Daily Papers

The Wilson-Cowan model for metapopulation, a Neural Mass Network Model, treats different subcortical regions of the brain as connected nodes, with connections representing various types of structural, functional, or effective neuronal connectivity between these regions. Each region comprises interacting populations of excitatory and inhibitory cells, consistent with the standard Wilson-Cowan model. By incorporating stable attractors into such a metapopulation model's dynamics, we transform it into a learning algorithm capable of achieving high image and text classification accuracy. We test it on MNIST and Fashion MNIST, in combination with convolutional neural networks, on CIFAR-10 and TF-FLOWERS, and, in combination with a transformer architecture (BERT), on IMDB, always showing high classification accuracy. These numerical evaluations illustrate that minimal modifications to the Wilson-Cowan model for metapopulation can reveal unique and previously unobserved dynamics.

Humans rapidly learn abstract knowledge when encountering novel environments and flexibly deploy this knowledge to guide efficient and intelligent action. Can modern AI systems learn and plan in a similar way? We study this question using a dataset of complex human gameplay with concurrent fMRI recordings, in which participants learn novel video games that require rule discovery, hypothesis revision, and multi-step planning. We jointly evaluate models by their ability to play the games, match human learning behavior, and predict brain activity during the same task, comparing a suite of frontier Large Reasoning Models (LRMs) against model-free and model-based deep reinforcement learning agents and a Bayesian theory-based agent. We find that frontier LRMs most closely match human behavioral patterns during game discovery and predict brain activity an order of magnitude better than both reinforcement learning alternatives across cortical and subcortical regions, with effects robust to permutation controls. Through targeted manipulations, we further show that brain alignment reflects the model's in-context representation of the game state rather than its downstream planning or reasoning. Our results establish LRMs as compelling computational accounts of human learning and decision making in complex, naturalistic environments. Project page with interactive replays: https://botcs.github.io/reason-to-play/

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

Cortical circuits exhibit intricate recurrent architectures that are remarkably similar across different brain areas. Such stereotyped structure suggests the existence of common computational principles. However, such principles have remained largely elusive. Inspired by gated-memory networks, namely long short-term memory networks (LSTMs), we introduce a recurrent neural network in which information is gated through inhibitory cells that are subtractive (subLSTM). We propose a natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical microcircuits. Our empirical evaluation across sequential image classification and language modelling tasks shows that subLSTM units can achieve similar performance to LSTM units. These results suggest that cortical circuits can be optimised to solve complex contextual problems and proposes a novel view on their computational function. Overall our work provides a step towards unifying recurrent networks as used in machine learning with their biological counterparts.

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

White matter tract segmentation is crucial for studying brain structural connectivity and neurosurgical planning. However, segmentation remains challenging due to issues like class imbalance between major and minor tracts, structural similarity, subject variability, symmetric streamlines between hemispheres etc. To address these challenges, we propose TractoEmbed, a modular multi-level embedding framework, that encodes localized representations through learning tasks in respective encoders. In this paper, TractoEmbed introduces a novel hierarchical streamline data representation that captures maximum spatial information at each level i.e. individual streamlines, clusters, and patches. Experiments show that TractoEmbed outperforms state-of-the-art methods in white matter tract segmentation across different datasets, and spanning various age groups. The modular framework directly allows the integration of additional embeddings in future works.

Large Language Models (LLMs) demonstrate human-level or even superior language abilities, effectively modeling syntactic structures, yet the specific computational modules responsible remain unclear. A key question is whether LLM behavioral capabilities stem from mechanisms akin to those in the human brain. To address these questions, we introduce the Hierarchical Frequency Tagging Probe (HFTP), a tool that utilizes frequency-domain analysis to identify neuron-wise components of LLMs (e.g., individual Multilayer Perceptron (MLP) neurons) and cortical regions (via intracranial recordings) encoding syntactic structures. Our results show that models such as GPT-2, Gemma, Gemma 2, Llama 2, Llama 3.1, and GLM-4 process syntax in analogous layers, while the human brain relies on distinct cortical regions for different syntactic levels. Representational similarity analysis reveals a stronger alignment between LLM representations and the left hemisphere of the brain (dominant in language processing). Notably, upgraded models exhibit divergent trends: Gemma 2 shows greater brain similarity than Gemma, while Llama 3.1 shows less alignment with the brain compared to Llama 2. These findings offer new insights into the interpretability of LLM behavioral improvements, raising questions about whether these advancements are driven by human-like or non-human-like mechanisms, and establish HFTP as a valuable tool bridging computational linguistics and cognitive neuroscience. This project is available at https://github.com/LilTiger/HFTP.

Computed tomography perfusion (CTP) at admission is routinely used to estimate the ischemic core and penumbra, while follow-up diffusion-weighted MRI (DWI) provides the definitive infarct outcome. However, single time-point segmentations fail to capture the biological heterogeneity and temporal evolution of stroke. We propose a bi-temporal analysis framework that characterizes ischemic tissue using statistical descriptors, radiomic texture features, and deep feature embeddings from two architectures (mJ-Net and nnU-Net). Bi-temporal refers to admission (T1) and post-treatment follow-up (T2). All features are extracted at T1 from CTP, with follow-up DWI aligned to ensure spatial correspondence. Manually delineated masks at T1 and T2 are intersected to construct six regions of interest (ROIs) encoding both initial tissue state and final outcome. Features were aggregated per region and analyzed in feature space. Evaluation on 18 patients with successful reperfusion demonstrated meaningful clustering of region-level representations. Regions classified as penumbra or healthy at T1 that ultimately recovered exhibited feature similarity to preserved brain tissue, whereas infarct-bound regions formed distinct groupings. Both baseline GLCM and deep embeddings showed a similar trend: penumbra regions exhibit features that are significantly different depending on final state, whereas this difference is not significant for core regions. Deep feature spaces, particularly mJ-Net, showed strong separation between salvageable and non-salvageable tissue, with a penumbra separation index that differed significantly from zero (Wilcoxon signed-rank test). These findings suggest that encoder-derived feature manifolds reflect underlying tissue phenotypes and state transitions, providing insight into imaging-based quantification of stroke evolution.

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that primarily affects the aging population by impairing cognitive and motor functions. Early detection of AD through accessible methodologies like magnetic resonance imaging (MRI) is vital for developing effective interventions to halt or slow the disease's progression. This study aims to perform a comprehensive analysis of machine learning techniques for selecting MRI-based biomarkers and classifying individuals into healthy controls (HC) and unstable controls (uHC) who later show mild cognitive impairment within five years. The research utilizes MRI data from the Alzheimer's Disease Neuroinformatics Initiative (ADNI) and the Open Access Series of Imaging Studies 3 (OASIS-3), focusing on both HC and uHC participants. The study addresses the challenges of imbalanced data by testing classification methods on balanced and unbalanced datasets, and harmonizes data using polynomial regression to mitigate nuisance variables like age, gender, and intracranial volume. Results indicate that Gaussian Naive Bayes and RusBoost classifiers shows an optimal performance, achieving accuracies of up to 76.46% and 72.48% respectively on the ADNI dataset. For the OASIS-3 dataset, Kernel Naive Bayes and RusBoost yield accuracies ranging from 64.66% to 75.71%, improving further in age-matched datasets. Brain regions like the entorhinal cortex, hippocampus, lateral ventricle, and lateral orbitofrontal cortex are identified as significantly impacted during early cognitive decline. Despite limitations such as small sample sizes, the study's harmonization approach enhances the robustness of biomarker selection, suggesting the potential of this semi-automatic machine learning pipeline for early AD detection using MRI.

