brain-computer interface developers

Abstract: Brain foundation models have transformed medical artificial intelligence and computational neuroscience by reducing the reliance on task-specific data through large-scale pretraining. While they have been successful with non-invasive neuroimaging data, their adoption in functional near-infrared spectroscopy (fNIRS) has lagged due to the limited size and heterogeneity of public datasets, which are collected under varying protocols, devices, and sensor configurations. In addition, no single fNIRS dataset is comparable in size to the largest datasets in functional magnetic resonance imaging (fMRI), electroencephalography (EEG), or magnetoencephalography (MEG). The fNIRS datasets are also spread across different platforms and often have insufficient information, or lack the protocols that would make them easier to use. Given the advances in EEG foundation models that enable flexible modeling across diverse EEG montages, we curated 1,955 hours of fNIRS data from 67 public datasets spanning 2,798 participants, representing the largest fNIRS curation effort to date. The curated data include oxygenated (HbO) and deoxygenated (HbR) hemoglobin signals along with the three-dimensional position of every channel in the standard space of the Montreal Neurological Institute (MNI), which makes positions comparable across datasets. We release dataloaders that handle each dataset automatically, along with the minimal preprocessing pipeline used to prepare the data, at https://github.com/sposso/fnirs-datasets. This work aims to facilitate the future development of foundation models for fNIRS.

Abstract: Electroencephalography (EEG) has proven to be a powerful tool for decoding neural activity in real-life scenarios, including the perception and processing of emotions elicited by music. Among the various musical features that modulate these responses, musical mode and melodic direction (or contour) play a central role. This work proposes a novel EEG feature extraction framework based on Empirical Mode Decomposition (EMD) to decompose EEG signals recorded during active piano performance for the detection of these two musical features. Energy-based descriptors were computed from the first four Intrinsic Mode Functions (IMFs) obtained through EMD and used to train a Wide Neural Network classifier. The model performance was benchmarked against several standard classifiers commonly employed in EEG classification tasks. Two experimental scenarios were explored: intra-subject and intersubject. In the former case, the proposed framework achieved average accuracies of 84%, whereas in the inter-subject case, accuracies reached 81% on average using the first IMF, with AUC-ROC values of 0.9 on average in both cases. A frequency-domain analysis revealed a strong correspondence between the IMFs and conventional EEG sub-bands, except for certain specific frequency components that were not fully represented. Predominant activations were observed over the frontal, temporal, and parietooccipital regions, areas consistently associated with music processing. Furthermore, the proposed method demonstrated robustness to handedness, successfully classifying EEG data across participants regardless of their dominant hand. These findings highlight the potential of EMD-based feature extraction for identifying music-related neural patterns and contribute to advancing research in Music Information Retrieval (MIR), affective neuroscience, and the broader understanding of the neural encoding of musical structure.

Abstract: When one time series informs another, the delay at which that information arrives determines if models can utilize this relationship effectively. A source may be strongly predictive at one delay but uninformative at neighboring lags. Therefore, fixed input windows may obscure this structure by bundling informative and irrelevant history together. Transfer entropy (TE) can recover these delays by measuring how much a source's past tells us about a target beyond the target's own history. However, existing TE estimators require separate fits across source and conditioning depths, with further estimation on local windows to track delays over time. We introduce ATEMPO, a diffusion-based transfer entropy estimator amortized over lags and time. ATEMPO samples source and conditioning depths during training and conditions explicitly on temporal position, allowing a single score network to estimate the full TE surface without refitting. Differencing this surface recovers when information arrives. Across synthetic datasets with ground-truth TE, ATEMPO achieves the lowest mean relative error among baselines, and on datasets with known lags, ATEMPO achieves $0.98\pm0.04$ lag-detection accuracy. ATEMPO requires a single fit across source depths $K=6$ and target depths $L=3$, whereas existing estimators require 18 separate fits to evaluate the same $K \times L$ grid. On three systems with time-varying lag, ATEMPO is the only estimator to maintain perfect lag-detection accuracy across all evaluated window lengths. These recovered delays improve downstream forecasting: ATEMPO-selected inputs reduce MSE on WEATHER-5K by 7.25%, while 120 selected inputs outperform the benchmark's 240-feature default by 4.6%. Across three brain-computer interface tasks, using ATEMPO-selected lags achieves the highest or equal-best $R^2$, improving mean $R^2$ by 4.1% relative to the strongest competing baseline.

Abstract: Electroencephalography (EEG) is widely used in clinical assessment, brain-computer interfaces, and cognitive-state analysis, yet EEG modeling remains fragmented across task paradigms. Recent multimodal large language models (MLLMs) provide a promising interface for flexible multimodal reasoning, but their ability to understand EEG inputs remains limited. In this work, we propose OneEEG, a unified EEG-MLLM framework for multi-task EEG understanding. By training on our curated OneEEG-Instruct, a multi-task EEG instruction-tuning dataset, OneEEG jointly models numerical EEG representations and visual EEG representations, and introduces a task-aware Mixture of Projectors (MoP) to align heterogeneous EEG features across different task families with the LLM embedding space. We further establish OneEEG-Bench, a benchmark for evaluating current MLLMs and our method on multi-task EEG understanding. Experiments show that existing MLLMs have limited ability to interpret EEG inputs, while OneEEG achieves stronger performance by integrating numerical and visual EEG representations with task-aware EEG-to-LLM projection. Extensive ablations and analyses further reveal the effects of visual EEG renderings, MoP variants, router behavior, and feature dispersion across EEG tasks.

Abstract: Sustained attention is critical for academic performance, yet existing auditory support tools are static and not grounded in real-time neural evidence. This paper presents EEGBiFormer, a hybrid CNN-Transformer model for realtime binary classification of attention states, focus versus nonfocus, from 16-channel EEG signals. A custom analog front-end acquisition board was designed and built to collect a task-based EEG dataset. Before model training, spectral and connectivity analysis, using Power Spectral Density and Phase Locking Value, confirmed distinct neural signatures between attention states, providing physiological grounding for the classification approach. EEGBiFormer achieved 91.3 percent window-level validation accuracy with an F1 score of 94.5 percent, and 88.2 percent recording-level accuracy across 17 independent sessions. End-to-end system latency was measured below 100 ms, supporting real-time responsiveness. The trained model was further used to objectively rank auditory stimuli by focus-state confidence, yielding EEG-informed audio protocols. In a paired within-subject behavioral study with 37 participants, these protocols produced a statistically significant 20 percent improvement in composite attention scores over silent controls, with a medium-to-large effect size. This work demonstrates a complete pipeline from custom EEG hardware through neural signal analysis, deep learning classification, and evidence-based auditory protocol design.

