Papers

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.

Cortical circuits must respond flexibly to new inputs while integrating information about the past, yet the way in which neural activity reconciles these competing demands remains unclear. Combining Neuropixels recordings from six mouse visual areas with mechanistic circuit modeling, we identify a dynamical regime in which heavy-tailed superdiffusive fluctuations coexist with long-range temporal dependence and oscillations. We formalize this regime as the adaptive fractional (AF) state, using an effective mean-field theory in which spatial and temporal fractional derivatives capture heavy-tailed excursions and long-range memory, respectively. We find that dynamical exponents characterizing the AF state vary systematically across the visual hierarchy: higher visual areas exhibit weaker superdiffusion and stronger temporal memory. In the circuit model, this hierarchical shift emerges from a progressive weakening of effective inhibition. These findings extend the classical hierarchy of timescales to a hierarchy of dynamical regimes and suggest that the AF state allows cortical areas to jointly express rapid responses and long-term temporal integration.

Modern imaging produces terabyte-scale segmentation volumes, assigning each voxel an object label. These categorical, boundary-sensitive and label-rich data underpin connectomics and other imaging-driven fields, yet their scale often forces interpretation through slices, approximate meshes or distributed workflows that obscure spatial context and voxel-level defects. Here we show that such volumes can be explored directly on commodity hardware with Volcanite, an open-source framework for dense-segmentation rendering. Combining compression-aware data handling, a Vulkan GPU backend and segmentation-specific rendering, Volcanite enables low-latency exploration without meshing or distributed infrastructure, including for unpublished, sensitive or proprietary data. Across multi-domain datasets, it preserves voxel labels, adds shadows and global illumination, and renders up to half a trillion voxels at 100 frames per second. By replacing lengthy preprocessing with direct inspection, Volcanite decouples hypothesis generation from data preparation and turns teravoxel label fields into interactive evidence for discovery, validation and cross-domain spatial analysis

Speech brain-computer interfaces (BCIs) aim to restore communication by transforming neural activity related to speech, language, or communicative intent into external outputs such as text, synthesized voice, or avatar control. Recent advances in intracortical and electrocorticographic recording, deep sequence models, and language-model-assisted decoding have enabled rapid progress, including high-performance attempted-speech decoding and increasingly naturalistic speech synthesis. Yet these achievements also reveal that speech BCIs are not simply neural-to-text decoders. They are adaptive clinical systems in which neural representations, recording hardware, decoding architectures, language priors, feedback, and user learning interact over time. Here, we synthesize speech BCI research from a system-level perspective. We first examine the neural substrates of speech and language, emphasizing their hierarchical, distributed, temporally structured, and non-stationary organization. We then examine recording and decoding choices, closed-loop adaptation, evaluation, clinical translation, and ethics. Across these domains, we highlight recurring trade-offs between signal resolution and invasiveness, low-level motor and high-level semantic targets, decoder accuracy and user agency, and language-model fluency and faithful neural evidence. We argue the next generation of speech BCIs should be evaluated not only by offline accuracy, but also by robustness across sessions, calibration burden, latency, uncertainty, usability, and safeguards against unintended decoding. By reframing speech BCIs as adaptive, user-centred systems, we outline the interdisciplinary priorities spanning speech neuroscience, neural engineering, machine learning, clinical practice, and neuroethics needed to move from proof-of-concept decoding toward reliable, expressive, and controllable communication neuroprostheses.

Structural reasoning, the ability to recognize and make inferences over the relational structure between objects and concepts, is a hallmark of human cognition, yet prevailing methods often collapse relational topology into flat embeddings, cannot discover hidden structure and lack interpretability. We introduce Neural Structural Reasoner (NSR), a brain-inspired network that preserves relational structure directly in the connectivity and dynamics of coupled neuronal populations. NSR draws inspiration from three biological mechanisms: multi-layered architecture for encoding hierarchical knowledge, stable representations of entity and concepts, and path integration for input-driven state inference. At query time, NSR parallelizes computation over candidate relational structures and leverages confidence-weighted scores to perform link prediction. Across standard knowledge-graph benchmarks, NSR achieves competitive accuracy without leading on every dataset, and has lower reported training times than several neural baselines. Because reasoning is implemented through sequences of human-readable neuron activations, NSR affords native interpretability by tracking intermediate inference steps. The model further extracts latent relational hierarchies and compositional rules, demonstrating the brain-inspired architecture as an effective, efficient, and highly interpretable substrate for structural reasoning.