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

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

Understanding the functional organization of higher visual cortex is a central focus in neuroscience. Past studies have primarily mapped the visual and semantic selectivity of neural populations using hand-selected stimuli, which may potentially bias results towards pre-existing hypotheses of visual cortex functionality. Moving beyond conventional approaches, we introduce a data-driven method that generates natural language descriptions for images predicted to maximally activate individual voxels of interest. Our method -- Semantic Captioning Using Brain Alignments ("BrainSCUBA") -- builds upon the rich embedding space learned by a contrastive vision-language model and utilizes a pre-trained large language model to generate interpretable captions. We validate our method through fine-grained voxel-level captioning across higher-order visual regions. We further perform text-conditioned image synthesis with the captions, and show that our images are semantically coherent and yield high predicted activations. Finally, to demonstrate how our method enables scientific discovery, we perform exploratory investigations on the distribution of "person" representations in the brain, and discover fine-grained semantic selectivity in body-selective areas. Unlike earlier studies that decode text, our method derives voxel-wise captions of semantic selectivity. Our results show that BrainSCUBA is a promising means for understanding functional preferences in the brain, and provides motivation for further hypothesis-driven investigation of visual cortex.

Sparse autoencoders have recently produced dictionaries of high-dimensional vectors corresponding to the universe of concepts represented by large language models. We find that this concept universe has interesting structure at three levels: 1) The "atomic" small-scale structure contains "crystals" whose faces are parallelograms or trapezoids, generalizing well-known examples such as (man-woman-king-queen). We find that the quality of such parallelograms and associated function vectors improves greatly when projecting out global distractor directions such as word length, which is efficiently done with linear discriminant analysis. 2) The "brain" intermediate-scale structure has significant spatial modularity; for example, math and code features form a "lobe" akin to functional lobes seen in neural fMRI images. We quantify the spatial locality of these lobes with multiple metrics and find that clusters of co-occurring features, at coarse enough scale, also cluster together spatially far more than one would expect if feature geometry were random. 3) The "galaxy" scale large-scale structure of the feature point cloud is not isotropic, but instead has a power law of eigenvalues with steepest slope in middle layers. We also quantify how the clustering entropy depends on the layer.

Over the past decade, predictive modeling of neural responses in the primate visual system has advanced significantly, largely driven by various DNN approaches. These include models optimized directly for visual recognition, cross-modal alignment through contrastive objectives, neural response prediction from scratch, and large language model embeddings.Likewise, different readout mechanisms, ranging from fully linear to spatial-feature factorized methods have been explored for mapping network activations to neural responses. Despite the diversity of these approaches, it remains unclear which method performs best across different visual regions. In this study, we systematically compare these approaches for modeling the human visual system and investigate alternative strategies to improve response predictions. Our findings reveal that for early to mid-level visual areas, response-optimized models with visual inputs offer superior prediction accuracy, while for higher visual regions, embeddings from LLMs based on detailed contextual descriptions of images and task-optimized models pretrained on large vision datasets provide the best fit. Through comparative analysis of these modeling approaches, we identified three distinct regions in the visual cortex: one sensitive primarily to perceptual features of the input that are not captured by linguistic descriptions, another attuned to fine-grained visual details representing semantic information, and a third responsive to abstract, global meanings aligned with linguistic content. We also highlight the critical role of readout mechanisms, proposing a novel scheme that modulates receptive fields and feature maps based on semantic content, resulting in an accuracy boost of 3-23% over existing SOTAs for all models and brain regions. Together, these findings offer key insights into building more precise models of the visual system.

Attention Deficit Hyperactive Disorder (ADHD) is a common behavioral problem affecting children. In this work, we investigate the automatic classification of ADHD subjects using the resting state Functional Magnetic Resonance Imaging (fMRI) sequences of the brain. We show that the brain can be modeled as a functional network, and certain properties of the networks differ in ADHD subjects from control subjects. We compute the pairwise correlation of brain voxels' activity over the time frame of the experimental protocol which helps to model the function of a brain as a network. Different network features are computed for each of the voxels constructing the network. The concatenation of the network features of all the voxels in a brain serves as the feature vector. Feature vectors from a set of subjects are then used to train a PCA-LDA (principal component analysis-linear discriminant analysis) based classifier. We hypothesized that ADHD-related differences lie in some specific regions of the brain and using features only from those regions is sufficient to discriminate ADHD and control subjects. We propose a method to create a brain mask that includes the useful regions only and demonstrate that using the feature from the masked regions improves classification accuracy on the test data set. We train our classifier with 776 subjects and test on 171 subjects provided by The Neuro Bureau for the ADHD-200 challenge. We demonstrate the utility of graph-motif features, specifically the maps that represent the frequency of participation of voxels in network cycles of length 3. The best classification performance (69.59%) is achieved using 3-cycle map features with masking. Our proposed approach holds promise in being able to diagnose and understand the disorder.

White matter bundle segmentation is crucial for studying brain structural connectivity, neurosurgical planning, and neurological disorders. White Matter Segmentation remains challenging due to structural similarity in streamlines, subject variability, symmetry in 2 hemispheres, etc. To address these challenges, we propose TractoGPT, a GPT-based architecture trained on streamline, cluster, and fusion data representations separately. TractoGPT is a fully-automatic method that generalizes across datasets and retains shape information of the white matter bundles. Experiments also show that TractoGPT outperforms state-of-the-art methods on average DICE, Overlap and Overreach scores. We use TractoInferno and 105HCP datasets and validate generalization across dataset.

The article explores an encoding and structural information processing approach using sparse bit vectors and fixed-length linear vectors. The following are presented: a discrete method of speculative stochastic dimensionality reduction of multidimensional code and linear spaces with linear asymptotic complexity; a geometric method for obtaining discrete embeddings of an organised code space that reflect the internal structure of a given modality. The structure and properties of a code space are investigated using three modalities as examples: morphology of Russian and English languages, and immunohistochemical markers. Parallels are drawn between the resulting map of the code space layout and so-called pinwheels appearing on the mammalian neocortex. A cautious assumption is made about similarities between neocortex organisation and processes happening in our models.

Neurons in the brain are spatially organized such that neighbors on tissue often exhibit similar response profiles. In the human language system, experimental studies have observed clusters for syntactic and semantic categories, but the mechanisms underlying this functional organization remain unclear. Here, building on work from the vision literature, we develop TopoLM, a transformer language model with an explicit two-dimensional spatial representation of model units. By combining a next-token prediction objective with a spatial smoothness loss, representations in this model assemble into clusters that correspond to semantically interpretable groupings of text and closely match the functional organization in the brain's language system. TopoLM successfully predicts the emergence of the spatio-functional organization of a cortical language system as well as the organization of functional clusters selective for fine-grained linguistic features empirically observed in human cortex. Our results suggest that the functional organization of the human language system is driven by a unified spatial objective, and provide a functionally and spatially aligned model of language processing in the brain.

