EEG Foundation Models

Clinical electroencephalogram (EEG) analysis rests on a hand-crafted feature catalog refined over decades, \emph{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: \emph{what does the model learn}, \emph{what does the model use}, and \emph{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.

Learning transferable representations for electroencephalography (EEG) remains challenging because EEG signals are inherently multi-channel and non-stationary. Channels observed at the same time provide coupled measurements of neural activity, while the relevant temporal dynamics vary across contexts. This structure is poorly matched by architectures that apply uniform computation across time or route each channel patch independently. To this end, we propose TRACE, an autoregressive EEG pre-training framework that predicts future EEG patches from causal context while performing temporally adaptive and cross-channel coherent computation. At each temporal step, TRACE derives an expert routing decision from the causal cross-channel history and applies it jointly to all channels at that step. This preserves instantaneous cross-channel coherence while allowing different temporal regimes to activate different computation. Since routing is defined over the available channel set and causal temporal context, TRACE is compatible with heterogeneous pre-training across corpora with different channel counts, montages, sequence lengths, and recording domains. Across eight downstream EEG benchmarks, TRACE is evaluated in both settings: when downstream domains are seen only as unlabeled pre-training data and when downstream datasets are completely unseen during pre-training. It obtains the best results on several benchmarks while remaining competitive on motor imagery and clinical event classification tasks, with ablations supporting the importance of cross-channel temporal routing.

Clinical EEG interpretation requires reasoning over full EEG sessions and integrating signal patterns with clinical context. Existing EEG foundation models are largely designed for short-window decoding and do not incorporate clinical context. We introduce CLEF, a clinically grounded long-context EEG foundation model. CLEF represents EEG sessions as 3D multitaper spectrogram tokens, enabling tractable Transformer modeling at session scale, and aligns embeddings with neurologist reports and structured EHR data through contrastive objectives. We evaluate CLEF on a new 234-task benchmark spanning disease phenotypes, medication exposures, and EEG findings, with more than 260k EEG sessions from over 108k patients. CLEF outperforms prior EEG foundation models on 229 of 234 tasks, improving mean AUROC from 0.65 to 0.74. Reconstruction-only pretraining surpasses prior EEG foundation models, while report and EHR alignment yields further gains. Held-out concept and external-cohort experiments suggest that these representations transfer beyond observed alignment targets. These results support session-scale, clinically grounded representation learning as a promising foundation-model paradigm for clinical EEG.

Intracranial electrocorticography (ECoG) offers high-signal-to-noise access to cortical activity for brain-computer interfaces, yet limited per-patient data has led most prior work to rely on small, subject-specific decoders that neglect information shared across patients. We investigate whether large pretrained scalp-EEG foundation models (EEG FMs) can be adapted to ECoG, enabling cross-patient learning and competitive decoding performance while calibrating to a held-out patient in 10-30 minutes on a single GPU. We introduce CORTEG, a cross-modality transfer framework that combines a pretrained EEG FM backbone, an electrode-aware KNNSoftFourier spatial adapter, a dual-stream tokenizer for low-frequency and high-gamma activity, and a leave-one-subject-out fine-tuning strategy. We evaluate CORTEG on two challenging regression tasks: public finger trajectory regression (n=9) and private audio envelope regression (n=16). CORTEG matches or exceeds the strongest task-specific baselines on both tasks: it reaches the highest mean correlation among compared methods on the public finger benchmark (gain not statistically significant on n=9 subjects), with larger and statistically significant gains on the audio task and in low-data per-patient calibration. Feature analyses align with neurophysiology, and latent manifolds capture low-dimensional finger-movement structure. CORTEG provides systematic evidence that scalp-EEG pretraining can be repurposed for ECoG decoding, enabling data-efficient intracranial BCIs that can adapt to new patients.

Deep learning and large public datasets have recently catalyzed the proliferation of AI models for processing brain recordings. However, systematically evaluating these models remains a challenge: not only do the preprocessing pipelines, training and finetuning approaches largely vary across studies, but their downstream evaluation is often limited to small sets of tasks and/or datasets. Here, we present NeuralBench: a unified framework for benchmarking AI models of brain activity. We accompany this framework with NeuralBench-EEG v1.0 -- a large EEG benchmark that includes 36 electroencephalography (EEG) tasks and 14 deep learning architectures, and is evaluated on 94 datasets accessed through a standardized interface. This first EEG-focused release already highlights two main findings. First, current foundation models only marginally outperform task-specific models. Second, a large set of tasks (e.g. cognitive decoding, clinical predictions) remain highly challenging, even for the best models. Critically, NeuralBench is designed for the integration of new tasks, datasets, models, and neuroimaging modalities, as illustrated by preliminary extensions to MEG and fMRI datasets and models. Through this white paper, we invite the community to expand this open-source framework and work together toward a unified benchmarking standard for neuroimaging models.

