EEG Foundation Models

Decoding the orchestration of neural activity in electroencephalography (EEG) signals is a central challenge in bridging neuroscience with artificial intelligence. Foundation models have made strides in generalized EEG decoding, yet many existing frameworks primarily relying on separate temporal and spectral masking of raw signals during self-supervised pretraining. Such strategies often tend to bias learning toward high-frequency oscillations, as low-frequency rhythmic patterns can be easily inferred from the unmasked signal. We introduce a foundation model that utilizes a novel Gaussian-smoothed masking scheme applied to short-time Fourier transform (STFT) maps. By jointly applying time, frequency, and time-frequency Gaussian masks, we make the reconstruction task much more challenging, forcing the model to learn intricate neural patterns across both high- and low-frequency domains. To effectively recover signals under this aggressive masking strategy, we design SpecHi-Net, a U-shaped hierarchical architecture with multiple encoding and decoding stages. To accelerate large-scale pretraining, we partition the data into three subsets, each used to train an independent expert model. We then combine these models through SpecMoE, a mixture of experts framework guided by a learned spectral gating mechanism. SpecMoE achieves state-of-the-art performance across a diverse set of EEG decoding tasks, including sleep staging, emotion recognition, motor imagery classification, abnormal signal detection, and drug effect prediction. Importantly, the model demonstrates strong cross-species and cross-subject generalization, maintaining high accuracy on both human and murine EEG datasets.

Electroencephalography (EEG) is a widely used tool for studying brain function, with applications in clinical neuroscience, diagnosis, and brain-computer interfaces (BCIs). Recent EEG foundation models trained on large unlabeled corpora aim to learn transferable representations, but their effectiveness remains unclear; reported improvements over smaller task-specific models are often modest, sensitive to downstream adaptation and fine-tuning strategies, and limited under linear probing. We hypothesize that one contributing factor is the reliance on signal reconstruction as the primary self-supervised learning (SSL) objective, which biases representations toward high-variance artifacts rather than task-relevant neural structure. To address this limitation, we explore an SSL paradigm based on Joint Embedding Predictive Architectures (JEPA), which learn by predicting latent representations instead of reconstructing raw signals. We introduce Laya, the first EEG foundation model based on LeJEPA. We show that latent prediction yields representations that encode semantic structure in EEG: Laya embeddings track clinically meaningful state changes such as seizure onset, are resilient to noise, and achieve the strongest mean clinical accuracy under frozen linear probing, with particular gains on tasks where relevant neural patterns are subtle and easily obscured by artifacts. Controlled ablations against matched MAE variants confirm that the choice of pretraining objective, rather than architecture or data, is the primary driver of these gains.

Pretraining for electroencephalogram (EEG) foundation models has predominantly relied on self-supervised masked reconstruction, a paradigm largely adapted from and inspired by the success of vision and language foundation models. However, unlike images and text, EEG datasets are notoriously expensive to collect and characterized by low signal-to-noise ratio. These challenges introduce difficulties in scaling the EEG foundation models and capturing the underlying neural semantics through reconstruction. In this work, we ask the question: can we stand on the shoulders of well-established foundation models from well-represented modalities to bootstrap the pretraining of EEG foundation models? We first demonstrate that mainstream foundation models, such as those from vision and time series, transfer surprisingly well to EEG domain. To this end, we propose the Multi-Teacher Distillation Pretraining (MTDP) framework for pretraining EEG foundation models via a two-stage multi-teacher distillation. In the first stage, we introduce a learnable gating network to fuse representations from diverse teachers (e.g., DINOv3 and Chronos) via a masked latent denoising objective. In the second stage, we distill the fused representation into an EEG foundation model. Extensive evaluations across 9 downstream tasks and 12 datasets demonstrate that our MTDP-based EEG foundation model outperforms its self-supervised counterparts while requiring only 25% of the pretraining data.

EEG foundation models are typically pretrained on narrow-source clinical archives and evaluated on benchmarks from the same ecosystem, leaving unclear whether representations encode neural physiology or recording-distribution artifacts. We introduce PRISM (Population Representative Invariant Signal Model), a masked autoencoder ablated along two axes -- pretraining population and downstream adaptation -- with architecture and preprocessing fixed. We compare a narrow-source EU/US corpus (TUH + PhysioNet) against a geographically diverse pool augmented with multi-center South Asian clinical recordings across multiple EEG systems. Three findings emerge. First, narrow-source pretraining yields stronger linear probes on distribution-matched benchmarks, while diverse pretraining produces more adaptable representations under fine-tuning -- a trade-off invisible under single-protocol evaluation. Trained on three source corpora, PRISM matches or outperforms REVE (92 datasets, 60,000+ hours) on the majority of tasks, demonstrating that targeted diversity can substitute for indiscriminate scale and that dataset count is a confounding variable in model comparison. Second, on a clinically challenging and previously untested task -- distinguishing epilepsy from diagnostic mimickers via interictal EEG -- the diverse checkpoint outperforms the narrow-source checkpoint by +12.3 pp balanced accuracy, the largest gap across all evaluations. Third, systematic inconsistencies between EEG-Bench and EEG-FM-Bench reverse model rankings on identical datasets by up to 24 pp; we identify six concrete sources including split construction, checkpoint selection, segment length, and normalization, showing these factors compound non-additively.

