Daily Papers

Deep Learning has revolutionized various fields, including Computer Vision, Natural Language Processing, as well as Biomedical research. Within the field of neuroscience, specifically in electrophysiological neuroimaging, researchers are starting to explore leveraging deep learning to make predictions on their data without extensive feature engineering. The availability of large-scale datasets is a crucial aspect of allowing the experimentation of Deep Learning models. We are publishing the first large-scale clinical EEG dataset that simplifies data access and management for Deep Learning. This dataset contains eyes-closed EEG data prepared from a collection of 1,574 juvenile participants from the Healthy Brain Network. We demonstrate a use case integrating this framework, and discuss why providing such neuroinformatics infrastructure to the community is critical for future scientific discoveries.

Neuroscience employs diverse neuroimaging techniques, each offering distinct insights into brain activity, from electrophysiological recordings such as EEG, which have high temporal resolution, to hemodynamic modalities such as fMRI, which have increased spatial precision. However, integrating these heterogeneous data sources remains a challenge, which limits a comprehensive understanding of brain function. We present the Spatiotemporal Alignment of Multimodal Brain Activity (SAMBA) framework, which bridges the spatial and temporal resolution gaps across modalities by learning a unified latent space free of modality-specific biases. SAMBA introduces a novel attention-based wavelet decomposition for spectral filtering of electrophysiological recordings, graph attention networks to model functional connectivity between functional brain units, and recurrent layers to capture temporal autocorrelations in brain signal. We show that the training of SAMBA, aside from achieving translation, also learns a rich representation of brain information processing. We showcase this classify external stimuli driving brain activity from the representation learned in hidden layers of SAMBA, paving the way for broad downstream applications in neuroscience research and clinical contexts.

Generating images from brain waves is gaining increasing attention due to its potential to advance brain-computer interface (BCI) systems by understanding how brain signals encode visual cues. Most of the literature has focused on fMRI-to-Image tasks as fMRI is characterized by high spatial resolution. However, fMRI is an expensive neuroimaging modality and does not allow for real-time BCI. On the other hand, electroencephalography (EEG) is a low-cost, non-invasive, and portable neuroimaging technique, making it an attractive option for future real-time applications. Nevertheless, EEG presents inherent challenges due to its low spatial resolution and susceptibility to noise and artifacts, which makes generating images from EEG more difficult. In this paper, we address these problems with a streamlined framework based on the ControlNet adapter for conditioning a latent diffusion model (LDM) through EEG signals. We conduct experiments and ablation studies on popular benchmarks to demonstrate that the proposed method beats other state-of-the-art models. Unlike these methods, which often require extensive preprocessing, pretraining, different losses, and captioning models, our approach is efficient and straightforward, requiring only minimal preprocessing and a few components. Code will be available after publication.

Current techniques of neuroimaging, including electrical devices, are either of low spatiotemporal resolution or invasive, impeding multiscale monitoring of brain activity at both single cell and network levels. Overcoming this issue is of great importance to assess brain's computational ability and for neurorehabilitation projects that require real-time monitoring of neurons and concomitant networks activities. Currently, that information could be extracted from functional MRI when combined with mathematical models. Novel methods enabling quantitative and long-lasting recording at both single cell and network levels will allow to correlate the MRI data with intracortical activity at single cell level, and to refine those models. Here, we report the fabrication and validation of ultra-thin, optically transparent and flexible intracortical microelectrode arrays for combining extracellular multi-unit and fMRI recordings. The sensing devices are compatible with large-scale manufacturing, and demonstrate both fMRI transparency at 4.7 T, and high electrical performance, and thus appears as a promising candidate for simultaneous multiscale neurodynamic measurements.

Functional magnetic resonance imaging (fMRI) is an indispensable tool in modern neuroscience, providing a non-invasive window into whole-brain dynamics at millimeter-scale spatial resolution. However, fMRI is constrained by issues such as high operation costs and immobility. With the rapid advancements in cross-modality synthesis and brain decoding, the use of deep neural networks has emerged as a promising solution for inferring whole-brain, high-resolution fMRI features directly from electroencephalography (EEG), a more widely accessible and portable neuroimaging modality. Nonetheless, the complex projection from neural activity to fMRI hemodynamic responses and the spatial ambiguity of EEG pose substantial challenges both in modeling and interpretability. Relatively few studies to date have developed approaches for EEG-fMRI translation, and although they have made significant strides, the inference of fMRI signals in a given study has been limited to a small set of brain areas and to a single condition (i.e., either resting-state or a specific task). The capability to predict fMRI signals in other brain areas, as well as to generalize across conditions, remain critical gaps in the field. To tackle these challenges, we introduce a novel and generalizable framework: NeuroBOLT, i.e., Neuro-to-BOLD Transformer, which leverages multi-dimensional representation learning from temporal, spatial, and spectral domains to translate raw EEG data to the corresponding fMRI activity signals across the brain. Our experiments demonstrate that NeuroBOLT effectively reconstructs unseen resting-state fMRI signals from primary sensory, high-level cognitive areas, and deep subcortical brain regions, achieving state-of-the-art accuracy with the potential to generalize across varying conditions and sites, which significantly advances the integration of these two modalities.

Seeing is believing, however, the underlying mechanism of how human visual perceptions are intertwined with our cognitions is still a mystery. Thanks to the recent advances in both neuroscience and artificial intelligence, we have been able to record the visually evoked brain activities and mimic the visual perception ability through computational approaches. In this paper, we pay attention to visual stimuli reconstruction by reconstructing the observed images based on portably accessible brain signals, i.e., electroencephalography (EEG) data. Since EEG signals are dynamic in the time-series format and are notorious to be noisy, processing and extracting useful information requires more dedicated efforts; In this paper, we propose a comprehensive pipeline, named NeuroImagen, for reconstructing visual stimuli images from EEG signals. Specifically, we incorporate a novel multi-level perceptual information decoding to draw multi-grained outputs from the given EEG data. A latent diffusion model will then leverage the extracted information to reconstruct the high-resolution visual stimuli images. The experimental results have illustrated the effectiveness of image reconstruction and superior quantitative performance of our proposed method.

Neural electrical activity is fundamental to brain function, underlying a range of cognitive and behavioral processes, including movement, perception, decision-making, and consciousness. Abnormal patterns of neural signaling often indicate the presence of underlying brain diseases. The variability among individuals, the diverse array of clinical symptoms from various brain disorders, and the limited availability of diagnostic classifications, have posed significant barriers to formulating reliable model of neural signals for diverse application contexts. Here, we present BrainWave, the first foundation model for both invasive and non-invasive neural recordings, pretrained on more than 40,000 hours of electrical brain recordings (13.79 TB of data) from approximately 16,000 individuals. Our analysis show that BrainWave outperforms all other competing models and consistently achieves state-of-the-art performance in the diagnosis and identification of neurological disorders. We also demonstrate robust capabilities of BrainWave in enabling zero-shot transfer learning across varying recording conditions and brain diseases, as well as few-shot classification without fine-tuning, suggesting that BrainWave learns highly generalizable representations of neural signals. We hence believe that open-sourcing BrainWave will facilitate a wide range of clinical applications in medicine, paving the way for AI-driven approaches to investigate brain disorders and advance neuroscience research.

Scalp electroencephalography (EEG) and intracranial EEG (iEEG) are vital for epilepsy diagnosis and treatment. Their unified analysis offers the potential to harness the complementary strengths of each modality but is challenging due to variations in recording montages, amplitude and signal-to-noise ratio (SNR), and frequency components. To address the aforementioned challenges, this paper introduces EpiNT, a novel Transformer-based pre-trained model for unified EEG and iEEG analysis. EpiNT employs channel-independent modeling with masked autoencoders (MAE) and vector quantization (VQ), along with a frequency domain mapping quantizer to capture crucial frequency features. Pre-trained on over 2,700 hours of multi-modal clinical neurophysiological data from 1,199 patients, EpiNT outperformed both randomly initialized models and other pre-trained methods on six downstream classification tasks, demonstrating robust representation learning capabilities. This work presents a promising approach for unified epilepsy neurophysiology analysis.

Intracranial recordings have opened a unique opportunity to simultaneously measure activity across multiregional networks in the human brain. Recent works have focused on developing transformer-based neurofoundation models of such recordings that can generalize across subjects and datasets. However, these recordings exhibit highly complex spatiotemporal interactions across diverse spatial scales, from the single-channel scale to the scale of brain regions. As such, there remain critical open questions regarding how best to encode spatial information and how to design self-supervision tasks that enable the learning of brain network patterns and enhance downstream decoding performance using such high-dimensional, multiregional recordings. To allow for exploring these questions, we propose a new spatiotemporal transformer model of multiregional neural activity and a corresponding self-supervised masked latent reconstruction task, designed to enable flexibility in the spatial scale used for token encoding and masking. Applying this model on publicly available multiregional intracranial electrophysiology (iEEG) data, we demonstrate that adjusting the spatial scale for both token encoding and masked reconstruction significantly impacts downstream decoding. Further, we find that spatial encoding at larger scales than channel-level encoding, which is commonly used in existing iEEG transformer models, improves downstream decoding performance. Finally, we demonstrate that our method allows for region-level token encoding while also maintaining accurate channel-level neural reconstruction. Taken together, our modeling framework enables exploration of the spatial scales used for token encoding and masking, reveals their importance towards self-supervised pretraining of neurofoundation models of multiregional human brain activity, and enhances downstream decoding performance.

Event-related potential (ERP), a specialized paradigm of electroencephalographic (EEG), reflects neurological responses to external stimuli or events, generally associated with the brain's processing of specific cognitive tasks. ERP plays a critical role in cognitive analysis, the detection of neurological diseases, and the assessment of psychological states. Recent years have seen substantial advances in deep learning-based methods for spontaneous EEG and other non-time-locked task-related EEG signals. However, their effectiveness on ERP data remains underexplored, and many existing ERP studies still rely heavily on manually extracted features. In this paper, we conduct a comprehensive benchmark study that systematically compares traditional manual features (followed by a linear classifier), deep learning models, and pre-trained EEG foundation models for ERP analysis. We establish a unified data preprocessing and training pipeline and evaluate these approaches on two representative tasks, ERP stimulus classification and ERP-based brain disease detection, across 12 publicly available datasets. Furthermore, we investigate various patch-embedding strategies within advanced Transformer architectures to identify embedding designs that better suit ERP data. Our study provides a landmark framework to guide method selection and tailored model design for future ERP analysis. The code is available at https://github.com/DL4mHealth/ERP-Benchmark.

Intracranial EEG (iEEG) provides direct, millisecond-scale recordings of human neural activity, but reusable representation learning is difficult because electrode layouts, anatomical coverage, referencing schemes, and recording conditions vary across patients and centers. We introduce DIVER-1, a self-supervised iEEG foundation model for variable-input recordings that combines any-variate electrode-time attention, spatio-temporal resampling, input-conditioned positional embeddings, and multi-domain masked reconstruction without assuming a fixed electrode montage. We pretrain two variants, DIVER-1-0.1s and DIVER-1-1s, on 5,310 hours of ECoG and SEEG spanning 352k channel-hours, roughly 54x the BrainTreeBank-based pretraining volume. We evaluate DIVER-1 on two held-out benchmarks: Neuroprobe for naturalistic cognitive decoding and MAYO for seizure detection. On leakage-aware Neuroprobe, DIVER-1-0.1s outperforms prior evaluated iEEG foundation models despite using no BrainTreeBank recordings, the corpus underlying Neuroprobe, during pretraining; it also exceeds the linear spectrogram decoder in mean AUROC and remains competitive with stronger nonlinear baselines, a level prior evaluated iEEG foundation models did not reach. DIVER-1-1s also achieves the top AUROC on MAYO seizure detection. Finally, we conduct, to our knowledge, the first controlled compute-aware scaling study for self-supervised iEEG pretraining, sweeping data scale, subject count, training duration, and model size up to 1.8B parameters. Our results indicate a data-constrained regime: expanding unique recordings and training sufficiently long are more reliable scaling axes than increasing parameter count alone. Code is available at link.

Multimodal functional neuroimaging enables systematic analysis of brain mechanisms and provides discriminative representations for brain-computer interface (BCI) decoding. However, its acquisition is constrained by high costs and feasibility limitations. Moreover, underrepresentation of specific groups undermines fairness of BCI decoding model. To address these challenges, we propose a unified representation framework for multimodal functional neuroimaging via generative artificial intelligence (AI). By mapping multimodal functional neuroimaging into a unified representation space, the proposed framework is capable of generating data for acquisition-constrained modalities and underrepresented groups. Experiments show that the framework can generate data consistent with real brain activity patterns, provide insights into brain mechanisms, and improve performance on downstream tasks. More importantly, it can enhance model fairness by augmenting data for underrepresented groups. Overall, the framework offers a new paradigm for decreasing the cost of acquiring multimodal functional neuroimages and enhancing the fairness of BCI decoding models.

Exploring brain activity in relation to visual perception provides insights into the biological representation of the world. While functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG) have enabled effective image classification and reconstruction, their high cost and bulk limit practical use. Electroencephalography (EEG), by contrast, offers low cost and excellent temporal resolution, but its potential has been limited by the scarcity of large, high-quality datasets and by block-design experiments that introduce temporal confounds. To fill this gap, we present CrossPT-EEG, a benchmark for cross-participant and cross-time generalization of visual decoding from EEG. We collected EEG data from 16 participants while they viewed 4,000 images sampled from ImageNet, with image stimuli annotated at multiple levels of granularity. Our design includes two stages separated in time to allow cross-time generalization and avoid block-design artifacts. We also introduce benchmarks tailored to non-block design classification, as well as pre-training experiments to assess cross-time and cross-participant generalization. These findings highlight the dataset's potential to enhance EEG-based visual brain-computer interfaces, deepen our understanding of visual perception in biological systems, and suggest promising applications for improving machine vision models.

Electroencephalography (EEG) signals, known for convenient non-invasive acquisition but low signal-to-noise ratio, have recently gained substantial attention due to the potential to decode natural images. This paper presents a self-supervised framework to demonstrate the feasibility of learning image representations from EEG signals, particularly for object recognition. The framework utilizes image and EEG encoders to extract features from paired image stimuli and EEG responses. Contrastive learning aligns these two modalities by constraining their similarity. With the framework, we attain significantly above-chance results on a comprehensive EEG-image dataset, achieving a top-1 accuracy of 15.6% and a top-5 accuracy of 42.8% in challenging 200-way zero-shot tasks. Moreover, we perform extensive experiments to explore the biological plausibility by resolving the temporal, spatial, spectral, and semantic aspects of EEG signals. Besides, we introduce attention modules to capture spatial correlations, providing implicit evidence of the brain activity perceived from EEG data. These findings yield valuable insights for neural decoding and brain-computer interfaces in real-world scenarios. The code will be released on https://github.com/eeyhsong/NICE-EEG.

We present a new large-scale electroencephalography (EEG) dataset as part of the THINGS initiative, comprising over 1.6 million visual stimulus trials collected from 20 participants, and totaling more than twice the size of the most popular current benchmark dataset, THINGS-EEG2. Crucially, our data was recorded using a 32-channel consumer-grade wet electrode system costing ~$2.2k, around 27x cheaper than research-grade EEG systems typically used in cognitive neuroscience labs. Our work is one of the first open-source, large-scale EEG resource designed to closely reflect the quality of hardware that is practical to deploy in real-world, downstream applications of brain-computer interfaces (BCIs). We aim to explore the specific question of whether deep neural network-based BCI research and semantic decoding methods can be effectively conducted with such affordable systems, filling an important gap in current literature that is extremely relevant for future research. In our analysis, we not only demonstrate that decoding of high-level semantic information from EEG of visualized images is possible at consumer-grade hardware, but also that our data can facilitate effective EEG-to-Image reconstruction even despite significantly lower signal-to-noise ratios. In addition to traditional benchmarks, we also conduct analyses of EEG-to-Image models that demonstrate log-linear decoding performance with increasing data volume on our data, and discuss the trade-offs between hardware cost, signal fidelity, and the scale of data collection efforts in increasing the size and utility of currently available datasets. Our contributions aim to pave the way for large-scale, cost-effective EEG research with widely accessible equipment, and position our dataset as a unique resource for the democratization and development of effective deep neural models of visual cognition.

