SCOPE: Structured Prototype-Guided Adaptation for EEG Foundation Models with Limited Labels

EEG foundation models pretrained via self-supervised learning promise transferable representations, but their generalization remains limited, especially across diverse clinical datasets. Full fine-tuning is impractical for resource-constrained clinical settings due to high computational requirements. In this work, we investigate whether parameter-efficient self-supervised adaptation, updating only 9% of parameters suffices to align representations to target tasks. We evaluate our method on two state-of-the-art models with different pretraining objectives: BIOT (contrastive) and CBraMod (masked reconstruction), and evaluate on three clinical EEG datasets for abnormality detection (TUAB), event classification (TUEV), and seizure detection (CHB-MIT) under both in-distribution and out-of-distribution conditions. SSL adaptation yields consistent gains over linear probing, up to 20x AUCPR. Under a fixed compute budget, peak performance requires only 20--50% of available unlabeled data. Critically, when total window count is fixed, performance remains invariant to patient count, suggesting that performance is dependent on overall temporal window diversity only. Our findings demonstrate that parameter-efficient adaptation enables effective deployment of EEG Foundation models (EEG-FM) with minimal computational overhead and data collection burden. Code available at: https://github.com/c3n-group/efficient-eeg-adapt

Scaling EEG foundation models requires pooling data across heterogeneous electrode montages, a prerequisite both for larger pretraining corpora and for downstream deployment. We present the first systematic comparison of four channel adaptation methods (Conv1d projection, spherical spline interpolation (SSI), source-space decomposition, and Riemannian re-centering) across five pretrained EEG foundation models (5M--157M parameters), five downstream tasks, and two training regimes with 10--15 random seeds each. We find that rigid-montage models (BENDR, Neuro-GPT) require external adaptation, while flexible models (EEGPT, CBraMod) match or exceed it natively when fine-tuned but benefit from external methods under frozen-encoder deployment. A probe-SFT asymmetry exists: external adaptation can cause severe negative transfer during fine-tuning of flexible models. The optimal method is architecture-dependent (Conv1d for BENDR, SSI/Riemannian for Neuro-GPT, source-space decomposition for depression detection), and 5M-parameter CBraMod outperforms models up to 31$\times$ larger on 4/5 datasets, consistent with independent findings that compact EEG-specific architectures can match larger models.

EEG foundation models (EFMs) capture reusable knowledge from large-scale EEG data, while many EEG recordings also include companion physiological signals that provide complementary information beyond the EEG-only interface. The challenge is to preserve this pretrained knowledge while extending the EFM to heterogeneous multimodal recordings through an adaptation inferred from unlabeled target data. We introduce ZeroMAG, a zero-shot multimodal adapter generation framework that extends a frozen EEG encoder and prediction head using unlabeled target recordings, without target labels or target-side optimization. The target datasets are held out from all model training and selection in the ZeroMAG pipeline. ZeroMAG organizes companion modalities around a configuration-invariant adapter, constructs a modality-subject-task condition from unlabeled recordings and task context, and generates adapter weights in a function-constrained latent space learned from source adapters. Across six held-out target datasets and three EFM backbones, ZeroMAG improves balanced accuracy by 7.22 percentage points over EEG-only inference and 4.89 points over direct weight regression, while coming within 0.50 points of supervised multimodal adaptation on average. Ablations further show that removing functional supervision from either representation learning or conditional generation degrades generated-adapter performance, confirming the contribution of both components.