MAGNET: Manifold-Aware Graph Diffusion Network for Connectome Generation

Task-based fMRI provides a direct readout of task-evoked neural dynamics, but it is expensive and difficult to acquire at scale, motivating rest-to-task synthesis from widely available resting-state fMRI (rsfMRI). We propose FM-fMRI, an event-conditioned flow-matching model that learns a continuous-time conditional vector field to generate task ROI time series from a subject's rsfMRI and the task event information. The formulation enables fast ODE-based sampling and flexible conditioning over heterogeneous event schedules. Rather than optimizing for pointwise reconstruction, we evaluated generated signals using complementary criteria that probe temporal and spectral structure, subject and group-level connectome consistency, and distributional alignment. On the public Human Connectome Project and internal BioPoint autism cohort, FM-fMRI achieves the strongest spectral and connectivity agreement and improved distribution-level matching over conditional diffusion, generative adversarial networks (GANs), and variational autoencoders (VAEs) baselines. Furthermore, we augment the BioPoint cohort by synthesizing task-fMRI ROI time series with our method, improving downstream autism classification and demonstrating practical utility in data-limited clinical settings. The code will be available on GitHub.

Connectomes, graph-level maps of neurons and their synaptic connections, provide a structural basis for understanding how brain circuits support function and computation. However, mapping connectome structure to computation remains difficult because these graphs are high-dimensional, sparse, and sensitive to local structural variation. Existing approaches often depend on hand-crafted structural descriptors or task-specific predictors, which limits their ability to represent connectomes in a form that is both generative and functionally meaningful. We propose a conditional generative latent framework that encodes connectome graphs into a compact structural space while using available node-level conditions to guide reconstruction and generation. From this space, the model can reconstruct observed connectivity with a mean edge-reconstruction AUC up to 0.910 and generate new candidate connectomes, enabling a unified analysis of graph structure and computational behavior. Using connectome-derived graphs as recurrent computational substrates, we found that the learned latent space captures functional variation across reservoir-computing experiments, with cross-validated $R^2$ values up to approximately 0.87. Interpretability analysis further revealed task-specific structural mechanisms: in our examples, memory performance is associated with reciprocal recurrent connectivity, whereas prediction and classification are more strongly associated with spectral properties of the recurrent network. These findings suggest an AI-for-science approach to linking neural connectivity to computation and provide a generative and interpretable basis for studying how distinct structural mechanisms shape computational capacity.

Functional connectome analysis examines brain-region interactions to understand and identify disorders such as autism spectrum disorder and Alzheimer's disease. Existing methods typically use GNNs and Transformers to model the full functional connectivity matrix. However, processing tens of thousands of connections introduces redundancy and noise, increases computational cost, and limits connection-level interpretability. This raises a central question: do we really need complex interaction modeling, or is identifying a small set of disease-relevant connectivity patterns sufficient? To answer this question, we propose BrainLinear, a lightweight geometry-aware framework for mining disease-discriminative connectome patterns. BrainLinear first maps each functional connectivity matrix to a shared tangent space centered at the Fréchet mean of the training set, capturing subject-specific deviations while respecting matrix geometry. It then scores each ROI-pair tangent direction by its classification contribution and disease--control difference, retaining Top-$K$ directions as a compact representation. Finally, a shallow multilayer perceptron performs classification on the selected representation. Experiments on ABIDE and ADNI show that BrainLinear matches or exceeds strong GNN and Transformer baselines at a fraction of their cost: it improves AUC and ACC over the best baseline for each metric by up to $3.54$ and $1.39$ percentage points, while reducing runtime and peak GPU memory by $84.0\%$ and $68.4\%$ relative to the closest baseline in AUC. The selected directions are directionally consistent with between-group displacements and organized across major functional systems, supporting connection-level interpretation.