Large Language Models (LLMs) possess vast amounts of knowledge within their parameters, prompting research into methods for locating and editing this knowledge. Previous work has largely focused on locating entity-related (often single-token) facts in smaller models. However, several key questions remain unanswered: (1) How can we effectively locate query-relevant neurons in decoder-only LLMs, such as Llama and Mistral? (2) How can we address the challenge of long-form (or free-form) text generation? (3) Are there localized knowledge regions in LLMs? In this study, we introduce Query-Relevant Neuron Cluster Attribution (QRNCA), a novel architecture-agnostic framework capable of identifying query-relevant neurons in LLMs. QRNCA allows for the examination of long-form answers beyond triplet facts by employing the proxy task of multi-choice question answering. To evaluate the effectiveness of our detected neurons, we build two multi-choice QA datasets spanning diverse domains and languages. Empirical evaluations demonstrate that our method outperforms baseline methods significantly. Further, analysis of neuron distributions reveals the presence of visible localized regions, particularly within different domains. Finally, we show potential applications of our detected neurons in knowledge editing and neuron-based prediction.

Attending to what is relevant is fundamental to both the mammalian brain and modern machine learning models such as Transformers. Yet, determining relevance remains a core challenge, traditionally offloaded to learning algorithms like backpropagation. Inspired by recent cellular neurobiological evidence linking neocortical pyramidal cells to distinct mental states, this work shows how models (e.g., Transformers) can emulate high-level perceptual processing and awake thought (imagination) states to pre-select relevant information before applying attention. Triadic neuronal-level modulation loops among questions (Q), clues (keys, K), and hypotheses (values, V) enable diverse, deep, parallel reasoning chains at the representation level and allow a rapid shift from initial biases to refined understanding. This leads to orders-of-magnitude faster learning with significantly reduced computational demand (e.g., fewer heads, layers, and tokens), at an approximate cost of O(N), where N is the number of input tokens. Results span reinforcement learning (e.g., CarRacing in a high-dimensional visual setup), computer vision, and natural language question answering.

In this paper, we identify a sparse reward subsystem within the hidden states of Large Language Models (LLMs), drawing an analogy to the biological reward subsystem in the human brain. We demonstrate that this subsystem contains value neurons that represent the model's internal expectation of state value, and through intervention experiments, we establish the importance of these neurons for reasoning. Our experiments reveal that these value neurons are robust across diverse datasets, model scales, and architectures; furthermore, they exhibit significant transferability across different datasets and models fine-tuned from the same base model. By examining cases where value predictions and actual rewards diverge, we identify dopamine neurons within the reward subsystem which encode reward prediction errors (RPE). These neurons exhibit high activation when the reward is higher than expected and low activation when the reward is lower than expected.

Deep Learning (DL) in neuroimaging has become increasingly relevant for detecting neurological conditions and neurodegenerative disorders. One of the most predominant biomarkers in neuroimaging is represented by brain age, which has been shown to be a good indicator for different conditions, such as Alzheimer's Disease. Using brain age for weakly supervised pre-training of DL models in transfer learning settings has also recently shown promising results, especially when dealing with data scarcity of different conditions. On the other hand, anatomical information of brain MRIs (e.g. cortical thickness) can provide important information for learning good representations that can be transferred to many downstream tasks. In this work, we propose AnatCL, an anatomical foundation model for brain MRIs that i.) leverages anatomical information in a weakly contrastive learning approach, and ii.) achieves state-of-the-art performances across many different downstream tasks. To validate our approach we consider 12 different downstream tasks for the diagnosis of different conditions such as Alzheimer's Disease, autism spectrum disorder, and schizophrenia. Furthermore, we also target the prediction of 10 different clinical assessment scores using structural MRI data. Our findings show that incorporating anatomical information during pre-training leads to more robust and generalizable representations. Pre-trained models can be found at: https://github.com/EIDOSLAB/AnatCL.

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

Recently, Ultra-High Field MRI (UHF-MRI) has become more available and one of the best tools to study the brain. One common step in quantitative neuroimaging is to segment the brain into several regions, which has been done using software packages like FreeSurfer , FastSurferVINN or SynthSeg. However, the differences between UHF-MRI and 1.5T or 3T images are such that the automatic segmentation techniques optimized at these field strengths usually produce unsatisfactory segmentation results for UHF images. Thus, it has been particularly challenging to perform region-based quantitative analyses as typically done with 1.5-3T data, underscoring the crucial need for developing new automatic segmentation techniques designed to handle UHF images. Hence, we propose a novel Deep Learning (DL)-based segmentation technique called GOUHFI: Generalized and Optimized segmentation tool for Ultra-High Field Images, designed to segment UHF images of various contrasts and resolutions. For training, we used a total of 206 label maps from datasets acquired at 3T, 7T and 9.4T. In contrast to most DL strategies, we used a domain randomization approach, where synthetic images were used to train a 3D U-Net. GOUHFI was tested on seven different datasets and compared to existing techniques like FastSurferVINN,SynthSeg and CEREBRUM-7T. GOUHFI was able to segment the six contrasts and seven resolutions tested at 3T, 7T and 9.4T. Average Dice scores of 0.90, 0.90 and 0.93 were computed against the ground truth segmentations at 3T, 7T and 9.4T, respectively. Ultimately, GOUHFI is a promising new segmentation tool, being the first of its kind proposing a contrast- and resolution-agnostic alternative for UHF-MRI without requiring fine-tuning or retraining, making it the forthcoming alternative for neuroscientists working with UHF-MRI or even lower field strengths.

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

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

Understanding how the human brain represents visual concepts, and in which brain regions these representations are encoded, remains a long-standing challenge. Decades of work have advanced our understanding of visual representations, yet brain signals remain large and complex, and the space of possible visual concepts is vast. As a result, most studies remain small-scale, rely on manual inspection, focus on specific regions and properties, and rarely include systematic validation. We present a large-scale, automated framework for discovering and explaining visual representations across the human cortex. Our method comprises two main stages. First, we discover candidate interpretable patterns in fMRI activity through unsupervised, data-driven decomposition methods. Next, we explain each pattern by identifying the set of natural images that most strongly elicit it and generating a natural-language description of their shared visual meaning. To scale this process, we introduce an automated pipeline that tests multiple candidate explanations, assigns quantitative reliability scores, and selects the most consistent description for each voxel pattern. Our framework reveals thousands of interpretable patterns spanning many distinct visual concepts, including fine-grained representations previously unreported.

Many AI models trained on natural images develop representations that resemble those of the human brain. However, the factors that drive this brain-model similarity remain poorly understood. To disentangle how the model, training and data independently lead a neural network to develop brain-like representations, we trained a family of self-supervised vision transformers (DINOv3) that systematically varied these different factors. We compare their representations of images to those of the human brain recorded with both fMRI and MEG, providing high resolution in spatial and temporal analyses. We assess the brain-model similarity with three complementary metrics focusing on overall representational similarity, topographical organization, and temporal dynamics. We show that all three factors - model size, training amount, and image type - independently and interactively impact each of these brain similarity metrics. In particular, the largest DINOv3 models trained with the most human-centric images reach the highest brain-similarity. This emergence of brain-like representations in AI models follows a specific chronology during training: models first align with the early representations of the sensory cortices, and only align with the late and prefrontal representations of the brain with considerably more training. Finally, this developmental trajectory is indexed by both structural and functional properties of the human cortex: the representations that are acquired last by the models specifically align with the cortical areas with the largest developmental expansion, thickness, least myelination, and slowest timescales. Overall, these findings disentangle the interplay between architecture and experience in shaping how artificial neural networks come to see the world as humans do, thus offering a promising framework to understand how the human brain comes to represent its visual world.

