Machine learning provides a valuable tool for analyzing high-dimensional functional neuroimaging data, and is proving effective in predicting various neurological conditions, psychiatric disorders, and cognitive patterns. In functional magnetic resonance imaging (MRI) research, interactions between brain regions are commonly modeled using graph-based representations. The potency of graph machine learning methods has been established across myriad domains, marking a transformative step in data interpretation and predictive modeling. Yet, despite their promise, the transposition of these techniques to the neuroimaging domain has been challenging due to the expansive number of potential preprocessing pipelines and the large parameter search space for graph-based dataset construction. In this paper, we introduce NeuroGraph1, a collection of graph-based neuroimaging datasets, and demonstrated its utility for predicting multiple categories of behavioral and cognitive traits.

Recent developed graph-based methods for diagnosing brain disorders using functional connectivity highly rely on predefined brain atlases, but overlook the rich information embedded within atlases and the confounding effects of site and phenotype variability. To address these challenges, we propose a two-stage Brain-to-Population Graph Learning (B2P-GL) framework that integrates the semantic similarity of brain regions and condition-based population graph modeling. In the first stage, termed brain representation learning, we leverage brain atlas knowledge from GPT-4 to enrich the graph representation and refine the brain graph through an adaptive node reassignment graph attention network. In the second stage, termed population disorder diagnosis, phenotypic data is incorporated into population graph construction and feature fusion to mitigate confounding effects and enhance diagnosis performance. Experiments on the ABIDE I, ADHD-200, and Rest-meta-MDD datasets show that B2P-GL outperforms state-of-the-art methods in prediction accuracy while enhancing interpretability. Overall, our proposed framework offers a reliable and personalized approach to brain disorder diagnosis, advancing clinical applicability.

Brain graph learning has demonstrated significant achievements in the fields of neuroscience and artificial intelligence. However, existing methods struggle to selectively learn disease-related knowledge, leading to heavy parameters and computational costs. This challenge diminishes their efficiency, as well as limits their practicality for real-world clinical applications. To this end, we propose a lightweight Brain PathoGraph Learning (BrainPoG) model that enables efficient brain graph learning by pathological pattern filtering and pathological feature distillation. Specifically, BrainPoG first contains a filter to extract the pathological pattern formulated by highly disease-relevant subgraphs, achieving graph pruning and lesion localization. A PathoGraph is therefore constructed by dropping less disease-relevant subgraphs from the whole brain graph. Afterwards, a pathological feature distillation module is designed to reduce disease-irrelevant noise features and enhance pathological features of each node in the PathoGraph. BrainPoG can exclusively learn informative disease-related knowledge while avoiding less relevant information, achieving efficient brain graph learning. Extensive experiments on four benchmark datasets demonstrate that BrainPoG exhibits superiority in both model performance and computational efficiency across various brain disease detection tasks.

The construction of brain graphs from functional Magnetic Resonance Imaging (fMRI) data plays a crucial role in enabling graph machine learning for neuroimaging. However, current practices often rely on rigid pipelines that overlook critical data-centric choices in how brain graphs are constructed. In this work, we adopt a Data-Centric AI perspective and systematically define and benchmark a data-centric design space for brain graph construction, constrasting with primarily model-centric prior work. We organize this design space into three stages: temporal signal processing, topology extraction, and graph featurization. Our contributions lie less in novel components and more in evaluating how combinations of existing and modified techniques influence downstream performance. Specifically, we study high-amplitude BOLD signal filtering, sparsification and unification strategies for connectivity, alternative correlation metrics, and multi-view node and edge features, such as incorporating lagged dynamics. Experiments on the HCP1200 and ABIDE datasets show that thoughtful data-centric configurations consistently improve classification accuracy over standard pipelines. These findings highlight the critical role of upstream data decisions and underscore the importance of systematically exploring the data-centric design space for graph-based neuroimaging. Our code is available at https://github.com/GeQinwen/DataCentricBrainGraphs.

Brain connectomes, representing neural connectivity as graphs, are crucial for understanding brain organization but costly and time-consuming to acquire, motivating generative approaches. Recent advances in graph generative modeling offer a data-driven alternative, enabling synthetic connectome generation and reducing dependence on large neuroimaging datasets. However, current models face key limitations: (i) compressing the whole graph into a single latent code (e.g., VGAEs) blurs fine-grained local motifs; (ii) relying on rich node attributes rarely available in connectomes reduces reconstruction quality; (iii) edge-centric models emphasize topology but overlook accurate edge-weight prediction, harming quantitative fidelity; and (iv) computationally expensive designs (e.g., edge-conditioned convolutions) impose high memory demands, limiting scalability. We propose GraphTreeGen (GTG), a subtree-centric generative framework for efficient, accurate connectome synthesis. GTG decomposes each connectome into entropy-guided k-hop trees capturing informative local structure, encoded by a shared GCN. A bipartite message-passing layer fuses subtree embeddings with global node features, while a dual-branch decoder jointly predicts edge existence and weights to reconstruct the adjacency matrix. GTG outperforms state-of-the-art baselines in self-supervised tasks and remains competitive in supervised settings, delivering higher structural fidelity and more precise weights with far less memory. Its modular design enables extensions to connectome super-resolution and cross-modality synthesis. Code: https://github.com/basiralab/GTG/

