Taming foundation model with invariance-oriented pre-training for broad-spectrum EEG analysis across signal-level, brain-state, and brain-health tasks

Electroencephalography (EEG) is a widely used window into human brain function, but most EEG models remain tied to a one-dataset-one-model supervised paradigm. Recent EEG foundation models offer a route toward reusable representations, but most remain reconstruction-centered, assuming that EEG content predictable from local context is necessarily transferable neural information. Here we present INCEPT, an invariance-oriented EEG foundation model trained on over 11,000 hours of unlabelled clinical EEG. Rather than prioritizing signal recovery alone, INCEPT learns representation-level stability across correlated EEG observations, separating stable neural structure and essential subject-sensitive information from the nuisance variability that dominates scalp recordings while preserving subject-, state- and condition-discriminative information. We evaluate INCEPT on a broad-spectrum benchmark of ten datasets spanning three levels of post-acquisition EEG analysis: signal-level assessment, brain-state decoding, and brain-health evaluation. INCEPT ranks first among recent EEG foundation models on 26 of 30 linear-probing metrics and 24 of 30 fine-tuning metrics, and also surpasses strong task-specific specialist encoders across diverse downstream settings. Objective ablations and representation analyses further show that invariance-oriented pre-training improves transfer and organizes subject-sensitive neural representations beyond reconstruction alone. These results establish invariance learning as a promising principle for building reusable EEG foundation models.

EEG-JEPA: Structured Latent Prediction for EEG Foundation Models

Electroencephalography (EEG) foundation models aim to learn reusable representations from large-scale unlabeled recordings. A common pretraining strategy is masked waveform reconstruction, but applying supervision directly to noisy EEG may encourage models to recover predictable background activity, acquisition effects, and artifacts rather than neural structure that transfers across tasks. This raises a central question: what should an EEG foundation model predict to learn transferable representations? We introduce EEG-JEPA a structured latent-prediction framework for EEG foundation modeling. Rather than reconstructing masked voltage samples, a masked context encoder and predictor infer contextual latent states produced by an exponential-moving-average target encoder that observes the complete input. EEG-JEPA organizes target design along three complementary dimensions: target content specifies what representation is predicted, target support specifies where prediction occurs over structured electrode--time regions through Neurotopology-Aware Multi-scale Electrode-Temporal Masking (N-MET), and target depth specifies at which encoder layers supervision is applied. Together, these designs shift EEG pretraining from recovering missing measurements to inferring latent states from structured electrode--time context. We evaluate EEG-JEPA through controlled objective comparisons, frozen multitask transfer, and full fine-tuning. Under the same backbone, pretraining corpus, and training duration, EEG-JEPA improves the 14-task frozen macro balanced accuracy from 40.49% to 50.42% over CBraMod-style masked waveform reconstruction. Multi-source continuation further raises this result to 52.94%, the highest average among the EEG foundation models evaluated on EEG-FM-Bench. Under protocol-matched full fine-tuning, EEG-JEPA also improves the nine-task average balanced accuracy from 68.98% to 70.65%.

B[FM]$^2$: Brain Foundation Model via Flow Matching with SplitUNet

EEG foundation models can learn generalizable representations from large-scale EEG corpora to enable single-backbone transfer across diverse clinical and brain-computer interface tasks. Existing models typically discretize the continuous multi-channel EEG waveform into patches or codebook tokens and train a transformer with masked self-supervision. Recognizing that this discretization fragments continuous brain rhythms and obscures fine-grained temporal dynamics, we present B[FM]$^2$(Brain Foundation Model via Flow Matching), whose inductive bias aligns with the data by pretraining directly on the raw signal using continuous-time flow matching without patches, tokenization, or masking. However, multi-channel EEG signals pose an architectural challenge for flow matching: time is densely sampled and highly autocorrelated (thousands of timepoints), while the electrode axis is short (tens of channels) at distinct scalp positions. To address this time-electrode asymmetry, we introduce SplitUNet, a velocity network that factorizes each block into separate 1D temporal and 1D electrode convolutions and downsamples only along time, preserving electrode topology throughout the hierarchy. B[FM]$^2$ sets a new state of the art on 7 of 9 standard downstream EEG classification tasks, using a pretraining budget of only 36,895 segments ($\approx$ 307h), 1-2 orders of magnitude ($\approx$ 30x) less than required by existing EEG foundation models. Further, it generates synthetic EEGs that two board-certified neurologists cannot distinguish from brain data (Cohen's $κ=$ -0.096). https://jd730.github.io/projects/BFM2