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

Understanding the property of neural populations (or voxels) in the human brain can advance our comprehension of human perceptual and cognitive processing capabilities and contribute to developing brain-inspired computer models. Recent encoding models using deep neural networks (DNNs) have successfully predicted voxel-wise activity. However, interpreting the properties that explain voxel responses remains challenging because of the black-box nature of DNNs. As a solution, we propose LLM-assisted Visual Cortex Captioning (LaVCa), a data-driven approach that uses large language models (LLMs) to generate natural-language captions for images to which voxels are selective. By applying LaVCa for image-evoked brain activity, we demonstrate that LaVCa generates captions that describe voxel selectivity more accurately than the previously proposed method. Furthermore, the captions generated by LaVCa quantitatively capture more detailed properties than the existing method at both the inter-voxel and intra-voxel levels. Furthermore, a more detailed analysis of the voxel-specific properties generated by LaVCa reveals fine-grained functional differentiation within regions of interest (ROIs) in the visual cortex and voxels that simultaneously represent multiple distinct concepts. These findings offer profound insights into human visual representations by assigning detailed captions throughout the visual cortex while highlighting the potential of LLM-based methods in understanding brain representations. Please check out our webpage at https://sites.google.com/view/lavca-llm/

Vision-language models are increasingly deployed in high-stakes settings, yet their susceptibility to sycophantic manipulation remains poorly understood, particularly in relation to how these models represent visual information internally. Whether models whose visual representations more closely mirror human neural processing are also more resistant to adversarial pressure is an open question with implications for both neuroscience and AI safety. We investigate this question by evaluating 12 open-weight vision-language models spanning 6 architecture families and a 40times parameter range (256M--10B) along two axes: brain alignment, measured by predicting fMRI responses from the Natural Scenes Dataset across 8 human subjects and 6 visual cortex regions of interest, and sycophancy, measured through 76,800 two-turn gaslighting prompts spanning 5 categories and 10 difficulty levels. Region-of-interest analysis reveals that alignment specifically in early visual cortex (V1--V3) is a reliable negative predictor of sycophancy (r = -0.441, BCa 95\% CI [-0.740, -0.031]), with all 12 leave-one-out correlations negative and the strongest effect for existence denial attacks (r = -0.597, p = 0.040). This anatomically specific relationship is absent in higher-order category-selective regions, suggesting that faithful low-level visual encoding provides a measurable anchor against adversarial linguistic override in vision-language models. We release our code on https://github.com/aryashah2k/Gaslight-Gatekeep-Sycophantic-Manipulation{GitHub} and dataset on https://huggingface.co/datasets/aryashah00/Gaslight-Gatekeep-V1-V3{Hugging Face}

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron.

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

Attention sinks are tokens, often the beginning-of-sequence (BOS) token, that receive disproportionately high attention despite limited semantic relevance. In this work, we identify a class of attention sinks, which we term secondary sinks, that differ fundamentally from the sinks studied in prior works, which we term primary sinks. While prior works have identified that tokens other than BOS can sometimes become sinks, they were found to exhibit properties analogous to the BOS token. Specifically, they emerge at the same layer, persist throughout the network and draw a large amount of attention mass. Whereas, we find the existence of secondary sinks that arise primarily in middle layers and can persist for a variable number of layers, and draw a smaller, but still significant, amount of attention mass. Through extensive experiments across 11 model families, we analyze where these secondary sinks appear, their properties, how they are formed, and their impact on the attention mechanism. Specifically, we show that: (1) these sinks are formed by specific middle-layer MLP modules; these MLPs map token representations to vectors that align with the direction of the primary sink of that layer. (2) The ell_2-norm of these vectors determines the sink score of the secondary sink, and also the number of layers it lasts for, thereby leading to different impacts on the attention mechanisms accordingly. (3) The primary sink weakens in middle layers, coinciding with the emergence of secondary sinks. We observe that in larger-scale models, the location and lifetime of the sinks, together referred to as sink levels, appear in a more deterministic and frequent manner. Specifically, we identify three sink levels in QwQ-32B and six levels in Qwen3-14B.

We present a simple mathematical model for the mammalian low visual pathway, taking into account its key elements: retina, lateral geniculate nucleus (LGN), primary visual cortex (V1). The analogies between the cortical level of the visual system and the structure of popular CNNs, used in image classification tasks, suggests the introduction of an additional preliminary convolutional module inspired to precortical neuronal circuits to improve robustness with respect to global light intensity and contrast variations in the input images. We validate our hypothesis on the popular databases MNIST, FashionMNIST and SVHN, obtaining significantly more robust CNNs with respect to these variations, once such extra module is added.

Historically, neuroscience has progressed by fragmenting into specialized domains, each focusing on isolated modalities, tasks, or brain regions. While fruitful, this approach hinders the development of a unified model of cognition. Here, we introduce TRIBE, the first deep neural network trained to predict brain responses to stimuli across multiple modalities, cortical areas and individuals. By combining the pretrained representations of text, audio and video foundational models and handling their time-evolving nature with a transformer, our model can precisely model the spatial and temporal fMRI responses to videos, achieving the first place in the Algonauts 2025 brain encoding competition with a significant margin over competitors. Ablations show that while unimodal models can reliably predict their corresponding cortical networks (e.g. visual or auditory networks), they are systematically outperformed by our multimodal model in high-level associative cortices. Currently applied to perception and comprehension, our approach paves the way towards building an integrative model of representations in the human brain. Our code is available at https://github.com/facebookresearch/algonauts-2025.

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

Alzheimer's disease (AD) is a degenerative brain disease impairing a person's ability to perform day to day activities. The clinical manifestations of Alzheimer's disease are characterized by heterogeneity in age, disease span, progression rate, impairment of memory and cognitive abilities. Due to these variabilities, personalized care and treatment planning, as well as patient counseling about their individual progression is limited. Recent developments in machine learning to detect hidden patterns in complex, multi-dimensional datasets provides significant opportunities to address this critical need. In this work, we use unsupervised and supervised machine learning approaches for subtype identification and prediction. We apply machine learning methods to the extensive clinical observations available at the Alzheimer's Disease Neuroimaging Initiative (ADNI) data set to identify patient subtypes and to predict disease progression. Our analysis depicts the progression space for the Alzheimer's disease into low, moderate and high disease progression zones. The proposed work will enable early detection and characterization of distinct disease subtypes based on clinical heterogeneity. We anticipate that our models will enable patient counseling, clinical trial design, and ultimately individualized clinical care.

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

Neural Network movement controllers promise a variety of advantages over conventional control methods however they are not widely adopted due to their inability to produce reliably precise movements. This research explores a bilateral neural network architecture as a control system for motor tasks. We aimed to achieve hemispheric specialisation similar to what is observed in humans across different tasks; the dominant system (usually the right hand, left hemisphere) excels at tasks involving coordination and efficiency of movement, and the non-dominant system performs better at tasks requiring positional stability. Specialisation was achieved by training the hemispheres with different loss functions tailored toward the expected behaviour of the respective hemispheres. We compared bilateral models with and without specialised hemispheres, with and without inter-hemispheric connectivity (representing the biological Corpus Callosum), and unilateral models with and without specialisation. The models were trained and tested on two tasks common in the human motor control literature: the random reach task, suited to the dominant system, a model with better coordination, and the hold position task, suited to the non-dominant system, a model with more stable movement. Each system out-performed the non-favoured system in its preferred task. For both tasks, a bilateral model outperforms the 'non-preferred' hand, and is as good or better than the 'preferred' hand. The Corpus Callosum tends to improve performance, but not always for the specialised models.