Abstract: Electroencephalography (EEG)-to-language models offer a promising approach for translating complex neural signals into human-readable descriptions. However, generating plausible language does not necessarily demonstrate that a model has learned to interpret the underlying EEG signal. A direct way to assess such interpretation is to probe objectively measurable properties of the signal itself. We therefore construct an EEG-language dataset of 160,781 segments annotated with signal-level question answering (QA) pairs, where each question targets one of five property families and requires a quantitative comparison involving spectral, spatial, temporal, or lateral signal properties. Each segment is also paired with a feature-grounded EEG caption. We further propose a Dual-Domain EEG Encoder that jointly models temporal waveforms and spectral-spatial representations, and introduce EEG-Captioner, a unified EEG-to-language framework trained with both signal-level QA and EEG caption supervision. Experiments show that the proposed encoder achieves the highest overall macro-averaged balanced accuracy (Macro-BA) among the compared EEG encoders, while EEG-Captioner achieves a Macro-BA of 88.81% on signal-level QA and improves caption factual consistency from 82.06% to 83.46% over caption-only language adaptation, demonstrating the complementary benefits of signal-level QA and caption supervision.

Abstract: Electrophysiological source imaging is severely underdetermined because the lead-field matrix has limited rank relative to the source dimension and strongly correlated columns. Scalp EEG measurements constrain only the observable row-space component, leaving a high-dimensional null space unobservable. We propose a two-stage framework coupling posterior diffusion refinement with deterministic null-space completion. A minimum-norm-initialized, singular-coordinate Posterior-DDIM sampler combines a spatiotemporal diffusion prior with direction-dependent measurement reliability to refine the observable component. A frozen ridge predictor and nonlinear temporal residual network then estimate the null component under explicit projection constraints, preserving the refined row estimate and its predicted EEG exactly. All learned components are trained exclusively on simulated cortical activity and its row-null decomposition, without paired EEG-source training data. Across simulations with varying noise levels, the method achieved higher frame-level area under the receiver operating characteristic curve and average precision, together with lower localization error, than conventional and learning-based baselines. Exploratory evaluations on evoked EEG and simultaneous scalp EEG-stereo-EEG recordings showed condition- and event-dependent concordance with cross-modal and intracranial references.

Abstract: EEG analysis and decoding underpin brain-computer interfaces, cognitive assessment, and sleep monitoring. Fixed pipelines and reward-driven search do not explicitly determine how signal structure, representations, predictor behavior, and training dynamics contribute to performance or generalization gaps, leaving intervention choice underdetermined. We introduce NeuroAct, an autonomous research agent framework for EEG analysis and decoding. NeuroAct implements dual-loop autonomous research across EEG foundation models, task-specific predictors, and model combinations. In an inner loop, research, development, and review roles use evidence on signal structure, representations, predictor behavior, and training dynamics to test hypotheses, select analyses or interventions, and refine candidates using performance, stability, and cost feedback. An outer loop distills outcomes into conditional, testable recommendations with task and model conditions, then validates and revises them on subsequent tasks.We evaluate four settings: (A) EEG General Analysis, (B) Cross-task Model Optimization, (C) Single-task Open Research, and (D) Collaborative Prediction. In Setting A, NeuroAct's 80.88 macro-average exceeds BrainAgent's 63.13 by 17.75 points. In Setting B, NeuroAct raises EEGPT's mean balanced accuracy (BA) by 7.34 points and HBN Pearson's (r) from 0.6894 to 0.7362; in Setting C, it improves ADFTD BA by 16.33 points; and in Setting D, it raises Workload BA from 79.69% to 85.02%. Experience reuse raises BCIC-IV-2a BA from 34.66% to 50.81% while reducing LLM tokens by 64.02%, indicating recommendations improve cross-task performance. NeuroAct enables evidence-guided EEG research improved by cross-task experience.

Abstract: Motor imagery brain-computer interfaces require reliable decoding from multichannel EEG, but practical acquisition often yields sparse or corrupted electrode montages. We propose TriRouter, an electrode-space routing framework with discriminative-preservation, mask-robustness, and latent-compensation paths. A validation-calibrated router uses observable channel availability to allocate path contributions, preserving complete-channel discrimination while increasing representation recovery under severe missingness. In BNCI2014-001, TriRouter outperforms standard public backbones and a dynamic-spatial-filtering corrupted-EEG baseline. It improves accuracy over the strongest corrupted-EEG baseline by 3.68, 4.02, and 6.46 percentage points at nominal 25%, 50%, and 75% missing settings, and remains effective under structured regional missingness and additional low-channel dataset evaluation.

Abstract: Cross-dataset EEG decoding often treats montage, reference, and active-sensor changes as representation shift, although they also alter the observation operator. We study target-statistics-blind transfer: fitting receives no target signal, label, or empirical statistic, and electrode coordinates only instantiate a fixed prediction operator. method removes the active-set common-reference gauge and transports each native mask through a template motor leadfield. A source-fitted spectral classifier anchors the decision; a bounded state-space-model (SSM) residual is secondary. We establish restricted identifiability and an operator-perturbation bound. Across five leave-one-dataset-out targets (253 participants), dynamic method achieved 60.865% equal-target balanced accuracy versus 52.684% for strict-clean 5/5 BIOT (hierarchical difference +8.182 points; 95% CI +6.382 to +10.196; positive in every target). On four EEGPT-clean targets, the descriptive means were 61.520% and 59.057%. In four post-hoc exact same-parent tests, FULL exceeded coordinate-basis, matched-spectrum, row-shuffled, and wrong-anatomy controls by 9.959, 9.698, 11.241, and 3.985 points, respectively (all 95% CIs excluded zero; Holm-adjusted P<0.001). A separate 60-participant same-paradigm evaluation retained a positive physical-operator contrast (+4.029 points; +2.338 to +5.773), whereas dynamic--static was inconclusive; its preregistered status is partial confirmation rather than unrestricted external validation. The SSM added +1.059 points (+0.013 to +1.892). Claims remain bounded to five binary motor-imagery domains and the tested operators.

