Neurophysiological Correlates

EEG foundation models such as BIOT, LaBraM, and EEGMamba have achieved remarkable performance in neural signal decoding, but their black-box nature limits clinical trust and neuroscientific validation. We propose a unified attribution framework for interpreting EEG foundation models across heterogeneous architectures. The framework integrates gradient-, perturbation-, and activation-based explanation methods to analyze model behavior in spatial, temporal, and frequency dimensions. Spatially, it identifies critical EEG channels and visualizes their distributions using topographic maps. Temporally, it highlights decision-relevant signal segments through attribution heatmaps. In the frequency domain, it quantifies the contributions of canonical EEG rhythms via spectral perturbation analysis. To assess explanation reliability, we introduce a population-level evaluation combining Area Over the Perturbation Curve (AOPC) and cross-method consistency analysis. The framework further leverages Large Language Models (LLMs) to transform structured attribution outputs into natural-language reports, bridging low-level neural representations and high-level semantic reasoning. Experiments on benchmark datasets, including Mumtaz2016 and TUAB, demonstrate that the generated explanations are consistent with established neurophysiological markers, validating meaningful neural representations while exposing potential dependencies on artifacts and spurious patterns. The proposed framework provides a standardized approach for evaluating the interpretability, reliability, and physiological plausibility of EEG foundation models.

Clinical electroencephalography (EEG) data are valuable for healthcare research and for developing artificial intelligence (AI)-based clinical decision-support systems, but EEG recordings and derived features may contain sensitive patient-specific information. This creates privacy risks when data are reused, analyzed, or shared across clinical and research environments. Conventional anonymization methods are often insufficient for high-dimensional biomedical signals, since removing direct identifiers does not necessarily prevent re-identification, linkage, or inference risks. At the same time, strong privacy protection may distort clinically relevant signal characteristics and reduce data utility. This paper studies subject-level differential privacy for protecting clinical EEG-derived feature representations using Gaussian and Laplace perturbations. The proposed framework considers three deployment scenarios: client-side anonymization, centralized server-side anonymization, and decentralized local training. Following EEG preprocessing and feature extraction, Gaussian and Laplace perturbations are applied to the resulting patient-level EEG feature representations. The Laplace experiments evaluate the implemented noise scales, while the scales required for formal full-vector calibration are derived separately. The effects of both perturbations are assessed using statistical utility measures and a downstream machine-learning-based utility check. The results show that differentially private perturbation can be integrated into EEG processing workflows, but the selected mechanism, privacy parameters, and sensitivity calibration strongly influence data utility. The study highlights the practical privacy-utility trade-off in DP-based EEG feature anonymization and the challenges of preserving downstream utility in small and imbalanced clinical EEG datasets.

We present an alternative characterization of the occupancy measure of reinforcement learning, obtained by embedding the planning criterion into the dynamics through a resetting planning process. Its stationary measure, which we term visitation measure, is the object on which the information geometry of decision making is most naturally expressed. The achievable visitation measures form a dually flat statistical manifold whose two affine charts are the visitation probabilities and the log-policies, dual under the conditional entropy. This structure makes planning-as-inference generalize from linear rewards to nonlinear functionals of the visitation, each iterate solved by one natural-gradient step, and gives the temporal-difference error the interpretation of a marginal-utility estimate. We develop the geometry and its consequences for reinforcement learning and theoretical neuroscience.

The rising prevalence of psychological disorders necessitates effective emotion monitoring, yet current methods relying on facial or physiological signals often suffer from intrusiveness and privacy issues. This paper proposes an intelligent decision support system and pervasive edge-computing framework that leverages smart glasses and a companion smartphone to infer emotional states from microscopic visual fixation patterns. Moving beyond traditional macroscopic gaze metrics, the proposed system extracts and decomposes three distinct neurophysiological micro-movements: microsaccades, ocular drifts, and ocular microtremors. We introduce an interpretable hybrid artificial intelligence pipeline combining a multi-head attention mechanism, extreme gradient boosting, and a support vector machine to extract deep temporal features, quantify their physiological importance, and perform efficient on-device classification. Through an extensive evaluation involving 60 volunteers, we rigorously validate the framework under a strict leave-one-subject-out cross-validation protocol across both controlled and naturalistic mobile scenarios. Ablation studies unequivocally demonstrate that these fixational micro-movements are substantially more discriminative for emotion inference than traditional macroscopic features. Furthermore, aligned with contemporary affective science, the system incorporates a few-shot personalization mechanism to bridge universal physiological baselines with individual emotional heterogeneity, achieving a highly robust personalized F1-score of 83.6%. This work establishes a physiologically interpretable, unobtrusive, and deployable paradigm for continuous real-time emotion monitoring.

Discovering stable neuron behavior across entire domains remains a challenge in mechanistic interpretability. Existing methods often rely on instance-level point estimates or computationally expensive procedures, which either obscure population-level variability or limit scalable domain-wide analysis. We present RACE (Residual Alignment for Consistency Estimation), a forward-pass statistical framework that evaluates the domain-wide functional consistency of Transformer neurons. Compared with gradient-based point estimates, RACE produces neuron rankings that yield more domain-specific effects under perturbation. Token-distribution shifts support the connection between the selected neurons and the target domain, while scoring requires roughly one-hundredth of the computational overhead of the gradient-based methods. Code is available at https://github.com/Nexround/RACE.

