Papers for
neurotechnology developers
Papers whose findings have a practical use for this group, as judged from the abstract. Open a paper to read what it means in practice.
C elegans brain signals follow strongest routes not all paths
Every route counts, but some count more: a max-plus view of the C. elegans brain
Abstract: Brains do not simply add up every signal they receive: they select which routes dominate. Yet connectomes are usually analyzed with tools that sum over all paths and place neural states in Euclidean spaces, blurring the feedback circuits that may sustain internal states. Here we treat neural signaling as routing instead of diffusion and describe it with max-plus algebra, in which signals accumulate along a path and the strongest route prevails. We propose a model in which the functional connectome of Caenorhabditis elegans emerges from the time-varying combination of electrical, synaptic, monoaminergic, neuropeptidergic and hormonal layers, and analyze five networks within this framework. Each collapses onto a handful of dominant feedback loops, which recover well-characterized circuits and point to new candidates for experimental study. Unlike linear spectra, these structures keep the biological meaning of the data, and their order-based description suggests that brain states live in lattices rather than Euclidean spaces.
Semantic correspondence reveals shared geometry in neural networks
The Geometry of Meaning in Neural Manifolds
Abstract: Just as different languages express the same concept through different words, neural networks express similar functions through incompatible coordinate systems. Different architectures, random initializations, and optimization trajectories produce incompatible parameterizations in extrinsic coordinates, obscuring functional relationships between independently trained models. When models independently solve similar tasks on related data, do their learned representations share exploitable structure despite incompatible coordinates? This thesis shows that semantic correspondence is a fundamental primitive revealing shared geometric structure beneath incompatible parameterizations. By identifying which elements refer to the same semantic content, correspondence breaks the symmetry of arbitrary implementation choices, anchoring incompatible systems to a shared semantic frame and revealing the intrinsic geometry that enables zero-shot transformation between independently trained models. Building on this principle, fourteen contributions explore correspondence-based alignment across zero-shot model stitching, cross-modal translation, policy transfer, activation steering, and neural decoding. They span domains (vision, language, reinforcement learning, neuroscience), architectures (CNNs, Transformers, graph networks), and scales (from small supervised models to billion-parameter generative systems). Each exploits different geometric properties (angular, metric, spectral, sparse, or distributional), yet all instantiate the same principle. It extends beyond artificial systems: fMRI data show that different human brains processing identical stimuli exhibit alignable geometric structure. By revealing intrinsic geometric structure beneath extrinsic parameterization, semantic correspondence transforms model isolation into interoperability.
EEG foundation models vary in how they use brain signal details
Probing Spatial and Spectral Grounding in EEG Foundation Models
Abstract: EEG foundation models are advancing at an unprecedented pace, yet their evaluation is driven by downstream accuracy, which reveals little about whether their predictions rely on physiologically interpretable signal structure. We introduce a set of perturbation probes in two grounding axes: spatial grounding in channel identity and topographic locality, and spectral grounding in oscillatory content and waveform morphology. We apply these probes to five published EEG foundation models across motor-imagery and seizure recordings. Our experiments reveal differences in both representational sensitivity and downstream reliance. Electrode identity may be encoded without influencing downstream classification: permuting LaBraM's positional codes heavily displaced its embeddings yet reduced motor-imagery accuracy by only 1.2 points, while spectral details may be discriminable without producing specific responses to simulated clinical markers, as only REVE exceeded a spectral baseline on this task. These dissociations are hidden in common benchmarks, demonstrating how grounding probes can complement performance-based evaluation by revealing what EEG foundation models encode and what their predictions depend on.
Cnn classifies extraversion from brief eeg segments efficiently
CNN-based classifier for subject-independent MBTI Extraversion/Introversion preference classification from short-time EEG signals
Abstract: This study examines whether short, minimally preprocessed EEG segments contain sufficient information to distinguish between individuals classified as extraverted or introverted according to the Myers--Briggs Type Indicator (MBTI). EEG recordings from 50 participants were divided into 4-s segments and analyzed using a subject-independent nested 5-fold cross-validation procedure to compare EEGNet, EEGProgress, and a newly proposed compact convolutional architecture, SSCNet. SSCNet achieved the highest mean accuracy (0.6481), AUC (0.7063), and F1-score (0.6276). The proposed architecture also showed the lowest variability across folds. SSCNet demonstrated the best computational efficiency, with the shortest median training epoch time and the highest training throughput despite having a similar number of trainable parameters to EEGProgress. The results suggest that MBTI Extraversion--Introversion preferences may be moderately predictable from short time-domain EEG segments without manual spectral feature extraction, while highlighting the importance of subject-independent validation and computationally efficient model design.