Abstract: Understanding how the human brain constructs meaning from real-world language remains a fundamental challenge, as semantics depend on context that varies in natural settings. To enable the study of real-world linguistic meaning in the brain, we introduce SCRIBE, a framework grounded in a neuroscience-informed semantic space that leverages an ensemble of open-source large language models to generate interpretable, word-level semantic representations of arbitrary text. In a behavioral study with 921 participants, we show that human semantic feature judgments vary systematically with context, and that SCRIBE captures these shifts, reaching 75-81% of the estimated human noise ceiling. Using brain activity recorded while participants listen to naturalistic stories, we further demonstrate that SCRIBE predicts neural responses in language-selective brain regions, significantly outperforming non-contextual semantic representations. Variance partitioning reveals that SCRIBE explains unique brain-predictive information beyond syntactic features, suggesting that its representations capture aspects of linguistic meaning not accounted for by the measured syntactic features. Together, these findings establish SCRIBE as a scalable and interpretable foundation for studying natural language semantics in the brain.

Abstract: Objective. A decoder of imagined speech that works for a new user without calibration would make a non-invasive speech interface practical. We tested whether imagined-speech content recorded with scalp electroencephalography (EEG) transfers across people, and examined why accuracy within a single person remains low. Approach. We analyzed three public corpora, ds003626, KaraOne and Track 3 of the 2020 International Brain-Computer Interface Competition, under a protocol that enforces split integrity by assertion and reports exact binomial thresholds, group tests and bootstrap confidence intervals. We trained decoders on each participant and tested them on every other, compared representational geometry across participants without a classifier, applied subject-level alignment, and tested five explanations for the within-subject ceiling. Main results. Across 482 ordered pairs of participants, no pair survived correction for multiple comparisons; mean pair-transfer accuracy lay within 0.006 of chance on every corpus, while every within-subject reference lay above it. Imagery against pre-stimulus rest generalized at about 0.61 after artifact and elapsed-time controls, but its decoder labelled the interval preceding imagery as imagery as often as imagery itself, so the contrast reflects a post-stimulus state, not imagery. Within subject, only the competition corpus decoded above threshold for every participant (0.3147; chance 0.200); syllable count explained little of this, but its frequency profile failed an artifact audit. Significance. In these corpora, imagined-speech content did not transfer between people through any representation we examined. Trial count per class was the only variable that ordered the corpora, which favors larger single-condition datasets over further model development.

Abstract: Imagined speech decoding from EEG offers a promising route toward naturalistic brain-computer interfaces. Traditional closed-set classifiers treat semantic categories as independent labels and do not explicitly exploit relationships among linguistic intents, limiting output flexibility. We adapt a multimodal contrastive learning framework to imagined speech, aligning EEG trials with language representations in the embedding space of a frozen pretrained text encoder. An EEG encoder is trained with a composite objective combining semantically reweighted EEG-sentence alignment and text-prototype-based class discrimination, encouraging semantic structure while preserving separability among 39 intent categories. We evaluate the approach on the Chisco imagined speech dataset across five subjects, reporting Top-k accuracy, macro-F1, and balanced pairwise matching accuracy (2v2). We also investigate maximum EEG-text cosine similarity (MaxCosine) as an intrinsic indicator of decoding reliability and probe semantic structure beyond category labels using five evaluation-time semantic axes and a qualitative Semantic Gallery Probe (SGP) with previously unseen candidate sentences. The contrastive framework achieved decoding performance comparable to a task-optimized closed-set classifier while mapping EEG into a frozen language embedding space. MaxCosine identified subsets of held-out trials with higher Top-1 and Top-5 accuracy across subjects. Evaluation-time semantic axes showed mean agreement above the 50% chance reference across all five dimensions, and the SGP qualitatively illustrated direct comparison with unseen candidate sentences. Together, these findings suggest that EEG-language alignment can retain comparable fixed-intent decoding while supporting similarity-based retrieval, intrinsic reliability ranking, and evaluation of broader semantic structure.

Abstract: Asynchronous EEG event detection supports practical brain-computer interfaces by identifying event classes and temporal boundaries directly from continuous recordings without predefined event boundaries at inference time. The primary challenge lies in extracting event-related patterns embedded in ongoing background activity. To address this, we propose \textbf{NeuroDETR}, a discrete spatiotemporal multiscale framework that combines structured tokenization with event-aware feature refinement. Multiscale temporal codebooks capture brief responses and sustained dynamics, while Spatial-Pyramid VQ hierarchically encodes spatial structure across EEG channels. These complementary representations form a compact event memory for jointly classifying events and estimating their onsets and offsets. Before tokenization, we apply FOCAL, an event-aware sparse attention module that uses predicted event presence to guide temporal feature refinement and spatial aggregation, emphasizing likely event periods while preserving context across the recording. Experiments on eight EEG datasets that span diverse paradigms demonstrate state-of-the-art performance. These findings provide a basis for the development of BCI systems that recognize meaningful neural activity during continuous interaction and monitoring.