Large language models (LLMs) are increasingly reported to exhibit human-like neural and cognitive signatures, including concept cells, mental number lines, and cognitive maps. These claims often rely on linear probing and activation steering applied to a single model, yet both methods are highly sensitive to measurement choices. A reported parallel may therefore reflect the model, the measurement procedure, or both. We audit four representative neuroscience-inspired paradigms across 17 models from five families, spanning $0.6$B to $72$B parameters. Our main experiment examines the causal steerability of concept directions. With raw activation units and a fixed layer and coefficient, steerability appears to increase with model scale, resembling an emergent capability. However, this pattern is produced by an uncalibrated pipeline rather than by a claim established in the steering literature. The trend depends jointly on raw units, the readout metric, and the operating point; correcting any one of these removes it. With residual-norm-comparable interventions and held-out operating-point selection, concept steering remains significant at every scale, but shows no significant trend across the Qwen3 series, although the confidence interval does not rule out a moderate positive slope. The remaining results are mixed. A linear geographic world map is consistently decodable in every tested checkpoint up to $72$B. Number magnitude is strongly encoded, but whether individual neurons appear bell-shaped or monotonic depends on the selection criterion. Language-specific structure is localizable, but the direction of the cross-lingual asymmetry reverses under a different attribution method. These results suggest that the main constraint on AI neuroscience is not a lack of phenomena, but a lack of comparable measurements and adequate controls. We release the protocol, stimuli, and code.

Modern neuroscience relies on integrating multi-scale, multimodal datasets to uncover the neural principles underlying intelligence. However, analytical challenges posed by highly heterogeneous data and fragmented workflows increasingly constrain discoveries. Here we introduce SeekBrain, an autonomous multi-agent framework designed to accelerate neuroscience discovery through domain-grounded hierarchical planning and cross-modal data analysis. SeekBrain dynamically constructs a repertoire of analysis recipes extracted from code-paper pairs. By coupling this codified expertise with agentic planning and execution engines, the framework scalably generates hypotheses and analytical pipelines on demand. Systematic evaluation on the expert-annotated BrainArena benchmark demonstrates that SeekBrain substantially outperforms state-of-the-art agent baselines across various analysis tasks. Crucially, when deployed in real-world research, SeekBrain integrated behavioral, neural, and anatomical data to reveal structured, distributed neural representations of larval zebrafish behavior and a shared axis of regional decoding strength across the brain in a mouse decision-making task. These results establish SeekBrain as a scalable and practical tool for accelerating data-driven discoveries in neuroscience.

Sleep occupies roughly one-third of human life, yet many aspects of its physiology remain poorly understood. Large polysomnography (PSG) datasets offer new opportunities to study sleep and its links to disease, but extracting insight from these recordings requires substantial expert effort and remains difficult for general-purpose AI systems. We developed AI Sleep Co-Scientist, an expert-guided environment in which human scientists direct specialist agents for hypothesis development, signal preprocessing, and statistical analysis, reviewing intermediate outputs. Each reported result is linked to the executable code that produced it. Across four cohorts of approximately 124,000 PSG recordings and more than 50 TB of raw signals, we conducted five case studies spanning how sleep physiology relates to future disease, how it distinguishes clinical phenotypes, and how sleep is organized and regulated. Diminished network-level physiological coupling during sleep was associated with incident Parkinson's disease (HR 1.48) and Alzheimer's disease (HR 1.38). A physiologically structured late-fusion sleep-age model outperformed an unconstrained early-fusion approach, and its age residual was associated with incident disease across multiple organ systems. Arousal dynamics characterized comorbid insomnia and sleep apnoea as an intermediate phenotype skewed towards obstructive sleep apnoea, distinguished by prolonged post-arousal wakefulness. Rapid eye movement (REM) bout duration tracked preceding non-REM sleep more closely than intervening wakefulness. Transient-oscillation analysis identified a fast-sigma deficit and excess centrofrontal theta activity in narcolepsy type 1. Together, these findings connect sleep to disease risk, clinical classification, and its own regulation, and show how agentic AI can support large-scale, multimodal discovery.

Electroencephalography (EEG) offers a noninvasive approach for examining neurophysiological correlates of dimensional psychopathology, yet systematic evidence across EEG paradigms and feature granularities remains limited. Here, we develop a granularity-aware EEG feature pipeline that organizes multi-scale descriptors into global, regional, and channel levels. Using the Healthy Brain Network (HBN) cohort, we evaluate the prediction of four psychopathology dimensions: p-factor, internalizing, externalizing, and attention problems, across four EEG paradigms. Given the heterogeneity of pediatric psychopathology and the moderate reliability of questionnaire-derived scores, this setting represents a challenging feasibility test rather than a clinical screening scenario. Tree-based models and granularity-balanced feature selection showed promising improvements over conventional approaches in selected conditions, although effect sizes remained modest. Visualization of selected markers revealed dimension-specific spatial and spectral patterns that were broadly aligned with existing neurophysiological knowledge. An exploratory cross-dataset sanity check on the independent PEARL cohort suggested that the proposed selection principle remains technically feasible under protocol shifts, without claiming cross-dataset generalizability. Overall, multi-scale EEG features contain weak but detectable signals related to dimensional psychopathology, and granularity-aware selection may serve as a useful feature-reduction strategy for future EEG-based phenotyping studies.

