our proposed model allows us to perform prediction even if individuals are missing certain modalities. Our method addresses the missing modalities problem via knowledge transfer from two generative adversarial networks. The model exhibits superior performance for predicting AD versus healthy control, even with missing modalities. This could have an important impact from the patient point of view since certain clinical tests may not be necessary or available to a given individual.

The birth of wireless communication systems nearly a century ago has transformed and redefined the way humans communicate and interact. This transformation has evolved over many years and has brought along not only seamless connectivity for human interactions but also communication between machines and devices. While these communication systems are manmade artifacts, the research community has more recently turned its attention to other communication strategies that have spontaneously evolved in nature.

Imaging genomics focuses on characterizing genomic influence on the variation of neurobiological traits, holding promise for illuminating the pathogenesis, reforming the diagnostic system, and precision medicine of mental disorders. This paper aims to provide an overall picture of the current status of neuroimaging-genomic analyses in mental disorders, and how we can increase their translational potential into clinical practice. The review is organized around three perspectives. (a) Towards reliability, generalizability and interpretability, where we summarize the multivariate models and discuss the considerations and trade-offs of using these methods and how reliable findings may be reached, to serve as ground for further delineation. (b) Towards improved diagnosis, where we outline the advantages and challenges of constructing a dimensional transdiagnostic model and how imaging genomic analyses map into this framework to aid in deconstructing heterogeneity and achieving an optimal stratification of patients that better inform treatment planning. (c) Towards improved treatment. Here we highlight recent efforts and progress in elucidating the functional annotations that bridge between genomic risk and neurobiological abnormalities, in detecting genomic predisposition and prodromal neurodevelopmental changes, as well as in identifying imaging genomic biomarkers for predicting treatment response. Providing an overview of the challenges and promises, this review hopefully motivates imaging genomic studies with multivariate, dimensional and transdiagnostic designs for generalizable and interpretable findings that facilitate development of personalized treatment.

Human brain connectivity is complex. Graph theory based analysis has become a powerful and popular approach for analyzing brain imaging data, largely because of its potential to quantitatively illuminate the networks, the static architecture in structure and function, the organization of dynamic behavior over time, and disease related brain changes. The first step in creating brain graphs is to define the nodes and edges connecting them. We review a number of approaches for defining brain nodes including fixed versus data-driven nodes. Expanding the narrow view of most studies which focus on static and/or single modality brain connectivity, we also survey advanced approaches and their performances in building dynamic and multi-modal brain graphs. We show results from both simulated and real data from healthy controls and patients with mental illnesse. We outline the advantages and challenges of these various techniques. By summarizing and inspecting recent studies which analyzed brain imaging data based on graph theory, this article provides a guide for developing new powerful tools to explore complex brain networks.

By exploiting cross-information among multiple imaging data, multimodal fusion has often been used to better understand brain diseases. However, most current fusion approaches are blind, without adopting any prior information. There is increasing interest to uncover the neurocognitive mapping of specific clinical measurements on enriched brain imaging data; hence, a supervised, goal-directed model that employs prior information as a reference to guide multimodal data fusion is much needed and becomes a natural option. Here, we proposed a fusion with reference model called "multi-site canonical correlation analysis with reference + joint-independent component analysis" (MCCAR+jICA), which can precisely identify co-varying multimodal imaging patterns closely related to the reference, such as cognitive scores. In a three-way fusion simulation, the proposed method was compared with its alternatives on multiple facets; MCCAR+jICA outperforms others with higher estimation precision and high accuracy on identifying a target component with the right correspondence. In human imaging data, working memory performance was utilized as a reference to investigate the co-varying working memory-associated brain patterns among three modalities and how they are impaired in schizophrenia. Two independent cohorts (294 and 83 subjects respectively) were used. Similar brain maps were identified between the two cohorts along with substantial overlaps in the central executive network in fMRI, salience network in sMRI, and major white matter tracts in dMRI. These regions have been linked with working memory deficits in schizophrenia in multiple reports and MCCAR+jICA further verified them in a repeatable, joint manner, demonstrating the ability of the proposed method to identify potential neuromarkers for mental disorders.

Multiple types of signals or images are often collected from the same participants in biomedical research. Multimodal analyses have been shown to better capture the joint information. We propose a new method named parallel group independent component analysis (para-GICA) to address a special need for parallel processing of multimodal brain images or signals where it is desirable to partition into groups, for example to stratify by age. Para-GICA is designed to identify associated components between two modalities based on their loading variations in participants, while allowing components to show group specificity. Simulation using synthetic MRI and genetic data demonstrates that para-GICA is able to recover group specific brain networks and the connection between brain networks and genetic factors. A real data application on brain gray matter concentration and whiter matter fractional anisotropy images extracts associated gray matter and white matter components, and ageing induced spatial differences of the components.