Abstract: Decoding visual experience from fMRI is important for understanding human perception and developing brain-computer interfaces. Recent generative decoding methods can reconstruct plausible images and videos, but visual plausibility alone does not ensure that the output is faithfully grounded in brain activity. In this work, we propose Neurons++, a visual-stream fMRI reconstruction framework for both static image and dynamic video reconstruction. Compared with our conference version Neurons, Neurons++ extends the paradigm from video-only reconstruction to visual-stream reconstruction for both images and videos, and replaces parallel task conditioning with serial cortex-inspired decoding. The model first uses image-fMRI pretraining to obtain a stable spatial-semantic initialization, and then performs subject-specific fine-tuning for image and video reconstruction separately. The serial design organizes fMRI-derived representations into explicit spatial, semantic, language-level, and temporal cues. Extensive experiments show that Neurons++ achieves state-of-the-art video reconstruction and competitive image reconstruction across standard benchmarks. Beyond reconstruction fidelity, neural-to-visual analyses indicate that Neurons++ exhibits qualitative directional controllability under neural perturbation, that its fMRI encoder read-out is sensitive to stimulus-relevant cortical features, and that it supports ROI-guided semantic modulation. Code and model weights are available at: https://github.com/xmed-lab/NeuronsPlusPlus.

Abstract: The brain maintains stable cognition despite continuously changing neural activity. How to extract stable cognitive states from variable neural observations remains a central problem in neural decoding. Existing neural decoding methods map neural observations to predefined external labels based on the stimulus-response principle, often capturing recording-specific spurious correlations. Inspired by how the brain infers the world, and specifically by Bayesian brain theory, we recast neural decoding as cognitive inference constrained by brain-intrinsic priors, yielding high-level meta-neural semantic representations. In decoding experiments spanning five neural recording modalities and three cognitive domains (motor, perception and internal mentation), our cognitive inference method reorganized the geometry of neural observation representations, yielding meta-neural semantic representations that exhibited consistent geometric relationships across cognitive tasks and enabled the recovery of stable cognitive states from variable neural observations. Our work provides an account of how the brain maintains relatively stable cognition despite continual changes in the external environment. Cognitive stability is sustained through cognitive inference from changing neural activity, without requiring fixed neural activity patterns.

Abstract: Brain signal decoding is challenging because neural recordings are noisy and vary across individuals, while labeled data are often limited. Recent attention-based models on the symmetric positive definite (SPD) manifold have nevertheless achieved strong performance using covariance and connectivity representations, yet the contribution of learned token weighting remains unclear. We examine two representative architectures, MAtt (based on log-Euclidean geometry) and GBWAtt (based on generalized Bures--Wasserstein geometry), and find that their learned attention weights remain close to uniform after training. We relate this behavior to bounded similarity parameterizations that, under the original softmax scaling, limit attention-weight contrast. Moreover, replacing learned weights with uniform weights, throughout training and evaluation, has little effect on mean predictive performance while preserving each model's original aggregation geometry. Motivated by these findings, we introduce SPD-MetaFormer, an attention-free architecture built on uniformly weighted Fréchet aggregation under log-Euclidean geometry. Its backbone uses a geodesic residual to update a summary token and a shared spectral feedforward map to transform all tokens, followed by a learned weighted readout. Token states remain SPD-valued until tangent-space classification. Across three EEG benchmarks, SPD-MetaFormer achieves competitive results relative to published Euclidean and manifold baselines. Separate matched reproductions test learned versus uniform weighting within MAtt and GBWAtt. These results suggest that, in the short-sequence and limited-data regimes studied, carefully designed SPD architectures can provide a simpler and effective alternative to adaptive manifold attention.

Abstract: Electroencephalography (EEG) is highly susceptible to electromyographic (EMG) artifacts, whose temporal heterogeneity and spatial-spectral overlap with neural activity can leave mixed sources after blind source separation. Existing artifact-removal methods are further limited by scarce reliable component-level ground truth: expert annotations are costly and subjective, while no established method provides realistic simulation-based ground truth for EMG contamination in multichannel scalp EEG. To address these limitations, we propose a framework combining a frequency-aware high-dimensional representation with Multi-Instance Learning. The representation unfolds separated components into frequency-resolved intra-components, creating a space in which mixed neural and muscular activity becomes more separable, while the weakly supervised learning formulation enables artifact-likelihood scores for individual intra-components to be learned from epoch-level labels without finer-grained ground truth. The resulting intra-component classifier supports fine-grained EMG artifact detection and score-guided attenuation. Experiments on held-out subjects show that the framework learns informative intra-component scores and reduces artifact-related spectral deviations most clearly for jaw tension, with moderate effects for raising eyebrows and limited effects for frowning.

Abstract: Visual decoding from fMRI is typically siloed by participant and experiment, obscuring whether heterogeneous neural measurements can be organized within a common computational geometry. Here we introduce BRAID-fMRI (Brain Representation Alignment across Individuals and Datasets), a shared CLIP-supervised decoding framework. BRAID-fMRI uses a single ROI-wise Transformer with optional participant conditioning across eight visual-fMRI datasets comprising 93 dataset-specific participant entries, 430,007 single-trial responses and 162,839 unique stimuli. Regional brain activity is aligned with 512-dimensional CLIP ViT-B/32 representations using a multi-positive contrastive objective that treats repeated stimuli across participants and datasets as positives. BRAID-fMRI supports retrieval across seven evaluation datasets. On eight matched participant entries, it achieves 35.0 +/- 11.1% Top-10 accuracy, exceeding the observed mean accuracy of the two evaluated baselines - the MindEye-style pooled-CLIP decoder (27.1 +/- 5.1%) and ridge regression (21.1 +/- 9.1%) - and attaining the highest observed accuracy for seven of eight entries. In separately trained participant-agnostic models, expanding the source pool increased target-dataset holdout accuracy by up to 92.1% relative to the initial source-training condition. The learned space preserves graded semantic structure, while ablations and saliency highlight ventral and early visual cortex and category-specific motion and attentional systems. These results support scalable cross-dataset decoding into a common CLIP-aligned space, with model sensitivity concentrated in ventral and early visual inputs.

