Electroencephalography Spatial Super-Resolution

Evaluating foundation models under appropriate adaptation settings is essential for understanding the quality and transferability of the learned representations. Recent EEG foundation models have demonstrated promising transfer capabilities across tasks and datasets, motivating their growing use in neurotechnology and clinical applications. However, these models are typically evaluated under full fine-tuning on well-curated downstream datasets, a setting that does not reflect biomedical domain constraints such as limited labeled data, reduced sensor coverage, or parameter-efficient adaptation. In this work, we propose a multi-dimensional evaluation framework for assessing EEG models under realistic low-resource conditions. Empirical analysis of both supervised EEG models and recent EEG foundation models, including LaBraM, CSBrain, and CBraMod, across 6 different datasets is performed under the proposed multi-dimensional evaluation framework. We find that EEG foundation models consistently provide performance gains on long-context tasks such as sleep stage prediction and mental health state classification. In contrast, for short-window Brain Computer Interface style tasks, supervised models achieve comparable despite having substantially fewer parameters. Additional analyses demonstrate that current foundation models provide limited robustness to short-window tasks and channel constrained settings. Together, these findings motivate the use of multi-dimensional evaluation protocols that characterize model behavior under realistic use constraints.

Brain-computer interfaces (BCIs) are limited by low signal-to-noise ratio in modalities such as electroencephalography, which requires multiple trials to reliably decode user intentions. This induces a speed-accuracy trade-off, whereby higher accuracy comes at the cost of speed. The speed-accuracy balance is application-dependent, motivating controllable trade-offs. Conventional metrics, such as the Information Transfer Rate, combine speed and accuracy obscuring their dependence and potentially introducing biases. In this study, we propose an evaluation framework independent of classifier, paradigm, and early-stopping strategy that separates speed and accuracy. We employ two measures, Gain (relative speed improvement) and Conservation (relative accuracy preservation), and combine them into a tunable Gain-Cons Balance controlled by α, regulating the speed-accuracy trade-off. The parameter adjusts the operating point without modifying the classifier, facilitating deployment across scenarios. The framework was evaluated on P300 event-related potential paradigms using public recordings from 63 subjects as well as multiple classifiers and early-stopping strategies to achieve distinct operating points in speed-accuracy and bitrate. Results show that tuning α yields fast, accurate, or balanced BCI behaviours, demonstrating explicit control of the speed-accuracy trade-off. The method supports subject-level performance prediction and improves explainability of BCI behaviour. Further analysis of the Information Transfer Rate reveals a systematic bias toward speed, explained by the proposed framework through the Gain and Conservation measurements. Overall, this work establishes the speed-accuracy trade-off as a controllable design variable validated on public P300-based paradigms, enabling transparent evaluation and application-specific optimization of BCIs.

Large EEG Foundation Models (FMs) have shown great potential for decoding EEG signals across diverse cognitive tasks. However, existing EEG-FM studies exhibit three critical limitations: opaque supervised baseline tuning, unverified contributions of complex learning paradigms, and a lack of transparency in model decision-making. To address these, we propose EEG-FM-Audit, a comprehensive evaluation and analysis pipeline designed to systematize the assessment of EEG-FMs. EEG-FM-Audit consists of three primary components: (1) an ASHA-driven benchmarking protocol that ensures fair comparisons by transparently optimizing supervised baselines; (2) paradigm-level ablation studies to evaluate the effectiveness of learning paradigms in FMs; and (3) a neurophysiological probing (NPP) framework, which explores whether FMs leverage valid temporal, spatial, and spectral EEG properties. We apply EEG-FM-Audit to four state-of-the-art EEG-FMs and five representative supervised models across three public datasets. Our results reveal that properly tuned supervised baselines can match or outperform advanced FMs, despite requiring significantly fewer parameters. Furthermore, we find that the effectiveness of learning paradigms of FMs is highly dependent on dataset scale and architecture. Finally, NPP analysis demonstrates how FMs rely on specific physiological features, establishing a framework for more interpretable neural decoding.

Electroencephalogram (EEG)-based emotion recognition is an important affective computing task, and recent EEG foundation models provide useful generic representations for downstream adaptation. However, under the fine-tuning setting, three limitations remain prominent: insufficient modeling of multi-scale emotional dynamics, inadequate exploitation of inter-channel functional connectivity, and the limited expressive power of simple linear classification heads. To address these issues, this paper proposes a new EEG emotion recognition method, termed MSCGC-KAN, which introduces a structured task head composed of multi-scale causal graph convolution and Kolmogorov--Arnold feature mapping. Built on a pre-trained CBraMod backbone, MSCGC-KAN enhances downstream adaptation by jointly strengthening multi-scale temporal modeling, learnable inter-channel connectivity modeling, and nonlinear discriminative mapping within a compact task-specific head. This design preserves the representation advantage of the foundation model while making the classifier more sensitive to emotion-related spatiotemporal patterns. Extensive experiments are conducted on the public FACED and SEED-VII datasets. The proposed method achieves a balanced accuracy of 60.66%, a Cohen's Kappa of 0.5525, and a weighted F1-score of 60.40% on FACED, and obtains 33.27%, 0.2223, and 33.64%, respectively, on SEED-VII. Compared with the CBraMod+Linear baseline, the balanced accuracy is improved by 5.91 and 2.03 percentage points on the two datasets, respectively. These results indicate that structured task-head design is an effective way to improve EEG emotion recognition when fine-tuning pre-trained EEG models.

EEG foundation models, pre-trained on large-scale unlabelled EEG data, have emerged as a promising direction towards learning generalizable EEG representations. Despite showing positive results in data-rich regimes, they often fail to outperform significantly smaller supervised models in low-resource settings compared to fully supervised models. We provide a mechanistic account of this shortcoming, attributing it to a fundamental mismatch between reconstruction-based pretext tasks and the idiosyncratic spectral structure of EEG signals, which decompose into distinct high-power aperiodic and low-power oscillatory components. Using controlled, synthetically-generated EEG inputs, we demonstrate that EEG foundation model embeddings are biased to capture the aperiodic components of the EEG signal while under-representing oscillatory components, particularly at higher frequencies. Additionally, linear probe evaluations on real-world BCI datasets further reveal that embeddings encode subject identity more strongly than task-relevant information, thereby reinforcing the low-frequency and aperiodic component bias in foundation model embeddings trained primarily on reconstruction based objectives. Together, these findings elucidate a failure mode in reconstruction based EEG foundation models and motivate future work to incorporate auxiliary losses explicitly targeting high-frequency oscillatory structure as a path toward more capable and generalizable EEG representations.

Accurate classification of sleep stages is crucial for diagnosing sleep disorders and automating this process can significantly enhance clinical assessments. This study aims to explore the use of a self-supervised model (more specifically, an adapted version of mulEEG) combined with a Linear SVM classifier to improve sleep stage classification. \textbf{Methods:} The mulEEG model, which learns electroencephalogram signal representations in a self-supervised manner, was simplified here by replacing ResNet-50 with 1D-convolutions used as time series encoder by a ResNet-18 backbone. Two other adaptations were conducted: the first one evaluated different configurations of the model and data volume for training, while the second tested the effectiveness of time series features, spectrogram features, and their concatenation as inputs to a Linear SVM classifier. \textbf{Results:} The results showed that reducing the volume of data offered a better cost-benefit ratio compared to simplifying the model. Using the concatenated features with ResNet-18 also outperformed the linear evaluations of the original mulEEG model, achieving higher classification performance. \textbf{Conclusions:} Simplifying the mulEEG model to extract features and pairing it with a robust classifier leads to more efficient and accurate sleep stage classification. This approach holds promise for improving clinical sleep assessments and can be extended to other biological signal classification tasks.