A defining feature of human intelligence is the ability to adapt to changing environments by inferring latent task structure from sparse observations. Neuroscientific research indicates that this capability relies on the hippocampus constructing abstract representations, expressed as low-dimensional, approximately orthogonal manifolds in neural state space. However, the internal mechanisms of large language models (LLMs) remain largely opaque, making it unclear whether they form comparable abstract representations or instead rely on task-specific statistical regularities when performing comparable reasoning tasks. Here we adapt a contextual reversal-learning paradigm to a text-based setting and compare humans and LLMs at both the Behavioural and representational levels. We report that although LLMs exhibit generalizable reasoning less frequently than humans, when such inference occurs, their internal states exhibit abstract geometric structures that resemble those reported in the hippocampus. Notably, this representational geometry is not uniformly distributed but is organized hierarchically across model depth: whereas lower layers show early, stable encoding of stimulus identity, higher layers form a hippocampal-like functional band enriched for abstract context geometry associated with inference. Furthermore, complementary intervention experiments mechanistically implicate geometry in reasoning: task-sequence language modelling induces geometric disentanglement, whereas geometric regularization of higher layers increases the emergence of generalizable inference. Together, these findings establish abstract representational geometry as a mechanistic principle supporting inference in large language models.

Neuroscientific research has revealed that the brain encodes complex behaviors by leveraging structured, low-dimensional manifolds and dynamically fusing multiple sources of information through adaptive gating mechanisms. Inspired by these principles, we propose a novel reinforcement learning (RL) framework that encourages the disentanglement of dynamics-specific and reward-specific features, drawing direct parallels to how neural circuits separate and integrate information for efficient decision-making. Our approach leverages locally linear embeddings (LLEs) to capture the intrinsic, locally linear structure inherent in many environments, mirroring the local smoothness observed in neural population activity, while concurrently deriving reward-specific features through the standard RL objective. An attention mechanism, analogous to cortical gating, adaptively fuses these complementary representations on a per-state basis. Experimental results on benchmark tasks demonstrate that our method, grounded in neuroscientific principles, improves learning efficiency and overall performance compared to conventional RL approaches, highlighting the benefits of explicitly modeling local state structures and adaptive feature selection as observed in biological systems.

Biological plausibility is a key concept in neuromorphic computing and spiking neural networks, yet it remains inconsistently defined and difficult to quantify. In this work, we present an open-source framework for the automated assessment of biological plausibility in spiking neuron models. Our method builds on the idea of evaluating a model's ability to replicate canonical neuronal firing patterns observed in biological systems, following the classification proposed by Izhikevich. By encoding these patterns into objective functions and optimizing model parameters accordingly, our framework enables empirical assessment without requiring prior analytical modeling. Treating neuron models as black boxes, it provides a practical and flexible means of characterizing their dynamic capabilities. We demonstrate the effectiveness of the framework on several established models and a previously unexplored custom model. Implemented in Python and compatible with PyTorch and the Norse library, the framework is tailored for machine learning contexts. It is intended as a starting point for systematic research into the relationship between biological plausibility and network-level performance metrics such as accuracy, energy efficiency, robustness, and adaptability.

While non-verbal behaviors and expressive movements are essential for natural human-robot interaction, existing methods often overlook a crucial element: the human's internal cognitive state. Frequently, proactive multi-agent systems can interrupt humans at inopportune moments, leading to cognitive overload and decreased task performance. This paper introduces a framework for generating "cognitively aligned" multi-agent interactions, enhancing the ability of robotic systems to contextually defer communications to the user of an agent system during moments of high human mental workload and engagement. We present the design and implementation of a closed-loop architecture that explores the interplay between autonomous task execution and real-time neurophysiological focus. Using a consumer-grade Brain-Computer Interface (BCI), our approach continuously monitors Electroencephalography (EEG) spectral band powers while a human performs an engagement-inducing task. We propose an engagement-driven pipeline where an HTTP-based signaling mechanism places a primary agent's sensory inputs and audio outputs into a holding state upon detecting high engagement. This allows secondary agents to seamlessly process complex, delegated tasks in the background. Once the human's cognitive state returns to a lower cognitive load baseline, the primary agent releases the queued agent message. Our preliminary results demonstrate the feasibility of leveraging real-time signal processing, Large Language Models (LLMs), and physical robotic embodiments to create cognitively-aware, non-intrusive multi-agent systems.