A common assumption in language model development is that cognitive abilities are organized around a general, domain-free intelligence factor, like fluid intelligence in humans. This assumption is rarely tested directly, and prior attempts have done so only at a much smaller scale. We take a latent variable approach to intelligence in language models, similar to how psychometricians study psychological constructs. Performance in every specific problem set is influenced by a domain-specific and a domain-agnostic latent factor. Using factor analysis as a dimension-reduction technique, we analyzed 13,251 published evaluation scores covering 1,618 language models across 456 different text-only benchmarks. Due to the super-sparse nature of the dataset, we triangulate our analysis across different data densifiers and imputation methods. A robust pattern across different modes of bias is that 1. A general intelligence factor accounts for 70.8% of variance in model performance at our most generous estimate, and far less than that in most of our solutions, 2. Content-similar benchmarks do not necessarily cluster together, and 3. The $g$ factor is not dominated by any common theme, and there is a lack of evidence that it is well-proxied by standard "intelligence" benchmarks. Our findings go against current endeavors of defining, identifying, and targeting general intelligence as a tangible construct in language model development. This leaves the strategy of targeting a single conceptual ability without support, since the first-order abilities it would have to reach are often partially idiosyncratic and not identifiable in practice.

An ongoing challenge in sensory neuroscience is to characterize the feature dimensions encoded by cortical populations. Recent approaches probe feature selectivity in a data-driven way, by synthesizing a most-exciting-input (MEI) for a target neural population. While this approach has been successfully applied to human higher visual cortex using fMRI data, generating MEIs for early- and mid-level retinotopic visual areas requires additional modeling constraints due to small receptive field sizes. To address this challenge, we introduce two novel MEI generation frameworks, Receptive Field Diffusion for Visual Exploration (RF-DiVE) and Receptive Field Gradient Optimization (RF-GO). Both methods use a population receptive field (pRF)-constrained voxelwise encoding model; RF-DiVE combines this with a pretrained latent diffusion model, while RF-GO uses regularized gradient ascent. When applied to single voxels in retinotopically defined areas V1-hV4, using data from the Natural Scenes Dataset, we obtain MEIs that exhibit consistent structure within the pRF, suggesting selectivity for local features like contour, color, and texture. We systematically compare MEIs generated by RF-DiVE and RF-GO using two encoding backbones, performing in-silico validation of predicted responses to MEIs using independent encoding models. Across all methods and all visual areas, MEIs elicit higher model-predicted responses than the most activating natural images. We further find that the choice of generation framework and encoding backbone differentially affects MEI properties, including their visual appearance, structural interpretability, and cross-model generalizability. These results offer a new approach for performing data-driven characterization of spatial and feature selectivity across human visual cortex.

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

Collective patch-foraging experiments in the laboratory provide a controlled setting in which social information use can be quantified. Here, we consider a go/no-go task in which groups choose between two patches differing in food reward probability. We use agent-based simulations, underpinned by an augmented collective drift-diffusion model, to investigate alternative mechanisms for representing and integrating social information. We consider two representations, continuous (counting representation) and discrete (pulsatile representation), and two integration mechanisms, biasing the decision threshold (threshold modulation) and modifying the accumulated belief (belief modulation), yielding four distinct social models, in addition to a non-interacting model. We first characterize the collective dynamics generated by these models across cognitive parameters and experimental conditions. The temporal dynamics of group accuracy provide informative signatures of the underlying mechanisms. We then assess model selection and parameter identifiability using Bayesian inference and Wasserstein distance minimization, applied to group-accuracy and departure-time distributions. Bayesian inference using distributions of group accuracy provides the most reliable identification across the conditions considered. Importantly, model selection and parameter identifiability are associated with different aspects of collective behavior: model selection is closely linked to the presence of oscillations in the temporal dynamics, whereas parameter identifiability is more closely related to the global accuracy value. Thus, the information available for distinguishing the underlying cognitive mechanisms is not necessarily the same as that required to recover their parameters. Our results further show that identification depends not only on model structure but also on the experimental conditions.