Recent self-supervised pre-training methods for electroencephalogram (EEG) have shown promising results. However, the pre-trained models typically require full fine-tuning on each downstream task individually to achieve good performance. In practical applications involving multiple tasks, utilizing a separate model for each task is not ideal regarding computational and spatial cost. In this study, we go one step further and explore the simultaneous adaptation of a pre-trained model to multiple different tasks. The EEG signals exhibit significant heterogeneity due to their collection from various subjects using diverse devices and experimental setups, resulting in potential conflicts among different tasks that impede joint optimization. To tackle this challenge, we propose MTEEG, a multi-task EEG analysis framework which incorporates task-specific low-rank adaptation (LoRA) modules to disentangle the parameter space and alleviate task conflicts. To investigate the trade-off between task specification and interaction, we propose three variants of MTEEG that integrate the LoRA modules in different ways and evaluate them on six downstream tasks, demonstrating that MTEEG can surpass state-of-the-art single-task methods on the majority of metrics. MTEEG shows the potential of multi-task EEG analysis and promotes the development of general-purpose brain-computer interfaces in the future.

Scaling EEG foundation models requires pooling data across heterogeneous electrode montages, a prerequisite both for larger pretraining corpora and for downstream deployment. We present the first systematic comparison of four channel adaptation methods (Conv1d projection, spherical spline interpolation (SSI), source-space decomposition, and Riemannian re-centering) across five pretrained EEG foundation models (5M--157M parameters), five downstream tasks, and two training regimes with 10--15 random seeds each. We find that rigid-montage models (BENDR, Neuro-GPT) require external adaptation, while flexible models (EEGPT, CBraMod) match or exceed it natively when fine-tuned but benefit from external methods under frozen-encoder deployment. A probe-SFT asymmetry exists: external adaptation can cause severe negative transfer during fine-tuning of flexible models. The optimal method is architecture-dependent (Conv1d for BENDR, SSI/Riemannian for Neuro-GPT, source-space decomposition for depression detection), and 5M-parameter CBraMod outperforms models up to 31$\times$ larger on 4/5 datasets, consistent with independent findings that compact EEG-specific architectures can match larger models.

Source-free domain adaptation (SFDA) provides a practical solution to cross-subject EEG decoding by adapting source-pretrained models to unlabeled target domains without accessing source data. However, existing SFDA methods rely solely on the limited internal knowledge of source-pretrained models, leading to inferior cross-domain generalization and unreliable pseudo-labels. Although EEG Foundation Models (FMs) pretrained on large-scale data exhibit strong generalizability, their potential in SFDA remains largely unexplored. To this end, we propose FUSED, a Foundation-guided Source-free EEG Decoding framework that integrates a large-scale FM with a compact Specialist Model (SM) via dual-branch co-adaptation. Specifically, we introduce a Co-adaptation mechanism equipping both branches with linear and prototype views, enabling cross-branch pseudo-label generation. Additionally, we design a Consensus Filtering Mechanism that exploits the FM's inherent stability to identify high-quality samples, along with a Two-Stage Pseudo-Label Refinement scheme to suppress error accumulation through cross-branch arbitration. Finally, we calibrate the FM's decision boundaries via mutual information maximization with the SM, followed by knowledge distillation from FM to SM, forming a principled calibrate-then-distill pipeline. To our knowledge, FUSED is the first work to leverage EEG FMs within the SFDA framework for cross-subject EEG decoding. Extensive experiments across three EEG paradigms, including motor imagery, emotion recognition, and SSVEP, demonstrate consistent state-of-the-art performance, validating the effectiveness of foundation-guided synergy for robust and privacy-preserving EEG decoding.

Electroencephalography (EEG) foundation models have shown strong potential for learning generalizable representations from large-scale neural data, yet their clinical deployment is hindered by distribution shifts across clinical settings, devices, and populations. Test-time adaptation (TTA) offers a promising solution by enabling models to adapt to unlabeled target data during inference without access to source data, a valuable property in healthcare settings constrained by privacy regulations and limited labeled data. However, its effectiveness for EEG remains largely underexplored. In this work, we introduce NeuroAdapt-Bench, a systematic benchmark for evaluating test-time adaptation methods on EEG foundation models under realistic distribution shifts. We evaluate representative TTA approaches from other domains across multiple pretrained foundation models, diverse downstream tasks, and heterogeneous datasets spanning in-distribution, out-of-distribution, and extreme modality shifts (e.g., Ear-EEG). Our results show that standard TTA methods yield inconsistent gains and often degrade performance, with gradient-based approaches particularly prone to heavy degradation. In contrast, optimization-free methods demonstrate greater stability and more reliable improvements. These findings highlight the limitations of existing TTA techniques in EEG, provide guidance for future development, and underscore the need for domain-specific adaptation strategies.

EEG foundation models (EFMs) achieve strong cross-subject and cross-task generalization through large-scale pretraining and downstream fine-tuning. Through empirical analysis, we observe that (i) task-adapted EFMs provide strong decoding performance but incur substantial overhead when retained as inference backbones, making knowledge distillation a natural route for optimizing compact students; and (ii) direct distillation from a fixed teacher representation underutilizes EFM knowledge, as task-discriminative information is distributed across intermediate layers rather than concentrated in the final layer. These observations motivate DLink (Distilling Layer-wise and Dominant Knowledge), a spectrally guided distillation framework with input-conditioned layer routing for transferring EFM knowledge into compact students. DLink uses a lightweight router to aggregate teacher layers for each input, and aligns magnitude and phase spectra to mitigate compression-induced spectral distortion in learned representations. The routed teacher knowledge is internalized by a project-then-compress student; the teacher and router are used only during training. Experiments on four EEG benchmarks show that DLink improves matched compact students and remains competitive with lightweight baselines, narrowing the gap to fine-tuned EFMs while substantially reducing parameters, FLOPs, and CPU-only inference latency.

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.