In the past five years, the use of generative and foundational AI systems has greatly improved the decoding of brain activity. Visual perception, in particular, can now be decoded from functional Magnetic Resonance Imaging (fMRI) with remarkable fidelity. This neuroimaging technique, however, suffers from a limited temporal resolution (approx0.5 Hz) and thus fundamentally constrains its real-time usage. Here, we propose an alternative approach based on magnetoencephalography (MEG), a neuroimaging device capable of measuring brain activity with high temporal resolution (approx5,000 Hz). For this, we develop an MEG decoding model trained with both contrastive and regression objectives and consisting of three modules: i) pretrained embeddings obtained from the image, ii) an MEG module trained end-to-end and iii) a pretrained image generator. Our results are threefold: Firstly, our MEG decoder shows a 7X improvement of image-retrieval over classic linear decoders. Second, late brain responses to images are best decoded with DINOv2, a recent foundational image model. Third, image retrievals and generations both suggest that high-level visual features can be decoded from MEG signals, although the same approach applied to 7T fMRI also recovers better low-level features. Overall, these results, while preliminary, provide an important step towards the decoding -- in real-time -- of the visual processes continuously unfolding within the human brain.

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

Electroencephalography (EEG) provides a non-invasive, highly accessible, and cost-effective approach for detecting Alzheimer's disease (AD). However, existing methods, whether based on handcrafted feature engineering or standard deep learning, face three major challenges: 1) the lack of large-scale EEG-based AD datasets for robust representation learning and evaluation; 2) limited cross-subject generalizability; and 3) difficulty in adapting to highly heterogeneous data. To address these challenges, we curate the world's largest EEG-AD corpus to date, comprising 2,238 subjects. Leveraging this unique resource, we propose LEAD, the first foundation model for EEG-based AD detection. Specifically, we design a gated temporal-spatial Transformer that can adapt to EEG recordings with diverse lengths, channel configurations, and sampling rates. In addition, we introduce a subject-regularized training strategy to enhance end-to-end subject-level detection. We further employ medical contrastive learning to pre-train on 13 datasets, including 4 AD datasets and 9 non-AD neurological disorder datasets, and fine-tune/test the model on the other 5 AD datasets. LEAD achieves the best average ranking across all 20 evaluations on 5 downstream datasets, substantially outperforming existing approaches, including state-of-the-art (SOTA) EEG foundation models. These results strongly demonstrate the effectiveness of our proposed method and significant progress for EEG-based AD detection. Source code: https://github.com/DL4mHealth/LEAD

Magnetic resonance imaging (MRI) is a crucial tool to identify brain abnormalities in a wide range of neurological disorders. In focal epilepsy MRI is used to identify structural cerebral abnormalities. For covert lesions, machine learning and artificial intelligence algorithms may improve lesion detection if abnormalities are not evident on visual inspection. The success of this approach depends on the volume and quality of training data. Herein, we release an open-source dataset of preprocessed MRI scans from 442 individuals with drug-refractory focal epilepsy who had neurosurgical resections, and detailed demographic information. The MRI scan data includes the preoperative 3D T1 and where available 3D FLAIR, as well as a manually inspected complete surface reconstruction and volumetric parcellations. Demographic information includes age, sex, age of onset of epilepsy, location of surgery, histopathology of resected specimen, occurrence and frequency of focal seizures with and without impairment of awareness, focal to bilateral tonic-clonic seizures, number of anti-seizure medications (ASMs) at time of surgery, and a total of 1764 patient years of post-surgical follow up. Crucially, we also include resection masks delineated from post-surgical imaging. To demonstrate the veracity of our data, we successfully replicated previous studies showing long-term outcomes of seizure freedom in the range of around 50%. Our imaging data replicates findings of group level atrophy in patients compared to controls. Resection locations in the cohort were predominantly in the temporal and frontal lobes. We envisage our dataset, shared openly with the community, will catalyse the development and application of computational methods in clinical neurology.

Electroencephalography (EEG) analysis extends beyond assigning predefined labels to recordings; it requires workflows connecting natural-language instructions, signal processing, quantitative evidence, and scientific interpretation. We term this capability comprehensive EEG understanding. Existing evaluations, however, primarily target isolated decoding tasks or system-specific demonstrations, leaving the competence of large language models (LLMs) insufficiently quantified. We introduce , a unified benchmark for comprehensive, instruction-conditioned EEG understanding. It comprises four subsets---Foundational Analysis, Sleep Assessment, Neurocognitive Assessment, and Physiological Integration---covering 17 datasets, tasks, and over real-data instances. Given an instruction and EEG recordings with optional physiological signals, a system must perform the analysis and produce a scientifically grounded report and, when required, artifacts. Outputs are assessed through numerical, categorical, set, sequence, semantic, and artifact validation. We evaluate representative LLMs across more than 100K executions under two paradigms: autonomous code execution with CodeAct and structured agentic analysis with BrainAgent. Results vary substantially across models, subsets, difficulty levels, and execution paradigms, showing that EEG competence depends on the model and its operationalization. provides a reproducible testbed for advancing LLM-based EEG understanding. The code and benchmark will be released soon, with evaluation results continuously updated.

Brain-computer interfaces (BCIs) decode neural activity to restore lost function. Typically, training a high-performance neural decoder requires a large labeled dataset to be collected from every new subject. One way to reduce the labeled data cost is self-supervised pretraining, which learns general neural representations from unlabeled recordings that accumulate across subjects. However, for intracranial electroencephalography (iEEG) recordings, self-supervised learning has been challenging due to differences in contact placement and neuroanatomy between subjects. We propose MAPA, an otherwise vanilla masked autoencoder with two spatial encodings, an anatomical region embedding and a relative positional encoding, which together enable it to learn neural representations that transfer to unseen subjects and across various tasks. MAPA sets a new state of the art across all three regimes of the Neuroprobe benchmark without fine-tuning: within-session, cross-session, and cross-subject. In the cross-subject regime, a linear probe on MAPA's features needs only {sim}164 labeled trials to reach the accuracy that takes 3,500 without pretraining. Our results show that self-supervised pretraining can scale across heterogeneous iEEG recordings and reduce the labeled data needed for accurate decoding in new subjects.

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.

Invasive brain-computer interfaces have garnered significant attention due to their high performance. The current intracranial stereoElectroEncephaloGraphy (sEEG) foundation models typically build univariate representations based on a single channel. Some of them further use Transformer to model the relationship among channels. However, due to the locality and specificity of brain computation, their performance on more difficult tasks, e.g., speech decoding, which demands intricate processing in specific brain regions, is yet to be fully investigated. We hypothesize that building multi-variate representations within certain brain regions can better capture the specific neural processing. To explore this hypothesis, we collect a well-annotated Chinese word-reading sEEG dataset, targeting language-related brain networks, over 12 subjects. Leveraging this benchmark dataset, we developed the Du-IN model that can extract contextual embeddings from specific brain regions through discrete codebook-guided mask modeling. Our model achieves SOTA performance on the downstream 61-word classification task, surpassing all baseline models. Model comparison and ablation analysis reveal that our design choices, including (i) multi-variate representation by fusing channels in vSMC and STG regions and (ii) self-supervision by discrete codebook-guided mask modeling, significantly contribute to these performances. Collectively, our approach, inspired by neuroscience findings, capitalizing on multi-variate neural representation from specific brain regions, is suitable for invasive brain modeling. It marks a promising neuro-inspired AI approach in BCI.

As the prevalence of Alzheimer's disease (AD) rises, improving mechanistic insight from non-invasive biomarkers is increasingly critical. Recent work suggests that circuit-level brain alterations manifest as changes in electroencephalography (EEG) spectral features detectable by machine learning. However, conventional deep learning approaches for EEG-based AD detection are computationally intensive and mechanistically opaque. Spiking neural networks (SNNs) offer a biologically plausible and energy-efficient alternative, yet their application to AD diagnosis remains largely unexplored. We propose a neuro-bridge framework that links data-driven learning with minimal, biophysically grounded simulations, enabling bidirectional interpretation between machine learning signatures and circuit-level mechanisms in AD. Using resting-state clinical EEG, we train an SNN classifier that achieves competitive performance (AUC = 0.839) and identifies the aperiodic 1/f slope as a key discriminative marker. The 1/f slope reflects excitation-inhibition balance. To interpret this mechanistically, we construct spiking network simulations in which inhibitory-to-excitatory synaptic ratios are systematically varied to emulate healthy, mild cognitive impairment, and AD-like states. Using both membrane potential-based and synaptic current-based EEG proxies, we reproduce empirical spectral slowing and altered alpha organization. Incorporating empirical functional connectivity priors into multi-subnetwork simulations further enhances spectral differentiation, demonstrating that large-scale network topology constrains EEG signatures more strongly than excitation-inhibition balance alone. Overall, this neuro-bridge approach connects SNN-based classification with interpretable circuit simulations, advancing mechanistic understanding of EEG biomarkers while enabling scalable, explainable AD detection.

In the pursuit to understand the intricacies of human brain's visual processing, reconstructing dynamic visual experiences from brain activities emerges as a challenging yet fascinating endeavor. While recent advancements have achieved success in reconstructing static images from non-invasive brain recordings, the domain of translating continuous brain activities into video format remains underexplored. In this work, we introduce NeuroCine, a novel dual-phase framework to targeting the inherent challenges of decoding fMRI data, such as noises, spatial redundancy and temporal lags. This framework proposes spatial masking and temporal interpolation-based augmentation for contrastive learning fMRI representations and a diffusion model enhanced by dependent prior noise for video generation. Tested on a publicly available fMRI dataset, our method shows promising results, outperforming the previous state-of-the-art models by a notable margin of {20.97%}, {31.00%} and {12.30%} respectively on decoding the brain activities of three subjects in the fMRI dataset, as measured by SSIM. Additionally, our attention analysis suggests that the model aligns with existing brain structures and functions, indicating its biological plausibility and interpretability.

Large language models (LLMs) can make scientific software easier to use. However, a general model does not automatically know which measurements a particular sensor can support, which algorithms are implemented in the current software, or which conclusions are justified by a computed result. These distinctions are especially important for low-channel electroencephalography (EEG), where sparse spatial coverage and variable signal quality make plausible but unsupported interpretations easy to produce. We present NeuraDock Agent, an open-source architecture that separates a deterministic local EEG engine from a hardware-aware language layer. The numerical engine parses recordings, performs quality control, executes reviewed spectral workflows, and writes machine-readable artifacts. The LLM receives only a compact, allowlisted summary and a versioned context pack. The context describes the seven-channel hardware, reviewed workflows, result fields, implementation boundaries, scientific limits, and reference cases. Raw EEG and dense per-sample arrays remain local We evaluate the system at three levels. First, 12 recordings produced identical structured results over ten numerical repetitions, and a complete Rest/Task run produced identical result, report, and figure hashes over three repetitions. Second, request-capture and failure-injection experiments confirmed the tested data boundary and preservation of local artifacts under HTTP, malformed-output, and connection failures. Third, a boundary-awareness benchmark tested 36 ordinary and adversarial questions under four context ablations and two LLMs, yielding 288 outputs.These results support hardware- and implementation-aware grounding as a practical mechanism for calibrating what an EEG agent accepts, qualifies, or refuses; they do not establish clinical validity or a validated absolute cognitive-load index.

Brain computer interfaces (BCI) enable direct communication with a computer, using neural activity as the control signal. This neural signal is generally chosen from a variety of well-studied electroencephalogram (EEG) signals. For a given BCI paradigm, feature extractors and classifiers are tailored to the distinct characteristics of its expected EEG control signal, limiting its application to that specific signal. Convolutional Neural Networks (CNNs), which have been used in computer vision and speech recognition, have successfully been applied to EEG-based BCIs; however, they have mainly been applied to single BCI paradigms and thus it remains unclear how these architectures generalize to other paradigms. Here, we ask if we can design a single CNN architecture to accurately classify EEG signals from different BCI paradigms, while simultaneously being as compact as possible. In this work we introduce EEGNet, a compact convolutional network for EEG-based BCIs. We introduce the use of depthwise and separable convolutions to construct an EEG-specific model which encapsulates well-known EEG feature extraction concepts for BCI. We compare EEGNet to current state-of-the-art approaches across four BCI paradigms: P300 visual-evoked potentials, error-related negativity responses (ERN), movement-related cortical potentials (MRCP), and sensory motor rhythms (SMR). We show that EEGNet generalizes across paradigms better than the reference algorithms when only limited training data is available. We demonstrate three different approaches to visualize the contents of a trained EEGNet model to enable interpretation of the learned features. Our results suggest that EEGNet is robust enough to learn a wide variety of interpretable features over a range of BCI tasks, suggesting that the observed performances were not due to artifact or noise sources in the data.

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.

Understanding how the brain represents visual information is a fundamental challenge in neuroscience and artificial intelligence. While AI-driven decoding of neural data has provided insights into the human visual system, integrating multimodal neuroimaging signals, such as EEG, MEG, and fMRI, remains a critical hurdle due to their inherent spatiotemporal misalignment. Current approaches often analyze these modalities in isolation, limiting a holistic view of neural representation. In this study, we introduce BrainFLORA, a unified framework for integrating cross-modal neuroimaging data to construct a shared neural representation. Our approach leverages multimodal large language models (MLLMs) augmented with modality-specific adapters and task decoders, achieving state-of-the-art performance in joint-subject visual retrieval task and has the potential to extend multitasking. Combining neuroimaging analysis methods, we further reveal how visual concept representations align across neural modalities and with real world object perception. We demonstrate that the brain's structured visual concept representations exhibit an implicit mapping to physical-world stimuli, bridging neuroscience and machine learning from different modalities of neural imaging. Beyond methodological advancements, BrainFLORA offers novel implications for cognitive neuroscience and brain-computer interfaces (BCIs). Our code is available at https://github.com/ncclab-sustech/BrainFLORA.

Neuroimaging is a ubiquitous tool for evaluating patients with neurological diseases. The global demand for magnetic resonance imaging (MRI) studies has risen steadily, placing significant strain on health systems, prolonging turnaround times, and intensifying physician burnout. These challenges disproportionately impact patients in low-resource and rural settings. Here, we utilized a large academic health system as a data engine to develop Prima, the first vision language model (VLM) serving as an AI foundation for neuroimaging that supports real-world, clinical MRI studies as input. Trained on over 220,000 MRI studies, Prima uses a hierarchical vision architecture that provides general and transferable MRI features. Prima was tested in a 1-year health system-wide study that included 30K MRI studies. Across 52 radiologic diagnoses from the major neurologic disorders, including neoplastic, inflammatory, infectious, and developmental lesions, Prima achieved a mean diagnostic area under the ROC curve of 92.0, outperforming other state-of-the-art general and medical AI models. Prima offers explainable differential diagnoses, worklist priority for radiologists, and clinical referral recommendations across diverse patient demographics and MRI systems. Prima demonstrates algorithmic fairness across sensitive groups and can help mitigate health system biases, such as prolonged turnaround times for low-resource populations. These findings highlight the transformative potential of health system-scale VLMs and Prima's role in advancing AI-driven healthcare.

Deciphering brain function through non-invasive recordings requires synthesizing complementary high-frequency electromagnetic (EEG/MEG) and low-frequency metabolic (fMRI) signals. However, despite their shared neural origins, extreme discrepancies have traditionally confined these modalities to isolated analysis pipelines, hindering a holistic interpretation of brain activity. To bridge this fragmentation, we introduce NOBEL, a neuro-omni-modal brain-encoding large language model (LLM) that unifies these heterogeneous signals within the LLM's semantic embedding space. Our architecture integrates a unified encoder for EEG and MEG with a novel dual-path strategy for fMRI, aligning non-invasive brain signals and external sensory stimuli into a shared token space, then leverages an LLM as a universal backbone. Extensive evaluations demonstrate that NOBEL serves as a robust generalist across standard single-modal tasks. We also show that the synergistic fusion of electromagnetic and metabolic signals yields higher decoding accuracy than unimodal baselines, validating the complementary nature of multiple neural modalities. Furthermore, NOBEL exhibits strong capabilities in stimulus-aware decoding, effectively interpreting visual semantics from multi-subject fMRI data on the NSD and HAD datasets while uniquely leveraging direct stimulus inputs to verify causal links between sensory signals and neural responses. NOBEL thus takes a step towards unifying non-invasive brain decoding, demonstrating the promising potential of omni-modal brain understanding.

Neurophysiological recordings such as electroencephalography (EEG) offer accessible and minimally invasive means of estimating physiological activity for applications in healthcare, diagnostic screening, and even immersive entertainment. However, these recordings yield high-dimensional, noisy time-series data that typically require extensive pre-processing and handcrafted feature extraction to reveal meaningful information. Recently, there has been a surge of interest in applying representation learning techniques from large pre-trained (foundation) models to effectively decode and interpret biosignals. We discuss the challenges posed for incorporating such methods and introduce BioCodec, an alternative representation learning framework inspired by neural codecs to capture low-level signal characteristics in the form of discrete tokens. Pre-trained on thousands of EEG hours, BioCodec shows efficacy across multiple downstream tasks, ranging from clinical diagnostic tasks and sleep physiology to decoding speech and motor imagery, particularly in low-resource settings. Additionally, we provide a qualitative analysis of codebook usage and estimate the spatial coherence of codebook embeddings from EEG connectivity. Notably, we also document the suitability of our method to other biosignal data, i.e., electromyographic (EMG) signals. Overall, the proposed approach provides a versatile solution for biosignal tokenization that performs competitively with state-of-the-art models. The source code and model checkpoints are shared.