Abstract: Electroencephalography (EEG) offers millisecond temporal resolution, but inferring underlying neural sources is a severely ill-posed spatial inverse problem. While deep learning has advanced spatial reconstruction, current architectures face a critical dilemma: frame-by-frame models discard vital temporal context, whereas full 4D spatiotemporal networks introduce an architectural trade-off between reconstruction accuracy and inference cost. We propose a novel two-stream framework that explicitly decouples global temporal representation learning from per-time-point spatial refinement. A Transformer-based Temporal Condition Encoder processes the entire EEG sequence via factorized spatiotemporal attention, retaining sensor-resolved features. A fixed inverse then maps these features into source-indexed conditioning for a per-timestep Source-Space Transformer or volumetric convolutional refiner. Extensive evaluations on realistic synthetic data demonstrate that this temporal prior dramatically improves spatial localization, outperforming classical and spatiotemporal baselines, particularly in high-noise and multi-source regimes. Training across diverse leadfields and explicit operator mismatches improves transfer to unseen head geometries and brings template-based reconstruction closer to subject-specific inversion. Furthermore, we apply the model trained only on synthetic EEG data to real-world EEG. A logistic regressor fit on source power differences in eyes-open, eyes-closed conditions successfully decodes age groups.

Abstract: Cephalonauts One is a whole-brain 3 Tesla (3T) functional magnetic resonance imaging (fMRI) dataset recorded while subjects listened to audio podcasts. Three healthy subjects underwent multiple scanning sessions, each consisting of five 15-minute runs, while listening to podcasts in their native language. With 30 hours of fMRI data per subject, the current release is the deepest available fMRI dataset using naturalistic speech stimuli. The dataset pairs brain activity with the corresponding podcast audio, transcript annotations, and derived stimulus embeddings. Furthermore, we introduce a brain decoding benchmark formulated as audio segment retrieval: given fMRI activity from a held-out session, the decoder must identify the corresponding time-aligned podcast audio segment among candidate segments. We provide standardized splits, evaluation metrics, and baseline decoders for this task. Finally, a scaling analysis shows that decoding performance improves continuously with the amount of training data per subject.

Abstract: Understanding how neural activity represents higher-order cognition and how these representations evolve over time has long been a central pursuit in neuroscience. However, current analytical tools cannot easily distinguish representational plasticity from recording instability in chronic neural recordings. Here, we introduce NeuroLens (Latent Embeddings of Neural Semantics), a self-supervised model based on the Joint-Embedding Predictive Architecture (JEPA) framework that learns denoised, semantically informative latents from chronic neural recordings. An adaptive encoder maps changing neural populations into a common latent space, while a temporal predictor learns structure that supports prediction of future latent states. By predicting in latent space, NeuroLens captures temporally predictable structure and reduces sensitivity to transient, recording-specific variability. Across chronic intracortical data in mice and humans, the learned representations improve decoding of decision-making and semantic task variables. Multi-day pretraining enables generalization to future sessions, rapid few-shot adaptation to unseen neural populations, and more stable decoding over time than state-of-the-art baselines. Together, these results establish NeuroLens as a new paradigm for studying how neural representations change during learning and over long timescales.

Abstract: We find that major reported improvements in decoding words from non-invasive brain recordings are largely reproducible without any brain data. In the influential work of d'Ascoli et al. (2025), time series of brain activity from subjects perceiving continuous speech are segmented into fixed-length windows starting at each word. A neural network then generates predictions for all of the words in a sentence together. Neighbouring windows partially overlap, implicitly revealing the interval between words. Since these intervals indicate the duration of the words spoken, and different words tend to have different durations - for example, "the" is much shorter than "supercalifragilisticexpialidocious" - the neural network can improve its predictions of words without relying on the underlying brain activity. Consistent with this, the method reaches 22.0% balanced accuracy on synthetic signals containing no brain information, compared with 22.3% on real brain recordings. To prevent the network from learning this shortcut, we make a single, simple change. Instead of jointly encoding all windows in a sentence, we process each independently. As a result, the neural network achieves better performance by learning underlying word-specific information from brain recordings. This makes two existing strategies become much more effective than before. Both aggregating predictions from distinct neural responses to the same word and using a pretrained LLM as a linguistic prior now substantially improve results. On our perceived speech benchmark, this simple recipe (SimpleB2T) achieves a word error rate of 36.6% with five observations per word, approaching past invasive speech decoding performance, albeit under different conditions. The results in this work expose an important shortcut in brain-to-text decoding and show that removing it leads to a simple and considerably more effective strategy.

Abstract: Brain networks characterize structural and functional relationships among brain regions and support research on cognition, brain disorders, and brain-computer interfaces. Their time-varying topology and higher-order spatiotemporal dependencies are not adequately represented by conventional static networks. Existing tools primarily focus on static connectomes and provide limited integration of dynamic network modeling with modern graph and sequence learning methods. We present BrainNet Studio, an integrated toolkit for static and dynamic brain network analysis. It provides a unified workflow encompassing network construction, feature extraction, predictive modeling, candidate biomarker identification, visualization, and assisted interpretation. The toolkit integrates 27 algorithms, including deep learning, graph neural networks, and spatiotemporal sequence models, to support classification and the identification of discriminative brain regions and connections. A large language model generates researcher-verifiable summaries of functional connectivity, structural connectivity, and structure-function coupling at individual and group levels. Within a consistent computational framework, users can configure analytical tasks, compare methods, inspect outputs, and extend functionality without repeatedly assembling application-specific pipelines. BrainNet Studio provides a practical and extensible platform for connectome analysis in cognitive neuroscience, exploratory studies of brain disorders, and brain-computer interfaces. The toolkit is publicly available at https://github.com/xbrainnet/Brainnet-Studio.

Abstract: High-resolution dynamic functional connectivity (DFC) can reveal rapidly evolving brain-network interactions, but short temporal windows yield noisy, often low-rank covariance estimates. Graph-Variate Dynamic (GVD) connectivity addresses this by modulating fast instantaneous interactions with stable trial-level support. This suppresses spurious fluctuations and emphasizes persistent, informative connections. We show that the Hadamard construction lifts low-rank instantaneous connectivity from the positive-semidefinite to the positive-definite cone, keeping high-resolution trajectories on the SPD manifold without ridge regularisation or post-hoc projection. We introduce GVD-CFM, a class-conditional generative model for high-resolution dynamic connectivity. Each trial is represented as SPD GVD matrices on a product Riemannian manifold, then mapped through a global log-Euclidean diffeomorphism and an invertible temporal DCT basis. A Transformer-based conditional flow models all spectral modes jointly and generates the full trajectory non-autoregressively in Euclidean coordinates while preserving exact correspondence with valid SPD sequences. Retaining the full DCT basis also enables decoding on denser temporal grids without retraining. Across multiple EEG motor-imagery datasets, GVD-CFM delivers the strongest overall results for held-out distributional fidelity, temporal-dynamics preservation, and synthetic-to-real classification. It also remains computationally efficient relative to strong raw-signal and direct GVD-space generative baselines. GVD-CFM therefore provides a practical framework for realistic, temporally coherent, high-resolution brain-network generation with preserved manifold structure and resolution-flexible decoding from a single trained model.