The speed and accuracy of an artificial teammate fundamentally alter the failure states of Human-AI integration. While high-speed AI interventions risk inducing reflexive blind compliance, delayed interventions can induce ambiguous cognitive conflict. This study investigates how the fundamental characteristics of an in-task AI assistant, Fast/Less-Accurate (FLA-AI) versus Slow/Accurate (SA-AI) impact the synergy of Collaborative Brain-Computer Interface (cBCI) teams in a Virtual Reality drone task. Seventeen operators completed continuous search tasks under high cognitive workload while their spatial covariance was mapped using a 2D Adaptive Riemannian Oracle. The results mathematically demonstrate that AI timing dictates the mechanism of team failure. Fast AI induced instant, blind compliance; human accuracy under deception collapsed to 50.2%, and pure behavioural teams (N=8) failed to scale beyond 74.1%. In contrast, Slow AI induced delayed cognitive conflict; humans hesitated (61.1% accuracy), but N=8 behavioural teams eventually recovered to 100.0%. Crucially, the Riemannian Oracle mathematically adapted to these states: it heavily restricted temporal windows (< 0.8s) to intercept fast reflexive compliance, while widening windows (> 1.2s) to capture delayed cognitive conflict. Integrating these isolated veridical signals via Hybrid Fusion successfully rescued the Fast AI team (+7.6% at N=8) and significantly accelerated the recovery of smaller Slow AI teams (+6.9% at N=4). These findings prove that cBCI synergy is heavily contingent on the temporal dynamics of trust, providing a critical framework for designing dynamically gated Human-AI systems.

In the past decade, numerous studies have applied deep neural networks (DNNs) to decode auditory attention (AAD) from Electroencephalogram (EEG) signals via stimulus reconstruction. However, the influence of dataset balance on the decoding performance of stimulus reconstruction-based AAD remains unexplored. In this study, three publicly available EEG-AAD datasets - KUL, DTU, and NJU cEEGrid - are used to construct both balanced and unbalanced experimental conditions. We hypothesize and demonstrate that stimulus reconstruction-based DNN decoders tend to produce overestimated decoding performance on unbalanced datasets. To address this issue, we propose a leave-one-paired-envelope-out (LOPEO) cross-validation protocol. Experimental results confirm that LOPEO effectively prevents inflated decoding accuracy on unbalanced datasets. While balanced datasets are generally preferred in experimental design, LOPEO provides a principled evaluation framework for unbalanced datasets that have already been published, filling an important gap in the field.

A central challenge in electroencephalography (EEG) foundation modeling is learning transferable representations across recordings with diverse tasks, montages, references, and spectral characteristics. Existing masked modeling approaches often rely on broadband continuous patches or a single discrete representation, which may underrepresent frequency-specific activity. This paper proposes BandVQ, a band-wise vector-quantized EEG foundation model that decomposes EEG into delta, theta, alpha, beta, and gamma bands, trains an independent VQ-VAE tokenizer for each band, and pretrains a shared Transformer encoder on the resulting discrete VQ code indices. The encoder uses masked code tokens, quantized absolute log-power tokens, channel and temporal embeddings, and metadata prefix tokens representing reference, band, task family, and phase. Region-based masking is also introduced to reduce the trivial reconstruction of spatially adjacent electrodes. The model is pretrained on 71 public EEG corpora comprising over 9,200 subjects and 357,000 single-channel hours and evaluated on six subject-independent classification datasets. Under the current evaluation setting, the proposed model achieves strong transfer performance, with the highest reported results on three cognitive tasks and competitive performance on three motor imagery tasks.

In non-invasive neural language decoding, results can be inflated by sources that are not stimulus-evoked neural evidence: decoder priors, embedding-based metrics, and non-neural structural nuisances such as signal duration. The methodological challenge is therefore attribution: a reported gain is more informative when it can be traced to a specific source. We recast stimulus-locked MEG-to-audio retrieval as an auditing framework that separates apparent performance into three sources - structural shortcuts, window-level stimulus-locked evidence, and cross-window contextual aggregation - and provides a diagnostic for each. Signal-blind Gaussian noise reaches 66.3% Rank@1 (R@1) under variable-length decoding but collapses to near chance once fixed-duration windows and stimulus-identity splits are enforced, isolating structural leakage. Under these controls, fixed-window retrieval recovers measurable MEG-audio discriminability, while an oracle sentence-bucket diagnostic shows that 95.7% of Top-1 errors select the wrong sentence, localising the residual bottleneck to sentence-level competition. We audit this contextual source with Group Context Bias (GCB), an inference-time additive logit bias that pools sentence-consistent evidence across windows while leaving the base retrieval scores and candidate pool fixed. Used as a score-space intervention, GCB makes the contextual source measurable: R@1 shifts from 44% to 52% on Gwilliams and from 22% to 29% on MOUS under the same fixed setting. GCB is auditable under this design: its effect collapses under random-grouping perturbations and vanishes when local evidence is attenuated in MEG or is near chance in EEG, supporting its use as a controlled source-attribution intervention. These results suggest that brain-to-language performance should be source-attributed, not merely reported.

Visual decoding from brain signals is a key challenge at the intersection of computer vision and neuroscience, requiring methods that bridge neural representations and computational models of vision. We introduce a tri-modal contrastive framework for EEG-based visual decoding that aligns EEG, visual, and textual representations within a unified latent space. Our approach follows a two-stage design. First, we pre-train an EEG encoder via masked reconstruction on unlabeled trials, learning spatio-temporal regularities that transfer robustly to downstream tasks. Second, we jointly align EEG, image, and LLM-generated textual descriptions through contrastive learning, where text supervision acts as a semantic regularizer that injects linguistic structure into the shared space without overwhelming the primary EEG-image signal. The encoder integrates subject-specific adaptation, graph-attention over channels, and temporal-spatial convolutional embeddings. On the Things-EEG2 200-way zero-shot benchmark, our framework achieves 54.1% Top-1 and 83.4% Top-5 accuracy, substantially exceeding the strongest prior baseline (32.4% / 64.0%), with paired Wilcoxon tests confirming significance (p < 0.01) over all in-subject baselines. We validate generalization on Things-MEG. Analysis reveals that compact embedding geometries (CN-CLIP) outperform much larger backbones, and that decoding aligns with established neurophysiology of visual processing. This work is a critical step towards robust, semantically-grounded visual decoding from non-invasive temporal neural signals. The source code is publicly available in https://github.com/anon-eeg/eeg_image_decoding.

Accurate and generalizable estimation of cognitive workload from electroencephalography (EEG) is critical for human-centered and safety-critical systems. Although EEG is widely used for workload assessment, the consistency of region-level EEG contributions across tasks, datasets, and subjects remains unclear. This paper presents a region-level evaluation framework for EEG-based workload prediction in which models are trained and evaluated using features extracted exclusively from electrodes belonging to anatomically defined scalp regions. We perform a large-scale analysis across four publicly available EEG workload datasets spanning diverse task demands, recording hardware, and electrode montages. Region importance is quantified using a model-agnostic, performance-based approach under both mixed-subject and subject-independent evaluation protocols, with results aggregated using a rank-based strategy to ensure robustness across experimental configurations. Across all datasets and subject-independent evaluations, frontal electrode groups outperform the full-scalp baseline by approximately 15-20% in relative rank position while using substantially fewer electrodes. Fronto-central regions exhibit the most stable predictive utility, whereas posterior and occipital regions contribute less consistently across experimental conditions. These findings indicate that workload-relevant EEG information is most consistently retained within frontal and fronto-central electrode groups, supporting the design of efficient and generalizable EEG-based workload monitoring systems.

The development of brain-computer interfaces (BCIs) based on electroencephalograms (EEGs) has advanced significantly mainly to machine learning. Although the majority of earlier research has been on increasing classification accuracy, relatively little focus has been placed on security and robustness. According to recent research, EEG-based BCIs are susceptible to adversarial attacks, which can cause misdiagnosis due to minute, well-crafted disturbances. Evaluating model robustness against such perturbations is therefore critical for ensuring reliable deployment. In this study, we propose a lightweight custom Convolutional Neural Network (CNN) architecture to investigate adversarial robustness in EEG-based BCIs. The suggested method is assessed using two EEG datasets and contrasted with three novel CNN models tailored to EEG, namely EEGNet, DeepConvNet, and SleepEEGNet, under gradient-based adversarial attack scenarios. According to experimental findings, the suggested model continuously performs better in classification under adversarial perturbations compared to baseline models, indicating improved robustness. These findings highlight the potential of lightweight architectures for enhancing the reliability of EEG-based BCI systems under adversarial conditions.