Certain brain areas predict hypnotic susceptibility better than others
Region-Specific EEG Classification of Hypnotic Susceptibility Using a Sliding-Window 2D CNN: A Subject-Independent Evaluation
Abstract: We investigate whether a 2D Convolutional Neural Network (CNN) trained on minimally preprocessed EEG signals can classify hypnotic susceptibility across distinct brain regions. Sixty-two male participants (32 Control, 30 Guided Imagery / Hipno group) underwent a 20-minute EEG recording using a 256-channel EGI cap. A sliding-window approach evaluates all 10-second windows within the recording for each of seven predefined brain regions (prefrontal, frontal, temporal, central, parietal, occipital, and facial), yielding up to 868 independently trained models. Initial screening with a segment-level 90/10 random split showed that five regions exceeded the 0.67 accuracy threshold, with the occipital region achieving the highest mean accuracy (0.721) across 90.3% of windows. Subject-independent evaluation via Leave-One-Subject-Out (LOSO) cross-validation, however, substantially revised this picture: occipital performance collapsed to near-chance (mean ACC 0.453, AUC 0.429), revealing that high random-split accuracy was driven by subject-specific EEG fingerprints rather than genuine group differences. In contrast, the frontal and prefrontal regions maintained above-chance LOSO accuracy (0.646 and 0.624, respectively), demonstrating genuine generalisability. These results underscore the necessity of subject-independent validation in EEG-based classification studies and highlight anterior cortical regions as more reliable neural markers of hypnotic susceptibility.
EEG signals reveal word and context tracking across deep language model layers
Deep LLM layers expose passage-level context in EEG during silent reading
Abstract: In a previous report we showed that a decoder can recover open-vocabulary word-level information from 19-channel EEG recorded during silent reading, by aligning short EEG windows with hidden-state embeddings of the presented word taken from a large language model (LLM). That analysis contrasted two of the model's 33 layers: the context-free input embedding and one mid-depth layer. Here we ask how EEG-decodable structure is distributed over the full depth of the language model. We trained one decoder per layer of Llama-3.1-8B, with and without a causal transformer over the sequence of EEG windows. We distinguish word-level decodability from a context-tracking component. Word-level decodability peaks in early layers and declines steadily towards the last layer. In contrast, the context-tracking component of the retrieval gain rises with depth, both with and without a causal transformer. Unexpectedly, a decoder that sees a single 0.5-s window at a time tracks the text passage too. Two new controls dissect this component. A target-geometry control, a synthetic predictor made of the true target plus noise calibrated to each decoder's word-level accuracy, shows that context tracking is not a by-product of word decoding and target geometry. A control that permutes predictions across runs from either the same or from different sessions shows that most of the observed context-tracking is not caused by an EEG recording session signature. Instead, context tracking mostly follows the text. A single EEG window therefore carries passage-level information that a contextual target can absorb. The results locate word identity in the early layers of the language model, discourse state in the deeper layers, and make the choice of target layer a design dial for EEG language decoders.
