BrainCast: A Spatio-Temporal Forecasting Model for Whole-Brain fMRI Time Series Prediction

Modeling resting-state functional magnetic resonance imaging (rs-fMRI) data is crucial for understanding brain-wide neural activity. However, traditional methods struggle to capture complex temporal dynamics over long horizons, to account for the brain's anatomical spatial structure, and to model high-dimensional ambient signals that lie on a low-dimensional intrinsic subspace. We propose FAST-Brain, a unified flow-aligned spatio-temporal surrogate brain model that addresses all three challenges. At its core is a flow-aligned generative framework that directly predicts the clean blood-oxygen-level-dependent (BOLD) signal, paired with a graph convolutional network that captures spatial structural constraints and a Transformer that models long-range temporal dependencies. Theoretically, we show that under a low-dimensional subspace assumption, the approximation error of our model scales with the intrinsic dimension rather than the ambient dimension, which justifies our direct modeling of the BOLD signal. Extensive experiments on synthetic and Human Connectome Project datasets demonstrate that FAST-Brain achieves state-of-the-art performance in recovering functional connectivity, effective connectivity, and the implicit low-dimensional signal subspace.

Functional magnetic resonance imaging (fMRI) commonly characterizes large-scale brain organization through functional connectivity (FC). However, an observed FC matrix is not a fixed brain graph but a statistical estimate determined by the finite BOLD frames used to compute it. Conventional FC-based approaches typically represent each scan with a single Pearson-correlation matrix, leaving frame-resolved variations in regional interactions unexploited. To address this limitation, we introduce CoFlu-Brain, which organizes framewise cofluctuation observations into multiple retained and dropped views, each summarized as an FC matrix. The model learns connectivity structure reproducible across retained views and predicts the representations of the corresponding dropped views, while adopting SIGReg from LeJEPA to prevent representation collapse. We pretrained CoFlu-Brain on 13,444 subjects from eight dataset groups and evaluated its representations via frozen-encoder linear probing on seven classification and two age-prediction tasks across seven datasets. CoFlu-Brain showed strong transfer across demographic, developmental, and clinical prediction tasks, outperforming the evaluated released models on most tasks. Random frame partitioning improved aggregate transfer, while the complete objective achieved the strongest overall performance. Code is available.

Functional Magnetic Resonance Imaging (fMRI) is an imaging technique widely used to study human brain activity. fMRI signals in areas across the brain transiently synchronise and desynchronise their activity in a highly structured manner, even when an individual is at rest. These functional connectivity dynamics may be related to behaviour and neuropsychiatric disease. To model these dynamics, temporal brain connectivity representations are essential, as they reflect evolving interactions between brain regions and provide insight into transient neural states and network reconfigurations. However, conventional graph neural networks (GNNs) often struggle to capture long-range temporal dependencies in dynamic fMRI data. To address this challenge, we propose BrainATCL, an unsupervised, nonparametric framework for adaptive temporal brain connectivity learning, enabling functional link prediction and age estimation. Our method dynamically adjusts the lookback window for each snapshot based on the rate of newly added edges. Graph sequences are subsequently encoded using a GINE-Mamba2 backbone to learn spatial-temporal representations of dynamic functional connectivity in resting-state fMRI data of 1,000 participants from the Human Connectome Project. To further improve spatial modeling, we incorporate brain structure and function-informed edge attributes, i.e., the left/right hemispheric identity and subnetwork membership of brain regions, enabling the model to capture biologically meaningful topological patterns. We evaluate our BrainATCL on two tasks: functional link prediction and age estimation. The experimental results demonstrate superior performance and strong generalization, including in cross-session prediction scenarios.