Electron microscopy (EM) enables the reconstruction of neural circuits at the level of individual synapses, which has been transformative for scientific discoveries. However, due to the complex morphology, an accurate reconstruction of cortical axons has become a major challenge. Worse still, there is no publicly available large-scale EM dataset from the cortex that provides dense ground truth segmentation for axons, making it difficult to develop and evaluate large-scale axon reconstruction methods. To address this, we introduce the AxonEM dataset, which consists of two 30x30x30 um^3 EM image volumes from the human and mouse cortex, respectively. We thoroughly proofread over 18,000 axon instances to provide dense 3D axon instance segmentation, enabling large-scale evaluation of axon reconstruction methods. In addition, we densely annotate nine ground truth subvolumes for training, per each data volume. With this, we reproduce two published state-of-the-art methods and provide their evaluation results as a baseline. We publicly release our code and data at https://connectomics-bazaar.github.io/proj/AxonEM/index.html to foster the development of advanced methods.

The Backpropagation algorithm, widely used to train neural networks, has often been criticised for its lack of biological realism. In an attempt to find a more biologically plausible alternative, and avoid to back-propagate gradients in favour of using local learning rules, the recently introduced Forward-Forward algorithm replaces the traditional forward and backward passes of Backpropagation with two forward passes. In this work, we show that internal representations obtained with the Forward-Forward algorithm organize into robust, category-specific ensembles, composed by an extremely low number of active units (high sparsity). This is remarkably similar to what is observed in cortical representations during sensory processing. While not found in models trained with standard Backpropagation, sparsity emerges also in networks optimized by Backpropagation, on the same training objective of Forward-Forward. These results suggest that the learning procedure proposed by Forward-Forward may be superior to Backpropagation in modelling learning in the cortex, even when a backward pass is used.

Do brains and language models converge toward the same internal representations of the world? Recent years have seen a rise in studies of neural activations and model alignment. In this work, we review 25 fMRI-based studies published between 2023 and 2025 and explicitly confront their findings with two key hypotheses: (i) the Platonic Representation Hypothesis -- that as models scale and improve, they converge to a representation of the real world, and (ii) the Intermediate-Layer Advantage -- that intermediate (mid-depth) layers often encode richer, more generalizable features. Our findings provide converging evidence that models and brains may share abstract representational structures, supporting both hypotheses and motivating further research on brain-model alignment.

With the rise of Large Language Models (LLMs), the novel metric "Brainscore" emerged as a means to evaluate the functional similarity between LLMs and human brain/neural systems. Our efforts were dedicated to mining the meaning of the novel score by constructing topological features derived from both human fMRI data involving 190 subjects, and 39 LLMs plus their untrained counterparts. Subsequently, we trained 36 Linear Regression Models and conducted thorough statistical analyses to discern reliable and valid features from our constructed ones. Our findings reveal distinctive feature combinations conducive to interpreting existing brainscores across various brain regions of interest (ROIs) and hemispheres, thereby significantly contributing to advancing interpretable machine learning (iML) studies. The study is enriched by our further discussions and analyses concerning existing brainscores. To our knowledge, this study represents the first attempt to comprehend the novel metric brainscore within this interdisciplinary domain.

Magnetic resonance imaging (MRI) is the standard modality to understand human brain structure and function in vivo (antemortem). Decades of research in human neuroimaging has led to the widespread development of methods and tools to provide automated volume-based segmentations and surface-based parcellations which help localize brain functions to specialized anatomical regions. Recently ex vivo (postmortem) imaging of the brain has opened-up avenues to study brain structure at sub-millimeter ultra high-resolution revealing details not possible to observe with in vivo MRI. Unfortunately, there has been limited methodological development in ex vivo MRI primarily due to lack of datasets and limited centers with such imaging resources. Therefore, in this work, we present one-of-its-kind dataset of 82 ex vivo T2w whole brain hemispheres MRI at 0.3 mm isotropic resolution spanning Alzheimer's disease and related dementias. We adapted and developed a fast and easy-to-use automated surface-based pipeline to parcellate, for the first time, ultra high-resolution ex vivo brain tissue at the native subject space resolution using the Desikan-Killiany-Tourville (DKT) brain atlas. This allows us to perform vertex-wise analysis in the template space and thereby link morphometry measures with pathology measurements derived from histology. We will open-source our dataset docker container, Jupyter notebooks for ready-to-use out-of-the-box set of tools and command line options to advance ex vivo MRI clinical brain imaging research on the project webpage.

We propose a formal mathematical model for sparse representations and active dendrites in neocortex. Our model is inspired by recent experimental findings on active dendritic processing and NMDA spikes in pyramidal neurons. These experimental and modeling studies suggest that the basic unit of pattern memory in the neocortex is instantiated by small clusters of synapses operated on by localized non-linear dendritic processes. We derive a number of scaling laws that characterize the accuracy of such dendrites in detecting activation patterns in a neuronal population under adverse conditions. We introduce the union property which shows that synapses for multiple patterns can be randomly mixed together within a segment and still lead to highly accurate recognition. We describe simulation results that provide further insight into sparse representations as well as two primary results. First we show that pattern recognition by a neuron with active dendrites can be extremely accurate and robust with high dimensional sparse inputs even when using a tiny number of synapses to recognize large patterns. Second, equations representing recognition accuracy of a dendrite predict optimal NMDA spiking thresholds under a generous set of assumptions. The prediction tightly matches NMDA spiking thresholds measured in the literature. Our model matches many of the known properties of pyramidal neurons. As such the theory provides a mathematical framework for understanding the benefits and limits of sparse representations in cortical networks.

In this work, we present a network-specific approach for predicting brain responses to complex multimodal movies, leveraging the Yeo 7-network parcellation of the Schaefer atlas. Rather than treating the brain as a homogeneous system, we grouped the seven functional networks into four clusters and trained separate multi-subject, multi-layer perceptron (MLP) models for each. This architecture supports cluster-specific optimization and adaptive memory modeling, allowing each model to adjust temporal dynamics and modality weighting based on the functional role of its target network. Our results demonstrate that this clustered strategy significantly enhances prediction accuracy across the 1,000 cortical regions of the Schaefer atlas. The final model achieved an eighth-place ranking in the Algonauts Project 2025 Challenge, with out-of-distribution (OOD) correlation scores nearly double those of the baseline model used in the selection phase. Code is available at https://github.com/Corsi01/algo2025.

Blood vessels of the brain provide the human brain with the required nutrients and oxygen. As a vulnerable part of the cerebral blood supply, pathology of small vessels can cause serious problems such as Cerebral Small Vessel Diseases (CSVD). It has also been shown that CSVD is related to neurodegeneration, such as Alzheimer's disease. With the advancement of 7 Tesla MRI systems, higher spatial image resolution can be achieved, enabling the depiction of very small vessels in the brain. Non-Deep Learning-based approaches for vessel segmentation, e.g., Frangi's vessel enhancement with subsequent thresholding, are capable of segmenting medium to large vessels but often fail to segment small vessels. The sensitivity of these methods to small vessels can be increased by extensive parameter tuning or by manual corrections, albeit making them time-consuming, laborious, and not feasible for larger datasets. This paper proposes a deep learning architecture to automatically segment small vessels in 7 Tesla 3D Time-of-Flight (ToF) Magnetic Resonance Angiography (MRA) data. The algorithm was trained and evaluated on a small imperfect semi-automatically segmented dataset of only 11 subjects; using six for training, two for validation, and three for testing. The deep learning model based on U-Net Multi-Scale Supervision was trained using the training subset and was made equivariant to elastic deformations in a self-supervised manner using deformation-aware learning to improve the generalisation performance. The proposed technique was evaluated quantitatively and qualitatively against the test set and achieved a Dice score of 80.44 pm 0.83. Furthermore, the result of the proposed method was compared against a selected manually segmented region (62.07 resultant Dice) and has shown a considerable improvement (18.98\%) with deformation-aware learning.