Low-density EEG is more suitable for wearable and IoT-based brain sensing, but sparse electrode sampling often lacks sufficient spatial information to characterize cross-regional neural activity. EEG spatial super-resolution aims to recover dense-channel EEG from sparse recordings, yet remains challenging because channel missingness typically occurs at the whole-channel level, spatiotemporal dependencies over the full electrode layout are often underexplored, and the mapping from sparse to dense signals is inherently ambiguous. To address these issues, we propose TGSD, a topology-guided state-space diffusion framework for EEG spatial super-resolution. TGSD first employs a Hierarchical Spatial Prior Encoder to learn topology-aware priors over the complete electrode layout by integrating local geometric relationships with region-level contextual information. Based on these priors and sparse observations, a Conditional State-Space Diffusion Reconstructor progressively generates missing-channel signals through reverse diffusion, while alternating temporal and channel-wise state-space modeling captures long-range temporal dynamics and inter-channel dependencies in a unified framework. Experiments on the SEED and PhysioNet MM/I datasets show that TGSD consistently outperforms representative baselines under different super-resolution factors in both reconstruction fidelity and downstream classification performance. These results demonstrate the effectiveness of combining topology-aware spatial priors with conditional diffusion for enhancing practical low-density EEG sensing in wearable and IoT scenarios. The official implementation code is available at https://github.com/jtggz/TGSD.

Reliable seizure prediction is a prerequisite for closed-loop neurostimulation therapy, yet existing methods rarely account for the variability in EEG signal quality encountered in real-world deployment, and the overwhelming majority adopt non-strict evaluation protocols that overestimate generalisation performance. We propose CLSP-REQA (Closed-Loop Seizure Prediction with Real-time EEG Quality Assessment), a unified framework that embeds a lightweight signal quality estimator directly within the prediction pipeline. A Real-time EEG Quality Assessment (REQA) module runs in parallel with a Mamba-BiLSTM backbone, producing a scalar quality score q in [0,1] that modulates output confidence through a tiered non-linear fusion function (ECLO). Under strict cross-patient evaluation on the CHB-MIT Scalp EEG Database (n = 23 subjects, 198 seizures), CLSP-REQA achieves an AUC-ROC of 0.7426 +- 0.0199, outperforming the unadapted cross-patient baseline of 0.69 reported by Jemal et al., using only 16 EEG channels compared to 23 in prior work, and without requiring any target-patient data or domain adaptation. On the SIENA Scalp EEG Database (n = 14 subjects, 47 seizures), CLSP-REQA achieves AUC 0.7012 +- 0.0249, substantially surpassing the best domain-adapted cross-patient result of 0.61 on the same dataset, demonstrating strong cross-dataset generalisation. The framework outputs a structured four-tuple (p, q, c, Phi_SHAP) directly compatible with closed-loop neurostimulator interfaces.

We introduce a novel Longitudinal Focused Attention Meditation Electroencephalography (L-FAME) dataset and an accompanying benchmark, designed to foster research into the neural effects of various meditation practices and the evolution of these effects over a six-week training period. The dataset contains EEG recordings and psychological assessments from 74 healthy college participants, collected at two distinct time points: pre-intervention and post-intervention. Participants were randomly assigned to one of three distinct meditation groups: two mantra-based techniques (SA-TA-NA-MA and Hare Krishna) and one Breath Focus practice. Leveraging this unique longitudinal and comparative dataset, we propose a benchmark suite comprising three distinct classification tasks: (1) cognitive state decoding to distinguish between resting and meditation states, (2) fine-grained classification of the specific meditation techniques, and (3) cross-session adaptation to evaluate model generalization across the longitudinal time gap. We provide comprehensive baseline results for these tasks utilizing a range of classical machine learning algorithms and deep learning architectures. The complete dataset, preprocessing pipelines, and benchmark evaluation code will be publicly released, offering a valuable resource and a standardized framework for the development and comparison of new analytical methods in computational meditation research and EEG-based machine learning. The dataset is available at https://huggingface.co/datasets/L-FAME-Dataset-Benchmark/L-FAME

While Multimodal Large Language Models (MLLMs) have demonstrated remarkable proficiency in general video understanding, their capacity to interpret involuntary, and spatio-temporally evolving pathologic motor behaviors such as seizure semiology remains largely untested. To address this gap, we introduce Seizure-Semiology-Suite, a clinically grounded dataset and benchmark for fine-grained, structured seizure semiology understanding. The dataset includes 438 seizure videos annotated with over 35,000 dense labels covering 20 ILAE-defined semiological features. Building on this dataset, we propose a seven-task hierarchical benchmark that systematically evaluates MLLMs from low-level visual perception to temporal sequencing, narrative report generation, and seizure diagnosis. To enable clinically meaningful evaluation of generated reports, we further introduce the Report Quality Index for Seizure Semiology (Seizure-RQI). Extensive baselines across 11 open-weight MLLMs reveal systematic weaknesses in laterality reasoning, temporal localization, symptom sequencing, and clinically faithful reporting. We show that seizure-specific fine-tuning substantially improves performance across tasks, and that a two-stage neuro-symbolic framework achieves an F1 score of 0.96 on epileptic versus non-epileptic seizure classification. Seizure-Semiology-Suite establishes a rigorous benchmark for evaluating multimodal models in safety-critical medical video understanding and guides the development of clinically reliable, domain-adaptive multimodal intelligence.

High-fidelity EEG generation is critical for alleviating data scarcity and addressing privacy constraints in large-scale neural modeling. Despite recent progress, most existing approaches formulate EEG generation via discrete denoising objectives, which inadequately reflect the inherently continuous temporal dynamics and spectral structure of neural activity. As a result, these methods often struggle to preserve long-range temporal dependencies and exhibit mismatches in the spectral and temporal structure of the generated signals. In this work, we argue that effective EEG generation requires models that operate directly on the continuous evolution of neural signals. We introduce Just EEG Transformer (JET), a generative framework based on conditional flow matching that models EEG as raw sequences evolving along continuous trajectories. By learning a smooth vector field that transports noise to the EEG data distribution, JET captures temporal continuity and transient dynamics without relying on discretized denoising schemes or domain-specific representations. To ensure that the learned dynamics remain consistent with key properties of EEG signals, we introduce principled constraints that preserve spectral structure, temporal stationarity, and signal-level statistics. Across three large-scale benchmarks, JET consistently achieves state-of-the-art performance, reducing TS-FID by over 40% compared to strong baselines. Extensive analyses show that JET captures key structural properties of neural dynamics, providing a scalable and principled approach to EEG generation. Project page: https://y-research-sbu.github.io/JET/ .

Learning universal representations from electroencephalogram (EEG) signals is a cutting-edge approach in the field of neuroinformatics and brain-computer interfaces (BCIs). Conventionally, EEG is treated as a multivariate temporal signal, where time- or frequency-domain features are extracted for representation learning. This paper investigates a simple yet effective EEG representation, i.e., microstates. Microstates represent the building blocks of brain activity patterns at a microscopic time scale. We build a universal microstate tokenizer from a large medical EEG dataset by clustering continuous EEG signals into sequences of discrete microstates. The microstate tokenizer is then adopted universally across a series of downstream tasks, including sleep staging, emotion recognition, and motor imagery classification. Experimental results show that EEG representation learning with microstates outperforms traditional time-domain and frequency-domain features under different models and across different tasks. Further analysis shows that microstates offer greater interpretability and scalability, thereby opening up applications in both cognitive neuroscience and clinical research.

