SAMBA: Toward a Long-Context EEG Foundation Model via Spatial Embedding and Differential Mamba

Long-sequence electroencephalogram (EEG) modeling is essential for developing generalizable EEG representation models. This need arises from the high sampling rate of EEG data and the long recording durations required to capture extended neurological patterns in brain activity. Transformer-based models have shown promise in modeling short sequences of a few seconds; however, their quadratic complexity limits scalability to longer contexts. Moreover, variability in electrode montage across available datasets, along with inter-subject differences in brain signals, pose significant challenges to developing a generalizable and robust foundation model. We propose $\mathit{\text{SAMBA}}$, a self-supervised learning framework with a Mamba-based U-shaped encoder-decoder architecture, which effectively captures long-range temporal dependencies and spatial variability in EEG data. Leveraging the inherent ability of Mamba in processing long context sizes, we introduce: (1) $\mathit{\text{Temporal}}\mathit{\text{Semantic}}\mathit{\text{Random}}\mathit{\text{Masking}}$ for semantic-level sequence reconstruction, (2) a $\mathit{\text{Multi-Head}}\mathit{\text{Differential}}\mathit{\text{Mamba}}$ module to suppress redundancy and emphasize salient temporal structures, and (3) a $\mathit{\text{Spatial-Adaptive}}\mathit{\text{Input}}\mathit{\text{Embedding}}$ that learns unified embeddings in a three-dimensional Euclidean space, enabling robustness across devices. Experiments on thirteen EEG datasets across diverse tasks, electrode configurations, and sequence durations demonstrate that SAMBA consistently outperforms state-of-the-art methods while maintaining low memory consumption and inference time. We also show the learned spatial weight maps from our embedding module align closely with task-relevant neurophysiological regions, demonstrating the learnability and interpretability of SAMBA. These results highlight SAMBA’s scalability and practical potential as a foundation model for real-time brain-computer interface applications.