Large language models (LLMs) exhibit remarkable capabilities on not just language tasks, but also various tasks that are not linguistic in nature, such as logical reasoning and social inference. In the human brain, neuroscience has identified a core language system that selectively and causally supports language processing. We here ask whether similar specialization for language emerges in LLMs. We identify language-selective units within 18 popular LLMs, using the same localization approach that is used in neuroscience. We then establish the causal role of these units by demonstrating that ablating LLM language-selective units -- but not random units -- leads to drastic deficits in language tasks. Correspondingly, language-selective LLM units are more aligned to brain recordings from the human language system than random units. Finally, we investigate whether our localization method extends to other cognitive domains: while we find specialized networks in some LLMs for reasoning and social capabilities, there are substantial differences among models. These findings provide functional and causal evidence for specialization in large language models, and highlight parallels with the functional organization in the brain.

The process of reconstructing experiences from human brain activity offers a unique lens into how the brain interprets and represents the world. In this paper, we introduce a method for reconstructing music from brain activity, captured using functional magnetic resonance imaging (fMRI). Our approach uses either music retrieval or the MusicLM music generation model conditioned on embeddings derived from fMRI data. The generated music resembles the musical stimuli that human subjects experienced, with respect to semantic properties like genre, instrumentation, and mood. We investigate the relationship between different components of MusicLM and brain activity through a voxel-wise encoding modeling analysis. Furthermore, we discuss which brain regions represent information derived from purely textual descriptions of music stimuli. We provide supplementary material including examples of the reconstructed music at https://google-research.github.io/seanet/brain2music

Understanding and decoding brain activity from electroencephalography (EEG) signals is a fundamental challenge in neuroscience and AI, with applications in cognition, emotion recognition, diagnosis, and brain-computer interfaces. While recent EEG foundation models advance generalized decoding via unified architectures and large-scale pretraining, they adopt a scale-agnostic dense modeling paradigm inherited from NLP and vision. This design neglects a core property of neural activity: cross-scale spatiotemporal structure. EEG task patterns span a wide range of temporal and spatial scales, from short bursts to slow rhythms, and from localized cortical responses to distributed interactions. Ignoring this diversity leads to suboptimal representations and weak generalization. We propose CSBrain, a Cross-scale Spatiotemporal Brain foundation model for generalized EEG decoding. CSBrain introduces: (i) Cross-scale Spatiotemporal Tokenization (CST), which aggregates multi-scale features from localized temporal windows and anatomical brain regions into compact scale-aware tokens; and (ii) Structured Sparse Attention (SSA), which captures cross-window and cross-region dependencies, enhancing scale diversity while removing spurious correlations. CST and SSA are alternately stacked to progressively integrate multi-scale dependencies. Experiments on 11 EEG tasks across 16 datasets show that CSBrain consistently outperforms task-specific and foundation model baselines. These results establish cross-scale modeling as a key inductive bias and position CSBrain as a robust backbone for future brain-AI research.

The human brain is autonomously active, being characterized by a self-sustained neural activity which would be present even in the absence of external sensory stimuli. Here we study the interrelation between the self-sustained activity in autonomously active recurrent neural nets and external sensory stimuli. There is no a priori semantical relation between the influx of external stimuli and the patterns generated internally by the autonomous and ongoing brain dynamics. The question then arises when and how are semantic correlations between internal and external dynamical processes learned and built up? We study this problem within the paradigm of transient state dynamics for the neural activity in recurrent neural nets, i.e. for an autonomous neural activity characterized by an infinite time-series of transiently stable attractor states. We propose that external stimuli will be relevant during the sensitive periods, {\it viz} the transition period between one transient state and the subsequent semi-stable attractor. A diffusive learning signal is generated unsupervised whenever the stimulus influences the internal dynamics qualitatively. For testing we have presented to the model system stimuli corresponding to the bars and stripes problem. We found that the system performs a non-linear independent component analysis on its own, being continuously and autonomously active. This emergent cognitive capability results here from a general principle for the neural dynamics, the competition between neural ensembles.

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

Mapping behavioral actions to neural activity is a fundamental goal of neuroscience. As our ability to record large neural and behavioral data increases, there is growing interest in modeling neural dynamics during adaptive behaviors to probe neural representations. In particular, neural latent embeddings can reveal underlying correlates of behavior, yet, we lack non-linear techniques that can explicitly and flexibly leverage joint behavior and neural data. Here, we fill this gap with a novel method, CEBRA, that jointly uses behavioral and neural data in a hypothesis- or discovery-driven manner to produce consistent, high-performance latent spaces. We validate its accuracy and demonstrate our tool's utility for both calcium and electrophysiology datasets, across sensory and motor tasks, and in simple or complex behaviors across species. It allows for single and multi-session datasets to be leveraged for hypothesis testing or can be used label-free. Lastly, we show that CEBRA can be used for the mapping of space, uncovering complex kinematic features, and rapid, high-accuracy decoding of natural movies from visual cortex.

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

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors at different times. We introduce an unsupervised approach to learn the dynamic affinities between neurons in live, behaving animals, and to reveal which communities form among neurons at different times. The inference occurs in two major steps. First, pairwise non-linear affinities between neuronal traces from brain-wide calcium activity are organized by non-negative tensor factorization (NTF). Each factor specifies which groups of neurons are most likely interacting for an inferred interval in time, and for which animals. Finally, a generative model that allows for weighted community detection is applied to the functional motifs produced by NTF to reveal a dynamic functional connectome. Since time codes the different experimental variables (e.g., application of chemical stimuli), this provides an atlas of neural motifs active during separate stages of an experiment (e.g., stimulus application or spontaneous behaviors). Results from our analysis are experimentally validated, confirming that our method is able to robustly predict causal interactions between neurons to generate behavior. Code is available at https://github.com/dyballa/dynamic-connectomes.

Language understanding entails not just extracting the surface-level meaning of the linguistic input, but constructing rich mental models of the situation it describes. Here we propose that because processing within the brain's core language system is fundamentally limited, deeply understanding language requires exporting information from the language system to other brain regions that compute perceptual and motor representations, construct mental models, and store our world knowledge and autobiographical memories. We review the existing evidence for this hypothesis, and argue that recent progress in cognitive neuroscience provides both the conceptual foundation and the methods to directly test it, thus opening up a new strategy to reveal what it means, cognitively and neurally, to understand language.

The parcellation of Cranial Nerves (CNs) serves as a crucial quantitative methodology for evaluating the morphological characteristics and anatomical pathways of specific CNs. Multi-modal CNs parcellation networks have achieved promising segmentation performance, which combine structural Magnetic Resonance Imaging (MRI) and diffusion MRI. However, insufficient exploration of diffusion MRI information has led to low performance of existing multi-modal fusion. In this work, we propose a tractography-guided Dual-label Collaborative Learning Network (DCLNet) for multi-modal CNs parcellation. The key contribution of our DCLNet is the introduction of coarse labels of CNs obtained from fiber tractography through CN atlas, and collaborative learning with precise labels annotated by experts. Meanwhile, we introduce a Modality-adaptive Encoder Module (MEM) to achieve soft information swapping between structural MRI and diffusion MRI. Extensive experiments conducted on the publicly available Human Connectome Project (HCP) dataset demonstrate performance improvements compared to single-label network. This systematic validation underscores the effectiveness of dual-label strategies in addressing inherent ambiguities in CNs parcellation tasks.

