Probing Spatial and Spectral Grounding in EEG Foundation Models

EEG foundation models (EEG-FMs) have been evaluated predominantly on clean, in-distribution accuracy, demonstrating modest gains over supervised baselines and weak frozen representations. This study examines whether these conclusions hold beyond clean accuracy by evaluating six EEG-FMs and a supervised baseline across ten datasets along 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: using attribution methods in EEG-FMs, we show that models broadly concentrate relevance on task-appropriate brain regions consistent with known neurophysiology. (iii) Expressiveness: we demonstrate that the poor head-only performance previously attributed to low-quality pre-trained representations is largely explained by the pooling strategy and that EEG-FMs possess sufficient representational capacity when their token-level embeddings are preserved. Furthermore, with block-wise probing and attention analysis we show that late blocks are repurposed during fine-tuning, while early blocks already hold task-related information. Our results show that conclusions about EEG-FMs depend on evaluation choices and we recommend that future evaluation of EEG-FMs should report robustness per perturbation type, produce attribution maps and examine multiple pooling strategies.

Clinical electroencephalogram (EEG) analysis rests on a hand-crafted feature catalog refined over decades, e.g., band power, connectivity, complexity, and more. Modern EEG foundation models bypass this catalog, learn directly from raw signals via self-supervised pretraining, and match or outperform feature-engineered baselines on most clinical benchmarks. Whether the two representations align is an open question, which we decompose into three sub-questions: what does the model learn, what does the model use, and how much can be explained. We answer them with layer-wise ridge probing, LEACE-style cross-covariance subspace erasure, and a transparent classifier benchmarked against a random-feature baseline. The audit covers three foundation models (CSBrain, CBraMod, LaBraM), five clinical tasks (MDD, Stress, ISRUC-Sleep, TUSL, Siena), and a 6-family 63-feature lexicon. Of the $945$ (model, task, feature) units, $648$ ($68.6\%$) are representation-causal and $199$ ($21.1\%$) are encoded-only. Across tasks, $50$ features qualify as universal candidates with strong support (all three architectures RC) in two or more tasks. Frequency-domain features dominate, but the other five families each contribute substantial causal mass. Confirmed features recover, on average, $79.3\%$ of the foundation model's advantage over the random baseline, with a clean task gradient (MDD $\approx 0.99$ down to Stress $\approx 0.56$): tasks near ceiling are almost fully recovered by the lexicon, while harder tasks leave a non-trivial residual that pinpoints a concrete target for future concept discovery.

EEG foundation models (EEG-FMs) are intended to generalize across different datasets by learning representations that, ideally, are invariant to dataset-specific EEG configurations such as electrode montages. However, EEG-FMs that accept different montages as input do not guarantee that representations and predictions remain stable across different electrode configurations, especially outside the training setting. In this work, we investigate the effects of different electrode montages through a joint functional and representational analysis of four EEG foundation models selected to span distinct montage-handling designs. We evaluate embeddings on cross-subject resting-state eyes-open/closed and within-subject motor-imagery classification under spatially informed channel reduction. Functional robustness is tested through the generalizability of linear probes across channel counts, while representational robustness is assessed through within-subject similarity and preservation of between-subject geometry. The four models show distinct robustness profiles, and the two axes dissociate: large changes in embedding similarity need not come with comparable probe degradation, and stable embeddings can still lose downstream performance. Comparing two readouts of the same encoder further shows that aggregation, not the encoder alone, determines functional robustness: pooling into anatomically aligned regions degrades less than a learned global readout, despite being montage-invariant by construction. Montage robustness is therefore a joint property of the encoder and its aggregation, and characterizing it requires both a representational and a functional axis. Input compatibility alone is evidence for neither.