BrainCodes: A Lightweight EEG Foundation Model over Discrete Neural Codes

Evaluating foundation models under appropriate adaptation settings is essential for understanding the quality and transferability of the learned representations. Recent EEG foundation models have demonstrated promising transfer capabilities across tasks and datasets, motivating their growing use in neurotechnology and clinical applications. However, these models are typically evaluated under full fine-tuning on well-curated downstream datasets, a setting that does not reflect biomedical domain constraints such as limited labeled data, reduced sensor coverage, or parameter-efficient adaptation. In this work, we propose a multi-dimensional evaluation framework for assessing EEG models under realistic low-resource conditions. Empirical analysis of both supervised EEG models and recent EEG foundation models, including LaBraM, CSBrain, and CBraMod, across 6 different datasets is performed under the proposed multi-dimensional evaluation framework. We find that EEG foundation models consistently provide performance gains on long-context tasks such as sleep stage prediction and mental health state classification. In contrast, for short-window Brain Computer Interface style tasks, supervised models achieve comparable despite having substantially fewer parameters. Additional analyses demonstrate that current foundation models provide limited robustness to short-window tasks and channel constrained settings. Together, these findings motivate the use of multi-dimensional evaluation protocols that characterize model behavior under realistic use constraints.

A central challenge in electroencephalography (EEG) foundation modeling is learning transferable representations across recordings with diverse tasks, montages, references, and spectral characteristics. Existing masked modeling approaches often rely on broadband continuous patches or a single discrete representation, which may underrepresent frequency-specific activity. This paper proposes BandVQ, a band-wise vector-quantized EEG foundation model that decomposes EEG into delta, theta, alpha, beta, and gamma bands, trains an independent VQ-VAE tokenizer for each band, and pretrains a shared Transformer encoder on the resulting discrete VQ code indices. The encoder uses masked code tokens, quantized absolute log-power tokens, channel and temporal embeddings, and metadata prefix tokens representing reference, band, task family, and phase. Region-based masking is also introduced to reduce the trivial reconstruction of spatially adjacent electrodes. The model is pretrained on 71 public EEG corpora comprising over 9,200 subjects and 357,000 single-channel hours and evaluated on six subject-independent classification datasets. Under the current evaluation setting, the proposed model achieves strong transfer performance, with the highest reported results on three cognitive tasks and competitive performance on three motor imagery tasks.

Large-scale EEG foundation models have demonstrated promising transferability across neurological disorders, but often require millions of parameters and substantial computational resources. In this paper, we present the Universal Semantic EEG Foundation Model (USE-FM), a lightweight EEG foundation model that learns transferable neural representations through self-supervised signal reconstruction on the Temple University Hospital EEG Corpus (TUEG). After pretraining, the encoder is frozen and evaluated on two clinically distinct downstream tasks, abnormal EEG detection (TUAB) and epileptic seizure recognition (TUEP), using a unified frozen-transfer protocol against recent EEG foundation models, including LUNA-Base and CBraMod. With only 1.46 million parameters, approximately one-fifth the size of existing models, USE-FM achieves competitive overall performance, including strong sensitivity and F1-score on TUEP (SEN $75.00 \pm 14.14$, F1 $70.37 \pm 4.01$), while maintaining competitive performance on TUAB (AUC $85.24 \pm 5.61$). Beyond downstream classification, latent representation analysis using $k$-means clustering together with PCA and t-SNE demonstrates that USE-FM learns organized semantic EEG representations comparable to substantially larger foundation models. These results suggest that large-scale self-supervised pretraining enables lightweight architectures to learn transferable semantic EEG representations, providing a computationally efficient foundation for cross-disorder analysis and future clinical decision support in neurological disorders.