Modern neural recording techniques allow neuroscientists to obtain spiking activity of multiple neurons from different brain regions over long time periods, which requires new statistical methods to be developed for understanding structure of the large-scale data. In this paper, we develop a bi-clustering method to cluster the neural spiking activity spatially and temporally, according to their low-dimensional latent structures. The spatial (neuron) clusters are defined by the latent trajectories within each neural population, while the temporal (state) clusters are defined by (populationally) synchronous local linear dynamics shared with different periods. To flexibly extract the bi-clustering structure, we build the model non-parametrically, and develop an efficient Markov chain Monte Carlo (MCMC) algorithm to sample the posterior distributions of model parameters. Validating our proposed MCMC algorithm through simulations, we find the method can recover unknown parameters and true bi-clustering structures successfully. We then apply the proposed bi-clustering method to multi-regional neural recordings under different experiment settings, where we find that simultaneously considering latent trajectories and spatial-temporal clustering structures can provide us with a more accurate and interpretable result. Overall, the proposed method provides scientific insights for large-scale (counting) time series with elongated recording periods, and it can potentially have application beyond neuroscience.

Recent work in vision-and-language demonstrates that large-scale pretraining can learn generalizable models that are efficiently transferable to downstream tasks. While this may improve dataset-scale aggregate metrics, analyzing performance around hand-crafted subgroups targeting specific bias dimensions reveals systemic undesirable behaviors. However, this subgroup analysis is frequently stalled by annotation efforts, which require extensive time and resources to collect the necessary data. Prior art attempts to automatically discover subgroups to circumvent these constraints but typically leverages model behavior on existing task-specific annotations and rapidly degrades on more complex inputs beyond "tabular" data, none of which study vision-and-language models. This paper presents VLSlice, an interactive system enabling user-guided discovery of coherent representation-level subgroups with consistent visiolinguistic behavior, denoted as vision-and-language slices, from unlabeled image sets. We show that VLSlice enables users to quickly generate diverse high-coherency slices in a user study (n=22) and release the tool publicly.

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

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

A central question for neuroscience is how to characterize brain representations of perceptual and cognitive content. An ideal characterization should distinguish different functional regions with robustness to noise and idiosyncrasies of individual brains that do not correspond to computational differences. Previous studies have characterized brain representations by their representational geometry, which is defined by the representational dissimilarity matrix (RDM), a summary statistic that abstracts from the roles of individual neurons (or responses channels) and characterizes the discriminability of stimuli. Here we explore a further step of abstraction: from the geometry to the topology of brain representations. We propose topological representational similarity analysis (tRSA), an extension of representational similarity analysis (RSA) that uses a family of geo-topological summary statistics that generalizes the RDM to characterize the topology while de-emphasizing the geometry. We evaluate this new family of statistics in terms of the sensitivity and specificity for model selection using both simulations and functional MRI (fMRI) data. In the simulations, the ground truth is a data-generating layer representation in a neural network model and the models are the same and other layers in different model instances (trained from different random seeds). In fMRI, the ground truth is a visual area and the models are the same and other areas measured in different subjects. Results show that topology-sensitive characterizations of population codes are robust to noise and interindividual variability and maintain excellent sensitivity to the unique representational signatures of different neural network layers and brain regions.

We use (multi)modal deep neural networks (DNNs) to probe for sites of multimodal integration in the human brain by predicting stereoencephalography (SEEG) recordings taken while human subjects watched movies. We operationalize sites of multimodal integration as regions where a multimodal vision-language model predicts recordings better than unimodal language, unimodal vision, or linearly-integrated language-vision models. Our target DNN models span different architectures (e.g., convolutional networks and transformers) and multimodal training techniques (e.g., cross-attention and contrastive learning). As a key enabling step, we first demonstrate that trained vision and language models systematically outperform their randomly initialized counterparts in their ability to predict SEEG signals. We then compare unimodal and multimodal models against one another. Because our target DNN models often have different architectures, number of parameters, and training sets (possibly obscuring those differences attributable to integration), we carry out a controlled comparison of two models (SLIP and SimCLR), which keep all of these attributes the same aside from input modality. Using this approach, we identify a sizable number of neural sites (on average 141 out of 1090 total sites or 12.94%) and brain regions where multimodal integration seems to occur. Additionally, we find that among the variants of multimodal training techniques we assess, CLIP-style training is the best suited for downstream prediction of the neural activity in these sites.

Recent work in mechanistic interpretability has shown that behaviors in language models can be successfully reverse-engineered through circuit analysis. A common criticism, however, is that each circuit is task-specific, and thus such analysis cannot contribute to understanding the models at a higher level. In this work, we present evidence that insights (both low-level findings about specific heads and higher-level findings about general algorithms) can indeed generalize across tasks. Specifically, we study the circuit discovered in Wang et al. (2022) for the Indirect Object Identification (IOI) task and 1.) show that it reproduces on a larger GPT2 model, and 2.) that it is mostly reused to solve a seemingly different task: Colored Objects (Ippolito & Callison-Burch, 2023). We provide evidence that the process underlying both tasks is functionally very similar, and contains about a 78% overlap in in-circuit attention heads. We further present a proof-of-concept intervention experiment, in which we adjust four attention heads in middle layers in order to 'repair' the Colored Objects circuit and make it behave like the IOI circuit. In doing so, we boost accuracy from 49.6% to 93.7% on the Colored Objects task and explain most sources of error. The intervention affects downstream attention heads in specific ways predicted by their interactions in the IOI circuit, indicating that this subcircuit behavior is invariant to the different task inputs. Overall, our results provide evidence that it may yet be possible to explain large language models' behavior in terms of a relatively small number of interpretable task-general algorithmic building blocks and computational components.

Artificial intelligence has made great strides in the last decade but still falls short of the human brain, the best-known example of intelligence. Not much is known of the neural processes that allow the brain to make the leap to achieve so much from so little beyond its ability to create knowledge structures that can be flexibly and dynamically combined, recombined, and applied in new and novel ways. This paper proposes a mathematical approach using graph theory and spectral graph theory, to hypothesize how to constrain these neural clusters of information based on eigen-relationships. This same hypothesis is hierarchically applied to scale up from the smallest to the largest clusters of knowledge that eventually lead to model building and reasoning.

This article is about the neural conundrum behind the slowness of human behavior. The information throughput of a human being is about 10 bits/s. In comparison, our sensory systems gather data at ~10^9 bits/s. The stark contrast between these numbers remains unexplained and touches on fundamental aspects of brain function: What neural substrate sets this speed limit on the pace of our existence? Why does the brain need billions of neurons to process 10 bits/s? Why can we only think about one thing at a time? The brain seems to operate in two distinct modes: the "outer" brain handles fast high-dimensional sensory and motor signals, whereas the "inner" brain processes the reduced few bits needed to control behavior. Plausible explanations exist for the large neuron numbers in the outer brain, but not for the inner brain, and we propose new research directions to remedy this.