Abstract: Clinical scalp electroencephalography (EEG) offers a noninvasive window into neural dynamics of neuropsychiatric disorders. However, discriminative deep models often lack anatomically indexed physiological interpretability. We propose NeuroDyn-EEG, a pretraining framework integrating generative priors from neural dynamics. It couples an extended Jansen-Rit neural mass model, leadfield-based source projection, and simulation-based parameter inversion. Trained on synthetic parameter-EEG pairs within physiological ranges, NeuroDyn-EEG estimates 11 regional parameter families across 90 AAL regions plus one global parameter from standard 19-channel EEG, using only ~2.43M trainable parameters. We evaluate the framework across three levels. First, controlled simulations demonstrate robust parameter recovery under diverse noise conditions, while real resting-state EEG evaluations confirm spectral and phase consistency in an inverse-forward closed loop. Second, on four clinical benchmarks (AD65, PD31, Figshare MDD, and TUAB), NeuroDyn-EEG achieves competitive classification performance, securing the highest BACC, AUROC, and AUCPR on PD31 and MDD, and highest BACC on AD65. Third, post hoc regional analyses reveal disease-specific alterations: local synaptic connectivity C_1 involves the most altered regions in AD65, whereas the firing threshold theta ranks first in MDD, offering testable mechanistic hypotheses. Overall, NeuroDyn-EEG maps scalp EEG to anatomically indexed dynamical parameters, bridging representation learning and mechanistic neurophysiology. Code: https://github.com/Gnosis-Neurodynamics/NeuroDyn-EEG.

Abstract: Electroencephalography (EEG) analysis requires careful choices in preprocessing, statistical modeling, and machine learning because EEG signals are highly susceptible to artifacts, volume conduction, low signal-to-noise ratio, and substantial inter-subject variability. This chapter provides a practical and methodological guide to modern EEG analysis, spanning EEG preprocessing, artifact removal, filtering, bad-channel detection and interpolation, re-referencing, independent component analysis (ICA), and preprocessing of simultaneous EEG-fMRI recordings. We review major approaches for computational EEG analysis, including event-related potentials (ERPs), time-frequency analysis, functional and effective connectivity, source localization, multivariate decoding, permutation testing, and multiple-comparison correction. We then examine machine-learning methods for EEG, from feature-based classifiers to deep learning and emerging EEG foundation models, with emphasis on cross-subject generalization, limited-data regimes, data leakage, evaluation metrics, and fair benchmarking. Reproducibility is treated as a core requirement throughout, including transparent preprocessing, BIDS-EEG data organization, standardized derivatives, preservation of raw data, and FAIR data practices. The chapter is intended as a practical reference for researchers developing reliable, interpretable, and reproducible EEG analysis and machine-learning pipelines.

Abstract: Understanding how the brain parses actions and events from time-varying natural inputs is a central challenge in neuroscience. Recent work has used deep neural network (DNN) models to build stimulus-computable fMRI encoding models that predict single-voxel responses to complex natural videos. However, the majority of video-computable encoding models predict responses using simple linear mappings from model tokens, overlooking the spatiotemporal structure shared by video representations and neural responses. Recent cross-attention encoding models address this limitation for static images, enabling flexible stimulus-dependent weighting of image content across space. Here, we extend this framework to naturalistic video, using per-parcel cross-attention to dynamically route features from a self-supervised video model (V-JEPA-2) across both space and time, fitting this model to fMRI responses to short video clips. We compare joint spatiotemporal attention with factorized and selectively constrained alternatives, and find that joint routing improves predictions of brain responses to held-out videos across higher visual regions, most consistently in lateral and dorsal visual areas associated with dynamic motion perception. Moreover, our method provides interpretable, stimulus-specific attention maps that dynamically follow moving objects, revealing which locations and temporal moments contribute to each neural response. We further show that attention maps from parcels in different category-selective networks (face-, body-, scene-selective) differentially weight content in accordance with expected semantic selectivity. Together, this work provides a new computational framework for understanding how visual information is adaptively weighted by cortical populations during dynamic visual perception.

Abstract: Electroencephalography (EEG) records mixtures of brain-source activity. Even with a known anatomical forward model, experiments that excite only part of the source-state space leave the dynamics unidentified, and repetition cannot resolve the ambiguity. We show that unknown local mechanism changes can supply the missing information. We consider linear dynamics among fixed anatomical sources with known source-state initialization patterns. Changing one source's update rule for one transition leaves a rank-one, source-specific signature in subsequent EEG: subtracting matched baseline responses isolates it, and the forward model identifies the source and calibrates its response history. Combining these histories with initialization responses recovers source interactions without baseline reachability and without first identifying the intervention coefficients. We establish sufficient recovery conditions, a direct estimator, and a noise-sensitivity bound conditional on correct source labels. Simulated EEG on anatomy derived from magnetic resonance imaging confirms the information gain: with baseline excitation confined to four of twelve source coordinates, eight unknown changes recover all dynamics in 32/32 systems, whereas baseline realization, baseline regression through an invertible forward model, and changes that leave the tested states unexposed all fail, and explicitly constructed alternative dynamics reproduce every baseline mean. Where baseline information suffices, direct reconstruction is also more reliable than a matched-information spectral estimator. Nonlocal changes and forward-model error limit accuracy even when source labels are correct.