Persistence diagrams are common representations in topological data analysis, but they do not naturally live in a vector space, and the statistical tools developed for comparing them have largely evolved separately from those used for downstream prediction. We introduce STRAND (Survival Topological Representation ANalysis of Diagrams), which treats (collections of) PDs as survival data: each topological feature with persistence value $p = d - b$ is a fully observed time-to-event, and the persistence survival function $S(t) = \mathbb{P}(p > t)$ is the central object for comparing diagrams. From this single representation we derive (i) a non-parametric two-sample test with calibrated Type I error and high power from a small number of diagrams; (ii) interpretable effect sizes; and (iii) a 1-Wasserstein-stable feature vector for downstream machine learning. We validate calibration and power on synthetic manifolds with controlled topology, demonstrate competitive vectorisation across 14 graph and 3D point cloud benchmarks, and apply the method to study functional brain connectivity in fMRI/neuroscience data. To our knowledge, STRAND is the first method to provide hypothesis testing and vectorisation for persistence diagrams from a single coherent and interpretable representation.

Eye movements, including saccades, are widely regarded as highly sensitive and objective biomarkers of neurophysiologic states. Detecting saccadic signatures in neurologic diseases offers a rapid, portable alternative to brain imaging, avoiding access and cost barriers. Currently, there are no robust AI-enabled video-oculographic solutions (e.g., digital biomarkers) for screening, triaging, or localizing brain abnormalities due to privacy issues and scarce datasets. In this work, we propose the first fully synthetic, patient-free, multimodal eye movement generation pipeline for generalizable saccade analysis. Using this synthetic dataset, we trained a deep learning classifier to distinguish between normal and abnormal (hypometria and hypermetria) saccadic accuracies and evaluated its performance on real-world clinical data. The model achieved an AUROC of 0.76 and a sensitivity of 0.71, showing that the synthetic data has strong potential to generalize for clinical applications, including as a screening tool in at-home and emergency room settings or a tool for precise neuroanatomic localization.

Agentic AI tools offer a promising path to automating software development bottlenecks in scientific research pipelines, particularly for stages that take domain experts days to months to build, where scientists care about correctness and robustness, not implementation details. We present an empirical study of general-purpose coding agents on a fly optogenetics data-to-discovery pipeline. We assess agents on tasks substantially larger than existing benchmarks, datasets orders of magnitude bigger, and evaluation criteria grounded in domain expert standards. We show that agents can solve several individual pipeline stages, suggesting stage-level automation is tractable. By analyzing agents' code iterations, we show that they struggle most when there is not a pre-defined criterion to iterate on, and they must instead use their scientific judgment to assess their current solution, a key open challenge. Mirroring scientific practice, they sometimes attempt visual inspection of intermediate outputs for self-evaluation, but largely fail to interpret what they see or act on it appropriately. Solving the end-to-end pipeline correctly requires stringing together successes across all pipeline stages, and this is beyond agents' current abilities. We identify challenges largely absent from existing benchmarks, including computational resource management and generalization to large held-out data collections. Finally, we distill principles for constructing scientific tasks and rigorous evaluation criteria for open-ended problems.

Decoding emotional states from neural signals has been typically framed as a discrete, single-label classification task based on emotionally stable stimuli, a formulation that oversimplifies the continuous, fluid, and co-occurring nature of human affect. This study reconceptualizes emotion decoding by adopting a multi-target regression framework to track multiple overlapping emotional dimensions as continuous trajectories over time. Leveraging the robust generalization capabilities of Large Language Models (LLMs), we extracted fine-grained, continuous sentiment profiles from a naturalistic auditory narrative, Alice in Wonderland, to serve as scalable proxies for subjective affect from human fMRI dataset. Departing from standard classification paradigms or mass-univariate subtractive contrasts that filter out network dynamics, we leverage regularized and kernel-based machine learning algorithms as continuous estimators to track the magnitude of macroscale neural state variations. We demonstrate that models trained on temporal snapshots of Dynamic Functional Connectivity (DFC) significantly outperform static region-of-interest (ROI) amplitude representations, effectively capturing continuous emotional trajectories under rapidly fluctuating narrative input. Furthermore, by implementing graph-theoretical Explainable AI (XAI) techniques, we deconstruct the underlying predictive features to reveal highly interpretable, emotion-specific topological configurations. Collectively, these results highlight the utility of LLM-automated annotation in affective neuroscience and provide compelling empirical evidence for psychological constructionist frameworks, demonstrating that dynamic, distributed network interactions offer superior explanatory power over strictly locationist accounts of emotion.

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

Knowledge graph (KG) is an abstraction that can be extracted from text corpora and used for in-depth reasoning. Prior work has leveraged KGs to fine-tune language models (LMs), enabling domain-specific superintelligence. In this work, we explore whether KG-driven in-depth reasoning capabilities can emerge in neuroscience using only information contained within a single authoritative textbook. The central hypothesis is that structured knowledge, when distilled into a high-quality KG and converted into KG-grounded question-answer (QA) supervision, is sufficient to produce expert-level reasoning through a fine-tuned LM that surpasses large language models (LLMs) in accuracy, while employing orders of magnitude fewer parameters. We construct a textbook-derived KG via a dual-LLM validation pipeline, expand it with a masked LM trained on the KG topology, generate multi-hop QA items, which include QA pairs and reasoning traces, to fine-tune an LM exclusively on KG-derived supervision, and apply reinforcement learning using path-derived KG signals as implicit reward models. Our results demonstrate that deep, mechanistic neuroscience understanding can be induced in the model without reliance on large, heterogeneous web-scale corpora. The KG-based synthetic neuroscience curriculum that readers can quiz themselves on, and the fine-tuned LM, are available at the following GitHub location: https://kg-bottom-up-superintelligence.github.io/neuro-bench.