Brain models better match people’s picture similarity judgments
Alignment of visual brain encoding models with individual perceptual similarity judgments
Abstract: Encoding models that predict brain activation responses to images have traditionally been trained to maximize accuracy when predicting observed brain data. However, their internal representations may not reflect individual human perception. In this work, we investigate whether we can fine-tune brain encoding models to better align their representations with individuals' similarity judgments. Using similarity judgments of 100 images from 8 participants in the Natural Scenes Dataset (NSD), we adapt a generic human similarity judgment model (DreamSim) separately for each participant to obtain personalized perceptual similarity models. These models are then used to obtain subject-specific similarity structure across images in their encoding model training sets. We fine-tune each participant's baseline encoder in two conditions, aligning its representations with either generic or personalized similarity judgments, with the same initialization and objective. We find that baseline brain encoders reflect within-subject perceptual similarity more strongly than measured fMRI responses and preserve intersubject correlations present in measured fMRI, but fail to reflect those of human perceptual similarity judgments. Fine-tuning with generic, population-level perceptual similarity information results in better alignment with human judgments than baseline encoders, but these models still fail to capture intersubject correlations of human judgments. However, fine-tuning with personalized perceptual similarity information results in models that are the most aligned with human perceptual similarity judgments and also reflect intersubject correlations of human judgments. Our framework provides an approach for bootstrapping human similarity judgment data into more individualized, human-aligned brain encoding models of vision.
Extended reality offers new ways to study human brain and behavior
Moving Beyond the Flat Screen: Opportunities and Challenges of Extended Reality for Studying Human Brain and Behavior
Abstract: Much of what we know about human perception and cognition comes from austere experimental settings: static stimuli presented to sedentary observers on flat monitors, complex responses reduced to simple button presses, and brain activity recorded from immobilized heads using EEG or fMRI. These highly controlled paradigms have provided remarkable insights, but capture a small and often unusual slice of behavior, raising questions about how well the findings generalize to the real world. Extended reality (XR), spanning both immersive virtual reality (VR) and augmented reality (AR) that overlays digital content on the real world, offers a way beyond these constraints, supporting controlled, reproducible experiments in which participants actively engage with three-dimensional tasks. Drawing on a growing body of VR and AR studies of attention, memory, and language -- our own and others', some involving EEG -- we outline what XR makes newly possible for cognitive neuroscience and reflect on the practical and conceptual obstacles that remain. The opportunities are substantial, but realizing them requires solving practical problems of hardware, timing, and measurement, and being realistic about what a virtual or augmented world can and cannot stand in for.
Vision and language models represent children’s brain responses differently than adults
Vision Models Capture Complementary Representations in Children That Converge in Adults
Abstract: How the relationship between image-text aligned and vision-only models changes across development remains unknown. We applied time-resolved representational similarity analysis to EEG data from 8-year-olds, 12-year-olds, and adults. CLIP showed significant model-brain alignment already in children, whereas vision-only models aligned more strongly later in development. Residual analyses revealed complementary structure, with CLIP retaining alignment beyond an architecture-matched vision-only model from age 8. Much of the model-brain alignment reflected semantic structure, with EEG representations of category and animacy strengthening toward adulthood, while alignment with low-level image properties remained weak across age. Together, these findings suggest that image-text aligned and vision-only models capture complementary aspects of developing visual representations and may provide useful constraints for AI systems that aim to learn and adapt over time.
MindVLM turns brain activity into personalized image descriptions
MindVLM: Neural-Grounded Visual Captioning via Subject-Aware Semantic Evidence Selection
Abstract: Translating visual brain activity into natural language offers a powerful window into human cognition and neural semantic representation. Most prior brain-captioning approaches project fMRI signals into language space using paired supervision. However, the widely used Natural Scenes Dataset (NSD) was built based only on image-fMRI pairs, while existing methods rely on MS-COCO captions as indirect textual supervision. Critically, during fMRI acquisition, participants observe only cropped image regions, whereas the associated MS-COCO captions describe full scenes. This mismatch creates a fundamental gap between neural representations and textual supervision, introducing an inherent semantic loss in NSD-based brain captioning. To mitigate this limitation, we reformulate brain captioning as Neural-Grounded Visual Captioning, where language is generated directly from visually grounded neural evidence rather than text supervision. We propose MindVLM, a framework that maps fMRI signals into subject-aware visual tokens and leverages a frozen vision language model (VLM) to produce interpretable and personalized descriptions. Instead of point-wise regression, MindVLM focuses on extracting semantically relevant visual cues from neural activity, naturally accommodating partial observability and inter-subject variability. Extensive experiments on NSD show that MindVLM consistently improves caption quality across multiple VLM backbones, including LLaVA-v1.5, Qwen2.5-VL, and Gemma3, beyond intrinsic model priors. Despite requiring neither text supervision nor an LLM during training and operating under an image-grounded inference paradigm distinct from conventional captioning methods, MindVLM remains competitive with supervised approaches, suggesting that subject-specific neural grounding provides an efficient, scalable, and interpretable path toward faithful brain-to-language generation.
