clinical neuroimaging teams

Abstract: Electroencephalography (EEG) provides a non-invasive window into dynamic brain activity, yet modeling long-horizon EEG sequences remains challenging due to their high temporal complexity, substantial variability across subjects, and the lack of biologically meaningful sequence representations. Existing tokenization strategies, such as fixed-window and patch-based representations, discretize EEG signals according to artificial temporal boundaries, which may disrupt intrinsic brain-state dynamics. In this work, we propose Brain-Token Learning, a neuroscience-inspired framework that introduces Brain Tokenization for long-horizon EEG sequence modeling. Instead of partitioning EEG signals into predefined temporal segments, Brain Tokenization represents EEG as sequences of recurrent microstate-derived brain tokens, where each token corresponds to a quasi-stable large-scale brain state with variable temporal duration. Based on these biologically grounded tokens, we further develop a multi-scale token interaction module consisting of Latent State Aggregation and State Transition Modeling to jointly capture global brain-state context and local microstate transitions. We evaluate Brain-Token on five heterogeneous EEG datasets, including the newly collected long-horizon NeuroLong dataset and four affective or clinical EEG datasets (SEED, DEAP, MDD, and NSSI). Extensive experiments demonstrate that Brain-Token consistently outperforms conventional CNN/LSTM architectures, Transformer-based models, and domain adaptation methods across diverse EEG scenarios. Further analysis verifies the effectiveness of microstate-based tokenization and multi-scale interaction for learning robust and interpretable EEG representations. These results establish Brain-Token as a biologically grounded tokenization paradigm for long-horizon EEG sequence modeling.

Abstract: Masked reconstruction is widely used for EEG foundation models, but optimizing reconstruction on low-SNR waveforms does not necessarily produce the most useful latent representation. We introduce MANAS-2, a new EEG foundation model that combines a Raw-Band Hybrid (RBH) masked autoencoder with Constrained Reconstruction (ConRec), a physics-motivated regularizer. RBH jointly reconstructs temporal waveform patches and compact spectral-band targets, while ConRec acts only on the temporal decoder output, penalizing differences in RMS energy between adjacent short windows of the reconstructed waveform. ConRec is intended to shape the encoder by biasing it toward the organization of oscillatory-envelope information. Across seven held-out EEG datasets, adding ConRec to an otherwise identical RBH model increases frozen ridge recovery of six-band spectral power from mean R^2=0.860 to 0.906 and recovery of inter-patch band-energy dynamics from R^2=0.283 to 0.354, while temporal waveform information remains highly recoverable from the frozen latents. Applied to a temporal-only masked autoencoder, ConRec also improves frozen downstream transfer and frequency-dependent latent geometry despite receiving no spectral targets: i.e., the effects of ConRec are architecture-independent. MANAS-2 also outperforms leading EEG Foundation Models on most downstream knowledge-transfer tasks. From the effects of ConRec, we see that a physically motivated constraint imposed through the decoder can make for a more spectrally organized and transferable latent space. MANAS-2 therefore provides a new EEG foundation model built around constrained reconstruction as a mechanism for shaping representation--rather than reconstruction--quality.