Using predictive models to explain cognition requires more than accurate behavioral predictions. Input ablations offer an appealing route: remove information from a model and interpret the resulting performance change as evidence of its importance for behavior. Yet this inference assumes that the model's dependence on information reflects the dependence of the process generating the behavior. We test it in two synthetic sequential bandit tasks with known generating policies, where past choices can remain informative when feedback is unavailable to a predictor. We compare GRUs and Transformers trained from scratch, a fine-tuned LLaMA model, and cognitive models across systematically varied reward contributions. Our analyses distinguish prediction after training without reward observations from the response of a fixed predictor to donor-reward replacement. Three findings emerge. First, in the restless task, neural models trained without rewards predict held-out choices better than four simple training-fitted behavioral baselines. Second, under matched donor replacement, accurate predictors can respond much less than the known generator. Third, at some reward weights, neural networks predict better than a pooled reinforcement-learning model but have less faithful changes in choice probabilities; the model ordering differs between the two tasks. These independent-test results separate information sufficient for prediction from response fidelity under a specified ablation in sequential choice. They motivate validating model-ablation responses independently of predictive performance before using them to infer how the observed behavior was generated.

Effective central nervous system (CNS) intervention requires more than predicting biological responses: a scientific system must determine which intervention, observation, or additional evidence can improve a decision under uncertainty. However, in partially observed neuronal microenvironments, identical predicted outcomes may correspond to different exposure states, biological mechanisms, and intervention risks. We propose NeuronSifter, a decision-centric Agent-in-Twin framework, where an AI agent operates with an evolving biological digital twin rather than a fixed predictive model. NeuronSifter compiles interventions into state-conditional target-occupancy representations, propagates them through a mechanism-grounded World Action Model (WAM), and selects informative measurements based on their expected reduction in decision uncertainty. A shared probabilistic belief state couples intervention simulation, observation selection, and outcome assimilation, enabling the digital twin to continuously refine its decision-relevant representations through externally verified evidence. We evaluate NeuronSifter in Alzheimer's disease intervention scenarios using mechanistic neuronal microenvironment simulations and retrospective clinical endpoint references. The evaluation framework examines adaptive evidence acquisition, uncertainty-aware intervention planning, and robustness under model discrepancy through controlled environments and independent comparisons. NeuronSifter demonstrates how an AI system can actively identify missing evidence, refine biological hypotheses, and optimize intervention decisions under limited experimental budgets. Code is available at https://anonymous.4open.science/r/NeuronSifter.

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.

A major challenge in neuroscience and machine learning is to connect single-neuron influence, population dynamics, and circuit connectivity in a causal account of computation. Much previous work has shown that low-rank connectivity can generate low-dimensional dynamics in trained artificial neural networks, but this leaves unclear the functional relevance of the higher-rank structure of biological neural circuits and many artificial neuronal networks. Here we analyse recurrent neural networks trained to locate rewards by integrating continuously varying speed inputs in one- and two-dimensional spatial tasks. We find that dominant low-dimensional dynamics encode task locations, and can be causally manipulated to instruct behavioural outcomes. However, after decomposing the underlying circuitry we found that while low-rank connectivity accounts for the low-dimensional dynamics, accurate performance and generalisation to novel speed distributions requires high-rank connectivity. We demonstrate that this is achieved through distributed signalling that corrects errors in low-dimensional location representations. Thus, combined perturbation-, representation-, and circuit-level analyses demonstrate a novel mechanism for robust spatial computation and show how high-rank connectivity in neural circuits can provide a scaffold that supports precision and generalisation.