Social pain disrupts brain emotion action links in self injuring teens
Social Pain Disrupts Emotion-Action Brain-State Dynamics in Adolescents with Non-Suicidal Self-Injury
Abstract: Non-suicidal self-injury (NSSI) is prevalent among adolescents with depression, but the rapid brain-state dynamics linking social distress to maladaptive behavior remain unclear. We combine an experimental pain paradigm, electroencephalography (EEG) microstate analysis, and interpretable deep sequence modeling to investigate NSSI-related neurodynamics in 106 adolescents with depression, including 67 with NSSI (DN+) and 39 without NSSI (DN-), during social pain, physical pain, and resting-state conditions. A model integrating disease-specific, domain-adversarial, consistency, and contrastive learning captures higher-order dependencies in microstate sequences. Social pain yields the strongest NSSI discrimination, with 68.55% accuracy, outperforming the best baseline by 8.94% points. Model interpretation and conventional microstate analyses reveal weakened bidirectional transitions between MS3 and MS5 in DN+ adolescents during social pain. Source reconstruction associates MS3 with emotional/interoceptive processing and MS5 with action preparation, suggesting disrupted emotion-action coupling. Time-resolved analyses show greater early-to-middle action-state recruitment and later emotion-state recruitment in DN+ adolescents. In DN- adolescents, MS5-to-MS3 dynamics mediate associations between social-evaluation sensitivity and affective outcomes, whereas this mediation is absent in DN+; conversely, MS3-to-MS5 transitions are associated with greater negative affect in DN+. Together, these findings identify disrupted emotion-action coupling as a key neurodynamic mechanism underlying altered social pain processing in adolescents with NSSI, providing a mechanistically interpretable neural signature for objective identification of NSSI.
CircuitATLAS maps brain circuits to find new neurological drug targets
CircuitATLAS: Agentic reasoning over a systems neuroscience knowledge graph for target discovery in circuitopathies
Abstract: Drug discovery for neurological disease has traditionally centered on the molecules altered by disease. But the molecules that cause pathology are not necessarily the best points from which to reverse it. Here, we ask which otherwise unaltered molecular control points can be engaged to restore pathological neural circuits toward functional states. We present CircuitATLAS, a provenance-grounded systems-neuroscience knowledge graph and agentic framework for target discovery in circuitopathies. It structures literature-derived relationships across diseases, phenotypes, electrophysiology, circuits, brain regions, cell types and molecular effectors, while deliberately excluding direct disease-gene and disease-protein edges to reduce shortcut reasoning. The graph contains 3.83 million nodes and 7.66 million edges, including 5.31 million LLM-extracted relations, and incorporates structured datasets such as the Human Cell Atlas and new multimodal in vivo measurements. We then introduce an agentic workflow that reasons from measurable disease phenotypes through their circuit and cellular substrates to molecular interventions, therapeutic feasibility and clinical constraints. Finally, we introduce a human-governed in vivo lab-in-the-loop linking hypothesis generation to experimental iteration. Within this framework an agent nominated ATP1A3, the neuronal alpha3 Na+/K+-ATPase, as a control point on cortical excitability; interneuron-restricted expression of ATP1A3 abolished the beta- and gamma-band response to a focal 4-aminopyridine challenge in vivo, and the validated target was then carried into a structure-guided small-molecule campaign terminating in a defined assay to resolve the direction of modulation. CircuitATLAS thus provides a framework for discovering therapeutics based not only on what is molecularly disrupted in disease, but on what can be controlled to restore circuit function.