How to decode human vision through neural signals has attracted a long-standing interest in neuroscience and machine learning. Modern contrastive learning and generative models improved the performance of fMRI-based visual decoding and reconstruction. However, the high cost and low temporal resolution of fMRI limit their applications in brain-computer interfaces (BCIs), prompting a high need for EEG-based visual reconstruction. In this study, we present an EEG-based visual reconstruction framework. It consists of a plug-and-play EEG encoder called the Adaptive Thinking Mapper (ATM), which is aligned with image embeddings, and a two-stage EEG guidance image generator that first transforms EEG features into image priors and then reconstructs the visual stimuli with a pre-trained image generator. Our approach allows EEG embeddings to achieve superior performance in image classification and retrieval tasks. Our two-stage image generation strategy vividly reconstructs images seen by humans. Furthermore, we analyzed the impact of signals from different time windows and brain regions on decoding and reconstruction. The versatility of our framework is demonstrated in the magnetoencephalogram (MEG) data modality. We report that EEG-based visual decoding achieves SOTA performance, highlighting the portability, low cost, and high temporal resolution of EEG, enabling a wide range of BCI applications. The code of ATM is available at https://github.com/dongyangli-del/EEG_Image_decode.

Recent fMRI-to-image approaches mainly focused on associating fMRI signals with specific conditions of pre-trained diffusion models. These approaches, while producing high-quality images, capture only a limited aspect of the complex information in fMRI signals and offer little detailed control over image creation. In contrast, this paper proposes to directly modulate the generation process of diffusion models using fMRI signals. Our approach, NeuroPictor, divides the fMRI-to-image process into three steps: i) fMRI calibrated-encoding, to tackle multi-individual pre-training for a shared latent space to minimize individual difference and enable the subsequent cross-subject training; ii) fMRI-to-image cross-subject pre-training, perceptually learning to guide diffusion model with high- and low-level conditions across different individuals; iii) fMRI-to-image single-subject refining, similar with step ii but focus on adapting to particular individual. NeuroPictor extracts high-level semantic features from fMRI signals that characterizing the visual stimulus and incrementally fine-tunes the diffusion model with a low-level manipulation network to provide precise structural instructions. By training with over 60,000 fMRI-image pairs from various individuals, our model enjoys superior fMRI-to-image decoding capacity, particularly in the within-subject setting, as evidenced in benchmark datasets. Project page: https://jingyanghuo.github.io/neuropictor/.

In this paper, we introduce CineBrain, the first large-scale dataset featuring simultaneous EEG and fMRI recordings during dynamic audiovisual stimulation. Recognizing the complementary strengths of EEG's high temporal resolution and fMRI's deep-brain spatial coverage, CineBrain provides approximately six hours of narrative-driven content from the popular television series The Big Bang Theory for each of six participants. Building upon this unique dataset, we propose CineSync, an innovative multimodal decoding framework integrates a Multi-Modal Fusion Encoder with a diffusion-based Neural Latent Decoder. Our approach effectively fuses EEG and fMRI signals, significantly improving the reconstruction quality of complex audiovisual stimuli. To facilitate rigorous evaluation, we introduce Cine-Benchmark, a comprehensive evaluation protocol that assesses reconstructions across semantic and perceptual dimensions. Experimental results demonstrate that CineSync achieves state-of-the-art video reconstruction performance and highlight our initial success in combining fMRI and EEG for reconstructing both video and audio stimuli. Project Page: https://jianxgao.github.io/CineBrain.

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

Electroencephalography (EEG) and magnetoencephalography (MEG) measure neural activity non-invasively by capturing electromagnetic fields generated by dendritic currents. Although rooted in the same biophysics, EEG and MEG exhibit distinct signal patterns, further complicated by variations in sensor configurations across modalities and recording devices. Existing approaches typically rely on separate, modality- and dataset-specific models, which limits the performance and cross-domain scalability. This paper proposes BrainOmni, the first brain foundation model that generalises across heterogeneous EEG and MEG recordings. To unify diverse data sources, we introduce BrainTokenizer,the first tokenizer that quantises spatiotemporal brain activity into discrete representations. Central to BrainTokenizer is a novel Sensor Encoder that encodes sensor properties such as spatial layout, orientation, and type, enabling compatibility across devices and modalities. Building upon the discrete representations, BrainOmni learns unified semantic embeddings of brain signals by self-supervised pretraining. To the best of our knowledge, it is the first foundation model to support both EEG and MEG signals, as well as the first to incorporate large-scale MEG pretraining. A total of 1,997 hours of EEG and 656 hours of MEG data are curated and standardised from publicly available sources for pretraining. Experiments show that BrainOmni outperforms both existing foundation models and state-of-the-art task-specific models on a range of downstream tasks. It also demonstrates strong generalisation to unseen EEG and MEG devices. Further analysis reveals that joint EEG-MEG (EMEG) training yields consistent improvements across both modalities. Code and model checkpoints will be released upon acceptance.

Electroencephalography (EEG)-based brain-computer interfaces (BCIs) enable neural interaction by decoding brain activity for external communication. Motor imagery (MI) decoding has received significant attention due to its intuitive mechanism. However, most existing models rely on single-stream architectures and overlook the multi-view nature of EEG signals, leading to limited performance and generalization. We propose a multi-view contrastive network (MVCNet), a dual-branch architecture that parallelly integrates CNN and Transformer models to capture both local spatial-temporal features and global temporal dependencies. To enhance the informativeness of training data, MVCNet incorporates a unified augmentation pipeline across time, frequency, and spatial domains. Two contrastive modules are further introduced: a cross-view contrastive module that enforces consistency of original and augmented views, and a cross-model contrastive module that aligns features extracted from both branches. Final representations are fused and jointly optimized by contrastive and classification losses. Experiments on five public MI datasets across three scenarios demonstrate that MVCNet consistently outperforms seven state-of-the-art MI decoding networks, highlighting its effectiveness and generalization ability. MVCNet provides a robust solution for MI decoding by integrating multi-view information and dual-branch modeling, contributing to the development of more reliable BCI systems.

Electroencephalography (EEG) enables non-invasive monitoring of brain activity across clinical and neurotechnology applications, yet building foundation models for EEG remains challenging due to differing electrode topologies and computational scalability, as Transformer architectures incur quadratic sequence complexity. As a joint solution, we propose LuMamba (Latent Unified Mamba), a self-supervised framework combining topology-invariant encodings with linear-complexity state-space modeling, using LUNA's learned-query cross-attention mechanism for channel unification~luna, and FEMBA's bidirectional Mamba blocks for efficient temporal modeling~femba. Within this architecture, we provide the first systematic investigation of the Latent-Euclidean Joint-Embedding Predictive Architecture (LeJEPA) for biosignal learning. Pre-trained on over 21,000 hours of unlabeled EEG from the TUEG corpus, LuMamba is evaluated on five downstream tasks spanning abnormality detection, artifact recognition, and mental condition classification across electrode configurations ranging from 16 to 26 channels. In the pre-training objective, masked reconstruction alone yields structured but less generalizable representations, while LeJEPA alone produces diffuse embeddings; combining both objectives achieves the most robust performance. With only 4.6M parameters, LuMamba attains 80.99\% balanced accuracy on TUAB and achieves state-of-art performance on Alzheimer's detection (0.97 AUPR), while requiring 377times fewer FLOPS than state-of-art models at equivalent sequence lengths and scaling to 12times longer sequences before reaching typical GPU memory limits. Code is available at https://github.com/pulp-bio/biofoundation

Deciphering the intricacies of the human brain has captivated curiosity for centuries. Recent strides in Brain-Computer Interface (BCI) technology, particularly using motor imagery, have restored motor functions such as reaching, grasping, and walking in paralyzed individuals. However, unraveling natural language from brain signals remains a formidable challenge. Electroencephalography (EEG) is a non-invasive technique used to record electrical activity in the brain by placing electrodes on the scalp. Previous studies of EEG-to-text decoding have achieved high accuracy on small closed vocabularies, but still fall short of high accuracy when dealing with large open vocabularies. We propose a novel method, EEG2TEXT, to improve the accuracy of open vocabulary EEG-to-text decoding. Specifically, EEG2TEXT leverages EEG pre-training to enhance the learning of semantics from EEG signals and proposes a multi-view transformer to model the EEG signal processing by different spatial regions of the brain. Experiments show that EEG2TEXT has superior performance, outperforming the state-of-the-art baseline methods by a large margin of up to 5% in absolute BLEU and ROUGE scores. EEG2TEXT shows great potential for a high-performance open-vocabulary brain-to-text system to facilitate communication.

Electroencephalography (EEG) is a non-invasive technique to measure and record brain electrical activity, widely used in various BCI and healthcare applications. Early EEG decoding methods rely on supervised learning, limited by specific tasks and datasets, hindering model performance and generalizability. With the success of large language models, there is a growing body of studies focusing on EEG foundation models. However, these studies still leave challenges: Firstly, most of existing EEG foundation models employ full EEG modeling strategy. It models the spatial and temporal dependencies between all EEG patches together, but ignores that the spatial and temporal dependencies are heterogeneous due to the unique structural characteristics of EEG signals. Secondly, existing EEG foundation models have limited generalizability on a wide range of downstream BCI tasks due to varying formats of EEG data, making it challenging to adapt to. To address these challenges, we propose a novel foundation model called CBraMod. Specifically, we devise a criss-cross transformer as the backbone to thoroughly leverage the structural characteristics of EEG signals, which can model spatial and temporal dependencies separately through two parallel attention mechanisms. And we utilize an asymmetric conditional positional encoding scheme which can encode positional information of EEG patches and be easily adapted to the EEG with diverse formats. CBraMod is pre-trained on a very large corpus of EEG through patch-based masked EEG reconstruction. We evaluate CBraMod on up to 10 downstream BCI tasks (12 public datasets). CBraMod achieves the state-of-the-art performance across the wide range of tasks, proving its strong capability and generalizability. The source code is publicly available at https://github.com/wjq-learning/CBraMod.

Epilepsy affects over 50 million people worldwide, and one-third of patients suffer drug-resistant seizures where surgery offers the best chance of seizure freedom. Accurate localization of the epileptogenic zone (EZ) relies on intracranial EEG (iEEG). Clinical workflows, however, remain constrained by labor-intensive manual review. At the same time, existing data-driven approaches are typically developed on single-center datasets that are inconsistent in format and metadata, lack standardized benchmarks, and rarely release pathological event annotations, creating barriers to reproducibility, cross-center validation, and clinical relevance. With extensive efforts to reconcile heterogeneous iEEG formats, metadata, and recordings across publicly available sources, we present Omni-iEEG, a large-scale, pre-surgical iEEG resource comprising 302 patients and 178 hours of high-resolution recordings. The dataset includes harmonized clinical metadata such as seizure onset zones, resections, and surgical outcomes, all validated by board-certified epileptologists. In addition, Omni-iEEG provides over 36K expert-validated annotations of pathological events, enabling robust biomarker studies. Omni-iEEG serves as a bridge between machine learning and epilepsy research. It defines clinically meaningful tasks with unified evaluation metrics grounded in clinical priors, enabling systematic evaluation of models in clinically relevant settings. Beyond benchmarking, we demonstrate the potential of end-to-end modeling on long iEEG segments and highlight the transferability of representations pretrained on non-neurophysiological domains. Together, these contributions establish Omni-iEEG as a foundation for reproducible, generalizable, and clinically translatable epilepsy research. The project page with dataset and code links is available at omni-ieeg.github.io/omni-ieeg.

Frontier artificial intelligence (AI) models, such as OpenAI's GPT-5 and Meta's DINOv3, have advanced rapidly through training on internet-scale public data, yet such systems lack access to private clinical data. Neuroimaging, in particular, is underrepresented in the public domain due to identifiable facial features within MRI and CT scans, fundamentally restricting model performance in clinical medicine. Here, we show that frontier models underperform on neuroimaging tasks and that learning directly from uncurated data generated during routine clinical care at health systems, a paradigm we call health system learning, yields high-performance, generalist neuroimaging models. We introduce NeuroVFM, a visual foundation model trained on 5.24 million clinical MRI and CT volumes using a scalable volumetric joint-embedding predictive architecture. NeuroVFM learns comprehensive representations of brain anatomy and pathology, achieving state-of-the-art performance across multiple clinical tasks, including radiologic diagnosis and report generation. The model exhibits emergent neuroanatomic understanding and interpretable visual grounding of diagnostic findings. When paired with open-source language models through lightweight visual instruction tuning, NeuroVFM generates radiology reports that surpass frontier models in accuracy, clinical triage, and expert preference. Through clinically grounded visual understanding, NeuroVFM reduces hallucinated findings and critical errors, offering safer clinical decision support. These results establish health system learning as a paradigm for building generalist medical AI and provide a scalable framework for clinical foundation models.

In neural decoding research, one of the most intriguing topics is the reconstruction of perceived natural images based on fMRI signals. Previous studies have succeeded in re-creating different aspects of the visuals, such as low-level properties (shape, texture, layout) or high-level features (category of objects, descriptive semantics of scenes) but have typically failed to reconstruct these properties together for complex scene images. Generative AI has recently made a leap forward with latent diffusion models capable of generating high-complexity images. Here, we investigate how to take advantage of this innovative technology for brain decoding. We present a two-stage scene reconstruction framework called ``Brain-Diffuser''. In the first stage, starting from fMRI signals, we reconstruct images that capture low-level properties and overall layout using a VDVAE (Very Deep Variational Autoencoder) model. In the second stage, we use the image-to-image framework of a latent diffusion model (Versatile Diffusion) conditioned on predicted multimodal (text and visual) features, to generate final reconstructed images. On the publicly available Natural Scenes Dataset benchmark, our method outperforms previous models both qualitatively and quantitatively. When applied to synthetic fMRI patterns generated from individual ROI (region-of-interest) masks, our trained model creates compelling ``ROI-optimal'' scenes consistent with neuroscientific knowledge. Thus, the proposed methodology can have an impact on both applied (e.g. brain-computer interface) and fundamental neuroscience.

Understanding the hidden mechanisms behind human's visual perception is a fundamental question in neuroscience. To that end, investigating into the neural responses of human mind activities, such as functional Magnetic Resonance Imaging (fMRI), has been a significant research vehicle. However, analyzing fMRI signals is challenging, costly, daunting, and demanding for professional training. Despite remarkable progress in fMRI analysis, existing approaches are limited to generating 2D images and far away from being biologically meaningful and practically useful. Under this insight, we propose to generate visually plausible and functionally more comprehensive 3D outputs decoded from brain signals, enabling more sophisticated modeling of fMRI data. Conceptually, we reformulate this task as a {\em fMRI conditioned 3D object generation} problem. We design a novel 3D object representation learning method, Brain3D, that takes as input the fMRI data of a subject who was presented with a 2D image, and yields as output the corresponding 3D object images. The key capabilities of this model include tackling the noises with high-level semantic signals and a two-stage architecture design for progressive high-level information integration. Extensive experiments validate the superior capability of our model over previous state-of-the-art 3D object generation methods. Importantly, we show that our model captures the distinct functionalities of each region of human vision system as well as their intricate interplay relationships, aligning remarkably with the established discoveries in neuroscience. Further, preliminary evaluations indicate that Brain3D can successfully identify the disordered brain regions in simulated scenarios, such as V1, V2, V3, V4, and the medial temporal lobe (MTL) within the human visual system. Our data and code will be available at https://brain-3d.github.io/.

EEG-to-image evaluation should distinguish visual fidelity from recoverable meaning. Yet EEG-derived reconstructions are blurry, distorted, and low-detail, causing SSIM, LPIPS, and CLIP to penalize semantically recoverable outputs or reward plausible but incorrect ones. We analyze 6,855 ground-truth/reconstruction pairs from ATM, ENIGMA, BrainVis, and DreamDiffusion using semantic probes, caption harshness and blind-spot rates, and controlled degradations. Pixel metrics show near-zero correlation with semantic consistency, while representation metrics conflate perceptual and semantic errors. We therefore introduce a BCI-aware framework in which four VLMs assess image pairs through structured questions, producing Tolerant Perceptual Alignment Scores (T-PAS) and Tolerant Semantic Alignment Scores (T-SAS). Their consensus is distilled into the BCI-Coherence Score (BCS), a compact evaluator achieving a T-PAS MAE of 0.079 (r = 0.700) and a T-SAS MAE of 0.082 (r = 0.850) on our data. Human validation shows highly reliable joint coherence judgments, with Cohen's kappa = 0.882 +/- 0.174 and Krippendorff's alpha = 0.882, supporting perceptual-semantic recoverability over generic visual similarity. Code and resources are available at https://sukt03.github.io/BCS/.