Electroencephalography (EEG) foundation models have shown promise for learning generalizable representations, yet they remain sensitive to channel heterogeneity, such as changes in channel composition or ordering. We propose channel-aware multimodal EEG-text alignment contrastive language-image pretraining (CAMEL-CLIP), a contrastive EEG-text multimodal foundation model designed to be robust to heterogeneous channel configurations and widely applicable to diverse downstream tasks. CAMEL-CLIP introduces three key components: (1) channel attribute-based positional encoding, which identifies channels through semantic information; (2) dynamic channel projection, which generates variable-length embeddings by independently projecting each channel without feature compression; and (3) dual-level contrastive learning, which jointly performs channel-level and sample-level contrastive learning to capture both channel-specific and global signal characteristics. Experimental results demonstrate that CAMEL-CLIP achieves state-of-the-art performance under linear-probing and outperforms existing foundation models that rely on full-finetuning.

Electroencephalography (EEG) provides a non-invasive window into neural dynamics at high temporal resolution and plays a pivotal role in clinical neuroscience research. Despite this potential, prevailing computational approaches to EEG analysis remain largely confined to task-specific classification objectives or coarse-grained pattern recognition, offering limited support for clinically meaningful interpretation. To address these limitations, we introduce NeuroNarrator, the first generalist EEG-to-text foundation model designed to translate electrophysiological segments into precise clinical narratives. A cornerstone of this framework is the curation of NeuroCorpus-160K, the first harmonized large-scale resource pairing over 160,000 EEG segments with structured, clinically grounded natural-language descriptions. Our architecture first aligns temporal EEG waveforms with spatial topographic maps via a rigorous contrastive objective, establishing spectro-spatially grounded representations. Building on this grounding, we condition a Large Language Model through a state-space-inspired formulation that integrates historical temporal and spectral context to support coherent clinical narrative generation. This approach establishes a principled bridge between continuous signal dynamics and discrete clinical language, enabling interpretable narrative generation that facilitates expert interpretation and supports clinical reporting workflows. Extensive evaluations across diverse benchmarks and zero-shot transfer tasks highlight NeuroNarrator's capacity to integrate temporal, spectral, and spatial dynamics, positioning it as a foundational framework for time-frequency-aware, open-ended clinical interpretation of electrophysiological data.

Electroencephalography (EEG) foundation models (EFMs) have shown strong potential for transferable representation learning, yet their adaptation in realistic settings remains challenging when only a few labeled subjects are available. We show that this challenge stems from a structural mismatch between noisy, limited supervision and the highly plastic parameter space of EFMs, reflected in three key failure modes: overconfident miscalibration, prediction collapse, and representation drift caused by unconstrained parameter updates. To address these challenges, we propose SCOPE, a Structured COnfidence-aware Prototype-guided framework for label-limited EFM adaptation. SCOPE first constructs cohort-level external supervision to provide persistent guidance and further derives confidence-aware pseudo-labels to select reliable unlabeled samples for adaptation. Building on the constructed external supervision, SCOPE introduces ProAdapter, a lightweight prototype-conditioned adapter that modulates frozen EFMs to preserve pretrained representations. Experiments across 50 label-limited adaptation settings, covering 6 EEG tasks, 5 EFM backbones, and 5%-50% training labeled-subject ratios, show that SCOPE consistently achieves strong performance and efficiency.