Diagnosing epilepsy is challenging when routine EEGs lack interictal epileptiform discharges (IEDs). Intermittent photic stimulation (IPS) and hyperventilation (HV) can increase diagnostic yield, but their interpretation is subjective. We propose a reproducible pipeline that classifies EEG recordings acquired during stimulation procedures, using machine-learning features spanning temporal, spectral, wavelet, and connectivity domains, and a stacked ensemble to combine complementary feature sets. Performance is evaluated with leave-one-subject-out (LOSO) cross-validation on the TUH Epilepsy Corpus and a clinical Erasmus MC (EMC) cohort, including IED-free analyses on TUH. On TUH, ensembles achieve up to 97.8% AUC / 93.1% BAC on IED-free resting-state EEG and 94.1% AUC / 86.8% BAC on IED-free IPS. On EMC, IPS provides the strongest discrimination (79.4% AUC / 73.9% BAC), while HV performance benefits from stratifying subjects by responsiveness. These results indicate that stimulation-evoked activity, particularly IPS, contains meaningful discriminative information for IED-free epilepsy classification and that multi-domain ensembling improves robustness.

Advancements in clinical Brain-Computer Interfaces (BCIs) depend on precise and reliable signal interpretation. However, the high-dimensional and noisy nature of data captured from both implanted and non-implanted BCIs poses significant challenges, motivating the use of feature selection algorithms. We introduce BCI-sift (BCI Systematic and Interpretable Feature Tuning), a Python-based toolbox designed to streamline the application of diverse optimization algorithms to BCI datasets for identifying the most relevant features in machine learning tasks. Our scikit-learn-compatible toolbox (github.com/UMCU-RIBS/BCI-sift) simplifies feature selection in BCI tasks by integrating advanced optimization methods. We validated the toolbox on high-density electrocorticography (HD ECoG) data from eight able-bodied participants with 64-128 electrodes implanted over the sensorimotor cortex, who repeatedly spoke 12 words. BCI-sift identified informative neural features across electrode, temporal, and frequency dimensions. The anatomical locations of electrode selections were consistent across participants and aligned with known functional organization of the sensorimotor cortex. Relevant time points clustered around speech production, and the high-frequency band was identified as most informative, in line with prior work. Feature selection improved classification accuracy compared to using all features. BCI-sift provides an accessible and versatile platform for feature selection in BCI research, enabling improved decoding performance, automated feature analysis, and enhanced interpretability. While validated on HD ECoG data, the approach is broadly applicable to other BCI modalities. By enhancing classification accuracy and interpretability, BCI-sift addresses key challenges in developing efficient and transparent BCI systems.

Neuroscientists have recently turned to intracranial brain recording methods, like electrocorticography (ECoG), for human experiments because of the fine spatial and temporal resolution that they afford. Models trained on this data, however, are fundamentally restricted by the patient populations that can receive the implants necessary for recording. We propose using non-invasive fMRI to bridge the gap in training data. Using spoken language representations fine-tuned on fMRI, we build encoding models of ECoG. These representations showed improved prediction performance in ECoG, even though the temporal resolution of fMRI is two orders of magnitude worse. Prediction improved in frequency bands well beyond what is directly measured in fMRI. Next, to test the procedure's generalization ability, we fine-tuned models on fMRI responses that were temporally downsampled by a factor of 2. Despite the loss in resolution, these models were able to predict fMRI and ECoG responses at levels comparable to the original fMRI-tuned models. Finally, we showed that ECoG performance steadily scales with the amount of fMRI-tuning data. Our results show that "slow" data like fMRI can be a valuable resource for building better models of "fast" brain data like ECoG. In the future, integrating across multiple recording methods may further improve performance in other applications, like decoding.

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.

Self-initiated attention shifts play a critical role in voluntary behavior but are difficult to study due to the absence of explicit temporal markers. While previous studies have examined their neural correlates, it remains unclear how multi-dimensional electroencephalography (EEG) features contribute to their characterization within an interpretable computational framework. In this study, we build on an experimental paradigm developed in our previous work, which enables controlled comparison between task-constrained self-initiated shifts and externally instructed shifts under identical visual stimulation. Within this setting, we investigate whether preparatory EEG activity can distinguish these two types of attention shifts. We adopt a machine learning-based approach and conduct two complementary analyses: (1) a performance-oriented assessment of frequency-specific topographic patterns, and (2) a model-based feature attribution analysis using SHapley Additive exPlanations (SHAP). These analyses provide a structured view of how spectral features across regions of interest contribute to model behavior. Our results demonstrate reliable within-subject classification performance, indicating that preparatory EEG activity contains subject-specific discriminative information within this paradigm. The analysis shows that higher-frequency bands and frontal regions contribute strongly to model decisions, although such contributions should be interpreted cautiously due to the potential influence of non-neural artifacts in high-frequency EEG signals. Overall, this work highlights the value of interpretable machine learning for analyzing subject-specific EEG signal patterns in a controlled experimental setting, with potential applications in personalized and asynchronous brain-machine interface systems.

Leveraging the universal representations of pre-trained LLMs and MLLMs offers a promising path toward brain foundation models. However, visually-evoked EEG datasets remain scarce, leading existing methods to align neural signals mainly with abstract text, a lossy translation that may discard fine-grained perceptual information encoded in brain activity. We propose Generative Visual Grounding (GVG), a framework that visualizes the invisible by using an EEG-to-image generative model as a visual translator. Instead of forcing EEG into text alone, GVG hallucinates instance-specific proxy images for non-visual EEG, providing structured visual contexts that allow MLLMs to exploit their visual priors for clinical-state interpretation. We validate this idea on two MLLM backbones, GVG-X-Omni and GVG-Janus. Image-only alignment is already competitive: the lightweight GVG-X-Omni matches 1.7B-parameter text-aligned baselines while tuning only 170M parameters on a frozen 7B backbone. We further extend GVG-Janus with trimodal Image+Text alignment, where text supplies categorical semantic anchors and visual proxies enrich neural representations with perceptual details. Experiments show consistent gains in EEG understanding and visual generation, suggesting visual proxy grounding as an effective complement to textual alignment.

EEG foundation models (EEG-FMs) have been evaluated predominantly on clean, in-distribution accuracy, leaving their robustness, interpretability and representational quality largely unexamined. This study addresses these gaps by benchmarking six EEG-FMs against a baseline deep learning model across eight datasets. Beyond clean accuracy, we conduct three layers of analysis: (i) Robustness: we apply test-time perturbations including additive noise, random and region-based channel dropout and region-specific noise injection. Our analyses show that no single model dominates all failure modes. The most noise-robust model is among the most fragile under channel dropout and much of the dropout fragility disappears when channels are removed rather than zero-padded. (ii) Interpretability: we present the first application of Attention-Aware Layer-Wise Relevance Propagation (AttnLRP) to EEG-FMs and show that models broadly concentrate relevance on task-appropriate brain regions consistent with known neurophysiology. However, attribution maps remain spatially stable under perturbation while predictions degrade, suggesting that the models attend to the correct brain regions but decode corrupted content. (iii) Expressiveness: With block-wise probing we show that late blocks are repurposed during fine-tuning, while early blocks already hold task-related information. Furthermore, we demonstrate that the poor head-only performance previously attributed to low-quality pre-trained representations is largely explained by pooling and that EEG-FMs possess sufficient representational capacity when their token-level embeddings are preserved. Together, these findings provide the first systematic assessment of robustness, interpretability and expressiveness for EEG-FMs and highlight critical considerations for their development.

Intracranial EEG (iEEG) provides high-fidelity neural recordings essential for clinical and brain-computer interface applications, but acquiring these signals requires invasive surgery. While recent studies have attempted to estimate iEEG from non-invasive scalp EEG, most rely on patient-specific models, creating a circular dependency: if surgery is required to collect training data, the non-invasive model offers limited practical benefit. In this study, we address the challenge of cross-subject iEEG reconstruction by predicting intracranial signals for unseen patients using models trained on other individuals. We propose CAST (Cross-Attention Spatial-Temporal Transformer), a machine learning framework that translates scalp EEG into multi-channel iEEG waveforms through a two-stage transfer learning strategy. First, a temporal encoder extracts multi-scale neural representations at three different resolutions. Then, because electrode placements vary substantially across patients, a channel-aware decoder is calibrated using only a few minutes of data from the target subject. We evaluated the proposed method using leave-one-subject-out cross-validation on two public datasets comprising 1,282 iEEG channels. Experimental results demonstrate that CAST reconstructs cortical signals located near the scalp surface substantially better than deep subcortical activity. In highly observable sensorimotor regions, the model achieved peak correlations of up to r=0.864 in the precentral gyrus. Furthermore, with a channel selection strategy, CAST obtained a mean correlation of r=0.545 on viable subjects, outperforming previous within-subject baselines. These findings indicate that cortical iEEG signals can be reconstructed for unseen subjects from scalp EEG without extensive patient-specific training, and that only a brief calibration phase is sufficient to adapt the model to new hardware configurations.