Detection transformers reveal fiber details from complex brain scans
Fiber-Resolved Microstructure Quantification from Multi-Shell Diffusion MRI using Detection Transformers
Abstract: Fiber orientation and compartmental microstructure are central to the characterization of white matter tissue in diffusion MRI, yet existing methods either resolve fiber orientations without quantifying microstructure, or quantify microstructure while assuming a fixed number of compartments and a single fiber direction. Nonparametric approaches that recover both require tensor-valued diffusion encoding and computationally expensive Monte-Carlo inversion of an ill-posed inverse Laplace transform. We propose to reframe this problem as an object detection-like task, adopting the Detection Transformer (DETR) architecture to jointly predict mean diffusivity (MD), fractional anisotropy (FA), main fiber direction, and signal fraction for a variable number of compartments per voxel from standard multi-shell diffusion MRI with linear encoding. Hungarian matching during training resolves permutation invariance across compartments. We introduce mean Average Precision as a reproducible benchmark metric. Evaluated on synthetic test data with up to five compartments per voxel, our model achieves $R^2=0.95$ for MD, $R^2=0.88$ for FA, and a median angular error of 4.2°, with performance scaling naturally with compartmental signal fraction.
Spectral filtering improves brain data models for personalized prediction
Flattening the Connectome Spectrum: A Spectral Filter for FC Induces a Pretraining Target for fMRI Encoders
Abstract: Self-supervised pretraining reshaped prediction in language and vision, and brain foundation models (BFMs) inherited its promise. Representations learned from large unlabelled corpora should capture individual functional dynamics and generalise across cohorts. However, kernel ridge regression (KRR) fitted on functional connectivity (FC) matrices still predicts individual phenotypes more accurately than any BFM we tested. In this paper, we show that KRR is weighted by the eigenvalues of the FC which are miscalibrated for phenotype prediction. We apply an efficient spectral filter to recalibrate the eigenvalues of each subject's FC matrix, enabling the model to exploit more inter-individual variance. Across the 5 datasets, 11 parcellations and 6 prediction targets we tested, we match or exceed the KRR baseline. Based on this finding, we then pretrain a small encoder model on about 4,000 hours of fMRI from 162 open datasets, whereby we align the pairwise similarities between the embeddings of recording snippets with those between the recalibrated connectomes. Our model performs on par with the best of the 6 published BFMs we tested while having an order of magnitude fewer parameters. Our encoder performs better than FC on short scans and in smaller cohorts, especially in fingerprinting. We release the pretrained model weights, the code and the pretraining data, preprocessed and parcellated.
NeuronDiscover separates causes of brain fluid transport in neurons
NeuronDiscover: Agent-in-Twin for Mechanistic Discovery in Neuronal Microenvironments with World Action Models
Abstract: Mechanistic discovery in neuronal microenvironments requires interventions and measurements that separate competing explanations of solute transport and neuronal response. Predictive accuracy cannot settle the question: a real mechanistic change and an error in the computational twin leave the same signature in sparse observations. We formalize this twin confounding and reason over a joint mechanism--discrepancy belief, designing experiments that separate the two. NeuronDiscover is an Agent-in-Twin framework whose shared, mechanism-grounded World Action Model (WAM) couples prediction, intervention proposals, and observation design; independently adjudicated outcomes revise a scoped Mechanism--Intervention--Observation--Outcome (MIOY) graph, whose supported relations compile into executable programs carrying discrepancy-adjusted acceptance bounds. We evaluate on simulated brain-fluid tracer-transport worlds adjudicated by an independently frozen finer-mesh reference solver, and on donor-disjoint public current-clamp recordings of cortical neurons. Counting only relations that reach a certified terminal status, and scoring abstentions as unresolved for every method, at a matched budget of 16 experiments over 32 source units NeuronDiscover resolves 4.0 relations per assigned world against 3.4 for the strongest baseline and 3.2 without graph revision, at 5% false support and 82% scope accuracy. Joint mechanism--discrepancy acquisition resolves 3.8 relations versus 2.9 for plug-in expected information gain; discrepancy-adjusted verification lowers accepted-program failure from 15% to 9% at 60% acceptance coverage; and transfer to the recordings yields 1.94 versus 1.53 relations per assigned world. Correctness is adjudicated within declared model worlds and archival recordings.