Deep learning has become a cornerstone of EEG-based brain decoding, with a growing number of architectures proposed every day. However, how the performance of these different models scales with data volume is not clear. Although this relationship has been characterized in other fields under the name of scaling laws, it remains poorly understood in the EEG domain. The present study addresses this gap by investigating how scan time and subject diversity affect the performance of different architectures. We evaluated five models across four EEG datasets. Training data volume was controlled by varying both subject count and trial volume under cross-subject validation. We then fitted power-law relationships to characterize the resulting behavior. Our findings reveal that as total data volume increases, the distinction between trial and subject scaling becomes largely irrelevant. Furthermore, we show that power-law relationships are both model and dataset-specific, yet they provide a robust descriptive framework for EEG decoding performance. Extrapolation to larger subject pools yields RMSE values below 0.1 in most cases. Our work contributes to the literature by providing a descriptive framework for data scaling in EEG and by demonstrating data-efficient experimental design in EEG research.

Reliable decisions depend on recognizing when an answer may be wrong. In biological cognition, metacognitive monitoring can dissociate from task performance, raising the question of how closely solving and judging are linked in language models. Here we study the confidence reports of four frontier models across 15 benchmarks. High task accuracy can coexist with weak error discrimination: a model solves 97% of competition mathematics problems while its answer-time confidence ranks correct answers above errors barely better than chance. Confidence separates correct answers from errors more effectively on questions solved by a separate reference model, while review brings limited improvement on reference-hard questions. Aggregate discrimination also rewards ranking correct answers on easy questions above errors on hard ones, which question-only forecasts already do well. Cross-evaluation helps most where the evaluator answered correctly, and errors shared by the two models usually retain high confidence. Hard questions and shared errors remain difficult targets for prompted self-review and peer oversight, even in models with strong problem-solving performance.

Foundation models are increasingly adapted to individual users, but an apparent personalization gain can simply reflect a stronger population model. This distinction matters for brain-computer interfaces, where every new user must be calibrated. We evaluated personal adaptation of three frozen EEG foundation models (CBraMod, REVE and LaBraM) in 235 held-out subjects from three motor-imagery datasets, comparing each subject's adapter with the population model and with adapters fitted to other subjects. Using all first-half session labels, personal adapters improved mean balanced accuracy over the population model by 1.5-5.4 percentage points and outperformed exchanged adapters by 2.3-7.3 points in all nine model-dataset combinations. The size of this benefit depended on population training: with four times the original budget, median gains remained positive (1.0-2.0 points) but were smaller for every model, and no population model reached a confirmed plateau. Acquiring the benefit cheaply was unreliable: few-label calibration was consistently non-negative on only one dataset, and in CBraMod neither unlabeled context nor meta-learned initialization outperformed matched controls. Personalization should therefore be evaluated against both a population reference and exchanged parameters, across population-training budgets.

Background & Objective Accurate segmentation of neurons in microscopy images of neuronal cultures is crucial for research on neurodegenerative diseases and neurotoxicity. Manual annotation of such images is time-consuming, subjective, and inconsistent across experts. Deep learning (DL) models offer an effective alternative, but require high-quality training datasets composed of microscopy images with accurately segmented neurons, typically created by experts. Neuronal cultures can be imaged using either phase-contrast or fluorescence microscopy. While live neurons are easily detected in fluorescence images, this modality requires staining, which affects cell viability. Conversely, phase-contrast imaging is non-invasive but makes neuron identification more challenging. Methods In this work we present a robust computer vision pipeline for the automatic generation of expert-level neuron segmentation masks from fluorescence microscopy images. These masks are used to train DL models for neuron identification in phase-contrast images. Our method relies on paired fluorescence and phase-contrast images captured simultaneously at the same magnification and coordinates, ensuring alignment across modalities. Once trained, the DL models can segment neurons in phase-contrast images alone, eliminating the need for fluorescence staining. Results We validate our approach by comparing the automatically generated masks with expert annotations using multiple agreement metrics, including IoU, Accuracy, and Gwet's AC1. Such metrics are calculated not only for the identification but also for the segmentation of instances. Conclusions This study presents a classical computer vision algorithm for generating neuron segmentation masks, which can be used for downstream applications such as non-invasive cell viability analyses by means of DL.