While scaling laws have established a fundamental framework for foundation models in natural language processing, their applicability to electrocardiogram (ECG) models remains poorly characterized. Indeed, recent studies do not always yield consistent downstream gains as one increases the model size or pre-training dataset size of ECG models, leaving the exact roles of architectural inductive biases, pre-training paradigms, and expected improvements with size largely unanswered. In this work, we systematically investigate neural and loss-to-loss scaling laws within the ECG domain. By pre-training over $120$ models (ranging from $20$K to $200$M parameters) on the large-scale CODE dataset ($2.3$M records), we decouple the effects of model architecture (ResNet vs. Transformer) and pre-training paradigm, namely supervised learning (SL) versus self-supervised learning (SSL). We found that (i) SL models are data-bottlenecked in-distribution, whereas SSL models scale robustly across both model and data sizes; (ii) for out-of-distribution (OOD) generalization, ResNets are $1.3$ to $2.5$ times more parameter-efficient than Transformers, while SSL is up to $16$ times more data-efficient and achieves up to $7.6$ times higher transfer efficiency than SL on unseen clinical tasks; (iii) across the observed scales, ResNet-based models generally achieve the lowest OOD loss, with SSL dominating on unseen clinical tasks and self-supervised Transformers overtaking at very large model sizes. Our results suggest that the path to effective ECG foundation models lies in the strategic alignment of architecture and paradigm rather than brute-force scaling.

Decoding visual information from electroencephalography (EEG) signals remains a fundamental challenge in brain-computer interfaces and medical rehabilitation. Existing EEG visual decoding methods mainly focus on learning a single global EEG embedding for cross-modal alignment, but they largely overlook the staged and hierarchical characteristics of human visual processing. To address this limitation, we propose a neuroscience-inspired staged representation learning framework that reformulates EEG visual decoding as a stage-specific representation decomposition problem. The proposed framework organizes EEG representation learning into three complementary phases: low-level visual representation learning, high-level semantic representation learning, and integrative information fusion. To strengthen semantic modeling, we further introduce a multimodal dual-level semantic learning mechanism that separates coarse label-level semantics from fine image-level visual-semantic information. In addition, semantic latent channels are introduced as computational representation channels generated from observed visual EEG signals, expanding the channel-level semantic representation space for structured semantic abstraction and cross-modal alignment. Extensive experiments on the THINGS-EEG benchmark demonstrate that the proposed method achieves superior performance under subject-dependent zero-shot evaluation and improved exact retrieval under subject-independent zero-shot evaluation. Additional analyses, including layer-wise retrieval, temporal accumulation, expanded multi-image retrieval, and ablation studies, further support the effectiveness of staged decomposition and structured semantic modeling. These results suggest that explicitly modeling staged perceptual, semantic, and integrative representations provides an effective neuroscience-inspired framework for EEG-based visual decoding.

Electroencephalograph (EEG) timeseries signals are characterized by significant noise and coarse spatial resolution, which complicates the classification of neurodegenerative diseases. Even SOTA deep learning architectures struggle to distinguish between healthy controls and diseased subjects, or between different disease types, due to high intergroup similarity. In this paper, we show that a spectrally selective approach to feature construction enhances class separability. By isolating signal strengths within the primary brainwave bands, we transform high dimensional raw data into high value spectral features. Our results demonstrate that in small datasets a) features derived from frequency and time frequency domain allow traditional machine learning models to match or exceed the performance of SOTA deep learning models, b) Attention mechanism is unable to distill the stable feature signatures that characterize healthy neural activity in both resting and task EEGs, and c) the limitations of attention based models in finding relevant spectral features appear to be robust in that providing frequency selective time domain input do not appreciably improve their performance. We validate our methodology across three open source resting EEG datasets and one task EEG dataset, providing robust empirical evidence for our claims.

Electroencephalogram (EEG) signals are highly susceptible to artifacts, resulting in a low signal-to-noise ratio which makes extraction of meaningful neural information challenging. Artifact Subspace Reconstruction (ASR) is one of the most widely used artifact filtering techniques in EEG-based BCI applications, owing to its real-time applicability. ASR reconstructs artifact-free signals by operating in Principal Component (PC) space within sliding windows. However, ASR performance is critically sensitive to its threshold parameter - an incorrect threshold risks removing task-relevant neural features alongside artifacts. Furthermore, since PCs are linear combinations of all channels, subspace reconstruction in PC space may alter the underlying data structure, potentially discarding essential neural information. To address these limitations, we propose nASR, a novel end-to-end trainable Keras layer that jointly optimizes artifact rejection and downstream decoding. nASR introduces two trainable threshold parameters: K, which governs artifact detection in PC variance space, and L, which quantifies eigen-spread to pinpoint the primary artifact--contributing channels, enabling selective channel-level reconstruction that preserves clean channel information. An ablation study comprising five model variants (m01 - m05), evaluated across two subjects from the BCI Competition IV Dataset 1, confirms that nASR variants consistently outperform traditional ASR on test classification metrics, while achieving a 6-8x reduction in inference time, making nASR a strong candidate for real-time BCI applications demanding both low latency and high decoding performance.

Spike activity has been the dominant neural signal for behavior decoding due to its high spatial and temporal resolution. However, as brain-computer interfaces (BCIs) move toward high channel counts and wireless operation, the high sampling frequency of spike signals becomes a bottleneck due to high power and bandwidth requirements. Local field potentials (LFPs) represent a different spatial-temporal scale of brain activity compared to spikes, offering key advantages including improved long-term stability, reduced energy consumption, and lower bandwidth requirement. Despite these benefits, LFP-based decoding models typically show reduced accuracy and often rely on non-causal architectures that are unsuitable for real-time deployment. To address these challenges, we propose REALM: a retrospective distillation framework that enables causal LFP decoding. Inspired by offline-to-online distillation strategies in speech recognition, REALM transfers representational knowledge from a pretrained multi-session bidirectional LFP model to a causal version for real-time deployment. We first pretrain a bidirectional Mamba-2 teacher model using a masked autoencoding objective. We then distill this teacher model into a compact student model via a combined objective of representation alignment and task supervision. REALM consistently outperforms both causal and non-causal LFP-based SOTA methods for behavior decoding. Notably, our REALM improves decoding performance while achieving a $2\times$ reduction in parameter count and a $10\times$ reduction in training time. These results demonstrate that retrospective distillation effectively bridges the gap between offline and real-time neural decoding. REALM shows that LFP-only models can achieve competitive decoding performance without reliance on spike signals, offering a practical and scalable alternative for next-generation wireless implantable BCIs.

Foundation models (FMs) promise to extract unified representations that generalize across downstream tasks. They have emerged across fields, including electroencephalography (EEG), but it is less clear how effective they are in this particular field. Published evaluations differ in datasets, in the EEG-specific preprocessing that might influence reported results, and in the reported metrics, frequently obscuring the clinical relevance in EEG. We introduce NeuroAtlas, the largest EEG benchmark to date: 42 datasets and 260k hours covering clinical EEG (epilepsy, sleep medicine, brain age estimation) and brain-computer interfaces, and include multiple datasets per task along with bespoke clinical evaluation metrics. Besides evaluating EEG-FMs with respect to supervised baselines, we present results from generic time-series FMs. We report three findings. First, EEG-specific FMs do not consistently outperform time-series FMs, which have neither EEG-focused architectures nor been pretrained on EEG. Second, standard machine learning metrics are insufficient to assess clinical utility: thus, we thoroughly evaluate more appropriate measures such as the quality of event-level decision-making, hypnogram-derived features, and the brain-age gap in the domains of epilepsy, sleep, and brain age, respectively. Third, model rankings and performance can vary substantially within domains. We conclude that pretrained models perform largely on par, with only narrow advantages for a few, and that current models do not yet deliver on the promise of an out-of-the-box unified EEG model. NeuroAtlas exposes this gap and provides the datasets and metrics for the next generation of unified EEG FMs.