Brain signal analysis improves by modeling complex noise patterns
Beyond Gaussian Assumptions: Distribution-Aware Channel Capacity for Effective Connectivity
Abstract: Effective-connectivity estimation from brain signals often relies on Gaussian residual modeling, which enables tractable estimation but can discard informative distributional structure and distort inferred directed interactions when empirical residuals are non-Gaussian. We show across multiple modalities, species, and experimental conditions that both brain signals and fitted channel residuals frequently deviate from Gaussianity. We therefore introduce a distribution-aware, information-theoretic measure of effective connectivity based on channel capacity under general residual distributions. To estimate the resulting capacity from empirical, potentially non-Gaussian residuals, we develop a dual-flow min-max estimator based on normalizing flows, in which a generator searches over admissible input distributions under a power constraint while an observer estimates output entropy. We provide a theoretical characterization of the estimator, showing that the observer objective recovers differential entropy up to a KL approximation term, that the formulation reduces to classical Gaussian capacity as a special case, and that residual entropy can alter achievable information rates beyond variance; game-gap and error analyses further characterize optimization and approximation sources. In brain-like simulations with known directed connectivity, Dual-flow achieves the highest AUROC and AUPRC across ten conditions spanning diverse network topologies, hidden drivers, feedback, and heterogeneous hemodynamics, compared with Gaussian capacity, Granger causality, VAR-LiNGAM, and GIMME. Applied to multimodal brain signals, the method reveals time- and condition-resolved directed interactions consistent with known neurobiological circuitry. Together, these results establish a principled distribution-aware framework for effective-connectivity estimation beyond Gaussian residual modeling.
EEG word tests show promise for adult ADHD screening
EEG-based Word Association Paradigm for Adult ADHD Screening: An Exploratory Pilot Study
Abstract: With the prevalence of Attention Deficit Hyperactivity Disorder (ADHD) over the past decades, healthcare systems across the globe face critical diagnostic challenges due to long diagnostic waiting times and a reliance on subjective behavioural assessments that cannot distinguish ADHD from comorbid psychiatric disorders, especially for adult patients. This exploratory study investigates whether EEG-based word association paradigms show promise as a complementary approach to screening for ADHD in adults. Using a mixed-method approach, the study examines neurological and cognitive differences between neurotypical individuals (NT), clinically diagnosed ADHD participants (ND), and self-reported ADHD cases awaiting formal diagnosis (SR) across three word association tasks. While established EEG biomarkers (ERP N400, Theta/Beta Ratio, and Alpha Suppression) show no significant group differences, semantic distance analysis reveals a statistically significant main effect ($p=0.003$), with the SR group showing the most divergent associations. These preliminary findings suggest that word association paradigms may capture cognitive differences not detected by standard EEG metrics and encourage further large-scale investigation as a potential complement to existing adult ADHD screening tools.
Adaptive optimizer improves eeg decoding across different people
Adaptive Forgetting for Nonstationary Optimization: Towards Robust EEG Decoding
Abstract: Electroencephalography (EEG) provides non-invasive monitoring of brain activity and is widely used in emotion recognition, motor imagery and sleep staging. Although within-subject decoding has achieved considerable progress, cross-subject generalization remains a central challenge in practical applications. EEG decoders are typically trained with Adam/AdamW under a fixed second-moment decay coefficient, even though cross-subject learning involves low signal-to-noise ratios, subject variability, and gradient nonstationarity. A fixed coefficient implicitly assumes that gradient statistics are homogeneous across layers and time, which can limit model's adaptability to cross-subject EEG signals and degrade generalization. To address these issues, we propose AFOR, a tensor-wise adaptive optimizer that converts the fixed second-moment decay coefficient into a dynamic coefficient estimated online from local gradient state. AFOR combines a Residual-Alignment Signal Scorer (RASS) and an Adaptive Forgetting Controller (AFC). RASS summarizes local gradient residuals and directional agreement into a signal-quality score, and AFC maps this score through self-referential normalization to a bounded per-step decay coefficient, with cumulative-product initialization correction maintaining consistency under time-varying decay. Under a strict cross-subject protocol on three EEG benchmarks that cover three representative fields, AFOR achieves the best average performance among the compared optimizers, improving the mean test accuracy over Adam by 3.00%, 2.07%, and 4.38%, respectively.