Modeling resting-state functional magnetic resonance imaging (rs-fMRI) data is crucial for understanding brain-wide neural activity. However, traditional methods struggle to capture complex temporal dynamics over long horizons, to account for the brain's anatomical spatial structure, and to model high-dimensional ambient signals that lie on a low-dimensional intrinsic subspace. We propose FAST-Brain, a unified flow-aligned spatio-temporal surrogate brain model that addresses all three challenges. At its core is a flow-aligned generative framework that directly predicts the clean blood-oxygen-level-dependent (BOLD) signal, paired with a graph convolutional network that captures spatial structural constraints and a Transformer that models long-range temporal dependencies. Theoretically, we show that under a low-dimensional subspace assumption, the approximation error of our model scales with the intrinsic dimension rather than the ambient dimension, which justifies our direct modeling of the BOLD signal. Extensive experiments on synthetic and Human Connectome Project datasets demonstrate that FAST-Brain achieves state-of-the-art performance in recovering functional connectivity, effective connectivity, and the implicit low-dimensional signal subspace.

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

Traditional models of collective behavior rely on prescribed interaction rules, leaving unresolved the question of how behavior arises from neural representations of space. Here, we develop a first-principles theory in which movement, decision-making, and collective organization emerge by coarse-graining fast neural dynamics on a topological representation of directional space. For a ring manifold encoding heading, this reduction yields a macroscopic theory of behavior: a decision landscape over directions that admits a harmonic decomposition. In this framework, behavior is governed by a spectral organization of directional information rather than ad hoc rules. We demonstrate that target-seeking, avoidance, choice, spatial decision-making, and diverse forms of collective motion arise as distinct organizations of the underlying harmonic landscape. The theory unifies neural representations, behavioral decisions, and collective dynamics in a single mathematical description.

Mapping resting-state brain organization to individual differences in cognitive ability remains a major challenge in population neuroinformatics. Although deep learning enables flexible modeling of brain connectivity, limited interpretability restricts its scientific and clinical utility. To address this objective, we developed an explainable deep learning framework based on sparse projected residual networks to predict fluid, crystallized, and total intelligence from resting-state functional magnetic resonance imaging in 5,285 participants from the Adolescent Brain Cognitive Development study. We incorporated three complementary explainability methods (Integrated Gradients, Gradient Shapley Additive Explanations, and Occlusion) to interpret model behavior. The framework outperformed existing approaches, achieving Pearson correlations of 0.44, 0.58, and 0.56 for fluid, crystallized, and total intelligence, respectively, corresponding to predictive improvements of 6 to 9 percent. All three explainability methods produced near-identical feature rankings (pairwise rank correlations greater than 0.99). Consensus maps revealed a dual-layered functional architecture where primary predictive hubs localized within canonical systems, while the strongest global predictive pathways frequently bypassed these hubs through distributed, long-range relay connections. These findings suggest that intelligence emerges from the interaction between localized computational hubs and distributed communication pathways. Ultimately, these normative network architectures provide clinical reference maps to detect individual deviations, supporting earlier diagnosis, cognitive subtype stratification, and treatment monitoring in atypical neurodevelopment.

If consciousness is functional, a basic question is what awareness of a content actually changes in how a system operates on it. We ask, for a particular content X and mental or bodily process Y, whether awareness of X changes whether, or how well, X can be used in process Y. Crucially, X-aware and X-unaware conditions must be compared in ways that rule out poorer information about X as a sufficient explanation. Our current literature sweep yields a small but informative functional profile. The clearest current evidence concerns goal-sensitive control, especially regulation of attentional influence, with additional evidence linking awareness to metacognitive evaluation. Meanwhile, one feature-binding paradigm suggests that short-lived feature-location binding and retrieval can remain possible without awareness. This preliminary profile suggests a selective rather than universal immediate functional role for awareness. But such a functional profile is not yet a theory of consciousness. A full-stack functionalist theory must also account for the broader phenomena associated with consciousness - the explanatory profile: the structure and manner of presentation of perceptual and affective experience, subject-world organisation, awareness judgments, and problem reports. Finally, the functional and explanatory profiles constrain theory construction from different directions, but neither determines the process architecture that could connect them. Bridging this gap requires abductive construction: proposing candidate architectures, implementing and intervening on them, and progressively revising them as further constraints accumulate. In sum, we propose a framework for constructing full-stack functionalist theories of consciousness, and take the first step towards detailing the functional profile.