EEG-based visual decoding aims to establish a mapping between neural signals and visual semantics. However, it remains constrained by the dual challenges of severe information granularity mismatch and the low signal-to-noise ratio (SNR) of EEG signals. Existing approaches typically treat static visual features, ignoring the dynamic selectivity of human vision and the frequency specificity of neural oscillations. To bridge this gap, we propose CAIA, a Cognitive-guided Adaptive blurring with Information-Constrained Alignment framework for Neural-Visual decoding. On the visual side, it simulates selective attention to adaptively reduce redundancy. Meanwhile, on the EEG side, it leverages neural oscillation priors and the information bottleneck mechanism to enhance SNR. Specifically, we devise a cognitive-dynamics-based adaptive blurring mechanism that dynamically integrates center-biased and saliency-guided visual cues via cross-modal attention. Furthermore, we introduce a distribution-aware boundary calibration loss to robustly rectify alignment bias caused by outlier samples. Moreover, a cognitively-guided information-screening method is proposed to select task-relevant EEG oscillations. Extensive experiments demonstrate that CAIA improves both subject-dependent and subject-independent average Top-1 and Top-5 accuracy in zero-shot brain-to-image retrieval, significantly outperforming prior methods. Our work validates that optimizing visual information density to match neural granularity offers a more interpretable and robust pathway for neural decoding.

Digital phenotyping enables continuous passive monitoring of behavior and physiology, offering a promising paradigm for early detection of psychotic relapse. In this work, we develop and systematically study two smartwatch-based frameworks for daily relapse detection. The first forecasts cardiac dynamics and flags deviations between predicted and observed features as indicators of abnormality. The second adopts a multi-task formulation that fuses sleep with motion and cardiac-derived signals, learning time-aware embeddings and predicting measurement timing. Both pipelines use Transformer encoders and output a daily anomaly score, derived from predictive uncertainty estimated via an ensemble of multilayer perceptrons to improve robustness to real-world wearable variability. While each framework independently demonstrates strong predictive power, we show that they capture complementary physiological signatures. Consequently, we propose a late-fusion strategy that synergistically combines the anomaly signals from both architectures into a unified decision score. We benchmark our methodology on the 2nd e-Prevention Grand Challenge dataset, where our fused model achieves a 8% relative improvement over the competition-winning baseline. Our results, supported by extensive ablation studies, suggest that the integration of diverse digital phenotypes, cardiac, motion, and sleep, is essential for the high-fidelity detection of psychotic relapse in real-world settings.

EEG foundation models achieve state-of-the-art clinical performance, yet the internal computations driving their predictions remain opaque: a barrier to clinical trust. We apply TopK Sparse Autoencoders (SAEs) across three architecturally distinct EEG transformers: SleepFM, REVE, and LaBraM to extract sparse feature dictionaries from their embeddings. By grounding these features in a clinical taxonomy (abnormality, age, sex, and medication), we benchmark monosemanticity and entanglement across architectures. A single hyperparameter procedure, driven by an intrinsic dictionary health audit, transfers robustly across all three architectures. Via concept steering, we introduce a "target vs. off-target" probe area metric to quantify steering selectivity and reveal three operational regimes: selectively steerable, encoded but entangled, and non-encoded. This framework exposes critical representational failures: "wrecking-ball" interventions that collapse global model performance, and clinical entanglements, such as age-pathology confounding, where it is impossible to suppress one concept without corrupting the other. Finally, a spectral decoder maps these interventions back to the amplitude spectrum, translating latent manipulations into physiologically interpretable frequency signatures, such as pathological slow-wave suppression and $α$-band restoration.

While EEG foundation models have shown significant potential in universal neural decoding across tasks, their advancement remains constrained by the inadequacy modeling of complex spatiotemporal topology, as well as the inherent modality gap between low-level physiological signals and high-level textual semantics. To address these challenges, we propose a Knowledge-Anchored Semantically-Dynamic Topology Brain Autoregressive Model (KAST-BAR), which dynamically aligns physiological representations derived from multi-level brain topology with an expert-level semantic space. Specifically, we design a Dual-Stream Hierarchical Attention (DSHA) encoder that accurately captures the brain's intrinsic non-Euclidean topology by modeling local temporal dynamics with global spatial contexts. On this basis, a Knowledge-Anchored Semantic Profiler (KASP) is proposed to synthesize physically-grounded and instance-level textual profiles, which subsequently drive a Semantic Text-Aware Refiner (STAR) to dynamically reconstruct EEG representations using Latent Expert Queries. By conducting large-scale pre-training on 21 diverse datasets to build a foundation model, KAST-BAR effectively integrates expert-level medical knowledge into EEG signal representations, consistently achieving superior performance across six downstream tasks. Our code is available at https://github.com/KAST-BAR/KAST-BAR

Decoding speech from non-invasive brain signals is challenging. For the LibriBrain 2025 Speech Detection task, we propose a novel two-step framework that bypasses direct reconstruction. First, a contrastive learning model retrieves the matching speech segment for the given test MEG from a large-scale audio library (LibriVox). Second, a speech detection model generates the binary silence/speech sequence directly from this retrieved audio. With this approach, our team Sherlock Holmes achieved first place in the extended track (F1-score: 0.962), demonstrating that leveraging external audio databases is a highly effective strategy.

Closed-loop brain-computer interfaces often require both a forecast of upcoming neural population activity and a readout of the animal's behavioral state. A single Mamba forecaster, trained only on next-step spike counts at Neuropixels scale, can deliver both in one forward pass. A lightweight per-session linear head reading the model's predicted rates decodes behavior better than the same linear classifier reading the raw spike counts, under matched temporal context. We test on the Steinmetz visual-discrimination benchmark, which spans 39 sessions, roughly 27,000 neurons, and 1,994 held-out trials. Across three training seeds, Mamba's predicted rates decode mouse choice at 75.7$\pm$0.2% trial vote, roughly 2.3 times chance level, and stimulus side at 66.1$\pm$0.6%, about twice chance. Compared to a matched 500 ms-context linear decoder on the raw spike counts, Mamba wins at trial vote by 4-6 pp on response and 4-6 pp on stimulus side. A session-start calibration block of about 100-150 trials brings the readout within 1-2 pp of asymptote, and the full pipeline fits inside the 50 ms bin budget on workstation-class GPUs typical of tethered chronic Neuropixels recordings.

Neuroscience data are highly fragmented across labs, formats, and experimental paradigms, and reuse often requires substantial manual effort. A persistent roadblock to data reuse and integration is the need to decipher bespoke and diverse data formatting choices. Common data formats have been proposed in response, but the field continues to struggle with a fundamental tension: formats flexible enough to accommodate diverse experiments are rarely descriptive enough to be self-explanatory, and sufficiently descriptive formats demand detailed documentation and curation effort that few labs can sustain. Agentic AI is a natural candidate to solve this problem: LLMs read code and text faster and with sustained attention to the low-level details humans tend to skim over. To measure how well agentic AI performs on this task, we selected eight recent papers studying large-scale mouse neural population recordings that shared both data and code, spanning diverse recording modalities, behavioral paradigms, and dataset formats (e.g., NWB, specialized APIs, and general-purpose Python or MATLAB files). We provided agents with the data, code, and paper, and prompted them to load, understand, and reformat the data for a common downstream task: training a decoder from neural activity to task or behavioral variables. General-purpose coding agents commonly used by scientists performed well on each sub-task, but rarely strung together a fully error-free end-to-end solution. We characterize the types of mistakes agents made and the dataset properties that elicited them, and propose data-sharing best practices for the agentic-AI era. We further find that agents-as-judges are unreliable at catching errors, especially without ground-truth references, so interactive, human-in-the-loop coding remains necessary.