Shared spatiotemporal motifs model brain spikes across tissue types
A discrete generative model of neuronal spiking activity on microelectrode arrays
Abstract: Generative models of neural activity could help characterize tissue dynamics, compare experimental conditions, and simulate population activity for applications ranging from disease and drug-response studies to closed-loop experimentation. Existing approaches, however, typically assume a fixed set of sorted neurons, whereas high-density microelectrode arrays produce extremely sparse, array-wide binary spike volumes in which the observed subset of electrodes varies across assays. We introduce a discrete generative model that represents this activity using a shared vocabulary of spatiotemporal motifs. A residual vector-quantized autoencoder learns the motif vocabulary, while a factorized masked transformer predicts where activity occurs and which motif appears at each active location. We evaluate the model on 31 assays spanning human brain organoids and acute \emph{ex vivo} human hippocampal tissue. The learned motifs are broadly reused: assay identity explains only $9%$ of the entropy in motif use, and motif overlap across tissue types is comparable to overlap within them. When representation quality is evaluated independently of the generative prior, our approach achieves $5.2\times$ the voxel-level reconstruction average precision of a matched flat tokenizer. For masked completion and free generation, the full model achieves $1.4$--$2.6\times$ the site-level average precision of the matched generative baseline and outperforms it across all four families of generation metrics. These results establish a compact, reusable representation for array-wide spiking activity without learned assay-specific parameters, providing a scalable foundation for generative modeling across diverse neural preparations.
Brainwidebench measures neural model transfer across mice and brain regions
BrainWideBench: Benchmarking large-scale pretraining and across-animal transfer in multi-region neural recordings
Abstract: Advances in large-scale neural recording have made it possible to collect data across many animals and distributed brain regions, raising the question of whether this scale can be exploited to learn general-purpose neural representations transferable across diverse downstream tasks. Yet, progress toward this goal has been limited by fragmented evaluation protocols and a narrow focus on individual task domains. Here, we present BrainWideBench, a benchmark for evaluating across-animal transfer on multi-region neural recordings, built on the International Brain Laboratory Brainwide Map dataset of neural and behavioral recordings spanning 276 brain regions from 139 mice performing a sensory-guided decision-making task. The benchmark is organized around three complementary task suites that evaluate whether learned representations support downstream decoding of behavior, can predict masked or future neural activity, and can recover biologically meaningful anatomical organization. With this benchmark, we systematically evaluate pretraining methods across transfer settings, including finetuning on downstream objectives and zero-shot generalization to unseen animals. Our results confirm pretraining improves performance over matched single-session baselines, but we show current methods exhibit heterogeneity in transfer capabilities: gains depend strongly on the alignment between pretraining objectives and downstream tasks. No single approach performs uniformly well across all three suites, and most methods are designed to only address a subset of them. Together, these findings suggest that learning representations that jointly generalize across behavior, dynamics, and anatomy remains an open challenge. By providing a unified and reproducible evaluation suite, BrainWideBench establishes a framework for measuring progress toward general-purpose models of the mouse brain.
Multimodal model improves brain signal analysis without retraining
A Language-Guided Multimodal Foundation Model for Zero-Shot and Multi-Task Brain Signal Analysis
Abstract: Brain signal analysis is essential for both neuroscience research and clinical diagnostics, yet current approaches face critical limitations. End-to-end models require task-specific retraining and exhibit limited generalization, while pre-trained models lack semantic depth and still depend on extensive fine-tuning. Meanwhile, general-purpose multimodal foundation models, though powerful in other domains, struggle to interpret brain signals due to representational misalignment and lack of domain knowledge. This study introduces a multimodal foundation model for zero-shot and multi-task brain signal analysis (METIS) through a unified language-signal alignment framework. METIS is pretrained on the largest and most diverse brain-signal corpus to date, comprising over 70,000 h of recordings from more than 11,000 subjects across 20 datasets. In a comprehensive zero-shot evaluation across 12 datasets, METIS outperformed the leading generalist model by over 20.9% in average accuracy. Remarkably, without any fine-tuning, METIS's performance matches or exceeds that of supervised, task-specific models. Furthermore, METIS demonstrates exceptional data efficiency and strong generalization, achieving an average AUROC advantage of over 16.0% in few-shot settings and 15.9% in cross-dataset transfer. This work establishes a new paradigm for general-purpose brain signal analysis, paving the way for next-generation neurotechnology.