Channel Adaptation for EEG Foundation Models: A Systematic Benchmark Across Architectures, Tasks, and Training Regimes

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.

Electroencephalography (EEG) foundation models have shown strong potential for learning generalizable representations from large-scale neural data, yet their clinical deployment is hindered by distribution shifts across clinical settings, devices, and populations. Test-time adaptation (TTA) offers a promising solution by enabling models to adapt to unlabeled target data during inference without access to source data, a valuable property in healthcare settings constrained by privacy regulations and limited labeled data. However, its effectiveness for EEG remains largely underexplored. In this work, we introduce NeuroAdapt-Bench, a systematic benchmark for evaluating test-time adaptation methods on EEG foundation models under realistic distribution shifts. We evaluate representative TTA approaches from other domains across multiple pretrained foundation models, diverse downstream tasks, and heterogeneous datasets spanning in-distribution, out-of-distribution, and extreme modality shifts (e.g., Ear-EEG). Our results show that standard TTA methods yield inconsistent gains and often degrade performance, with gradient-based approaches particularly prone to heavy degradation. In contrast, optimization-free methods demonstrate greater stability and more reliable improvements. These findings highlight the limitations of existing TTA techniques in EEG, provide guidance for future development, and underscore the need for domain-specific adaptation strategies.

EEG foundation models (EEG-FMs) have been evaluated predominantly on clean, in-distribution accuracy, leaving their robustness, interpretability and representational quality largely unexamined. This study addresses these gaps by benchmarking six EEG-FMs against a baseline deep learning model across eight datasets. Beyond clean accuracy, we conduct three layers of analysis: (i) Robustness: we apply test-time perturbations including additive noise, random and region-based channel dropout and region-specific noise injection. Our analyses show that no single model dominates all failure modes. The most noise-robust model is among the most fragile under channel dropout and much of the dropout fragility disappears when channels are removed rather than zero-padded. (ii) Interpretability: we present the first application of Attention-Aware Layer-Wise Relevance Propagation (AttnLRP) to EEG-FMs and show that models broadly concentrate relevance on task-appropriate brain regions consistent with known neurophysiology. However, attribution maps remain spatially stable under perturbation while predictions degrade, suggesting that the models attend to the correct brain regions but decode corrupted content. (iii) Expressiveness: With block-wise probing we show that late blocks are repurposed during fine-tuning, while early blocks already hold task-related information. Furthermore, we demonstrate that the poor head-only performance previously attributed to low-quality pre-trained representations is largely explained by pooling and that EEG-FMs possess sufficient representational capacity when their token-level embeddings are preserved. Together, these findings provide the first systematic assessment of robustness, interpretability and expressiveness for EEG-FMs and highlight critical considerations for their development.