Specialized foundation models are beginning to emerge in various medical subdomains, but pretraining methodologies and parametric scaling with the size of the pretraining dataset are rarely assessed systematically and in a like-for-like manner. This work focuses on foundation models for electrocardiography (ECG) data, one of the most widely captured physiological time series world-wide. We present a comprehensive assessment of pretraining methodologies, covering five different contrastive and non-contrastive self-supervised learning objectives for ECG foundation models, and investigate their scaling behavior with pretraining dataset sizes up to 11M input samples, exclusively from publicly available sources. Pretraining strategy has a meaningful and consistent impact on downstream performance, with contrastive predictive coding (slightly ahead of JEPA) yielding the most transferable representations across diverse clinical tasks. Scaling pretraining data continues to yield meaningful improvements up to 11M samples for most objectives. We also compare model architectures across all pretraining methodologies and find evidence for a clear superiority of structured state space models compared to transformers and CNN models. We hypothesize that the strong inductive biases of structured state space models, rather than pretraining scale alone, are the primary driver of effective ECG representation learning, with important implications for future foundation model development in this and potentially other physiological signal domains.

Emerging foundation models (FMs) in electroencephalography (EEG) promise a path to scale deep learning in diagnostics and brain-computer interfaces despite data scarcity, yet their opaque nature remains a barrier to wider adoption. We investigate attention-aware Layer-wise relevance propagation (LRP) as a post-hoc attribution method for EEG-FMs, extending LRP's use on convolutional neural network (CNN)-based EEG models to the Transformer architectures that current FMs are based on. We find that LRP can both verify EEG-FM decisions and surface novel, biologically plausible hypotheses from them. In motor imagery, it unmasks 'Clever Hans' behavior where models prioritize task correlated ocular signals over the intended motor correlates. In a naturalistic paradigm for affect prediction, it reveals a recurring reliance on a central electrode cluster, suggesting a candidate sensorimotor signature of arousal. Though heatmap interpretation remains ambiguous in this complex domain, the results position LRP as a tool for both verification and exploration of EEG-FMs, a role that will grow in both importance and discovery potential as the underlying models mature.

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.

Brain-computer interfaces (BCIs) are moving rapidly from laboratory research into clinical, edge, and real-world settings. Under ISO/IEC 8663:2025, a BCI is a direct communication link between central nervous system activity and external software or hardware systems. This link expands privacy risk beyond raw neural-signal leakage: neural data, derived representations, model assets, and decoded outputs can be re-associated with individuals across collection, transmission, storage, training, inference, and feedback, or used to infer information beyond what a task requires. Starting from the general BCI paradigm, this review deffnes privacy-protection boundaries, protection objects, and the relationship between user data privacy and model privacy within a shared risk pathway. It then proposes a three-dimensional framework - protection object, lifecycle stage, and dominant protection-strength level - to classify existing work into four levels of protection strength. Finally, mental privacy and neuroethical risks are treated as open issues, emphasizing that BCI privacy protection should not only obscure data but also disentangle task-irrelevant sensitive information while preserving downstream utility. Keywords: Brain-computer interface, Neural data privacy, User data privacy, Model privacy, Disentanglement of task-irrelevant sensitive information, Protection-strength grading, Neuroethical risks

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.

Existing multi-model and tool-augmented systems communicate by generating text, serializing every exchange through the output vocabulary. Can two pretrained language models instead coordinate through a continuous, concurrent channel? The Bicameral Model couples two frozen language models through a trainable neural interface on their intermediate hidden states. At every generation step, both models run in lockstep: a primary model drives the task while an auxiliary model operates tools, solves constraints, or executes code, with both conditioning on each other's activations through a translation network and a learned suppression gate ($\sim$1% of combined parameters). The gate learns a selective communication protocol from task loss alone, without a prescribed format. We demonstrate the mechanism across three tool backends. On arithmetic, coupling two 0.5B models with a calculator raises accuracy from 36% to 96%. On logic grid puzzles, coupling two 0.6B models with a Z3 solver achieves $1.7\times$ the unaugmented baseline on ZebraLogic. On mathematical reasoning, coupling with a Python sandbox enables the auxiliary to generate problem-specific code from hidden-state signals alone, without ever seeing the problem text.

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.

Event identification in continuous neural recordings is a critical task in neuroscience. Decoding in EEG is dominated by classifying windows aligned to known event onsets. However, while available in controlled experiments, such onsets are absent in continuous real-world monitoring. Here, we introduce DANCE, a deep learning pipeline that frames neural decoding as a set-prediction problem and jointly detects and classifies events directly from raw, unaligned signals. Evaluated separately on ten datasets curated from the literature with a wide variety of event types (ranging from milliseconds to minutes in duration), our model outperforms existing methods on a broad range of cognitive, clinical and BCI tasks. This single architecture establishes a new state of the art in the competitive task of seizure monitoring and matches the accuracy of onset-informed models for BCI tasks. Overall, our method marks a step towards end-to-end asynchronous neural decoding models

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.

Brain-Computer Interfaces (BCIs) based on P300 event-related potentials offer promising applications in health, education, and assistive technologies. However, challenges related to inter- and intra-subject variability and the explainability of Deep Learning (DL) models limit their practical deployment. In this work, we present the Post-Recurrent Module (PRM), an additional layer designed to improve both performance and transparency, incorporated into a Recurrent Neural Network (RNN) architecture for classifying P300 signals from EEG data. Our approach enables a dual analysis of spatio-temporal signals through both global and local explainability techniques, allowing us not only to identify the most relevant brain regions and critical time intervals involved in classification, but also to interpret model decisions in terms of spatio-temporal EEG patterns consistent with well-stablished neurophysiological descriptions of the P300. Experimental results show a 9% improvement in performance over state of the art, while also revealing the importance of inter- and intra-subject variability, in alignment with established neuroscience literature. By making model decisions transparent and efficient, we present a framework for explainable EEG-based models. This framework is not limited to more efficient P300 detection, but can be generalized to a wide range of EEG-based tasks. Its ability to identify key spatial and temporal features makes it suitable for applications such as motor imagery, steady-state visual evoked potentials, and even cognitive workload assessment.

Motor imagery electroencephalography (MI-EEG) decoding offers a non-invasive route for post-stroke rehabilitation, but cross-patient use remains difficult because pathological neural reorganization changes task-related EEG dynamics, aperiodic activity, local excitability, cross-regional coordination, and trial-level brain-state context. This makes source-learned MI representations unreliable for unseen patients. To address this problem, we propose CFSPMNet, a cross-patient adaptation framework that models post-stroke MI-EEG as latent neural-state organization. CFSPMNet combines a Fourier-Reorganized State Mamba Network (FRSM) with Shared-Private Prototype Matching (SPPM). FRSM represents each trial as a latent physiological token sequence, reorganizes token states in the Fourier domain, and uses Fourier-derived trial context to guide Mamba state-space propagation. SPPM improves target pseudo-label updating by combining semantic confidence with shared-private physiological consistency, filtering confident but physiologically inconsistent target predictions. Leave-one-subject-out experiments on two stroke MI-EEG datasets show that CFSPMNet outperforms representative CNN-, Transformer-, Mamba-, and adaptation-based baselines, achieving average accuracies of 68.23% on XW-Stroke and 73.33% on 2019-Stroke, with gains of 5.63 and 8.25 percentage points over the strongest competitors. Ablation, sensitivity, feature-alignment, pseudo-label selection, and neurophysiological visualization analyses further support the roles of Fourier-domain token-state reorganization and calibrated pseudo-label updating. These results suggest that latent neural-state modeling can improve rehabilitation-oriented cross-patient BCI decoding. Code is available at https://github.com/wxk1224/CFSPMNet.

Spike-based encodings are sparse and energy-efficient, but have largely been formulated probabilistically, disconnected from most signal processing literature. We recast spike encoders as time-causal wavelet frames with quantitative bandwidths and reconstruction error bounds. The proposed wavelets preserve the sparsity and locality of spiking representations, with reconstruction up to spike quantization and time discretization. We demonstrate reconstruction on ECG and audio datasets, achieving a normalized RMSE comparable to continuous wavelet transforms. The spiking wavelets map directly to neuromorphic hardware.