Ablation studies have been widely used in the field of neuroscience to tackle complex biological systems such as the extensively studied Drosophila central nervous system, the vertebrate brain and more interestingly and most delicately, the human brain. In the past, these kinds of studies were utilized to uncover structure and organization in the brain, i.e. a mapping of features inherent to external stimuli onto different areas of the neocortex. considering the growth in size and complexity of state-of-the-art artificial neural networks (ANNs) and the corresponding growth in complexity of the tasks that are tackled by these networks, the question arises whether ablation studies may be used to investigate these networks for a similar organization of their inner representations. In this paper, we address this question and performed two ablation studies in two fundamentally different ANNs to investigate their inner representations of two well-known benchmark datasets from the computer vision domain. We found that features distinct to the local and global structure of the data are selectively represented in specific parts of the network. Furthermore, some of these representations are redundant, awarding the network a certain robustness to structural damages. We further determined the importance of specific parts of the network for the classification task solely based on the weight structure of single units. Finally, we examined the ability of damaged networks to recover from the consequences of ablations by means of recovery training. We argue that ablations studies are a feasible method to investigate knowledge representations in ANNs and are especially helpful to examine a networks robustness to structural damages, a feature of ANNs that will become increasingly important for future safety-critical applications.

Most neuroimaging experiments are under-powered, limited by the number of subjects and cognitive processes that an individual study can investigate. Nonetheless, over decades of research, neuroscience has accumulated an extensive wealth of results. It remains a challenge to digest this growing knowledge base and obtain new insights since existing meta-analytic tools are limited to keyword queries. In this work, we propose Text2Brain, a neural network approach for coordinate-based meta-analysis of neuroimaging studies to synthesize brain activation maps from open-ended text queries. Combining a transformer-based text encoder and a 3D image generator, Text2Brain was trained on variable-length text snippets and their corresponding activation maps sampled from 13,000 published neuroimaging studies. We demonstrate that Text2Brain can synthesize anatomically-plausible neural activation patterns from free-form textual descriptions of cognitive concepts. Text2Brain is available at https://braininterpreter.com as a web-based tool for retrieving established priors and generating new hypotheses for neuroscience research.

Neuroimage processing tasks like segmentation, reconstruction, and registration are central to the study of neuroscience. Robust deep learning strategies and architectures used to solve these tasks are often similar. Yet, when presented with a new task or a dataset with different visual characteristics, practitioners most often need to train a new model, or fine-tune an existing one. This is a time-consuming process that poses a substantial barrier for the thousands of neuroscientists and clinical researchers who often lack the resources or machine-learning expertise to train deep learning models. In practice, this leads to a lack of adoption of deep learning, and neuroscience tools being dominated by classical frameworks. We introduce Neuralizer, a single model that generalizes to previously unseen neuroimaging tasks and modalities without the need for re-training or fine-tuning. Tasks do not have to be known a priori, and generalization happens in a single forward pass during inference. The model can solve processing tasks across multiple image modalities, acquisition methods, and datasets, and generalize to tasks and modalities it has not been trained on. Our experiments on coronal slices show that when few annotated subjects are available, our multi-task network outperforms task-specific baselines without training on the task.

Multi-site neuroimaging analysis is fundamentally confounded by scanner-induced covariate shifts, where the marginal distribution of voxel intensities P(x) varies non-linearly across acquisition protocols while the conditional anatomy P(y|x) remains constant. This is particularly detrimental to radiomic reproducibility, where acquisition variance often exceeds biological pathology variance. Existing statistical harmonization methods (e.g., ComBat) operate in feature space, precluding spatial downstream tasks, while standard deep learning approaches are theoretically bounded by local effective receptive fields (ERF), failing to model the global intensity correlations characteristic of field-strength bias. We propose SA-CycleGAN-2.5D, a domain adaptation framework motivated by the HΔH-divergence bound of Ben-David et al., integrating three architectural innovations: (1) A 2.5D tri-planar manifold injection preserving through-plane gradients nabla_z at O(HW) complexity; (2) A U-ResNet generator with dense voxel-to-voxel self-attention, surpassing the O(L) receptive field limit of CNNs to model global scanner field biases; and (3) A spectrally-normalized discriminator constraining the Lipschitz constant (K_D le 1) for stable adversarial optimization. Evaluated on 654 glioma patients across two institutional domains (BraTS and UPenn-GBM), our method reduces Maximum Mean Discrepancy (MMD) by 99.1% (1.729 to 0.015) and degrades domain classifier accuracy to near-chance (59.7%). Ablation confirms that global attention is statistically essential (Cohen's d = 1.32, p < 0.001) for the harder heterogeneous-to-homogeneous translation direction. By bridging 2D efficiency and 3D consistency, our framework yields voxel-level harmonized images that preserve tumor pathophysiology, enabling reproducible multi-center radiomic analysis.

Neural fields are increasingly used as a light-weight, continuous, and differentiable signal representation in (bio)medical imaging. However, unlike discrete signal representations such as voxel grids, neural fields cannot be easily extended. As neural fields are, in essence, neural networks, prior signals represented in a neural field will degrade when the model is presented with new data due to catastrophic forgetting. This work examines the extent to which different neural field approaches suffer from catastrophic forgetting and proposes a strategy to mitigate this issue. We consider the scenario in which data becomes available incrementally, with only the most recent data available for neural field fitting. In a series of experiments on cardiac cine MRI data, we demonstrate how knowledge distillation mitigates catastrophic forgetting when the spatiotemporal domain is enlarged or the dimensionality of the represented signal is increased. We find that the amount of catastrophic forgetting depends, to a large extent, on the neural fields model used, and that distillation could enable continual learning in neural fields.

Learning EEG representations that generalize across cognitive tasks, subjects, and recording conditions remains a key challenge in electroencephalography (EEG) decoding. Recent advances in foundation models have improved EEG decoding performance, yet a fundamental open question remains: how to effectively interface neural signals with these models to enable multi-task learning across datasets. To investigate this question, we introduce BraVista, a visual-language framework that encodes multichannel EEG signals as structured images and enables multi-task learning through instruction-conditioned vision-language models (VLMs). Our approach relies on continued post-training of a general-domain VLM, leveraging its visual and linguistic priors to adapt to neural signals without a separate large-scale EEG-specific pretraining stage. We evaluate BraVista on four datasets spanning sleep staging, emotion recognition, cognitive workload classification, and abnormal EEG detection, showing strong performance across these tasks. Further analyses show that the choice of EEG-to-image representation is critical to performance. Moreover, through controlled perturbations of the EEG signal, we observe a gradual performance degradation under increasing noise, suggesting that the model relies on EEG-relevant information rather than superficial visual patterns. Together, these findings establish structured visual representations as an effective and scalable interface between neural signals and general-domain foundation models for unified multi-task EEG decoding.

Electroencephalography (EEG) foundation models hold significant promise for universal Brain-Computer Interfaces (BCIs). However, existing approaches often rely on end-to-end fine-tuning and exhibit limited efficacy under frozen-probing protocols, lacking the intrinsic universality required for broad generalization. This limitation stems from adapting general-purpose sequence architectures that overlook the biophysical and dynamical principles of neural activity. To bridge this gap, we propose DeeperBrain, a neuro-grounded foundation model integrating domain-specific inductive biases into its model design and learning objectives. Architecturally, DeeperBrain incorporates a volume conduction-aware channel encoding to model spatial mixing via 3D geometry, and a neurodynamics-aware temporal encoding capturing slow adaptations using oscillatory and exponential bases. For pretraining, we introduce a dual-objective strategy combining Masked EEG Reconstruction (MER) for local fidelity and Neurodynamics Statistics Prediction (NSP). NSP enforces alignment with macroscopic brain states by predicting interpretable order parameters, including spectral power, functional connectivity, cross-frequency coupling, and dynamic complexity. Extensive experiments demonstrate that DeeperBrain achieves state-of-the-art or highly competitive performance under end-to-end fine-tuning. Crucially, it maintains superior efficacy under a rigorous frozen-probing protocol, verifying that embedding neuroscientific first principles endows learned representations with the intrinsic universality essential for universal BCI. The code will be publicly available.

We propose a novel deep learning method which combines classical regularization with data augmentation for estimating myelin water fraction (MWF) in the brain via biexponential analysis. Our aim is to design an accurate deep learning technique for analysis of signals arising in magnetic resonance relaxometry. In particular, we study the biexponential model, one of the signal models used for MWF estimation. We greatly extend our previous work on input layer regularization (ILR) in several ways. We now incorporate optimal regularization parameter selection via a dedicated neural network or generalized cross validation (GCV) on a signal-by-signal, or pixel-by-pixel, basis to form the augmented input signal, and now incorporate estimation of MWF, rather than just exponential time constants, into the analysis. On synthetically generated data, our proposed deep learning architecture outperformed both classical methods and a conventional multi-layer perceptron. On in vivo brain data, our architecture again outperformed other comparison methods, with GCV proving to be somewhat superior to a NN for regularization parameter selection. Thus, ILR improves estimation of MWF within the biexponential model. In addition, classical methods such as GCV may be combined with deep learning to optimize MWF imaging in the human brain.

Agentic artificial intelligence systems promise to accelerate scientific workflows, but neuroimaging poses unique challenges: heterogeneous modalities (sMRI, fMRI, dMRI, EEG), long multi-stage pipelines, and persistent reproducibility risks. To address this gap, we present NeuroClaw, a domain-specialized multi-agent research assistant for executable and reproducible neuroimaging research. NeuroClaw operates directly on raw neuroimaging data across formats and modalities, grounding decisions in dataset semantics and BIDS metadata so users need not prepare curated inputs or bespoke model code. The platform combines harness engineering with end-to-end environment management, including pinned Python environments, Docker support, automated installers for common neuroimaging tools, and GPU configuration. In practice, this layer emphasizes checkpointing, post-execution verification, structured audit traces, and controlled runtime setup, making toolchains more transparent while improving reproducibility and auditability. A three-tier skill/agent hierarchy separates user-facing interaction, high-level orchestration, and low-level tool skills to decompose complex workflows into safe, reusable units. Alongside the NeuroClaw framework, we introduce NeuroBench, a system-level benchmark for executability, artifact validity, and reproducibility readiness. Across multiple multimodal LLMs, NeuroClaw-enabled runs yield consistent and substantial score improvements compared with direct agent invocation. Project homepage: https://cuhk-aim-group.github.io/NeuroClaw/index.html

We present a multimodal dataset of 1020 hours of simultaneously recorded scalp electroencephalography (EEG), facial electromyography (EMG), and speech audio from three healthy native Japanese speakers during open-vocabulary overt speech. Recordings were acquired with three EEG systems-an ultra-high-density system (g.Pangolin) and two cap-type systems (g.SCARABEO and eegosports), spanning 62-128 channels-across many sessions over several months. Each session provides time-synchronized EEG, facial EMG, and audio, together with speech-event annotations and transcriptions. Although collected with speech decoding as a primary motivation, the dataset also supports work on multimodal signal processing, artifact modeling, longitudinal and cross-device adaptation, and EEG representation learning. Technical validation included power spectral density and event-related potential analyses across participants, devices, and tasks, which showed the expected 1/f spectral profile, task-related alpha-band attenuation, and time-locked evoked responses. The dataset is released in Brain Imaging Data Structure (BIDS) format via OpenNeuro under a CC0 waiver to support both speech-related and broader EEG research.

High-resolution brain imaging can now capture not just synapse locations but their molecular composition, with the cost of such mapping falling exponentially. Yet such ultrastructural data has so far told us little about local neuronal physiology - specifically, the parameters (e.g., synaptic efficacies, local conductances) that govern neural dynamics. We propose to translate molecularly annotated ultrastructure into physiology, introducing the concept of an ultrastructure-to-dynamics compiler: a learned mapping from molecularly annotated ultrastructure to simulator-ready, uncertainty-aware physiological parameters. The requirement is paired training data, with jointly acquired ultrastructure from imaging, and dynamical responses to perturbations from physiological experiments. With this data we can train models that predict local physiology directly from structure. Such a compiler would support biophysical simulations by turning anatomical maps into models of circuit dynamics, shifting structure-to-function from a descriptive program to a predictive one and opening routes to understanding neural computation and forecasting intervention effects.

Recent advances in multimodal large language models enable new possibilities for image-based decision support. However, their reliability and operational trade-offs in neuroimaging remain insufficiently understood. We present a comprehensive benchmarking study of vision-enabled large language models for 2D neuroimaging using curated MRI and CT datasets covering multiple sclerosis, stroke, brain tumors, other abnormalities, and normal controls. Models are required to generate multiple outputs simultaneously, including diagnosis, diagnosis subtype, imaging modality, specialized sequence, and anatomical plane. Performance is evaluated across four directions: discriminative classification with abstention, calibration, structured-output validity, and computational efficiency. A multi-phase framework ensures fair comparison while controlling for selection bias. Across twenty frontier multimodal models, the results show that technical imaging attributes such as modality and plane are nearly solved, whereas diagnostic reasoning, especially subtype prediction, remains challenging. Tumor classification emerges as the most reliable task, stroke is moderately solvable, while multiple sclerosis and rare abnormalities remain difficult. Few-shot prompting improves performance for several models but increases token usage, latency, and cost. Gemini-2.5-Pro and GPT-5-Chat achieve the strongest overall diagnostic performance, while Gemini-2.5-Flash offers the best efficiency-performance trade-off. Among open-weight architectures, MedGemma-1.5-4B demonstrates the most promising results, as under few-shot prompting, it approaches the zero-shot performance of several proprietary models, while maintaining perfect structured output. These findings provide practical insights into performance, reliability, and efficiency trade-offs, supporting standardized evaluation of multimodal LLMs in neuroimaging.

We characterise the dynamics of neuronal activity, in terms of field theory, using neural units placed on a 2D-lattice modelling the cortical surface. The electrical activity of neuronal units was analysed with the aim of deriving a neural field model with a simple functional form that still able to predict or reproduce empirical findings. Each neural unit was modelled using a neural mass and the accompanying field theory was derived in the continuum limit. The field theory comprised coupled (real) Klein-Gordon fields, where predictions of the model fall within the range of experimental findings. These predictions included the frequency spectrum of electric activity measured from the cortex, which was derived using an equipartition of energy over eigenfunctions of the neural fields. Moreover, the neural field model was invariant, within a set of parameters, to the dynamical system used to model each neuronal mass. Specifically, topologically equivalent dynamical systems resulted in the same neural field model when connected in a lattice; indicating that the fields derived could be read as a canonical cortical field theory. We specifically investigated non-dispersive fields that provide a structure for the coding (or representation) of afferent information. Further elaboration of the ensuing neural field theory, including the effect of dispersive forces, could be of importance in the understanding of the cortical processing of information.

Electroencephalography (EEG) offers a non-invasive lens into human brain activity, but building large-scale models is hampered by topological heterogeneity: each public EEG data defines its own electrode layout, limiting generalization. We introduce LUNA (Latent Unified Network Architecture), a self-supervised foundation model that reconciles disparate electrode geometries while scaling linearly -- not quadratically -- with channel count. LUNA compresses multi-channel EEG into a fixed-size, topology-agnostic latent space via learned queries and cross-attention. Downstream transformer blocks then operate exclusively on this latent representation using patch-wise temporal self-attention, decoupling computation from electrode count. Pre-trained on TUEG and Siena (over 21,000 hours of raw EEG across diverse montages) using a masked-patch reconstruction objective, LUNA transfers effectively to four downstream tasks: abnormality detection, artifact rejection, slowing classification, and emotion recognition. It demonstrates highly competitive performance across several benchmarks, achieving state-of-the-art results on TUAR and TUSL, e.g., 0.921 AUROC on TUAR, while reducing FLOPs by 300x and trimming GPU memory use by up to 10x. Critically, these gains are consistent across all evaluated electrode configurations. Code is available at https://github.com/pulp-bio/BioFoundation

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

In this paper, we introduce fastHDMI, a Python package designed for efficient variable screening in high-dimensional datasets, particularly neuroimaging data. This work pioneers the application of three mutual information estimation methods for neuroimaging variable selection, a novel approach implemented via fastHDMI. These advancements enhance our ability to analyze the complex structures of neuroimaging datasets, providing improved tools for variable selection in high-dimensional spaces. Using the preprocessed ABIDE dataset, we evaluate the performance of these methods through extensive simulations. The tests cover a range of conditions, including linear and nonlinear associations, as well as continuous and binary outcomes. Our results highlight the superiority of the FFTKDE-based mutual information estimation for feature screening in continuous nonlinear outcomes, while binning-based methods outperform others for binary outcomes with nonlinear probability preimages. For linear simulations, both Pearson correlation and FFTKDE-based methods show comparable performance for continuous outcomes, while Pearson excels in binary outcomes with linear probability preimages. A comprehensive case study using the ABIDE dataset further demonstrates fastHDMI's practical utility, showcasing the predictive power of models built from variables selected using our screening techniques. This research affirms the computational efficiency and methodological strength of fastHDMI, significantly enriching the toolkit available for neuroimaging analysis.