We report a pre-registered test of five hypotheses about the synapse-flow random walk on the connectome of the male Drosophila central nervous system (166,700 neurons, 124 million synapses), in which a walker moves to a postsynaptic partner in proportion to synapse number. The hypotheses concern the spectral gap and its dependence on the neck connective, the localisation of the leading modes of an input-normalised signed map, the certified mixing depth measured by the Dobrushin coefficient, its robustness to per-synapse detection confidence, and the dependence of the signed spectrum on the neurotransmitter sign convention. After public registration and a code freeze, each was tested once. Two held: the two-neuron photoreceptor modes that lead the signed spectrum are an artefact of normalising by very small inputs, removed by an input floor at the median, and they do not depend on the sign convention. Three failed: at a threshold of five synapses per connection the spectral gap is an order of magnitude smaller than predicted ($|\lambda_2| = 0.9965$) and the chain is certifiably far from mixed after 128 steps, and at no confidence level tested was the mixing depth certifiably robust. Exploratory analyses trace the slow mode to eleven neurons of the cord, seven of them mesothoracic efferent neurons, that become nearly closed once weak connections are dropped, find a similar boundary set in the lamina of the FlyWire female brain, show that null models preserving cell-type wiring reproduce the slow modes, and show that exact chains built from the confidence data change the depth profile after 32 steps by at most 0.017 at the pre-registered confidence level, far less than the worst-case certificate allows. Random-walk summaries of connectomes are dominated by nearly closed sets at the edges of the reconstruction unless these are treated explicitly.

Traveling waves of activity in neural tissue can be halted by spatial inhomogeneity in synaptic coupling. We study an integrate-and-fire network in which each neuron fires once and the coupling decays exponentially. For this model the leading-edge firing map reduces exactly to a scalar equation for the wave speed in space, with a slow unstable and a fast stable homogeneous speed, $c_1$ and $c_2$, and a periodic modulation of the coupling enters this equation pointwise. Positive periodic waves terminate in folds. For slowly varying modulation the fold amplitude approaches a plateau set by the trough of the modulation, where the local bottleneck speed is $\sqrt{c_1 c_2}$; the approach to the plateau is set by the local geometry of the trough. For rapidly varying modulation the fold amplitude grows linearly with frequency, with a slope given by a full-amplitude average over the integrated modulation profile; a weak-ripple truncation of that average overestimates the slope about 2.5-fold at the default coupling. A perturbative recursion in the amplitude gives the speed profile explicitly. We distinguish loss of the periodic wave from failure of a particular launch, and the excitatory regime $\epsilon\le 1$ from its sign-changing extension. The results are checked against direct integration of the reduced equation and first-spike firing-map simulations of the network.

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.

Engram cells in hippocampal CA1 represent contextual information associated with events experienced by animals and constitute a cellular substrate of episodic memory. Recent experiments have shown that a subset of hippocampal place cells is recruited as engram cells for individual contexts. However, the principle governing engram cell allocation across contexts remains unclear. Here, we develop an information-theoretic framework that quantifies the trade-off between spatial and contextual information encoded by CA1 neurons. Our theory shows that limited neural resources inevitably create competition among contexts for the recruitment of place cells as engram cells. Solving this optimization problem determines the fraction of engram cells allocated to each context as a function of its occurrence probability. The theory predicts a non-monotonic relationship between context probability and engram allocation, reflecting competition between spatial and contextual information under resource constraints. Consequently, the recruited fraction emerges through a discontinuous transition at a critical probability, reaches a maximum at intermediate probabilities, and decreases for highly frequent contexts. Furthermore, we analytically derive the phase boundary for the emergence of finite engram cell allocation as a function of contextual input strength and the relative importance of contextual information. These findings identify competition for limited neural resources as a key determinant of engram cell allocation and provide experimentally testable predictions for how memory representations are distributed across contexts under resource constraints.