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.

Decoding imagined speech from non-invasive brain recordings is challenging because imagined datasets are scarce and difficult to align temporally across subjects and sessions In this work, we propose a new approach to the decoding of imagined speech that leverages the richer and more reliably labeled recordings during listening to speech. We collected paired listened and imagined MEG recordings to rhythmic melodic and spoken stimuli from trained musicians. Using trained musicians helped improve temporal alignment across conditions. We then developed a three-stage decoding pipeline that revealed consistent and meaningful relationships between neural activity evoked by imagining and listening to the same stimuli. First, we trained six linear and neural models to map imagined MEG responses to listened responses. We evaluated these models against a null baseline from unseen subjects to validate that the predicted-listening responses preserve stimulus-specific information. In the second stage, we trained a contrastive word decoder exclusively on the listened MEG responses, and evaluated it using four embedding strategies including semantic, acoustic, and phonetic representations. In the third stage, we process the imagined MEG responses from held-out subjects through the mapping pipeline to compute the corresponding listening responses that are then decoded by the listened decoder. Using rank-based analysis, we show that the imagined words are decodable significantly above chance. We shall report here the results of a proof-of-concept implementation to decode imagined speech, where all evaluations are performed on held-out subjects. We also demonstrate that performance improves with training data size, suggesting that this approach is scalable and can directly be made applicable to realistic brain-computer interface scenarios.

Electroencephalography (EEG) is a cornerstone of brain-computer interfaces and clinical neuroscience, yet deep learning models are typically trained and evaluated under a single, unreported preprocessing pipeline. We formalize preprocessing choices as a counterfactual intervention space and show that EEG predictions are surprisingly unstable under this space: across six datasets spanning four paradigms, up to 42% of trial-level predictions flip when only the preprocessing changes, a variability that standard uncertainty methods do not explicitly quantify because they condition on a fixed preprocessing pipeline. We provide three tools to make this instability measurable, decomposable, and reducible. First, a Walsh-Hadamard decomposition of the 2^7 pipeline space reveals that sensitivity is near-additive in practice under the binary intervention design, enabling efficient step-by-step optimization. Second, we introduce Preprocessing Uncertainty (PU), a per-trial diagnostic that captures a dimension of instability complementary to model-based confidence. Third, we study Normalized Adaptive PGI (NA-PGI), a graph-structured regularizer that exploits the compositional structure of preprocessing interventions as one mitigation strategy with clear scope conditions.

Accurate sleep stage classification across datasets remains challenging due to variability in EEG channel montages, sampling rates, recording environments, and subject populations. Although deep learning has shown considerable promise for automated sleep staging, most existing cross-dataset methods rely on one-dimensional EEG signal representations, whereas the use of two-dimensional spectrogram-based inputs within an unsupervised domain adaptation framework has remained largely unexplored. Here, we propose STDA-Net (Spectrogram-based Temporal Domain Adaptation Network), a framework that combines a convolutional neural network (CNN) for spectrogram-based feature extraction, a bidirectional long short-term memory (BiLSTM) module for temporal modeling of sleep dynamics, and a domain-adversarial neural network (DANN) for source-to-target feature alignment without requiring any labeled target-domain data during training. Experiments are conducted on three publicly available datasets Sleep-EDF, SHHS-1, and SHHS-2 under six cross-dataset transfer settings. Results show that the proposed framework achieves an average accuracy of 89.03% and an average macro F1-score of 87.64%, consistently outperforming existing 1D baseline methods in terms of balanced classification performance, with substantially lower variance across five independent runs, indicating improved stability and reproducibility. Overall, these findings demonstrate that 2D spectrogram-based representations, combined with temporal modeling and adversarial domain adaptation, provide a robust and competitive alternative to conventional 1D EEG inputs for cross-dataset sleep staging.

Denoising wearable electroencephalogram (EEG) is inherently challenging since neural activity is not only subtle but also inseparable from spectrally overlapping noise artifacts. Classical signal processing methods, relying on fixed or heuristic rules, cannot handle the time-varying pervasive artifacts in wearable EEGs. Deep learning methods, on the other hand, show promise in decomposition-free EEG denoising using highly expressive neural networks, but the training requires artifact-free EEG, which is inherently unobtainable. To address this, we propose Intelligent Partitioning for Self-supervised Denoising (iPSD). Our method eliminates the need for clean references by learning to partition an input EEG segment into independent noisy realizations with the same underlying signal. This enables self-supervision of deep learning denoisers, even in zero-shot settings where only a single EEG segment to be denoised is available. We validate iPSD through extensive experiments, including validations on wearable EEG from in-ear sensors. The results show that iPSD achieves state-of-the-art performance, most notably under extremely low signal-to-noise ratios (down to -10 dB) and challenging artifacts (e.g., EMG), with spectral fidelity orders of magnitude higher than competitive baselines.

Classification of EEG signals using shallow Convolutional Neural Networks (CNNs) is a prevalent and successful approach across a variety of fields. Most of these models use independent one-dimensional (1D) convolutional layers along the spatial and temporal dimensions, which are concatenated without a non-linear activation layer between. In this paper, we investigate an alternative encoding that operates a bi-dimensional (2D) spatiotemporal convolution. While 2D convolutions are numerically identical to two concatenated 1D convolutions along the two dimensions, the impact on learning is still uncertain. We test 1D and 2D CNNs and a CNN+transformer hybrid model in a low-dimensional (3-channel) and a high-dimensional (22-channel) BCI motor imagery classification task. We observe that 2D convolutions significantly reduce training time in high-dimensional tasks while maintaining performance. We investigate the root of this improvement and find no difference in spectral feature importance. However, a clear pattern emerges in representational similarity across models: 1D and 2D models yield vastly different representational geometries. Overall, we suggest an improved model with a 2D convolutional layer for faster training and inference. We also highlight the importance of architecturally-driven encoding when processing complex multivariate signals, as reflected in internal representations rather than purely in performance metrics.

This research addresses a validated TMS EEG cleaning pipeline and a corresponding benchmark dataset. It evaluates two widely used artifact removal pipelines. A reference dataset of carefully preprocessed EEG signals was established to support future algorithm development and enable systematic comparison of automated artifact removal strategies, despite the absence of a true physiological ground truth. The study evaluates the effectiveness of two widely used source based artifact removal approaches and examines their impact on signal quality improvement and preservation of TMS-evoked potentials. The results support the robustness of the proposed preprocessing workflow and demonstrate its potential for improving data reliability in both research and clinical applications. A key goal is integrating TMS EEG and embedding it within a larger BCI framework. Ultimately, these efforts aim to enhance understanding of cortical dynamics and expand the clinical and research applications of TMS EEG.

Chronic neck pain is a leading cause of disability worldwide, and current treatment selection remains largely trial and error. We present a machine learning framework that uses electroencephalography to predict treatment efficacy in patients with chronic neck pain, with the goal of supporting individualized therapy and reducing the burden on healthcare systems. The framework centers on a rigorous data preprocessing stage tailored to the characteristics of each EEG recording type. For resting-state EEG, the preprocessing pipeline comprises baseline signal removal, bad channel identification and exclusion, re-referencing, bandpass and notch filtering, Independent Component Analysis, and power spectral density analysis. For motor execution and motor imagery recordings, the same initial steps are applied, after which signals are aligned to trigger events so that event-related desynchronization (ERD) and event-related synchronization (ERS) can be quantified. Synchronously recorded electromyography data are bandpass filtered and smoothed with a moving average, then correlated with the corresponding EEG channels to characterize the EEG EMG relationship during attempted movement. In parallel, we performed an extensive literature review of machine learning models applied to clinical EEG (763 records initially screened, 16 patient and 47 healthy-control studies retained), to inform the post-processing strategy. Through this combined preprocessing and review effort, we aim to develop a robust predictive model that can support personalized healthcare strategies in chronic pain management.