As large language models (LLMs) continue to revolutionize AI research, there is a growing interest in building large-scale brain foundation models to advance neuroscience. While most existing brain foundation models are pre-trained on time-series signals or connectome features, we propose a novel graph-based pre-training paradigm for constructing a brain graph foundation model. In this paper, we introduce the Brain Graph Foundation Model, termed BrainGFM, a unified framework that leverages graph contrastive learning and graph masked autoencoders for large-scale fMRI-based pre-training. BrainGFM is pre-trained on a diverse mixture of brain atlases with varying parcellations, significantly expanding the pre-training corpus and enhancing the model's ability to generalize across heterogeneous fMRI-derived brain representations. To support efficient and versatile downstream transfer, we integrate both graph prompts and language prompts into the model design, enabling BrainGFM to flexibly adapt to a wide range of atlases, neurological and psychiatric disorders, and task settings. Furthermore, we employ meta-learning to optimize the graph prompts, facilitating strong generalization to previously unseen disorders under both few-shot and zero-shot learning conditions via language-guided prompting. BrainGFM is pre-trained on 27 neuroimaging datasets spanning 25 common neurological and psychiatric disorders, encompassing 2 types of brain atlases (functional and anatomical) across 8 widely-used parcellations, and covering over 25,000 subjects, 60,000 fMRI scans, and a total of 400,000 graph samples aggregated across all atlases and parcellations. The code is available at: https://github.com/weixinxu666/BrainGFM

Recent deep learning approaches have shown promise in learning such individual brain parcellations from functional magnetic resonance imaging (fMRI). However, most existing methods assume consistent data distributions across domains and struggle with domain shifts inherent to real-world cross-dataset scenarios. To address this challenge, we proposed Graph Domain Adaptation for Individual Parcellation (GDAIP), a novel framework that integrates Graph Attention Networks (GAT) with Minimax Entropy (MME)-based domain adaptation. We construct cross-dataset brain graphs at both the group and individual levels. By leveraging semi-supervised training and adversarial optimization of the prediction entropy on unlabeled vertices from target brain graph, the reference atlas is adapted from the group-level brain graph to the individual brain graph, enabling individual parcellation under cross-dataset settings. We evaluated our method using parcellation visualization, Dice coefficient, and functional homogeneity. Experimental results demonstrate that GDAIP produces individual parcellations with topologically plausible boundaries, strong cross-session consistency, and ability of reflecting functional organization.

Alzheimer's disease (AD) affects 50 million people worldwide and is projected to overwhelm 152 million by 2050. AD is characterized by cognitive decline due partly to disruptions in metabolic brain connectivity. Thus, early and accurate detection of metabolic brain network impairments is crucial for AD management. Chief to identifying such impairments is FDG-PET data. Despite advancements, most graph-based studies using FDG-PET data rely on group-level analysis or thresholding. Yet, group-level analysis can veil individual differences and thresholding may overlook weaker but biologically critical brain connections. Additionally, machine learning-based AD prediction largely focuses on univariate outcomes, such as disease status. Here, we introduce explainable graph-theoretical machine learning (XGML), a framework employing kernel density estimation and dynamic time warping to construct individual metabolic brain graphs that capture the distance between pair-wise brain regions and identify subgraphs most predictive of multivariate AD-related outcomes. Using FDG-PET data from the Alzheimer's Disease Neuroimaging Initiative, XGML builds metabolic brain graphs and uncovers subgraphs predictive of eight AD-related cognitive scores in new subjects. XGML shows robust performance, particularly for predicting scores measuring learning, memory, language, praxis, and orientation, such as CDRSB ($r = 0.74$), ADAS11 ($r = 0.73$), and ADAS13 ($r = 0.71$). Moreover, XGML unveils key edges jointly but differentially predictive of several AD-related outcomes; they may serve as potential network biomarkers for assessing overall cognitive decline. Together, we show the promise of graph-theoretical machine learning in biomarker discovery and disease prediction and its potential to improve our understanding of network neural mechanisms underlying AD.

State-of-the-art brain graph analysis methods fail to fully encode the small-world architecture of brain graphs (accompanied by the presence of hubs and functional modules), and therefore lack biological plausibility to some extent. This limitation hinders their ability to accurately represent the brain's structural and functional properties, thereby restricting the effectiveness of machine learning models in tasks such as brain disorder detection. In this work, we propose a novel Biologically Plausible Brain Graph Transformer (BioBGT) that encodes the small-world architecture inherent in brain graphs. Specifically, we present a network entanglement-based node importance encoding technique that captures the structural importance of nodes in global information propagation during brain graph communication, highlighting the biological properties of the brain structure. Furthermore, we introduce a functional module-aware self-attention to preserve the functional segregation and integration characteristics of brain graphs in the learned representations. Hub2 (a) Hubs play essential roles (b) Functional modules in the brain. One Figure 1: Small-world architecture of brain graphs. of the most important characteristics of brain graphs is their small-world architecture, with scientific evidence supporting the presence of hubs and functional modules in brain graphs (Liao et al., 2017; Swanson et al., 2024). First, it is demonstrated that nodes in brain graphs exhibit a high degree of difference in their importance, with certain nodes having more central roles in information propagation (Lynn & Bassett, 2019; Betzel et al., 2024). These nodes are perceived as hubs, as shown in Figure 1 (a) (the visualization is based on findings by Seguin et al. (2023)), which are usually highly connected so as to support efficient communication within the brain. Second, human brain consists of various functional modules (e.g., visual cortex), where ROIs within the same module exhibit high functional coherence, termed functional integration, while ROIs from different modules show lower functional coherence, termed functional segregation (Rubinov & Sporns, 2010; Seguin et al., 2022). Therefore, brain graphs are characterized by community structure, reflecting functional modules. Our code is available at https://github.com/pcyyyy/BioBGT. ROIs in the same module have strong connections (high temporal correlations), while those from different modules show weaker connections. With the significant ability of graph transformers in capturing interactions between nodes (Ma et al., 2023a; Shehzad et al., 2024; Yi et al., 2024), Transformer-based brain graph learning methods have gained prominence (Kan et al., 2022; Bannadabhavi et al., 2023).