A major goal of neuroscience is to understand brain computations during visual processing in naturalistic settings. A dominant approach is to use image-computable deep neural networks trained with different task objectives as a basis for linear encoding models. However, in addition to requiring tuning a large number of parameters, the linear encoding approach ignores the structure of the feature maps both in the brain and the models. Recently proposed alternatives have focused on decomposing the linear mapping to spatial and feature components but focus on finding static receptive fields for units that are applicable only in early visual areas. In this work, we employ the attention mechanism used in the transformer architecture to study how retinotopic visual features can be dynamically routed to category-selective areas in high-level visual processing. We show that this computational motif is significantly more powerful than alternative methods in predicting brain activity during natural scene viewing, across different feature basis models and modalities. We also show that this approach is inherently more interpretable, without the need to create importance maps, by interpreting the attention routing signal for different high-level categorical areas. Our approach proposes a mechanistic model of how visual information from retinotopic maps can be routed based on the relevance of the input content to different category-selective regions.

EEG-based neural networks, pivotal in medical diagnosis and brain-computer interfaces, face significant intellectual property (IP) risks due to their reliance on sensitive neurophysiological data and resource-intensive development. Current watermarking methods, particularly those using abstract trigger sets, lack robust authentication and fail to address the unique challenges of EEG models. This paper introduces a cryptographic wonder filter-based watermarking framework tailored for EEG-based neural networks. Leveraging collision-resistant hashing and public-key encryption, the wonder filter embeds the watermark during training, ensuring minimal distortion (leq 5% drop in EEG task accuracy) and high reliability (100\% watermark detection). The framework is rigorously evaluated against adversarial attacks, including fine-tuning, transfer learning, and neuron pruning. Results demonstrate persistent watermark retention, with classification accuracy for watermarked states remaining above 90\% even after aggressive pruning, while primary task performance degrades faster, deterring removal attempts. Piracy resistance is validated by the inability to embed secondary watermarks without severe accuracy loss ( >10% in EEGNet and CCNN models). Cryptographic hashing ensures authentication, reducing brute-force attack success probabilities. Evaluated on the DEAP dataset across models (CCNN, EEGNet, TSception), the method achieves >99.4% null-embedding accuracy, effectively eliminating false positives. By integrating wonder filters with EEG-specific adaptations, this work bridges a critical gap in IP protection for neurophysiological models, offering a secure, tamper-proof solution for healthcare and biometric applications. The framework's robustness against adversarial modifications underscores its potential to safeguard sensitive EEG models while maintaining diagnostic utility.

Despite extensive standardization, diagnostic interviews for mental health disorders encompass substantial subjective judgment. Previous studies have demonstrated that EEG-based neural measures can function as reliable objective correlates of depression, or even predictors of depression and its course. However, their clinical utility has not been fully realized because of 1) the lack of automated ways to deal with the inherent noise associated with EEG data at scale, and 2) the lack of knowledge of which aspects of the EEG signal may be markers of a clinical disorder. Here we adapt an unsupervised pipeline from the recent deep representation learning literature to address these problems by 1) learning a disentangled representation using beta-VAE to denoise the signal, and 2) extracting interpretable features associated with a sparse set of clinical labels using a Symbol-Concept Association Network (SCAN). We demonstrate that our method is able to outperform the canonical hand-engineered baseline classification method on a number of factors, including participant age and depression diagnosis. Furthermore, our method recovers a representation that can be used to automatically extract denoised Event Related Potentials (ERPs) from novel, single EEG trajectories, and supports fast supervised re-mapping to various clinical labels, allowing clinicians to re-use a single EEG representation regardless of updates to the standardized diagnostic system. Finally, single factors of the learned disentangled representations often correspond to meaningful markers of clinical factors, as automatically detected by SCAN, allowing for human interpretability and post-hoc expert analysis of the recommendations made by the model.

Uncovering the fundamental neural correlates of biological intelligence, developing mathematical models, and conducting computational simulations are critical for advancing new paradigms in artificial intelligence (AI). In this study, we implemented a comprehensive visual decision-making model that spans from visual input to behavioral output, using a neural dynamics modeling approach. Drawing inspiration from the key components of the dorsal visual pathway in primates, our model not only aligns closely with human behavior but also reflects neural activities in primates, and achieving accuracy comparable to convolutional neural networks (CNNs). Moreover, magnetic resonance imaging (MRI) identified key neuroimaging features such as structural connections and functional connectivity that are associated with performance in perceptual decision-making tasks. A neuroimaging-informed fine-tuning approach was introduced and applied to the model, leading to performance improvements that paralleled the behavioral variations observed among subjects. Compared to classical deep learning models, our model more accurately replicates the behavioral performance of biological intelligence, relying on the structural characteristics of biological neural networks rather than extensive training data, and demonstrating enhanced resilience to perturbation.

Brain-computer interfaces (BCIs), transform neural signals in the brain into in-structions to control external devices. However, obtaining sufficient training data is difficult as well as limited. With the advent of advanced machine learning methods, the capability of brain-computer interfaces has been enhanced like never before, however, these methods require a large amount of data for training and thus require data augmentation of the limited data available. Here, we use spiking neural networks (SNN) as data generators. It is touted as the next-generation neu-ral network and is considered as one of the algorithms oriented to general artifi-cial intelligence because it borrows the neural information processing from bio-logical neurons. We use the SNN to generate neural spike information that is bio-interpretable and conforms to the intrinsic patterns in the original neural data. Ex-periments show that the model can directly synthesize new spike trains, which in turn improves the generalization ability of the BCI decoder. Both the input and output of the spiking neural model are spike information, which is a brain-inspired intelligence approach that can be better integrated with BCI in the future.

Electroencephalography (EEG)-based Brain-Computer Interfaces (BCIs) have emerged as a transformative technology with applications spanning robotics, virtual reality, medicine, and rehabilitation. However, existing BCI frameworks face several limitations, including a lack of stage-wise flexibility essential for experimental research, steep learning curves for researchers without programming expertise, elevated costs due to reliance on proprietary software, and a lack of all-inclusive features leading to the use of multiple external tools affecting research outcomes. To address these challenges, we present PyNoetic, a modular BCI framework designed to cater to the diverse needs of BCI research. PyNoetic is one of the very few frameworks in Python that encompasses the entire BCI design pipeline, from stimulus presentation and data acquisition to channel selection, filtering, feature extraction, artifact removal, and finally simulation and visualization. Notably, PyNoetic introduces an intuitive and end-to-end GUI coupled with a unique pick-and-place configurable flowchart for no-code BCI design, making it accessible to researchers with minimal programming experience. For advanced users, it facilitates the seamless integration of custom functionalities and novel algorithms with minimal coding, ensuring adaptability at each design stage. PyNoetic also includes a rich array of analytical tools such as machine learning models, brain-connectivity indices, systematic testing functionalities via simulation, and evaluation methods of novel paradigms. PyNoetic's strengths lie in its versatility for both offline and real-time BCI development, which streamlines the design process, allowing researchers to focus on more intricate aspects of BCI development and thus accelerate their research endeavors. Project Website: https://neurodiag.github.io/PyNoetic

Objective: Electroencephalography signals are recorded as a multidimensional dataset. We propose a new framework based on the augmented covariance extracted from an autoregressive model to improve motor imagery classification. Methods: From the autoregressive model can be derived the Yule-Walker equations, which show the emergence of a symmetric positive definite matrix: the augmented covariance matrix. The state-of the art for classifying covariance matrices is based on Riemannian Geometry. A fairly natural idea is therefore to extend the standard approach using these augmented covariance matrices. The methodology for creating the augmented covariance matrix shows a natural connection with the delay embedding theorem proposed by Takens for dynamical systems. Such an embedding method is based on the knowledge of two parameters: the delay and the embedding dimension, respectively related to the lag and the order of the autoregressive model. This approach provides new methods to compute the hyper-parameters in addition to standard grid search. Results: The augmented covariance matrix performed noticeably better than any state-of-the-art methods. We will test our approach on several datasets and several subjects using the MOABB framework, using both within-session and cross-session evaluation. Conclusion: The improvement in results is due to the fact that the augmented covariance matrix incorporates not only spatial but also temporal information, incorporating nonlinear components of the signal through an embedding procedure, which allows the leveraging of dynamical systems algorithms. Significance: These results extend the concepts and the results of the Riemannian distance based classification algorithm.

Human's perception of the visual world is shaped by the stereo processing of 3D information. Understanding how the brain perceives and processes 3D visual stimuli in the real world has been a longstanding endeavor in neuroscience. Towards this goal, we introduce a new neuroscience task: decoding 3D visual perception from EEG signals, a neuroimaging technique that enables real-time monitoring of neural dynamics enriched with complex visual cues. To provide the essential benchmark, we first present EEG-3D, a pioneering dataset featuring multimodal analysis data and extensive EEG recordings from 12 subjects viewing 72 categories of 3D objects rendered in both videos and images. Furthermore, we propose Neuro-3D, a 3D visual decoding framework based on EEG signals. This framework adaptively integrates EEG features derived from static and dynamic stimuli to learn complementary and robust neural representations, which are subsequently utilized to recover both the shape and color of 3D objects through the proposed diffusion-based colored point cloud decoder. To the best of our knowledge, we are the first to explore EEG-based 3D visual decoding. Experiments indicate that Neuro-3D not only reconstructs colored 3D objects with high fidelity, but also learns effective neural representations that enable insightful brain region analysis. The dataset and associated code will be made publicly available.

Artifacts in electroencephalography (EEG) -- muscle, eye movement, electrode, chewing, and shiver -- confound automated analysis yet are costly to label at scale. We study whether modern generative models can synthesize realistic, label-aware artifact segments suitable for augmentation and stress-testing. Using the TUH EEG Artifact (TUAR) corpus, we curate subject-wise splits and fixed-length multi-channel windows (e.g., 250 samples) with preprocessing tailored to each model (per-window min--max for adversarial training; per-recording/channel z-score for diffusion). We compare a conditional WGAN-GP with a projection discriminator to a 1D denoising diffusion model with classifier-free guidance, and evaluate along three axes: (i) fidelity via Welch band-power deltas (Deltadelta, Deltatheta, Deltaalpha, Deltabeta), channel-covariance Frobenius distance, autocorrelation L_2, and distributional metrics (MMD/PRD); (ii) specificity via class-conditional recovery with lightweight kNN/classifiers; and (iii) utility via augmentation effects on artifact recognition. In our setting, WGAN-GP achieves closer spectral alignment and lower MMD to real data, while both models exhibit weak class-conditional recovery, limiting immediate augmentation gains and revealing opportunities for stronger conditioning and coverage. We release a reproducible pipeline -- data manifests, training configurations, and evaluation scripts -- to establish a baseline for EEG artifact synthesis and to surface actionable failure modes for future work.

Most of the Brain-Computer Interface (BCI) publications, which propose artificial neural networks for Motor Imagery (MI) Electroencephalography (EEG) signal classification, are presented using one of the BCI Competition datasets. However, these databases contain MI EEG data from less than or equal to 10 subjects . In addition, these algorithms usually include only bandpass filtering to reduce noise and increase signal quality. In this article, we compared 5 well-known neural networks (Shallow ConvNet, Deep ConvNet, EEGNet, EEGNet Fusion, MI-EEGNet) using open-access databases with many subjects next to the BCI Competition 4 2a dataset to acquire statistically significant results. We removed artifacts from the EEG using the FASTER algorithm as a signal processing step. Moreover, we investigated whether transfer learning can further improve the classification results on artifact filtered data. We aimed to rank the neural networks; therefore, next to the classification accuracy, we introduced two additional metrics: the accuracy improvement from chance level and the effect of transfer learning. The former can be used with different class-numbered databases, while the latter can highlight neural networks with sufficient generalization abilities. Our metrics showed that the researchers should not avoid Shallow ConvNet and Deep ConvNet because they can perform better than the later published ones from the EEGNet family.

A long standing goal in neuroscience has been to elucidate the functional organization of the brain. Within higher visual cortex, functional accounts have remained relatively coarse, focusing on regions of interest (ROIs) and taking the form of selectivity for broad categories such as faces, places, bodies, food, or words. Because the identification of such ROIs has typically relied on manually assembled stimulus sets consisting of isolated objects in non-ecological contexts, exploring functional organization without robust a priori hypotheses has been challenging. To overcome these limitations, we introduce a data-driven approach in which we synthesize images predicted to activate a given brain region using paired natural images and fMRI recordings, bypassing the need for category-specific stimuli. Our approach -- Brain Diffusion for Visual Exploration ("BrainDiVE") -- builds on recent generative methods by combining large-scale diffusion models with brain-guided image synthesis. Validating our method, we demonstrate the ability to synthesize preferred images with appropriate semantic specificity for well-characterized category-selective ROIs. We then show that BrainDiVE can characterize differences between ROIs selective for the same high-level category. Finally we identify novel functional subdivisions within these ROIs, validated with behavioral data. These results advance our understanding of the fine-grained functional organization of human visual cortex, and provide well-specified constraints for further examination of cortical organization using hypothesis-driven methods.

Neural decoding, the process of understanding how brain activity corresponds to different stimuli, has been a primary objective in cognitive sciences. Over the past three decades, advancements in functional Magnetic Resonance Imaging and machine learning have greatly improved our ability to map visual stimuli to brain activity, especially in the visual cortex. Concurrently, research has expanded into decoding more complex processes like language and memory across the whole brain, utilizing techniques to handle greater variability and improve signal accuracy. We argue that "seeing" involves more than just mapping visual stimuli onto the visual cortex; it engages the entire brain, as various emotions and cognitive states can emerge from observing different scenes. In this paper, we develop algorithms to enhance our understanding of visual processes by incorporating whole-brain activation maps while individuals are exposed to visual stimuli. We utilize large-scale fMRI encoders and Image generative models pre-trained on large public datasets, which are then fine-tuned through Image-fMRI contrastive learning. Our models hence can decode visual experience across the entire cerebral cortex, surpassing the traditional confines of the visual cortex. We first compare our method with state-of-the-art approaches to decoding visual processing and show improved predictive semantic accuracy by 43%. A network ablation analysis suggests that beyond the visual cortex, the default mode network contributes most to decoding stimuli, in line with the proposed role of this network in sense-making and semantic processing. Additionally, we implemented zero-shot imagination decoding on an extra validation dataset, achieving a p-value of 0.0206 for mapping the reconstructed images and ground-truth text stimuli, which substantiates the model's capability to capture semantic meanings across various scenarios.

Foundation models have recently shown strong potential for learning generalizable EEG representations, yet their effectiveness for event-related potential (ERP) analysis remains unclear. In this work, we investigate two fundamental questions: 1) can foundation-model learning benefit ERP analysis, and what limits the transfer of existing EEG foundation models to ERP tasks? 2) can the complementary advantages of single-trial and averaged-trial ERP be integrated into a unified training pipeline? To study these questions, we curate a large-scale ERP corpus comprising 1,517,157 single-trial ERPs from 3,696 subjects across 38 datasets and 18 paradigms. Leveraging this corpus, we introduce ERP-FM, to the best of our knowledge, the first foundation model specifically developed for ERP representation learning. ERP-FM uses single-channel tokenization, temporal and spatial positional embeddings, and mixed masked autoencoding for large-scale single-trial pretraining. We compare our model against 17 existing methods on 12 downstream datasets covering ERP event/condition classification and neurological disease classification. Our model achieves the best overall average rank across all evaluated methods. Furthermore, our analyses reveal that both ERP and non-ERP EEG pretraining can provide transferable representations for ERP tasks, while fine-grained temporal tokenization is critical for effectively modeling transient ERP dynamics. We further find that single-trial and averaged-trial ERP play complementary rather than competing roles. Combining single-trial pretraining with averaged-trial downstream adaptation substantially improves neurological disease analysis. Overall, these findings establish an effective foundation-model training pipeline for ERP analysis and represent significant progress toward generalizable ERP representation learning. Source code: https://github.com/DL4mHealth/ERP-FM

Parkinsons disease (PD) alters cortical neural dynamics, yet reliable non-invasive electrophysiological biomarkers remain elusive. This study examined whether interpretable EEG features capturing complementary aspects of neural dynamics can discriminate Parkinsonian neural states. A comprehensive set of interpretable features was extracted and grouped into Standard descriptors (spectral power, phase synchronization, time-domain statistics) and Dynamical descriptors (aperiodic activity, cross-frequency coupling, scale-free dynamics, neuronal avalanche statistics, and instantaneous frequency measures). A multi-head attention transformer classifier was trained using strict LOSO validation. Group-level comparisons were performed to identify electrophysiological differences associated with disease and medication state. Standard feature sets achieved strongest performance in discriminating medication states (PDoff vs PDon), whereas Dynamical performed competitively in contrasts between PD patients and healthy controls. Random feature ablation analyses indicated that Dynamical descriptors provide complementary information distributed across features while correlation analysis revealed low redundancy within both feature sets. Group-level comparisons revealed medication-sensitive reductions in delta power and voltage variance, modulation of neuronal avalanche statistics, persistent increases in theta phase synchronization in PD patients, and disease-related alterations in cross-frequency interactions. Traditional spectral and synchronization features primarily reflect medication-related neural modulation, whereas dynamical descriptors reveal broader alterations in cortical network organization associated with disease but also with medication. These findings support multivariate EEG representations as a promising framework for developing non-invasive biomarkers of PD.