Ordinary differential equation models of biochemical reactions are often formulated as stoichiometric systems in which the dynamics arise from a collection of interacting processes. A central challenge is that the functional form of each process is rarely known a priori and may be difficult to infer from data. We propose biochemically informed neural ordinary differential equations (BINODEs), a neural-ODE framework that retains the stoichiometric structure of mechanistic models while representing individual processes by neural networks. In BINODEs, the outputs of neural network processes (NNPs) are mapped to state derivatives through a linear layer analogous to a stoichiometric matrix. This architecture allows biological side information, such as process-specific inputs, sign constraints, and monotonicity assumptions, to be built directly into the model. We characterize the approximation properties of NNPs for several standard biochemical rate laws and show that the proposed framework recovers both trajectories and process-level structure in Monod, Lotka--Volterra, pharmacokinetic, and ultradian endocrine models. These results suggest that BINODEs offer a useful compromise between mechanistic interpretability and data-driven flexibility for modeling partially known biochemical or biological dynamical systems.

Mechanistic interpretability produces circuit-level causal analyses of neural network behaviour, but discovered circuits often remain isolated experimental artefacts: there is no shared formal representation for what circuits compute, how they relate, or when two findings provide evidence for the same mechanism. This work provides a formal infrastructure for cumulative mechanistic science by treating circuit interpretation as inductive theory construction. Each circuit is characterised at two levels: a Causal Functional Signature (CFS), which grounds component behaviour in causal attribution evidence and token role profiles, and an architectural signature $τ_{\mathrm{arch}}$, learned by inductive logic programming (ILP) from scale-invariant structural predicates. Together, these constitute a formal coherence layer that makes mechanistic claims explicit, comparable via $θ$-subsumption, and portable across model scales. CFS reveals qualitatively distinct computational strategies across task types, including attention-mediated copying versus MLP-mediated binding. ILP signatures achieve substantially better structural separation than graph kernel and feature-vector baselines, and support principled transfer across model scales and architecture families.

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

AI-based code assistants are transforming software development, yet we lack empirical evidence on how they affect developers' cognitive processes. We present a multisite study investigating the neurophysiological correlates of AI-assisted programming through a within-subjects crossover design. We recruited participants at two universities (Bari, Italy, and Copenhagen, Denmark) and collected electroencephalography, eye-tracking, electrodermal activity, and heart rate variability data alongside a rubric-based performance score and self-reported workload across six dimensions using the NASA Task Load Index (NASA-TLX). We tested four hypotheses addressing physiological differences between AI-assisted and non-assisted conditions, the moderating role of developer experience, the association between physiology and performance, and the alignment between subjective perceptions and objective measures. Under AI assistance, the EEG $θ/α$ ratio was lower during the first task and the gaze blink rate was higher during the second, both consistent with reduced cognitive engagement when developers offload generative effort to the model. This pattern did not differ between undergraduate and graduate students. Electrodermal activity correlated with performance under the non-AI condition but not under AI. Among the six NASA-TLX dimensions of self-reported workload, only Physical demand was associated with performance under the non-AI condition but not under AI. These findings suggest that AI-assisted programming is not a faster version of solo coding but a cognitively distinct activity, with implications for the design of AI assistants and for biometric monitoring in AI-augmented development.

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

Transforming neuroimaging data into clinically actionable biomarkers is a knowledge-intensive and labor-intensive process. Standardized workflows such as fMRIPrep have improved robustness and efficiency, but they are statically configured and cannot reason about downstream objectives, deliberate over alternative strategies, or close the loop between intermediate evidence and subsequent decisions in the way a human researcher would. This lack of closed-loop adaptation often leaves domain experts trapped in a cycle of manual trial-and-error to tune parameters and remediate pipeline failures, severely constraining the scalability of clinical biomarker development. To bridge this gap, we introduce NEXUS, an autonomous multi-agent framework that integrates neuroimaging workflow execution with scientific-objective understanding. Unlike conventional flat toolcalling agents, NEXUS adopts a code-centric execution paradigm where specialist agents collaboratively synthesize and optimize executable programs over composable domain-specific primitives. This design enables robust, long-horizon workflow construction that adapts dynamically to runtime observations. Furthermore, we propose a hierarchical verification framework for autonomous quality control, integrating cohort-level metric screening with agentic visual inspection to drive evidence-grounded workflow remediation. Experiments on ADHD-200 and ADNI demonstrate that NEXUS outperforms standard workflow-based baselines in predictive performance while exhibiting sophisticated agentic behaviors, including strategy exploration and adaptive refinement. The code is available at https://github.com/LearningKeqi/Virtual-Neuroscientist-NEXUS.