Amortized neural likelihoods enable computationally expensive inference for models with analytically intractable or unspecified likelihoods, but their black-box nature limits interpretability. We introduce a symbolic distillation pipeline that converts trained neural likelihoods into explicit, interpretable expressions optimized for efficient parameter estimation. Our approach uses a recovery-directed objective to guide symbolic regression toward expressions that preserve parameter-recovery accuracy rather than merely approximating the likelihood function. Candidate expressions are evaluated on held-out datasets and selected using a criterion that jointly accounts for expression complexity, parameter-recovery performance, and distributional distance from the learned likelihood. We evaluate the pipeline on the diffusion decision model, a classical cognitive model, whose analytically tractable likelihood provides ground truth for controlled evaluation. The proposed recovery-directed objective improves parameter recovery over standard symbolic-regression objectives. The resulting symbolic likelihoods enable over 100 times faster parameter evaluation than both neural likelihoods and, when available, the exact likelihood, while maintaining a manageable loss in precision. We further demonstrate these computational benefits in Bayesian hierarchical inference on empirical data. Our pipeline provides a lightweight interface for integrating symbolic distillation with existing neural-likelihood estimation methods and can be adapted to a range of simulation-based inference settings.

Neural activity unfolds not as a set of independent signals, but as a coordinated dynamical process that can be described as a point moving through a high-dimensional state space. This perspective has contributed substantially to recent developments in systems neuroscience, especially through studies of directly recorded neuronal population activity, but remains comparatively underused in non-invasive human recordings such as EEG and MEG. In this primer, we present a neural trajectory analysis based on Principal Component Analysis (PCA) as an accessible route into extending the concepts of neural trajectories in state space to human electrophysiology. We explain how EEG/MEG activity can be organized into neural state representations, projected onto axes organized by decreasing covariance, truncated into low-dimensional representations, and visualized as trajectories that capture how distributed activity evolves over time. We show how trajectory geometry can be used to compare conditions and relate neural dynamics to behavior or clinical outcomes. An example of EEG motor execution and imagery, accompanied by a tutorial notebook, illustrates the workflow from conventional EEG summaries to trajectory-based analysis. We also clarify the limits of PCA, including its linear, variance-driven nature, and discuss EEG/MEG-specific challenges such as spatial mixing, preprocessing sensitivity, validation, and overinterpretation. Finally, we situate PCA within a broader family of state-space methods. By making neural trajectories practical and interpretable, this primer offers a guide for bringing the conceptual framework of population-level dynamics into mainstream human cognitive neuroscience.

Humans rely on gaze, head movements, and visual cues to attend to speakers in noisy environments, yet auditory attention decoding (AAD) has been studied primarily using electroencephalography (EEG). We introduce the Multimodal Auditory-attention Egocentric Speech-TRacking Open (MAESTRO) corpus, the first AAD dataset to simultaneously record EEG, eye gaze, pupillometry, egocentric video, and head inertial measurement unit (IMU) data. MAESTRO includes four competing speakers and background noise across multiple signal-to-noise ratio (SNR) conditions, enabling attention decoding under realistic listening scenarios. Through a four-speaker attention decoding benchmark, we show that combining behavioral and physiological signals improves decoding performance over EEG-only approaches, enabling future advances in multimodal auditory attention decoding. These findings open the door to new applications, analyses, and methodological advances in multimodal AAD. The complete dataset is publicly available at https://huggingface.co/datasets/aspire-osu/maestro-eeg-dataset . The official code repository is available at https://github.com/ASPIRE-OSU/MAESTRO .

Can the spatial organization of cortical activity help transfer frozen image representations to fMRI prediction? We introduce FlatClip, which renders cortical activity as anatomy-linked flatmaps and extracts features with a frozen SigLIP2 encoder. Only a lightweight downstream probe is trained, without fMRI-specific encoder pretraining or fine-tuning. Across four resting-state benchmarks, FlatClip outperforms the evaluated ROI-level baselines on HCP and ADNI, but is weaker on PPMI and below the strongest voxel-level models overall. On NSD visual-fMRI decoding, restricting inputs to visual or NSD-provided task-active cortex improves recognition over whole-cortex inputs. Spatial perturbations reduce performance with both retrained and fixed readouts, and anatomy-linked arrangements outperform cortical-pixel permutations across three colormaps. Together, these results demonstrate a practical route for reusing image-pretrained features in fMRI and highlight cortical arrangement and input-region selection as important design choices. Code is available at https://github.com/OneMore1/FlatClip.