Brain-computer interfaces (BCIs) enable direct communication between the brain and external devices. Recent EEG foundation models aim to learn generalized representations across diverse BCI paradigms. However, these approaches overlook fundamental paradigm-specific neurophysiological distinctions, limiting their generalization ability. Importantly, in practical BCI deployments, the specific paradigm such as motor imagery (MI) for stroke rehabilitation or assistive robotics, is generally determined prior to data acquisition. This paper proposes MIRepNet, the first EEG foundation model tailored for the MI paradigm. MIRepNet comprises a high-quality EEG preprocessing pipeline incorporating a neurophysiologically-informed channel template, adaptable to EEG headsets with arbitrary electrode configurations. Furthermore, we introduce a hybrid pretraining strategy that combines self-supervised masked token reconstruction and supervised MI classification, facilitating rapid adaptation and accurate decoding on novel downstream MI tasks with fewer than 30 trials per class. Extensive evaluations across five public MI datasets demonstrated that MIRepNet consistently achieved state-of-the-art performance, significantly outperforming both specialized and generalized EEG models. Our code will be available on GitHubhttps://github.com/staraink/MIRepNet.

Insufficient data is a long-standing challenge for Brain-Computer Interface (BCI) to build a high-performance deep learning model. Though numerous research groups and institutes collect a multitude of EEG datasets for the same BCI task, sharing EEG data from multiple sites is still challenging due to the heterogeneity of devices. The significance of this challenge cannot be overstated, given the critical role of data diversity in fostering model robustness. However, existing works rarely discuss this issue, predominantly centering their attention on model training within a single dataset, often in the context of inter-subject or inter-session settings. In this work, we propose a hierarchical personalized Federated Learning EEG decoding (FLEEG) framework to surmount this challenge. This innovative framework heralds a new learning paradigm for BCI, enabling datasets with disparate data formats to collaborate in the model training process. Each client is assigned a specific dataset and trains a hierarchical personalized model to manage diverse data formats and facilitate information exchange. Meanwhile, the server coordinates the training procedure to harness knowledge gleaned from all datasets, thus elevating overall performance. The framework has been evaluated in Motor Imagery (MI) classification with nine EEG datasets collected by different devices but implementing the same MI task. Results demonstrate that the proposed frame can boost classification performance up to 16.7% by enabling knowledge sharing between multiple datasets, especially for smaller datasets. Visualization results also indicate that the proposed framework can empower the local models to put a stable focus on task-related areas, yielding better performance. To the best of our knowledge, this is the first end-to-end solution to address this important challenge.

Electroencephalography (EEG) interpretation using multimodal large language models (MLLMs) offers a novel approach for analyzing brain signals. However, the complex nature of brain activity introduces critical challenges: EEG signals simultaneously encode both cognitive processes and intrinsic neural states, creating a mismatch in EEG paired-data modality that hinders effective cross-modal representation learning. Through a pivot investigation, we uncover complementary relationships between these modalities. Leveraging this insight, we propose mapping EEG signals and their corresponding modalities into a unified semantic space to achieve generalized interpretation. To fully enable conversational capabilities, we further introduce WaveMind-Instruct-338k, the first cross-task EEG dataset for instruction tuning. The resulting model demonstrates robust classification accuracy while supporting flexible, open-ended conversations across four downstream tasks, thereby offering valuable insights for both neuroscience research and the development of general-purpose EEG models.

We propose EEG-SimpleConv, a straightforward 1D convolutional neural network for Motor Imagery decoding in BCI. Our main motivation is to propose a simple and performing baseline to compare to, using only very standard ingredients from the literature. We evaluate its performance on four EEG Motor Imagery datasets, including simulated online setups, and compare it to recent Deep Learning and Machine Learning approaches. EEG-SimpleConv is at least as good or far more efficient than other approaches, showing strong knowledge-transfer capabilities across subjects, at the cost of a low inference time. We advocate that using off-the-shelf ingredients rather than coming with ad-hoc solutions can significantly help the adoption of Deep Learning approaches for BCI. We make the code of the models and the experiments accessible.

Data scarcity in the brain-computer interface field can be alleviated through the use of generative models, specifically diffusion models. While diffusion models have previously been successfully applied to electroencephalogram (EEG) data, existing models lack flexibility w.r.t.~sampling or require alternative representations of the EEG data. To overcome these limitations, we introduce a novel approach to conditional diffusion models that utilizes classifier-free guidance to directly generate subject-, session-, and class-specific EEG data. In addition to commonly used metrics, domain-specific metrics are employed to evaluate the specificity of the generated samples. The results indicate that the proposed model can generate EEG data that resembles real data for each subject, session, and class.

In this study, we present a technique that spans multi-scale views (global scale -- meaning brain network-level and local scale -- examining each individual ROI that constitutes the network) applied to resting-state fMRI volumes. Deep learning based classification is utilized in understanding neurodegeneration. The novelty of the proposed approach lies in utilizing two extreme scales of analysis. One branch considers the entire network within graph-analysis framework. Concurrently, the second branch scrutinizes each ROI within a network independently, focusing on evolution of dynamics. For each subject, graph-based approach employs partial correlation to profile the subject in a single graph where each ROI is a node, providing insights into differences in levels of participation. In contrast, non-linear analysis employs recurrence plots to profile a subject as a multichannel 2D image, revealing distinctions in underlying dynamics. The proposed approach is employed for classification of a cohort of 50 healthy control (HC) and 50 Mild Cognitive Impairment (MCI), sourced from ADNI dataset. Results point to: (1) reduced activity in ROIs such as PCC in MCI (2) greater activity in occipital in MCI, which is not seen in HC (3) when analysed for dynamics, all ROIs in MCI show greater predictability in time-series.

Cognitive neuroscience is enjoying rapid increase in extensive public brain-imaging datasets. It opens the door to large-scale statistical models. Finding a unified perspective for all available data calls for scalable and automated solutions to an old challenge: how to aggregate heterogeneous information on brain function into a universal cognitive system that relates mental operations/cognitive processes/psychological tasks to brain networks? We cast this challenge in a machine-learning approach to predict conditions from statistical brain maps across different studies. For this, we leverage multi-task learning and multi-scale dimension reduction to learn low-dimensional representations of brain images that carry cognitive information and can be robustly associated with psychological stimuli. Our multi-dataset classification model achieves the best prediction performance on several large reference datasets, compared to models without cognitive-aware low-dimension representations, it brings a substantial performance boost to the analysis of small datasets, and can be introspected to identify universal template cognitive concepts.

Brain-computer interfaces (BCIs) offer transformative potential, but decoding neural signals presents significant challenges. The core premise of this paper is built around demonstrating methods to elucidate the underlying low-dimensional geometric structure present in high-dimensional brainwave data in order to assist in downstream BCI-related neural classification tasks. We demonstrate two pipelines related to electroencephalography (EEG) signal processing: (1) a preliminary pipeline removing noise from individual EEG channels, and (2) a downstream manifold learning pipeline uncovering geometric structure across networks of EEG channels. We conduct preliminary validation using two EEG datasets and situate our demonstration in the context of the BCI-relevant imagined digit decoding problem. Our preliminary pipeline uses an attention-based EEG filtration network to extract clean signal from individual EEG channels. Our primary pipeline uses a fast Fourier transform, a Laplacian eigenmap, a discrete analog of Ricci flow via Ollivier's notion of Ricci curvature, and a graph convolutional network to perform dimensionality reduction on high-dimensional multi-channel EEG data in order to enable regularizable downstream classification. Our system achieves competitive performance with existing signal processing and classification benchmarks; we demonstrate a mean test correlation coefficient of >0.95 at 2 dB on semi-synthetic neural denoising and a downstream EEG-based classification accuracy of 0.97 on distinguishing digit- versus non-digit- thoughts. Results are preliminary and our geometric machine learning pipeline should be validated by more extensive follow-up studies; generalizing these results to larger inter-subject sample sizes, different hardware systems, and broader use cases will be crucial.

Electroencephalography (EEG) foundation models have recently emerged as a promising paradigm for brain-computer interfaces (BCIs), aiming to learn transferable neural representations from large-scale heterogeneous recordings. Despite rapid progresses, there lacks fair and comprehensive comparisons of existing EEG foundation models, due to inconsistent pre-training objectives, preprocessing choices, and downstream evaluation protocols. This paper fills this gap. We first review 50 representative models and organize their design choices into a unified taxonomic framework including data standardization, model architectures, and self-supervised pre-training strategies. We then evaluate 12 open-source foundation models and competitive specialist baselines across 13 EEG datasets spanning nine BCI paradigms. Emphasizing real-world deployments, we consider both cross-subject generalization under a leave-one-subject-out protocol and rapid calibration under a within-subject few-shot setting. We further compare full-parameter fine-tuning with linear probing to assess the transferability of pre-trained representations, and examine the relationship between model scale and downstream performance. Our results indicate that: 1) linear probing is frequently insufficient; 2) specialist models trained from scratch remain competitive across many tasks; and, 3) larger foundation models do not necessarily yield better generalization performance under current data regimes and training practices.

Conventional multi-lead electrocardiogram (ECG) systems capture cardiac signals from a fixed set of anatomical viewpoints defined by lead placement. However, certain cardiac conditions (e.g., Brugada syndrome) require additional, non-standard viewpoints to reveal diagnostically critical patterns that may be absent in standard leads. To systematically overcome this limitation, Nef-Net was recently introduced to reconstruct a continuous electrocardiac field, enabling virtual observation of ECG signals from arbitrary views (termed Electrocardio Panorama). Despite its promise, Nef-Net operates under idealized assumptions and faces in-the-wild challenges, such as long-duration ECG modeling, robustness to device-specific signal artifacts, and suboptimal lead placement calibration. This paper presents NEF-NET+, an enhanced framework for realistic panoramic ECG synthesis that supports arbitrary-length signal synthesis from any desired view, generalizes across ECG devices, and compensates for operator-induced deviations in electrode placement. These capabilities are enabled by a newly designed model architecture that performs direct view transformation, incorporating a workflow comprising offline pretraining, device calibration tuning steps as well as an on-the-fly calibration step for patient-specific adaptation. To rigorously evaluate panoramic ECG synthesis, we construct a new Electrocardio Panorama benchmark, called Panobench, comprising 5367 recordings with 48-view per subject, capturing the full spatial variability of cardiac electrical activity. Experimental results show that NEF-NET+ delivers substantial improvements over Nef-Net, yielding an increase of around 6 dB in PSNR in real-world setting. The code and Panobench will be released in a subsequent publication.

This article addresses the challenge of modeling the amplitude of spatially indexed low frequency fluctuations (ALFF) in resting state functional MRI as a function of cortical structural features and a multi-task coactivation network in the Adolescent Brain Cognitive Development (ABCD) Study. It proposes a generative model that integrates effects of spatially-varying inputs and a network-valued input using deep neural networks to capture complex non-linear and spatial associations with the output. The method models spatial smoothness, accounts for subject heterogeneity and complex associations between network and spatial images at different scales, enables accurate inference of each images effect on the output image, and allows prediction with uncertainty quantification via Monte Carlo dropout, contributing to one of the first Explainable AI (XAI) frameworks for heterogeneous imaging data. The model is highly scalable to high-resolution data without the heavy pre-processing or summarization often required by Bayesian methods. Empirical results demonstrate its strong performance compared to existing statistical and deep learning methods. We applied the XAI model to the ABCD data which revealed associations between cortical features and ALFF throughout the entire brain. Our model performed comparably to existing methods in predictive accuracy but provided superior uncertainty quantification and faster computation, demonstrating its effectiveness for large-scale neuroimaging analysis. Open-source software in Python for XAI is available.

Reliable automatic seizure detection from long-term EEG remains a challenge, as current machine learning models often fail to generalize across patients or clinical settings. Manual EEG review remains the clinical standard, underscoring the need for robust models and standardized evaluation. To rigorously assess algorithm performance, we organized a challenge using a private dataset of continuous EEG recordings from 65 subjects (4,360 hours). Expert neurophysiologists annotated the data, providing ground truth for seizure events. Participants were required to detect seizure onset and duration, with evaluation based on event-based metrics, including sensitivity, precision, F1-score, and false positives per day. The SzCORE framework ensured standardized evaluation. The primary ranking criterion was the event-based F1-score, reflecting clinical relevance by balancing sensitivity and false positives. The challenge received 30 submissions from 19 teams, with 28 algorithms evaluated. Results revealed wide variability in performance, with a top F1-score of 43% (sensitivity 37%, precision 45%), highlighting the ongoing difficulty of seizure detection. The challenge also revealed a gap between reported performance and real-world evaluation, emphasizing the importance of rigorous benchmarking. Compared to previous challenges and commercial systems, the best-performing algorithm in this contest showed improved performance. Importantly, the challenge platform now supports continuous benchmarking, enabling reproducible research, integration of new datasets, and clinical evaluation of seizure detection algorithms using a standardized framework.

Brain MRI underpins a wide range of neuroscientific and clinical applications, yet most learning-based methods remain task-specific and require substantial labeled data. Here we show that a single self-supervised representation can generalize across heterogeneous brain MRI endpoints. We trained BrainDINO, a self-distilled foundation model, on approximately 6.6 million unlabeled axial slices from 20 datasets encompassing broad variation in population, disease, and acquisition setting. Using a frozen encoder with lightweight task heads, BrainDINO supported transfer across tumor segmentation, neurodegenerative and neurodevelopmental conditions classification, brain age estimation, post-stroke temporal prediction, molecular status prediction, MRI sequence classification, and survival modeling. Across tasks and supervision regimes, BrainDINO consistently equaled or exceeded natural-image and MRI-specific self-supervised baselines, with particularly strong advantages under label scarcity. Representation analyses further showed anatomically organized and pathology-sensitive feature structure in the absence of task-specific supervision. Our findings indicate that large-scale slice-wise self-supervised learning can yield a unified brain MRI representation that supports diverse neuroimaging tasks without volumetric pretraining or full-network fine-tuning, establishing a scalable foundation for robust and data-efficient brain imaging analysis.

Cortical visual prostheses aim to restore sight by electrically stimulating neurons in early visual cortex (V1). With the emergence of high-density and flexible neural interfaces, electrode placement within three-dimensional cortex has become a critical surgical planning problem. Existing strategies emphasize visual field coverage and anatomical heuristics but do not directly optimize predicted perceptual outcomes under safety constraints. We present a percept-aware framework for surgical planning of cortical visual prostheses that formulates electrode placement as a constrained optimization problem in anatomical space. Electrode coordinates are treated as learnable parameters and optimized end-to-end using a differentiable forward model of prosthetic vision. The objective minimizes task-level perceptual error while incorporating vascular avoidance and gray matter feasibility constraints. Evaluated on simulated reading and natural image tasks using realistic folded cortical geometry (FreeSurfer fsaverage), percept-aware optimization consistently improves reconstruction fidelity relative to coverage-based placement strategies. Importantly, vascular safety constraints eliminate margin violations while preserving perceptual performance. The framework further enables co-optimization of multi-electrode thread configurations under fixed insertion budgets. These results demonstrate how differentiable percept models can inform anatomically grounded, safety-aware computer-assisted planning for cortical neural interfaces and provide a foundation for optimizing next-generation visual prostheses.

