BrainPro: Process-conditioned Pretraining with Topographic Retrieval for Large EEG Models

Electroencephalography (EEG) decoding models often generalize poorly across datasets and subjects due to domain shifts in acquisition protocols and individual neurophysiology. We propose EEG-PRIME, a two-stage EEG foundation model for cross-dataset multi-task decoding. EEG-PRIME combines masked pretraining with prototype-aligned instruction tuning to enable instruction-aware and subject-invariant decoding across diverse BCI paradigms. During pretraining, an EEG encoder learns transferable representations through masked reconstruction with frequency-cutoff spectral augmentation. During instruction tuning, EEG-PRIME incorporates task-semantic, dataset-specific, and subject-invariant conditioning. The resulting conditioning signal modulates the Q-Former through Layer-wise Query Modulation, while frozen text embeddings of class labels serve as prototypes for cosine-similarity-based prediction across heterogeneous label spaces. Experiments on sixteen datasets covering motor imagery, emotion recognition, ADHD detection, covert speech, and mental workload show consistent improvements over state-of-the-art baselines and prior EEG foundation models under cross-subject settings. On two additional held-out datasets, EEG-PRIME achieves balanced accuracy comparable to within-session calibration models without target-domain optimization, calibration, or linear probing, demonstrating promising zero-shot transfer capability.

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.

EEG visual decoding remains difficult because scalp recordings are noisy, spatially coarse, and variable across trials and subjects. Most systems align each trial with a dense image embedding, although that embedding mixes semantic content with instance-specific texture, pose, and background. This target can demand details absent from EEG and provides no explicit account of the visual factors supporting a prediction. We propose ProtoEEG, a prototype-mediated framework that reformulates EEG--image alignment as soft composition over a shared learnable visual codebook. A trainable EEG encoder and a frozen visual teacher produce assignment distributions over the same $K=64$ prototypes. Their weighted reconstructions form a structured representation for retrieval and image generation. Prototype contrast supplies the main cross-modal training signal, distribution alignment coordinates codebook use across modalities, an instance anchor preserves fine-grained discrimination, and diversity regularization prevents redundant prototypes. The shared assignment profile also makes the learned bottleneck directly testable through prototype retention, random selection, and identity shuffling. Across five seeds, ProtoEEG reaches 64.0% Top-1 and 91.5% Top-5 on THINGS-EEG2 200-way retrieval. After retraining on EEG-ImageNet, it obtains 44.8% Top-1 and 73.8% Top-5 in 80-way retrieval. ProtoEEG also ranks first on all seven reconstruction metrics. Removing prototype contrast lowers Top-1 by 56.9 percentage points, while shuffling prototype identities reduces it to 0.5%. Prototype analyses further show distributed assignments and broad codebook use rather than one-prototype routing. These results support structured alignment targets as a practical alternative to increasing encoder or teacher capacity alone.