DARE-EEG: A Foundation Model for Mining Dual-Aligned Representation of EEG
Authors: Yang Shao, Peiliang Gong, Qun Dai, Daoqiang Zhang
Abstract
Foundation models pre-trained through masked reconstruction on large-scale EEG data have emerged as a promising paradigm for learning generalizable neural representations across diverse brain-computer interface applications. However, a critical yet overlooked challenge is that EEG encoders must learn representations invariant to incomplete observations-when different masked views of the same signal have minimal overlap, existing methods fail to constrain them to a consistent latent subspace, leading to degraded transferability. To address this, we propose DARE-EEG, a self-supervised foundation model that explicitly enforces the mask-invariance property through dual-aligned representation learning during pre-training. Specifically, we introduce mask alignment that constrains representations from multiple masked views of the same EEG sample via contrastive learning, complementing anchor alignment that aligns masked representations to momentum-updated complete features for semantic stability. Additionally, we propose conv-linear-probing, a parameter-efficient strategy that adapts pre-trained representations to heterogeneous electrode configurations and sampling rates through decoupled spectro-spatial projections. Extensive experiments across diverse EEG benchmarks demonstrate that DARE-EEG consistently achieves state-of-the-art in accuracy performance while maintaining relatively low parameter complexity and superior cross-dataset portability compared to existing methods. Furthermore, DARE-EEG contributes to effectively discovering and utilizing the rich potential representations in EEG.
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%.
Increasing EEG pretraining data scale or model capacity does not consistently improve downstream performance. We identify a persistent low-frequency bias in representations learned by diverse EEG foundation models, which remains across dataset scales, model capacities, and pretraining objectives. Our analysis links this bias to the interaction between EEG's 1/fα-like spectral structure and neural networks' tendency to preferentially learn low-frequency components. In masked autoencoders, the ℓ2 reconstruction objective further amplifies this imbalance: under comparable relative reconstruction errors, high-power low-frequency components contribute disproportionately to the loss. To address this issue, we introduce FAME, a frequency-balanced masked autoencoding framework that reconstructs time--frequency activity in predefined EEG bands from masked EEG inputs. FAME independently standardizes the reconstruction targets within each band and assigns equal weight to all band-specific losses, thereby balancing supervision across the EEG spectrum. Evaluated on 41 downstream tasks in OmniEEG-Bench, FAME learns more spectrally balanced representations and achieves state-of-the-art performance on 24 of them. These results underscore the importance of balanced spectral supervision for learning transferable EEG representations.
Recent advances in self-supervised learning for EEG representation have largely relied on masked reconstruction, where models are trained to recover randomly masked signal segments. While effective at modeling local dependencies, the training objective of masked reconstruction does not compel the model to capture global generative constraints essential for characterizing neural activity. To address this limitation, we propose EEGDM, a novel self-supervised framework that leverages latent diffusion models to generate EEG signals as an objective. Unlike masked reconstruction, diffusion-based generation progressively denoises signals from noise to realism, compelling the model to capture holistic temporal patterns and cross-channel relationships. Specifically, EEGDM incorporates an EEG encoder that distills raw signals and their channel augmentations into a compact representation, which serves as conditional information to guide the diffusion denoising process, thereby enabling the encoder and diffusion model to be jointly optimized through the generative objective. This design endows EEGDM with a compact latent space, which not only offers ample control over the generative process but also can be leveraged for downstream tasks. Experimental results show that EEGDM (1) reconstructs high-quality EEG signals, (2) learns robust representations, and (3) achieves competitive performance across diverse downstream tasks, thus exploring a new direction for self-supervised EEG representation learning.