Magnetic resonance imaging (MRI) is a central modality for stroke imaging. It is used upon patient admission to make treatment decisions such as selecting patients for intravenous thrombolysis or endovascular therapy. MRI is later used in the duration of hospital stay to predict outcome by visualizing infarct core size and location. Furthermore, it may be used to characterize stroke etiology, e.g. differentiation between (cardio)-embolic and non-embolic stroke. Computer based automated medical image processing is increasingly finding its way into clinical routine. Previous iterations of the Ischemic Stroke Lesion Segmentation (ISLES) challenge have aided in the generation of identifying benchmark methods for acute and sub-acute ischemic stroke lesion segmentation. Here we introduce an expert-annotated, multicenter MRI dataset for segmentation of acute to subacute stroke lesions. This dataset comprises 400 multi-vendor MRI cases with high variability in stroke lesion size, quantity and location. It is split into a training dataset of n=250 and a test dataset of n=150. All training data will be made publicly available. The test dataset will be used for model validation only and will not be released to the public. This dataset serves as the foundation of the ISLES 2022 challenge with the goal of finding algorithmic methods to enable the development and benchmarking of robust and accurate segmentation algorithms for ischemic stroke.

Partially inspired by features of computation in visual cortex, deep neural networks compute hierarchical representations of their inputs. While these networks have been highly successful in machine learning, it remains unclear to what extent they can aid our understanding of cortical function. Several groups have developed metrics that provide a quantitative comparison between representations computed by networks and representations measured in cortex. At the same time, neuroscience is well into an unprecedented phase of large-scale data collection, as evidenced by projects such as the Allen Brain Observatory. Despite the magnitude of these efforts, in a given experiment only a fraction of units are recorded, limiting the information available about the cortical representation. Moreover, only a finite number of stimuli can be shown to an animal over the course of a realistic experiment. These limitations raise the question of how and whether metrics that compare representations of deep networks are meaningful on these datasets. Here, we empirically quantify the capabilities and limitations of these metrics due to limited image presentations and neuron samples. We find that the comparison procedure is robust to different choices of stimuli set and the level of subsampling that one might expect in a large-scale brain survey with thousands of neurons. Using these results, we compare the representations measured in the Allen Brain Observatory in response to natural image presentations to deep neural network. We show that the visual cortical areas are relatively high order representations (in that they map to deeper layers of convolutional neural networks). Furthermore, we see evidence of a broad, more parallel organization rather than a sequential hierarchy, with the primary area VISp(V1) being lower order relative to the other areas.

Brain simulation builds dynamical models to mimic the structure and functions of the brain, while brain-inspired computing (BIC) develops intelligent systems by learning from the structure and functions of the brain. The two fields are intertwined and should share a common programming framework to facilitate each other's development. However, none of the existing software in the fields can achieve this goal, because traditional brain simulators lack differentiability for training, while existing deep learning (DL) frameworks fail to capture the biophysical realism and complexity of brain dynamics. In this paper, we introduce BrainPy, a differentiable brain simulator developed using JAX and XLA, with the aim of bridging the gap between brain simulation and BIC. BrainPy expands upon the functionalities of JAX, a powerful AI framework, by introducing complete capabilities for flexible, efficient, and scalable brain simulation. It offers a range of sparse and event-driven operators for efficient and scalable brain simulation, an abstraction for managing the intricacies of synaptic computations, a modular and flexible interface for constructing multi-scale brain models, and an object-oriented just-in-time compilation approach to handle the memory-intensive nature of brain dynamics. We showcase the efficiency and scalability of BrainPy on benchmark tasks, highlight its differentiable simulation for biologically plausible spiking models, and discuss its potential to support research at the intersection of brain simulation and BIC.

Trustworthy interpretation of deep learning models is critical for neuroimaging applications, yet commonly used Explainable AI (XAI) methods lack rigorous validation, risking misinterpretation. We performed the first large-scale, systematic comparison of XAI methods on ~45,000 structural brain MRIs using a novel XAI validation framework. This framework establishes verifiable ground truth by constructing prediction tasks with known signal sources - from localized anatomical features to subject-specific clinical lesions - without artificially altering input images. Our analysis reveals systematic failures in two of the most widely used methods: GradCAM consistently failed to localize predictive features, while Layer-wise Relevance Propagation generated extensive, artifactual explanations that suggest incompatibility with neuroimaging data characteristics. Our results indicate that these failures stem from a domain mismatch, where methods with design principles tailored to natural images require substantial adaptation for neuroimaging data. In contrast, the simpler, gradient-based method SmoothGrad, which makes fewer assumptions about data structure, proved consistently accurate, suggesting its conceptual simplicity makes it more robust to this domain shift. These findings highlight the need for domain-specific adaptation and validation of XAI methods, suggest that interpretations from prior neuroimaging studies using standard XAI methodology warrant re-evaluation, and provide urgent guidance for practical application of XAI in neuroimaging.

Brain-computer interfaces (BCIs) hold great potential for aiding individuals with speech impairments. Utilizing electroencephalography (EEG) to decode speech is particularly promising due to its non-invasive nature. However, recordings are typically short, and the high variability in EEG data has led researchers to focus on classification tasks with a few dozen classes. To assess its practical applicability for speech neuroprostheses, we investigate the relationship between the size of EEG data and decoding accuracy in the open vocabulary setting. We collected extensive EEG data from a single participant (175 hours) and conducted zero-shot speech segment classification using self-supervised representation learning. The model trained on the entire dataset achieved a top-1 accuracy of 48\% and a top-10 accuracy of 76\%, while mitigating the effects of myopotential artifacts. Conversely, when the data was limited to the typical amount used in practice (sim10 hours), the top-1 accuracy dropped to 2.5\%, revealing a significant scaling effect. Additionally, as the amount of training data increased, the EEG latent representation progressively exhibited clearer temporal structures of spoken phrases. This indicates that the decoder can recognize speech segments in a data-driven manner without explicit measurements of word recognition. This research marks a significant step towards the practical realization of EEG-based speech BCIs.

To handle the scarcity and heterogeneity of electroencephalography (EEG) data for Brain-Computer Interface (BCI) tasks, and to harness the power of large publicly available data sets, we propose Neuro-GPT, a foundation model consisting of an EEG encoder and a GPT model. The foundation model is pre-trained on a large-scale data set using a self-supervised task that learns how to reconstruct masked EEG segments. We then fine-tune the model on a Motor Imagery Classification task to validate its performance in a low-data regime (9 subjects). Our experiments demonstrate that applying a foundation model can significantly improve classification performance compared to a model trained from scratch, which provides evidence for the generalizability of the foundation model and its ability to address challenges of data scarcity and heterogeneity in EEG. The code is publicly available at github.com/wenhui0206/NeuroGPT.

Multi-Frequency Electrical Impedance Tomography (MF-EIT) is a non-invasive, low-cost modality that reconstructs electrical property distributions from boundary voltages. For stroke imaging, progress in 3D deep-learning reconstruction is limited by the lack of large-scale datasets with paired ground-truth (GT) volumes and by non-standardized pipelines for data generation, simulation, and evaluation. We introduce BREIT, a modular framework for 3D MF-EIT stroke reconstruction providing: (i) a neuroimaging-to-EIT pipeline that converts CT/MRI into frequency-dependent GT admittivity volumes; (ii) a self-contained Python 3D Complete Electrode Model (CEM) forward solver for simulating MF-EIT voltages; and (iii) a 3D D-bar implementation supporting non-uniform electrode layouts. Building on BREIT, we propose dFNO-bar, which integrates Fourier Neural Operators into D-bar by learning a mapping from scattering data t(ξ) to conductivity σ(x){=}Re{γ}. We evaluate dFNO-bar against D-bar, Deep D-bar, and Gauss--Newton reconstructions on UCLH-matched synthetic data, and observe higher brain SSIM with comparable CC across noise settings.

Regeneration of the nervous system after injury remains an important therapeutic objective, especially in the central nervous system (CNS), in which regeneration is restricted by both neuronal limitations as well as adverse extracellular environments. Conversely, the peripheral nervous system (PNS) displays enhanced regenerative capability in the presence of supportive Schwann cells (SC) and pro-growth stimuli. While the structure and molecular mechanisms are thoroughly understood, functional biomarkers that can non-invasively monitor regeneration in real time are limited. In this review, we discuss the promise of electroencephalography (EEG) as well as electromyography (EMG) as real-time, non-invasive biomarkers to monitor damage to nerves and regeneration in both CNS and PNS contexts. First, we contrast biological and electrophysiological indicators of CNS/PNS injury, showing how EEG signs, including oscillatory power, connectivity, and evoked potential changes, reflect dysfunction due to injury as well as neuroplastic reorganization. Also, EMG provides direct insight into muscle activation and peripheral output, providing useful EEG complementation in neuromuscular pathway integrity and reactivation. In CNS injuries (e.g., stroke, spinal cord injury (SCI)), EEG typically shows global slowing, disrupted interhemispheric coherence, and partial recovery of higher frequencies. For PNS injuries, EEG can capture cortical remapping and return of somatosensory evoked responses with re-establishment of the peripheries' connectivity. EMG, in turn, enables monitoring of reinnervation and restoration of functional motor output. This review presents a dual-system perspective, positioning EEG and EMG not only as diagnostic tools but also as functional biomarkers of neural regeneration, thereby bridging electrophysiology, plasticity, and clinical recovery.

Diffusion-weighted magnetic resonance imaging (DW-MRI) can be used to characterise the microstructure of the nervous tissue, e.g. to delineate brain white matter connections in a non-invasive manner via fibre tracking. Magnetic Resonance Imaging (MRI) in high spatial resolution would play an important role in visualising such fibre tracts in a superior manner. However, obtaining an image of such resolution comes at the expense of longer scan time. Longer scan time can be associated with the increase of motion artefacts, due to the patient's psychological and physical conditions. Single Image Super-Resolution (SISR), a technique aimed to obtain high-resolution (HR) details from one single low-resolution (LR) input image, achieved with Deep Learning, is the focus of this study. Compared to interpolation techniques or sparse-coding algorithms, deep learning extracts prior knowledge from big datasets and produces superior MRI images from the low-resolution counterparts. In this research, a deep learning based super-resolution technique is proposed and has been applied for DW-MRI. Images from the IXI dataset have been used as the ground-truth and were artificially downsampled to simulate the low-resolution images. The proposed method has shown statistically significant improvement over the baselines and achieved an SSIM of 0.913pm0.045.

Brain MRIs are routinely acquired as multiple complementary sequences with unique contrast weighting, including T1-weighed imaging (T1w) anatomic and fluid-sensitive T2-weighted (T2w) contrasts. However, methods for learning unified representations across the multitude of MRI contrast mechanisms at health-system scale are lacking. In this study, we introduce Neuro-JEPA, a sparse multimodal neuroimaging foundation model that combines a latent predictive objective with a Mixture-of-Experts architecture to encode brain MRI across core T1w, T2w, and fluid-suppressed FLAIR imaging (FLAIR). We further provide a systematic methodological study of architectural, masking, objective, and sparsity design choices beneficial for robust neuroimaging multimodal representation learning. Neuro-JEPA was pretrained on 1,551,862 scans from 428,647 studies after modality-specific preprocessing with data curation across three core structural brain MRI sequences. We evaluated the learned representations across clinical and research settings, including 25 tasks from three health systems: NYU Langone, NYU Long Island, and Massachusetts General Hospital, and 22 tasks from 12 public datasets, covering unimodal, multimodal and cross-domain evaluation configurations. Across these benchmarks, existing neuroimaging foundation models showed inconsistent gains over a simple convolutional neural network (CNN) baseline, whereas Neuro-JEPA achieved stronger and more consistent performance across all evaluated settings. These results establish a scalable methodological framework for multimodal neuroimaging representation learning and highlight the need for foundation model evaluation protocols that include simple baselines, clinically heterogeneous cohorts and controlled multimodal comparisons.

Electroencephalography foundation models (EEG-FMs) have advanced brain signal analysis, but the lack of standardized evaluation benchmarks impedes model comparison and scientific progress. Current evaluations rely on inconsistent protocols that render cross-model comparisons unreliable, while a lack of diagnostic analyses obscures the internal mechanisms driving transfer efficiency and scaling behaviors. To address this, we introduce EEG-FM-Bench, a unified system for the standardized evaluation of EEG-FMs. The benchmark integrates 14 datasets across 10 paradigms and incorporates diverse experimental settings, including multiple fine-tuning strategies, task organizations, and classifier configurations, supported by tools for gradient and representation analysis. Our experiments and analysis reveal several critical insights: (1) multi-task learning acts as a critical regularizer to mitigate overfitting in data-scarce EEG contexts; (2) pre-training efficiency is currently limited by gradient conflicts between reconstruction objectives and downstream tasks; (3) model scaling deviates from typical laws, as compact architectures with domain-specific inductive biases consistently outperform significantly larger models. This benchmark enables fair comparison and reproducible analysis, shifting the field from fragmented results to interpretable advances. Code is available at https://github.com/xw1216/EEG-FM-Bench.

Generative modeling offers a promising solution to the scarcity of labeled clinical electroencephalography (EEG) data under strict privacy constraints. Although recent generative models report substantial improvements in generation fidelity, we show that these gains conceal a categorical failure. EEG is not an arbitrary multichannel signal: each channel records the voltage difference between two scalp electrodes. So, real recordings satisfy exact linear identities among their channels. Current generators invariably violate these identities, yet this has gone unnoticed. We therefore propose MontageFlow, a flow-matching model that enforces these identities by restricting its output to signals that satisfy them. We find that ensuring validity improves fidelity too. Furthermore, to retain the EEG characteristics that oversmoothing washes out, we also condition the model on a physiological state vector encoded from the whole EEG window. For generation, this vector is drawn from a prior fitted in latent space. Across 3 large-scale benchmarks, our model improves TS-FID by 1.6-3.6times over the closest rival while ensuring validity.

Decoding language from brain activity is a long-awaited goal in both healthcare and neuroscience. Major milestones have recently been reached thanks to intracranial devices: subject-specific pipelines trained on invasive brain responses to basic language tasks now start to efficiently decode interpretable features (e.g. letters, words, spectrograms). However, scaling this approach to natural speech and non-invasive brain recordings remains a major challenge. Here, we propose a single end-to-end architecture trained with contrastive learning across a large cohort of individuals to predict self-supervised representations of natural speech. We evaluate our model on four public datasets, encompassing 169 volunteers recorded with magneto- or electro-encephalography (M/EEG), while they listened to natural speech. The results show that our model can identify, from 3s of MEG signals, the corresponding speech segment with up to 72.5% top-10 accuracy out of 1,594 distinct segments (and 44% top-1 accuracy), and up to 19.1% out of 2,604 segments for EEG recordings -- hence allowing the decoding of phrases absent from the training set. Model comparison and ablation analyses show that these performances directly benefit from our original design choices, namely the use of (i) a contrastive objective, (ii) pretrained representations of speech and (iii) a common convolutional architecture simultaneously trained across several participants. Together, these results delineate a promising path to decode natural language processing in real time from non-invasive recordings of brain activity.

Interpretability methods for large language models (LLMs) typically derive directions from textual supervision, which can lack external grounding. We propose using human brain activity not as a training signal but as a coordinate system for reading and steering LLM states. Using the SMN4Lang MEG dataset, we construct a word-level brain atlas of phase-locking value (PLV) patterns and extract latent axes via ICA. We validate axes with independent lexica and NER-based labels (POS/log-frequency used as sanity checks), then train lightweight adapters that map LLM hidden states to these brain axes without fine-tuning the LLM. Steering along the resulting brain-derived directions yields a robust lexical (frequency-linked) axis in a mid TinyLlama layer, surviving perplexity-matched controls, and a brain-vs-text probe comparison shows larger log-frequency shifts (relative to the text probe) with lower perplexity for the brain axis. A function/content axis (axis 13) shows consistent steering in TinyLlama, Qwen2-0.5B, and GPT-2, with PPL-matched text-level corroboration. Layer-4 effects in TinyLlama are large but inconsistent, so we treat them as secondary (Appendix). Axis structure is stable when the atlas is rebuilt without GPT embedding-change features or with word2vec embeddings (|r|=0.64-0.95 across matched axes), reducing circularity concerns. Exploratory fMRI anchoring suggests potential alignment for embedding change and log frequency, but effects are sensitive to hemodynamic modeling assumptions and are treated as population-level evidence only. These results support a new interface: neurophysiology-grounded axes provide interpretable and controllable handles for LLM behavior.