Abstract: Decoding brain states requires models that capture both the evolution of neural activity and interactions among groups of brain regions. Existing EEG methods often treat recordings as multivariate time series or represent functional connectivity with pairwise graphs, leaving dynamic higher-order interactions largely unmodeled. We introduce the Temporal Simplicial Neural Network (T-SNN), which represents EEG recordings as sequences of evolving simplicial complexes. By combining simplicial convolutions with recurrent updates, T-SNN jointly learns higher-order interactions and their temporal evolution. On the seven-class SEED-VII emotion recognition task, T-SNN outperforms convolutional, recurrent, graph-based, and Transformer methods in both trial-wise and cross-subject evaluations. Incorporating eye-movement features further improves performance, demonstrating the framework's potential for multimodal brain-state decoding.

Abstract: Objective cognitive assessment from neural signals supports neurorehabilitation, but individual-level prediction from task-based fMRI (tfMRI) remains difficult because neural features coexist with substantial demographic and scanner-related variation. We present the Multi-task Activation and Contrast Network (MAC-Net), a covariate-aware deep learning framework for modeling individual cognitive function from regional tfMRI. By isolating tfMRI features into a dedicated neural pathway and restricting participant variables to a terminal late-fusion pathway, MAC-Net prevents dominant covariates from suppressing high-dimensional clinical representations during feature learning. Evaluating baseline data from 6,500 Adolescent Brain Cognitive Development Study participants under family-aware cross-validation, MAC-Net was benchmarked against linear models, random forests, and alternative deep architectures. The N-back plus Monetary Incentive Delay configuration achieved $R^{2}$ values of 0.174, 0.238, and 0.277 for fluid, crystallized, and total cognition, outperforming covariate-only baselines (0.178) and alternative deep models (0.217). N-back was the most informative paradigm, whereas incorporating the Stop Signal Task marginally degraded performance. Feature attributions via Integrated Gradients, DeepLIFT, and Input Gradient were highly concordant, localizing working-memory-related frontal, parietal, and cingulate regions. These findings demonstrate that covariate-aware multi-task modeling yields reproducible cognitive-function estimations, establishing a robust neural engineering framework for clinical translation.

Abstract: Analyzing neuroimaging data requires specialized coding and statistical expertise, which limits accessibility for researchers without computational backgrounds. We present the AI Neuroscientist, a language agent for interactive data exploration. The system integrates a large language model (LLM) with a neuroimaging toolset to perform quality control, modeling, and visualization. This allows researchers to query data quality and specify analysis parameters directly in natural language, providing a transparent and interactive alternative to conventional scripted pipelines for small-scale data exploration. We demonstrate these capabilities using functional near-infrared spectroscopy (fNIRS) data, and evaluate the agent on a custom fNIRS benchmarking suite against general-purpose LLM agents with code sandboxes. Future extensions will generalize the architecture to additional modalities, including functional magnetic resonance imaging (fMRI) data, and expand the benchmarking suite to additional fNIRS tasks.

Abstract: Zero-shot brain-to-image retrieval requires robust alignment between noisy EEG responses and visual representations. Existing EEG-vision alignment methods often operate in sensor space and apply fixed visual supervision to all responses, ignoring both spatial mixing in scalp EEG and response-wise variability in alignment reliability. We propose an adaptive cortically constrained EEG-vision alignment method for zero-shot brain-to-image retrieval. The method reconstructs EEG responses into predefined ROI-level source-pattern representations and encodes them with a Neuro-ROI Attention Encoder. To handle response-wise variability, we introduce an evidence-based adaptive visual supervision strategy that weights detail-controlled visual targets using model-based alignment evidence. On THINGS-EEG, the proposed method achieves strong 200-way zero-shot retrieval performance, with ROI-level attribution providing post hoc interpretability of the learned source-pattern representations. These results show that cortically constrained representation learning and adaptive supervision can jointly support EEG-vision alignment for zero-shot brain-to-image retrieval.

Abstract: Pretrained EEG foundation models are increasingly proposed as general-purpose encoders for brain-computer interfaces, yet recent benchmarks disagree about when their representations transfer to downstream tasks. We audit LaBraM and CBraMod on motor imagery under a validation-locked protocol in which preprocessing, architecture, optimization, freeze depth, checkpoint, temperature, and method selection are determined using training-session data only. On four-class BCI Competition IV-2a, every supervised comparator evaluated here outperforms every foundation-model configuration, including validation-selected fine-tuning. We then examine a key confound: foundation models and task-specific decoders are normally evaluated using different input pipelines. Retraining three supervised architectures on the broadband arrays consumed by the foundation models produces matched-input accuracy differences of opposite sign across architectures: broadband input improves ATCNet by 0.078 accuracy while reducing EEG Conformer accuracy by 0.088. None of the three individual matched-input terms is significant after multiple-comparison correction at n = 9, so we treat the sign variation descriptively rather than as a formal architecture-by-pipeline interaction. These observed sign differences suggest that a single comparator may not provide an architecture-invariant decomposition of a pretrained-versus-supervised performance gap. The four-class deficit also does not reproduce uniformly across motor-imagery datasets: on two-class BNCI2014-004 we cannot detect the same separation between fine-tuned CBraMod and the supervised comparators. Finally, validation-fitted temperature scaling returns foundation-model calibration error to the supervised range despite substantially lower four-class accuracy.

Abstract: Silent speech interfaces (SSIs) enable private communication without audible speech and may support people with post-stroke dysarthria. Everyday reuse requires articulation-related representations that generalize across days despite sensor repositioning and physiological changes. We present AESSI, an around-ear SSI using masked-context representation pretraining (MCRP): a student predicts teacher representations from masked time-frequency inputs to encourage robustness to recording variability. We collected 44 electrophysiological recordings from 24 participants for 25 everyday Mandarin sentences. With six participants' complete final recordings held out, AESSI achieved 92.24 percent mean accuracy without test-day calibration. AESSI exceeded the best adapted baseline by 50.57 percentage points. At least 21 days after each participant's last recording, five participants each completed 50 independently randomized online tests without calibration, achieving 98.0 percent overall accuracy. Median preprocessing and inference time in CPU replay was 31.70 ms. These results demonstrate end-to-end system operation and support online reuse without test-day calibration. Demo is included with the paper.