Cognitive neuroscience is fragmented into specialized models, each tailored to specific experimental paradigms, hence preventing a unified model of cognition in the human brain. Here, we introduce TRIBE v2, a tri-modal (video, audio and language) foundation model capable of predicting human brain activity in a variety of naturalistic and experimental conditions. Leveraging a unified dataset of over 1,000 hours of fMRI across 720 subjects, we demonstrate that our model accurately predicts high-resolution brain responses for novel stimuli, tasks and subjects, superseding traditional linear encoding models, delivering several-fold improvements in accuracy. Critically, TRIBE v2 enables in silico experimentation: tested on seminal visual and neuro-linguistic paradigms, it recovers a variety of results established by decades of empirical research. Finally, by extracting interpretable latent features, TRIBE v2 reveals the fine-grained topography of multisensory integration. These results establish artificial intelligence as a unifying framework for exploring the functional organization of the human brain.

Human attention is the gateway to conscious perception, memory and decision-making. However, its role in modern transformer models remains largely unexplored. As these systems increasingly influence what people see, prefer and buy, the question arises as to whether they encode principles of human interest or merely exploit large-scale correlations. Addressing this issue is crucial for understanding cognition and ensuring the responsible use of AI in communication and marketing. In order to address this issue, the concept of visual interest was examined within the multimodal vision-language-model Qwen3-VL-8B, using a pre-defined Common Interestingness (CI) score derived from large-scale human engagement data on the photo-sharing platform Flickr. Here, we analyzed internal representations across vision and language components using methods from the neurosciences. Our analyses revealed that CI information is linearly decodable from final-layer embeddings, indicating that it is aligned with human-derived measures of visual interestingness. Dimensionality reduction and Generalized Discrimination Value (GDV) analyses demonstrate that CI-related hidden representations emerge in intermediate vision transformer layers and becomes progressively more distinguishable across language model layers. Concept vectors derived using geometric, probe, and Sparse Auto-Encoder based methods converge in higher layers, as confirmed by representational similarity analysis. This indicates a robust and structured encoding of visual interestingness without explicit supervision. Future work will seek to identify shared computational principles linking human brain dynamics and transformer architectures, with the ultimate goal of uncovering the organizing mechanisms that give rise to attention and interest in both biological and artificial systems.

The Free Energy Principle (FEP) is a leading framework for mathematically modeling self-organization and learning, while Integrated Information Theory (IIT) is a computational ontology of consciousness oriented around irreducible cause and effect. While conceptual unifications have been proposed and appear to be supported by empirical findings, the absence of a rigorous mathematical mapping places upper bounds on their precision and testability. This work proposes that information can be defined as the deviation $ψ$ of realized dynamics from a constrained maximum-caliber (MaxCal) path ensemble over a finite time horizon. Under this definition, each of the cause/effect repertoires central to IIT 3.0 emerge directly from MaxCal variational principles, allowing IIT's phenomenological calculus to be re-derived from constrained entropy-maximization (CMEP). This framework supplies a theoretical bridge to active inference, which is mathematically dual to CMEP under Langevin dynamics, and offers a principled route for extending IIT to new dynamical regimes. When the approach is applied under the Central Limit Theorem (CLT) for Markov chains and via large deviations theory (LDT) to Ising models, information $ψ$ is shown to be equivalent to prediction error under accompanying predictive coding models. This may hold relevance to the ``hill-shaped trajectory'' of $Φ$ observed in neuronal cultures adapting to sensory inputs. Together, these results provide a physically and mathematically grounded rationale for studying the convergence of FEP, IIT, and thermodynamic frameworks of cognition such as recent work grounding consciousness in violations of the Fluctuation-Dissipation Theorem (FDT).

Current AI systems, grounded in oversimplified neuroscience, risk eroding the distinction between truth and falsehood. They maximize reward by amplifying attention to information without intrinsic precision mechanisms to assess whether it is valid or worth attending to. This increases both the volume of information and the inherent biases in what the system attends to, whether true, false, or irrelevant. If not corrected, this trend will accelerate, threatening to overload systems and individuals with biased and dubious information and increasing the risk of confusion, poor judgment, and irrational or harmful decisions and behaviour, a condition I term the mind-reality overload dilemma. I argue that this threat may be mitigated by providing the public with access to more advanced AI tools built on the biophysical dynamics of pyramidal neurons underlying awake thought and higher-order cognition. These neurons support an intrinsic active precision mechanism that, rather than merely maximizing reward, uses locally and globally coherent predictions to evaluate the validity and contextual adequacy of evidence before it is attended to or propagated through hierarchies, prioritizing coherence and adequacy before attention.~While this approach does not derive or prescribe moral rules from biology, it may give rise to AI with more "real understanding", helping restore epistemic conditions by reducing information overload and amplifying reliable information, thereby supporting the formation of better-informed beliefs and more coherent judgments that benefit society at large-though no guarantees exist.