Developing foundation models for electroencephalography (EEG) remains challenging due to the signal's low signal-to-noise ratio and complex spectro-temporal non-stationarity. Existing approaches often overlook the hierarchical latent structure inherent in neural dynamics, leading to suboptimal reconstruction of fine-grained information. In this work, we propose BrainRVQ, a general-purpose EEG foundation model pre-trained on a large-scale corpus of clinical EEG data. Unlike standard masked modeling, BrainRVQ features a Dual-Domain Residual Vector Quantization (DD-RVQ) tokenizer that disentangles temporal waveforms and spectral patterns into hierarchical discrete codes. We further introduce a hierarchical autoregressive pre-training objective that learns to reconstruct these codes in a coarse-to-fine manner, utilizing an importance-guided curriculum masking strategy to prioritize information-rich neural events over background noise. Extensive experiments across 8 diverse downstream datasets demonstrate that BrainRVQ consistently outperforms state-of-the-art baselines, validating its effectiveness in learning robust and generalizable neural representations. Our code and model weights are available:https://github.com/keqicmz/BrainRVQ

EEG foundation models are pretrained on heterogeneous corpora, but two challenges remain underexplored: (1) experimental protocols provide mental-process cues that are rarely used in masked pretraining, and (2) electrode montages vary across datasets, making spatial representations montage-dependent. Existing methods typically learn a single general-purpose representation and model spatial structure implicitly, limiting their ability to exploit process-related information under montage heterogeneity. We introduce BrainPro, a process-conditioned self-supervised pretraining framework that couples topographic retrieval with shared and process-associated representation learning. BrainPro maps dataset-specific montages to a universal channel-region template and retrieves channel- and region-level spatial filters to form a topographically aligned spatial basis. Over this basis, BrainPro learns a shared encoder for general EEG structure and additional affective, motor-related, and auxiliary residual branches for process-associated variation. Protocol-derived mental-process cues condition branch activation and region-weighted masked reconstruction, incorporating topographic spatial priors and process information. Across nine public BCI benchmarks, BrainPro achieves strong performance among evaluated baselines. Ablations, channel-drop analysis, encoder-configuration studies, and spatial-filter visualizations suggest that topographic retrieval and process-conditioned representation learning jointly improve EEG decoding. Our code is available at https://github.com/yi-ding-cs/BrainPro.

Current deep learning models for electroencephalography (EEG) are often task-specific and depend on large labeled datasets, limiting their adaptability. Although EEG foundation models seek broader applicability, many still rely on predefined multi-channel inputs, electrode-layout assumptions, or model-specific channel handling. To address these limitations, we introduce the Single-Channel Large EEG Model (SingLEM), a self-supervised foundation model whose hybrid convolutional--Transformer encoder maps each channel independently to a reusable representation capturing local and long-range temporal structure. These representations can be used individually or combined through channel-wise feature concatenation. We assembled 71 public EEG datasets comprising approximately 9,200 subjects and 357,000 single-channel hours. For leakage-controlled evaluation, downstream results were obtained with a model pretrained on 68 datasets after excluding the three source datasets underlying the six tasks. A model pretrained on all 71 datasets is provided for general reuse. Across six motor imagery and cognitive tasks under strict leave-one-subject-out (LOSO) evaluation, the leakage-controlled model with concatenated representations and a support vector machine (SVM) classifier achieved the best overall performance among the compared pretrained and classical feature-based methods. Additional classifier and subject-adapted analyses supported the robustness of its representations. These findings support single-channel self-supervised learning as a montage-flexible foundation for reusable EEG feature extraction and electrode-level spatial analysis. The source code and pretrained models are available at https://github.com/ttlabtuat/SingLEM.

Learning from multi-variate time-series with heterogeneous channel configurations remains a fundamental challenge for deep neural networks, particularly in clinical domains such as intracranial electroencephalography (iEEG), where channel setups vary widely across subjects. In this work, we introduce multi-variate parallel attention (MVPA), a novel self-attention mechanism that disentangles content, temporal, and spatial attention, enabling flexible, generalizable, and efficient modeling of time-series data with varying channel counts and configurations. We use MVPA to build MVPFormer, a generative foundation model for human electrophysiology, trained to predict the evolution of iEEG signals across subjects. To support this and future efforts by the community, we release the SWEC iEEG dataset, the largest publicly available iEEG dataset to date, comprising nearly 10,000 hours of recordings from heterogeneous clinical sources. MVPFormer leverages MVPA to achieve strong generalization across subjects, demonstrating expert-level performance in several iEEG tasks. MVPFormer surpasses state-of-the-art (SOTA) Transformer baselines in seizure detection across the SWEC, the MAYO, and the FNUSA datasets, while also achieving SOTA performance on four Brain TreeBank iEEG decoding tasks (volume, pitch, onset, and speech). We further validate MVPA on standard time-series forecasting and classification tasks, where it matches or exceeds the performance of existing attention-based models. Together, our contributions establish MVPA as a general-purpose attention mechanism for heterogeneous time-series and MVPFormer as the first open-source, open-weights, and open-data iEEG foundation model with SOTA clinical performance. The code is available at https://github.com/IBM/multi-variate-parallel-transformer. The SWEC iEEG dataset is available at https://huggingface.co/datasets/NeuroTec/SWEC_iEEG_Dataset.