Abstract: The categorization of cognitive and resting states derived from electroencephalography (EEG) signals is crucial for comprehending fluctuations in brain activity linked to various mental states. EEG provides a non-intrusive approach for documenting brain function in both resting and task-oriented cognitive conditions, whilst deep learning techniques enable the automatic extraction of significant patterns from intricate EEG data. This study presents a deep learning framework to distinguish between resting and cognitive states through EEG records. The proposed framework integrates a Convolutional Neural Network (CNN) stacked with a Gated Recurrent Unit (GRU) for the extraction of features from EEG signals. Time-frequency analysis is conducted to explore the salient aspects of signals, and the derived features are then assessed utilizing conventional deep learning and machine learning classifiers, including the suggested 2D-Net architecture. The proposed approach and feature extraction strategy outperform the evaluated comparative methods, achieving accuracies of 83.177% for resting-versus-mathematical task classification, 76.107% for resting-versus-memory task classification, and 83.432% for resting-versus-music task classification. The findings illustrate the efficacy of integrating signal processing with deep learning methodologies to discriminate resting from cognitive states utilizing EEG signals.

Abstract: Intracranial electroencephalography (iEEG) is widely used to record electrical activity directly from electrodes inside the human brain, making it an attractive modality for neural decoding. However, progress in iEEG decoding, especially toward general-purpose foundation models, remains difficult to measure reliably: datasets are task- or institution-specific, limiting evidence of generalization across tasks and recording environments, and preprocessing choices can strongly influence performance, making model improvements difficult to distinguish from preprocessing gains. Thus, we introduce iMINDBench, an iEEG Multi-Institution Neural Decoding Benchmark that evaluates models on a shared suite of fifteen decoding tasks across three naturalistic movie-watching datasets. The benchmark additionally defines standardized preprocessing tracks and fixed evaluation splits to support consistent model comparisons. Using iMINDBench, we find that the evaluated pretrained systems generally outperform baselines within their respective preprocessing tracks, while strong spectral baselines remain competitive across institutional datasets. In our scaling study, adding up to 25 times more supervised data from other subjects or institutions yields only small or task-dependent gains over within-session training. Together, these findings highlight the need for iEEG models that improve on strong preprocessing baselines and make more effective use of data across subjects and institutions. Project website: https://imindbench.github.io/

Abstract: Reconstructing 3D objects from brain signals offers a promising avenue for understanding human visual cognition. While prior work has shown initial success using EEG signals for 3D reconstruction, existing methods typically employ a uniform diffusion decoder, overlooking the evolving semantic granularity of both EEG representations and the diffusion denoising process. In this paper, we propose Mind2Cloud, a novel EEG-to-point-cloud generation framework based on two-granularity diffusion decoding. The core of Mind2Cloud is a time-aware decoder that integrates a global Transformer branch and a local Point-Voxel CNN (PVCNN) branch across diffusion timesteps through a learnable fusion mask. Specifically, Transformer layers are incorporated into the early upsampling stages to capture global object structure under high uncertainty, while PVCNN modules are used in later stages to refine local geometric details. Inspired by the hierarchical nature of EEG-based visual representations, this design dynamically adapts its spatial granularity in accordance with the coarse-to-fine trajectory of diffusion denoising. We further introduce an adversarial refinement module to enhance geometric realism and semantic consistency. Extensive experiments on the EEG-3D dataset across all 12 subjects demonstrate that Mind2Cloud outperforms prior work in both geometric accuracy and semantic alignment, setting a new benchmark for EEG-to-point-cloud generation. Our source code is available at https://github.com/duasoi/Mind2Cloud.

Abstract: Masked reconstruction is widely used for EEG foundation models, but optimizing reconstruction on low-SNR waveforms does not necessarily produce the most useful latent representation. We introduce MANAS-2, a new EEG foundation model that combines a Raw-Band Hybrid (RBH) masked autoencoder with Constrained Reconstruction (ConRec), a physics-motivated regularizer. RBH jointly reconstructs temporal waveform patches and compact spectral-band targets, while ConRec acts only on the temporal decoder output, penalizing differences in RMS energy between adjacent short windows of the reconstructed waveform. ConRec is intended to shape the encoder by biasing it toward the organization of oscillatory-envelope information. Across seven held-out EEG datasets, adding ConRec to an otherwise identical RBH model increases frozen ridge recovery of six-band spectral power from mean R^2=0.860 to 0.906 and recovery of inter-patch band-energy dynamics from R^2=0.283 to 0.354, while temporal waveform information remains highly recoverable from the frozen latents. Applied to a temporal-only masked autoencoder, ConRec also improves frozen downstream transfer and frequency-dependent latent geometry despite receiving no spectral targets: i.e., the effects of ConRec are architecture-independent. MANAS-2 also outperforms leading EEG Foundation Models on most downstream knowledge-transfer tasks. From the effects of ConRec, we see that a physically motivated constraint imposed through the decoder can make for a more spectrally organized and transferable latent space. MANAS-2 therefore provides a new EEG foundation model built around constrained reconstruction as a mechanism for shaping representation--rather than reconstruction--quality.

Abstract: Multimodal brain state decoding has largely focused on fusing paired modalities for prediction, but has rarely explored how their correspondence can be further exploited to enrich training data and improve multimodal representation learning. To address this gap, we propose CoMA-DiT, a bidirectional cross-modal Diffusion Transformer for latent augmentation that treats paired modalities as sources of mutual generative supervision rather than merely as inputs to be fused. CoMA-DiT conditions velocity prediction on the paired modality through cross-modal attention and adaptively injects the resulting variation via a reliability-gated residual mechanism. Experiments on multimodal auditory attention decoding and emotion recognition showed that CoMA-DiT consistently outperformed 20 representative baselines, achieving absolute gains of 4.28% and 6.70% in accuracy and macro-F1 over the no-augmentation baseline, respectively. Extensive ablation, sensitivity, visualization, and interpretability analyses further demonstrated its robustness, generalizability, and ability to capture functionally relevant cross-modal interactions. These findings support a broader view of multimodal learning: Paired modalities can serve not only as inputs for fusion but also as supervision sources that augment one another.