Large-scale neuroscience is generating rich datasets across animals, brain areas and behavioral contexts, yet our modeling efforts remains fragmented across isolated experiments. We argue that understanding behavior requires integrative neurocybernetic models: understandable dynamical models that capture the closed-loop coupling of brain, body and environment, treat the brain as a controller pursuing latent objectives, represent structured variation across scales, and scale to heterogeneous datasets. Such models shift the goal from predicting neural recordings in isolation to inferring the organizing principles that govern neural and behavioral dynamics. We outline a practical route toward this goal by combining nonlinear state-space models and meta-dynamical extensions with scalable inference, knowledge distillation, mixed open- and closed-loop training, and connectomics-informed architectures. By pooling complementary constraints from recordings, behavior, perturbations and anatomy, integrative neurocybernetic models can provide statistical amplification, few-shot generalization, and mechanistic insight into shared dynamical structure, individual variation, and the control objectives that govern behavior. This agenda offers a model-centric path from fragmented data to a mechanistic science of how brains produce behavior.

The analysis of neural representation has become an integral part of research aiming to better understand the inner workings of neural networks. While there are many different approaches to investigate neural representations, an important line of research has focused on doing so through the lens of intrinsic dimensions (IDs). Although this perspective has provided valuable insights and stimulated substantial follow-up research, important limitations of this approach have remained largely unaddressed. In this paper, we highlight a crucial discrepancy between theory and practice of IDs in neural representations, theoretically and empirically showing that common ID estimators are, in fact, not tracking the true underlying ID of the representation. We contrast this negative result with an investigation of the underlying factors that may drive commonly reported ID-related results on neural representation in the literature. Building on these insights, we offer a new perspective on ID estimation in neural representations.

In real-world applications of noninvasive electroencephalography (EEG), specialized decoders often show limited generalizability across diverse tasks under subject-independent settings. One central challenge is that task-relevant EEG signals often follow different temporal organization patterns across tasks, while many existing methods rely on task-tailored architectural designs that introduce task-specific temporal inductive biases. This mismatch makes it difficult to adapt temporal modeling across tasks without changing the model configuration. To address these challenges, we propose DSAINet, an efficient dual-scale attentive interaction network for general EEG decoding. Specifically, DSAINet constructs shared spatiotemporal token representations from raw EEG signals and models diverse temporal dynamics through parallel convolutional branches at fine and coarse scales. The resulting representations are then adaptively refined by intra-branch attention to emphasize salient scale-specific patterns and by inter-branch attention to integrate task-relevant features across scales, followed by adaptive token aggregation to yield a compact representation for prediction. Extensive experiments on five downstream EEG decoding tasks across ten public datasets show that DSAINet consistently outperforms 13 representative baselines under strict subject-independent evaluation. Notably, this performance is achieved using the same architecture hyperparameters across datasets. Moreover, DSAINet achieves a favorable accuracy-efficiency trade-off with only about 77K trainable parameters and provides interpretable neurophysiological insights. The code is publicly available at https://github.com/zy0929/DSAINet.

Neuroscience and Artificial Intelligence (AI) have made impressive progress in recent years but remain only loosely interconnected. Based on a workshop convened by the National Science Foundation in August 2025, we identify three fundamental capability gaps in current AI: the inability to interact with the physical world, inadequate learning that produces brittle systems, and unsustainable energy and data inefficiency. We describe the neuroscience principles that address each: co-design of body and controller, prediction through interaction, multi-scale learning with neuromodulatory control, hierarchical distributed architectures, and sparse event-driven computation. We present a research roadmap organized around these principles at near, mid, and long-term horizons. We argue that realizing this program requires a new generation of researchers trained across the boundary between neuroscience and engineering, and describe the institutional conditions: interdisciplinary training, hardware access, community standards, and ethics, needed to support them. We conclude that NeuroAI, neuroscience-informed artificial intelligence, has the potential to overcome limitations of current AI while deepening our understanding of biological neural computation.

Binge eating disorder (BED) is the most prevalent eating disorder. However, current diagnostic frameworks remain largely grounded in symptom-based criteria rather than underlying biological mechanisms, thereby limiting early detection and the development of biologically-informed interventions. Emerging studies have begun to investigate the neurobiological signatures of BED, yet their findings are often difficult to generalize due to the reliance on hypothesis-driven parametric models, single-modality analyses, and limited data diversity. Therefore, there is a critical need for advanced data-driven frameworks capable of modeling multimodal data to uncover generalizable and biologically meaningful signatures of BED. In this study, we propose the Interpretable Modality-Aware Mixture-of-Experts (IMA-MoE), a novel architecture designed to integrate heterogeneous neuroimaging, behavioral, hormonal, and demographic measures within a unified predictive framework. By encoding each measure as a distinct token, IMA-MoE enables flexible modeling of cross-modal dependencies while preserving modality-specific characteristics. We further introduce a token-importance mechanism to enhance interpretability by quantifying the contribution of each measure to model predictions. Evaluated on the large-scale Adolescent Brain Cognitive Development (ABCD) dataset, IMA-MoE demonstrates superior performance in differentiating BED from healthy controls compared with baseline methods, while revealing sex-specific predictive patterns, with hormonal measures contributing more prominently to prediction in females. Collectively, these findings highlight the promise of interpretable, data-driven multimodal modeling in advancing biologically-informed characterization of BED and facilitating more precise and personalized interventions in neuropsychiatric disorders.