Surface analysis of the cortex is ubiquitous in human neuroimaging with MRI, e.g., for cortical registration, parcellation, or thickness estimation. The convoluted cortical geometry requires isotropic scans (e.g., 1mm MPRAGEs) and good gray-white matter contrast for 3D reconstruction. This precludes the analysis of most brain MRI scans acquired for clinical purposes. Analyzing such scans would enable neuroimaging studies with sample sizes that cannot be achieved with current research datasets, particularly for underrepresented populations and rare diseases. Here we present the first method for cortical reconstruction, registration, parcellation, and thickness estimation for clinical brain MRI scans of any resolution and pulse sequence. The methods has a learning component and a classical optimization module. The former uses domain randomization to train a CNN that predicts an implicit representation of the white matter and pial surfaces (a signed distance function) at 1mm isotropic resolution, independently of the pulse sequence and resolution of the input. The latter uses geometry processing to place the surfaces while accurately satisfying topological and geometric constraints, thus enabling subsequent parcellation and thickness estimation with existing methods. We present results on 5mm axial FLAIR scans from ADNI and on a highly heterogeneous clinical dataset with 5,000 scans. Code and data are publicly available at https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all-clinical

Current medical vision-language models (VLMs) process volumetric brain MRI using 2D slice-based approximations, fragmenting the spatial context required for accurate neuroradiological interpretation. We developed Brain3D, a staged vision-language framework for automated radiology report generation from 3D brain tumor MRI. Our approach inflates a pretrained 2D medical encoder into a native 3D architecture and progressively aligns it with a causal language model through three stages: contrastive grounding, supervised projector warmup, and LoRA-based linguistic specialization. Unlike generalist 3D medical VLMs, Brain3D is tailored to neuroradiology, where hemispheric laterality, tumor infiltration patterns, and anatomical localization are critical. Evaluated on 468 subjects (BraTS pathological cases plus healthy controls), our model achieves a Clinical Pathology F1 of 0.951 versus 0.413 for a strong 2D baseline while maintaining perfect specificity on healthy scans. The staged alignment proves essential: contrastive grounding establishes visual-textual correspondence, projector warmup stabilizes conditioning, and LoRA adaptation shifts output from verbose captions to structured clinical reports\footnote{Our code is publicly available for transparency and reproducibility

Electroencephalography (EEG) provides real-time insights into brain activity and supports diverse applications in neuroscience. While EEG foundation models (EFMs) have emerged to address the scalability issues of task-specific models, current approaches still yield clinically uninterpretable and weakly discriminative representations, inefficiently capture global dependencies, and neglect important local neural events. We present CodeBrain, a two-stage EFM designed to fill this gap. In the first stage, we introduce the TFDual-Tokenizer, which decouples heterogeneous temporal and frequency EEG signals into discrete tokens, quadratically expanding the representation space to enhance discriminative power and offering domain-specific interpretability by suggesting potential links to neural events and spectral rhythms. In the second stage, we propose the multi-scale EEGSSM architecture, which combines structured global convolution with sliding window attention to efficiently capture both sparse long-range and local dependencies, reflecting the brain's small-world topology. Pretrained on the largest public EEG corpus, CodeBrain achieves strong generalization across 8 downstream tasks and 10 datasets under distribution shifts, supported by comprehensive ablations, scaling-law analyses, and interpretability evaluations. Both code and pretraining weights will be released in the future version.

State-of-the-art systems neuroscience experiments yield large-scale multimodal data, and these data sets require new tools for analysis. Inspired by the success of large pretrained models in vision and language domains, we reframe the analysis of large-scale, cellular-resolution neuronal spiking data into an autoregressive spatiotemporal generation problem. Neuroformer is a multimodal, multitask generative pretrained transformer (GPT) model that is specifically designed to handle the intricacies of data in systems neuroscience. It scales linearly with feature size, can process an arbitrary number of modalities, and is adaptable to downstream tasks, such as predicting behavior. We first trained Neuroformer on simulated datasets, and found that it both accurately predicted simulated neuronal circuit activity, and also intrinsically inferred the underlying neural circuit connectivity, including direction. When pretrained to decode neural responses, the model predicted the behavior of a mouse with only few-shot fine-tuning, suggesting that the model begins learning how to do so directly from the neural representations themselves, without any explicit supervision. We used an ablation study to show that joint training on neuronal responses and behavior boosted performance, highlighting the model's ability to associate behavioral and neural representations in an unsupervised manner. These findings show that Neuroformer can analyze neural datasets and their emergent properties, informing the development of models and hypotheses associated with the brain.

Modeling invasive neural spike data is fundamental to advancing high-performance brain-computer interfaces (BCIs). However, existing approaches face critical challenges, including limited-scale heterogeneous data, cross-domain distribution shift, and the intrinsic spatiotemporal complexity of invasive neural signals. In this work, we propose UniBCI, a unified pretrained model for invasive Brain-Computer Interfaces. The model integrates three key components: (1) a context-conditioned spatio-temporal tokenization (CST) scheme that embeds neural signals together with metadata into a shared representation space; (2) a hierarchical Interval-Area Attention (IAA) mechanism that captures patterns of spike dynamics in slots via linear attention and locality dependencies via sliding-window attention; and (3) a scalable self-supervised masked signals reconstruction objective for learning generalizable neural representations from large-scale unlabeled data. We construct a pretraining corpus spanning multiple species, subjects, brain regions, and behavioral experiment paradigms. These heterogeneous recordings are standardize via our proposed unified normalization and tokenization. Comprehensive experiments demonstrate that UniBCI achieves SOTA performance across diverse downstream tasks while improving generalization. Moreover, the model achieves a strong balance between accuracy and efficiency, with fewer trainable parameters and lower inference latency. These results suggest that UniBCI provides a practical step toward general-purpose neural foundation models, enabling robust, scalable, and transferable representation learning for invasive neural data. The code for this paper is available at: https://anonymous.4open.science/r/UniBCI-C805.

The objective of this study is to investigate the application of various channel attention mechanisms within the domain of brain-computer interface (BCI) for motor imagery decoding. Channel attention mechanisms can be seen as a powerful evolution of spatial filters traditionally used for motor imagery decoding. This study systematically compares such mechanisms by integrating them into a lightweight architecture framework to evaluate their impact. We carefully construct a straightforward and lightweight baseline architecture designed to seamlessly integrate different channel attention mechanisms. This approach is contrary to previous works which only investigate one attention mechanism and usually build a very complex, sometimes nested architecture. Our framework allows us to evaluate and compare the impact of different attention mechanisms under the same circumstances. The easy integration of different channel attention mechanisms as well as the low computational complexity enables us to conduct a wide range of experiments on four datasets to thoroughly assess the effectiveness of the baseline model and the attention mechanisms. Our experiments demonstrate the strength and generalizability of our architecture framework as well as how channel attention mechanisms can improve the performance while maintaining the small memory footprint and low computational complexity of our baseline architecture. Our architecture emphasizes simplicity, offering easy integration of channel attention mechanisms, while maintaining a high degree of generalizability across datasets, making it a versatile and efficient solution for EEG motor imagery decoding within brain-computer interfaces.

Electroencephalography (EEG) signals provide critical insights for applications in disease diagnosis and healthcare. However, the scarcity of labeled EEG data poses a significant challenge. Foundation models offer a promising solution by leveraging large-scale unlabeled data through pre-training, enabling strong performance across diverse tasks. While both temporal dynamics and inter-channel relationships are vital for understanding EEG signals, existing EEG foundation models primarily focus on the former, overlooking the latter. To address this limitation, we propose Graph-Enhanced EEG Foundation Model (GEFM), a novel foundation model for EEG that integrates both temporal and inter-channel information. Our architecture combines Graph Neural Networks (GNNs), which effectively capture relational structures, with a masked autoencoder to enable efficient pre-training. We evaluated our approach using three downstream tasks and experimented with various GNN architectures. The results demonstrate that our proposed model, particularly when employing the GCN architecture with optimized configurations, consistently outperformed baseline methods across all tasks. These findings suggest that our model serves as a robust foundation model for EEG analysis.

Closed-loop brain stimulation refers to capturing neurophysiological measures such as electroencephalography (EEG), quickly identifying neural events of interest, and producing auditory, magnetic or electrical stimulation so as to interact with brain processes precisely. It is a promising new method for fundamental neuroscience and perhaps for clinical applications such as restoring degraded memory function; however, existing tools are expensive, cumbersome, and offer limited experimental flexibility. In this article, we propose the Portiloop, a deep learning-based, portable and low-cost closed-loop stimulation system able to target specific brain oscillations. We first document open-hardware implementations that can be constructed from commercially available components. We also provide a fast, lightweight neural network model and an exploration algorithm that automatically optimizes the model hyperparameters to the desired brain oscillation. Finally, we validate the technology on a challenging test case of real-time sleep spindle detection, with results comparable to off-line expert performance on the Massive Online Data Annotation spindle dataset (MODA; group consensus). Software and plans are available to the community as an open science initiative to encourage further development and advance closed-loop neuroscience research.

This study examines the efficacy of various neural network (NN) models in interpreting mental constructs via electroencephalogram (EEG) signals. Through the assessment of 16 prevalent NN models and their variants across four brain-computer interface (BCI) paradigms, we gauged their information representation capability. Rooted in comprehensive literature review findings, we proposed EEGNeX, a novel, purely ConvNet-based architecture. We pitted it against both existing cutting-edge strategies and the Mother of All BCI Benchmarks (MOABB) involving 11 distinct EEG motor imagination (MI) classification tasks and revealed that EEGNeX surpasses other state-of-the-art methods. Notably, it shows up to 2.1%-8.5% improvement in the classification accuracy in different scenarios with statistical significance (p < 0.05) compared to its competitors. This study not only provides deeper insights into designing efficient NN models for EEG data but also lays groundwork for future explorations into the relationship between bioelectric brain signals and NN architectures. For the benefit of broader scientific collaboration, we have made all benchmark models, including EEGNeX, publicly available at (https://github.com/chenxiachan/EEGNeX).

Electroencephalography (EEG), with its broad range of applications, necessitates models that can generalize effectively across various tasks and datasets. Large EEG Models (LEMs) address this by pretraining encoder-centric architectures on large-scale unlabeled data to extract universal representations. While effective, these models lack decoders of comparable capacity, limiting the full utilization of the learned features. To address this issue, we introduce ECHO, a novel decoder-centric LEM paradigm that reformulates EEG modeling as sequence-to-sequence learning. ECHO captures layered relationships among signals, labels, and tasks within sequence space, while incorporating discrete support samples to construct contextual cues. This design equips ECHO with in-context learning, enabling dynamic adaptation to heterogeneous tasks without parameter updates. Extensive experiments across multiple datasets demonstrate that, even with basic model components, ECHO consistently outperforms state-of-the-art single-task LEMs in multi-task settings, showing superior generalization and adaptability.

Content-based image retrieval (CBIR) in neuroimaging enables the identification of structurally similar brain scans, supporting diagnosis, prognosis, and treatment planning; however, existing methods are often limited to small datasets, single brain regions, or coarse class labels, thereby restricting their clinical utility and generalizability. Here, we present NeuroCBIR, a framework for fast and flexible retrieval of both whole-brain and region-specific 3D T1w MRI scans. A total of 103 cortical and subcortical regions are extracted to enable both whole-brain and region-level queries. NeuroCBIR leverages latent representations learned by a variational autoencoder (VAE) combined with contrastive learning, producing scan-specific embeddings that capture anatomical patterns. These embeddings were evaluated for subject re-identification, zero-shot age prediction, and zero-shot multi-class pathology stratification. Re-identification performance was high across both whole-brain and brain-region levels (mean average precision across the top-5 retrieved images (mAP@5) >= 98.4%), with robust generalization across datasets and acquisition conditions. While NeuroCBIR is not trained for age prediction or pathology stratification, zero-shot evaluations for these two tasks demonstrate that the embeddings encode meaningful information for downstream tasks. Embedding extraction on a 4-core CPU required approximately 18.7 s per scan, whereas similarity search was effectively instantaneous (less than 0.01 s). NeuroCBIR is publicly available for brain MRI with more than 26,000 precomputed T1w MRI embeddings. It supports reproducible research, region-specific flexibility, and clinically meaningful personalized diagnostic support. The software is available at https://github.com/minnelab/NeuroCBIR.

Recent work has demonstrated that complex visual stimuli can be decoded from human brain activity using deep generative models, offering new ways to probe how the brain represents real-world scenes. However, many existing approaches first map brain signals into intermediate image or text feature spaces before guiding the generative process, which obscures the contributions of different brain areas to the final reconstruction output. In this work, we propose NeuroAdapter, a visual decoding framework that directly conditions a latent diffusion model on brain representations, bypassing the need for intermediate feature spaces. Our method demonstrates competitive visual reconstruction quality on public fMRI datasets compared to prior work, while providing greater transparency into how brain signals drive visual reconstruction. To this end, we introduce an Image-Brain BI-directional interpretability framework (IBBI) that analyzes cross-attention patterns across diffusion denoising steps to reveal how different cortical areas influence the unfolding generative trajectory. Our work highlights the potential of end-to-end brain-to-image reconstruction and establishes a path for interpretable neural decoding.

This paper introduces DreamDiffusion, a novel method for generating high-quality images directly from brain electroencephalogram (EEG) signals, without the need to translate thoughts into text. DreamDiffusion leverages pre-trained text-to-image models and employs temporal masked signal modeling to pre-train the EEG encoder for effective and robust EEG representations. Additionally, the method further leverages the CLIP image encoder to provide extra supervision to better align EEG, text, and image embeddings with limited EEG-image pairs. Overall, the proposed method overcomes the challenges of using EEG signals for image generation, such as noise, limited information, and individual differences, and achieves promising results. Quantitative and qualitative results demonstrate the effectiveness of the proposed method as a significant step towards portable and low-cost ``thoughts-to-image'', with potential applications in neuroscience and computer vision.

Pathology diagnosis based on EEG signals and decoding brain activity holds immense importance in understanding neurological disorders. With the advancement of artificial intelligence methods and machine learning techniques, the potential for accurate data-driven diagnoses and effective treatments has grown significantly. However, applying machine learning algorithms to real-world datasets presents diverse challenges at multiple levels. The scarcity of labelled data, especially in low regime scenarios with limited availability of real patient cohorts due to high costs of recruitment, underscores the vital deployment of scaling and transfer learning techniques. In this study, we explore a real-world pathology classification task to highlight the effectiveness of data and model scaling and cross-dataset knowledge transfer. As such, we observe varying performance improvements through data scaling, indicating the need for careful evaluation and labelling. Additionally, we identify the challenges of possible negative transfer and emphasize the significance of some key components to overcome distribution shifts and potential spurious correlations and achieve positive transfer. We see improvement in the performance of the target model on the target (NMT) datasets by using the knowledge from the source dataset (TUAB) when a low amount of labelled data was available. Our findings indicate a small and generic model (e.g. ShallowNet) performs well on a single dataset, however, a larger model (e.g. TCN) performs better on transfer and learning from a larger and diverse dataset.

Preclinical models poorly predict human drug efficacy, particularly in neurological disorders. Neural activity offers a uniquely rich source of translational information because it captures high-dimensional variation in nervous-system function that can be measured in both animals and humans. However, its high dimensionality makes it difficult to distinguish conserved disease-related features from variation arising from species, recording modality and experimental context. Here, we test whether shared neural dynamics can be identified directly from electrophysiology data by learning representations organized by biological state rather than species. We develop a dual-rule contrastive learning framework that aligns corresponding mouse and human states while preserving separation between distinct phenotypes. This framework recovered conserved sensory-response structure across species and, in epilepsy, resolved distinct relationships between three mouse models and heterogeneous human patient populations. When treated animals were projected into a frozen cross-species representation, drug-induced movement towards the human-aligned healthy state retrospectively tracked known clinical efficacy across ten model-drug combinations including a disease-specific detrimental effect. The framework also identified shared disease-associated neural dynamics between Fmr1-knockout mice and human 16p11.2 copy-number variant carriers despite differences in genetic aetiology and recording modality. Together, these findings show the potential of cross-species neural representation learning to map heterogeneous human disease onto experimentally tractable preclinical states and assess whether interventions restore human-relevant circuit function.

Deep networks for electroencephalogram (EEG) decoding are often only trained to solve one specific task, such as pathology or age decoding. A more general task-agnostic approach is to train deep networks to match a (clinical) EEG recording to its corresponding textual medical report and vice versa. This approach was pioneered in the computer vision domain matching images and their text captions and subsequently allowed to do successful zero-shot decoding using textual class prompts. In this work, we follow this approach and develop a contrastive learning framework, EEG-CLIP, that aligns the EEG time series and the descriptions of the corresponding clinical text in a shared embedding space. We investigated its potential for versatile EEG decoding, evaluating performance in a range of few-shot and zero-shot settings. Overall, we show that EEG-CLIP manages to non-trivially align text and EEG representations. Our work presents a promising approach to learn general EEG representations, which could enable easier analyses of diverse decoding questions through zero-shot decoding or training task-specific models from fewer training examples. The code for reproducing our results is available at https://github.com/tidiane-camaret/EEGClip