Elucidating the language-brain relationship requires bridging the methodological gap between the abstract theoretical frameworks of linguistics and the empirical neural data of neuroscience. Serving as an interdisciplinary cornerstone, computational neuroscience formalizes the hierarchical and dynamic structures of language into testable neural models through modeling, simulation, and data analysis. This enables a computational dialogue between linguistic hypotheses and neural mechanisms. Recent advances in deep learning, particularly large language models (LLMs), have powerfully advanced this pursuit. Their high-dimensional representational spaces provide a novel scale for exploring the neural basis of linguistic processing, while the "model-brain alignment" framework offers a methodology to evaluate the biological plausibility of language-related theories.

Effective analysis in neuroscience benefits significantly from robust conceptual frameworks. Traditional metrics of interbrain synchrony in social neuroscience typically depend on fixed, correlation-based approaches, restricting their explanatory capacity to descriptive observations. Inspired by the successful integration of geometric insights in network science, we propose leveraging discrete geometry to examine the dynamic reconfigurations in neural interactions during social exchanges. Unlike conventional synchrony approaches, our method interprets inter-brain connectivity changes through the evolving geometric structures of neural networks. This geometric framework is realized through a pipeline that identifies critical transitions in network connectivity using entropy metrics derived from curvature distributions. By doing so, we significantly enhance the capacity of hyperscanning methodologies to uncover underlying neural mechanisms in interactive social behavior.

Self-supervised learning has become an increasingly important paradigm in the domain of machine intelligence. Furthermore, evidence for self-supervised adaptation, such as contrastive formulations, has emerged in recent computational neuroscience and brain-inspired research. Nevertheless, current work on self-supervised learning relies on biologically implausible credit assignment -- in the form of backpropagation of errors -- and feedforward inference, typically a forward-locked pass. Predictive coding, in its mechanistic form, offers a biologically plausible means to sidestep these backprop-specific limitations. However, unsupervised predictive coding rests on learning a generative model of raw input (akin to "generative AI" approaches), which entails predicting a potentially high dimensional input; on the other hand, supervised predictive coding, which learns a mapping between inputs to target labels, requires human annotation, and thus incurs the drawbacks of supervised learning. In this work, we present a scheme for self-supervised learning, specifically for an emerging research sub-domain that we label as neuroscience-informed self-supervised learning (NeuroSSL), within a neurobiologically plausible framework that appeals to the free energy principle, constructing a new form of predictive coding that we call meta-representational predictive coding (MPC). MPC sidesteps the need for learning a generative model of sensory input (e.g., pixel-level features) by learning to predict representations of the input across parallel streams, resulting in an encoder-only learning and inference scheme. This formulation notably rests on active inference (in the form of sensory glimpsing) to drive the learning of representations, i.e., the representational dynamics are driven by sequences of decisions made by the model to sample informative portions of its sensorium.

The neurons of artificial neural networks were originally invented when much less was known about biological neurons than is known today. Our work explores a modification to the core neuron unit to make it more parallel to a biological neuron. The modification is made with the knowledge that biological dendrites are not simply passive activation funnels, but also compute complex non-linear functions as they transmit activation to the cell body. The paper explores a novel system of perforated'' backpropagation empowering the artificial neurons of deep neural networks to achieve better performance coding for the same features they coded for in the original architecture. After an initial network training phase, additional dendrite'' nodes are added to the network and separately trained with a different objective: to correlate their output with the remaining error of the original neurons. The trained dendrites are then frozen, and the original neurons are further trained, now taking into account the additional error signals provided by the dendrites. The cycle of training the original neurons and then adding and training dendrites can be repeated several times until satisfactory performance is achieved. Our algorithm was successfully added to modern state-of-the-art PyTorch networks across multiple domains, improving upon original accuracies and allowing for significant model compression without a loss in accuracy.

AI is rapidly advancing neuroscience, yet many laboratories fail to fully unleash its potential due to significant interdisciplinary barriers. While pre-trained neural models for physiological data are progressing quickly, their heterogeneous architectures and modality-specific constraints hinder systematic integration, selection, and evaluation. Despite recent advances in large language model (LLM)-based agent systems for intelligent scientific applications, existing approaches often still lack the domain expertise required to effectively select and coordinate diverse neuroscience pre-trained models and handle unique data types in this domain. We present NS-Copilot, an LLM-driven multi-agent system for neuroscience analysis that autonomously supports end-to-end workflows for diverse professional tasks. It unifies domain-specific pre-trained models and supports key neuroscience modalities, including EEG and extracellular spike data, through a natural-language interface. Given raw data and a task description, NS-Copilot orchestrates agents with specialized roles for planning, adaptive control, code generation, and result synthesis, enabling analysis without dataset-specific heuristics. We evaluate NS-Copilot on neuroscience benchmarks spanning Alzheimer's disease, Parkinson's disease, and working memory spike decoding. Across 8 trials per task, the system consistently outperforms strong baselines on the primary metric, demonstrating the ability of NS-Copilot for effective and scalable neuroscience analysis. Our code is publicly available at https://github.com/FrankLiu1102/ns-copilot.