Large Language Models (LLMs) have demonstrated notable proficiency in both code generation and comprehension across multiple programming languages. However, the mechanisms underlying this proficiency remain underexplored, particularly with respect to whether distinct programming languages are processed independently or within a shared parametric region. Drawing an analogy to the specialized regions of the brain responsible for distinct cognitive functions, we introduce the concept of Coding Spot, a specialized parametric region within LLMs that facilitates coding capabilities. Our findings identify this Coding Spot and show that targeted modifications to this subset significantly affect performance on coding tasks, while largely preserving non-coding functionalities. This compartmentalization mirrors the functional specialization observed in cognitive neuroscience, where specific brain regions are dedicated to distinct tasks, suggesting that LLMs may similarly employ specialized parameter regions for different knowledge domains.

Ultra-High Field MRI (UHF-MRI) is increasingly used in large-scale neuroimaging studies, yet automatic brain segmentation and cortical parcellation remain challenging due to signal inhomogeneities, heterogeneous contrasts and resolutions, and the limited availability of tools optimized for UHF data. Standard software packages such as FastSurferVINN and SynthSeg+ often yield suboptimal results when applied directly to UHF images, thereby restricting region-based quantitative analyses. To address this need, we introduce GOUHFI 2.0, an updated implementation of GOUHFI that incorporates increased training data variability and additional functionalities, including cortical parcellation and volumetry. GOUHFI 2.0 preserves the contrast- and resolution-agnostic design of the original toolbox while introducing two independently trained 3D U-Net segmentation tasks. The first performs whole-brain segmentation into 35 labels across contrasts, resolutions, field strengths and populations, using a domain-randomization strategy and a training dataset of 238 subjects. Using the same training data, the second network performs cortical parcellation into 62 labels following the Desikan-Killiany-Tourville (DKT) protocol. Across multiple datasets, GOUHFI 2.0 demonstrated improved segmentation accuracy relative to the original toolbox, particularly in heterogeneous cohorts, and produced reliable cortical parcellations. In addition, the integrated volumetry pipeline yielded results consistent with standard volumetric workflows. Overall, GOUHFI 2.0 provides a comprehensive solution for brain segmentation, parcellation and volumetry across field strengths, and constitutes the first deep-learning toolbox enabling robust cortical parcellation at UHF-MRI.

We present causal head gating (CHG), a scalable method for interpreting the functional roles of attention heads in transformer models. CHG learns soft gates over heads and assigns them a causal taxonomy - facilitating, interfering, or irrelevant - based on their impact on task performance. Unlike prior approaches in mechanistic interpretability, which are hypothesis-driven and require prompt templates or target labels, CHG applies directly to any dataset using standard next-token prediction. We evaluate CHG across multiple large language models (LLMs) in the Llama 3 model family and diverse tasks, including syntax, commonsense, and mathematical reasoning, and show that CHG scores yield causal, not merely correlational, insight validated via ablation and causal mediation analyses. We also introduce contrastive CHG, a variant that isolates sub-circuits for specific task components. Our findings reveal that LLMs contain multiple sparse task-sufficient sub-circuits, that individual head roles depend on interactions with others (low modularity), and that instruction following and in-context learning rely on separable mechanisms.

The ability to predict upcoming events has been hypothesized to comprise a key aspect of natural and machine cognition. This is supported by trends in deep reinforcement learning (RL), where self-supervised auxiliary objectives such as prediction are widely used to support representation learning and improve task performance. Here, we study the effects predictive auxiliary objectives have on representation learning across different modules of an RL system and how these mimic representational changes observed in the brain. We find that predictive objectives improve and stabilize learning particularly in resource-limited architectures, and we identify settings where longer predictive horizons better support representational transfer. Furthermore, we find that representational changes in this RL system bear a striking resemblance to changes in neural activity observed in the brain across various experiments. Specifically, we draw a connection between the auxiliary predictive model of the RL system and hippocampus, an area thought to learn a predictive model to support memory-guided behavior. We also connect the encoder network and the value learning network of the RL system to visual cortex and striatum in the brain, respectively. This work demonstrates how representation learning in deep RL systems can provide an interpretable framework for modeling multi-region interactions in the brain. The deep RL perspective taken here also suggests an additional role of the hippocampus in the brain -- that of an auxiliary learning system that benefits representation learning in other regions.

Reconstructing images seen by people from their fMRI brain recordings provides a non-invasive window into the human brain. Despite recent progress enabled by diffusion models, current methods often lack faithfulness to the actual seen images. We present "Brain-IT", a brain-inspired approach that addresses this challenge through a Brain Interaction Transformer (BIT), allowing effective interactions between clusters of functionally-similar brain-voxels. These functional-clusters are shared by all subjects, serving as building blocks for integrating information both within and across brains. All model components are shared by all clusters & subjects, allowing efficient training with a limited amount of data. To guide the image reconstruction, BIT predicts two complementary localized patch-level image features: (i)high-level semantic features which steer the diffusion model toward the correct semantic content of the image; and (ii)low-level structural features which help to initialize the diffusion process with the correct coarse layout of the image. BIT's design enables direct flow of information from brain-voxel clusters to localized image features. Through these principles, our method achieves image reconstructions from fMRI that faithfully reconstruct the seen images, and surpass current SotA approaches both visually and by standard objective metrics. Moreover, with only 1-hour of fMRI data from a new subject, we achieve results comparable to current methods trained on full 40-hour recordings.

Traveling waves of neural activity have been observed throughout the brain at a diversity of regions and scales; however, their precise computational role is still debated. One physically inspired hypothesis suggests that the cortical sheet may act like a wave-propagating system capable of invertibly storing a short-term memory of sequential stimuli through induced waves traveling across the cortical surface, and indeed many experimental results from neuroscience correlate wave activity with memory tasks. To date, however, the computational implications of this idea have remained hypothetical due to the lack of a simple recurrent neural network architecture capable of exhibiting such waves. In this work, we introduce a model to fill this gap, which we denote the Wave-RNN (wRNN), and demonstrate how such an architecture indeed efficiently encodes the recent past through a suite of synthetic memory tasks where wRNNs learn faster and reach significantly lower error than wave-free counterparts. We further explore the implications of this memory storage system on more complex sequence modeling tasks such as sequential image classification and find that wave-based models not only again outperform comparable wave-free RNNs while using significantly fewer parameters, but additionally perform comparably to more complex gated architectures such as LSTMs and GRUs.

Multi-modal brain tumor segmentation is critical for clinical diagnosis, and it requires accurate identification of distinct internal anatomical subregions. While the recent prompt-based segmentation paradigms enable interactive experiences for clinicians, existing methods ignore cross-modal correlations and rely on labor-intensive category-specific prompts, limiting their applicability in real-world scenarios. To address these issues, we propose a MSM-Seg framework for multi-modal brain tumor segmentation. The MSM-Seg introduces a novel dual-memory segmentation paradigm that synergistically integrates multi-modal and inter-slice information with the efficient category-agnostic prompt for brain tumor understanding. To this end, we first devise a modality-and-slice memory attention (MSMA) to exploit the cross-modal and inter-slice relationships among the input scans. Then, we propose a multi-scale category-agnostic prompt encoder (MCP-Encoder) to provide tumor region guidance for decoding. Moreover, we devise a modality-adaptive fusion decoder (MF-Decoder) that leverages the complementary decoding information across different modalities to improve segmentation accuracy. Extensive experiments on different MRI datasets demonstrate that our MSM-Seg framework outperforms state-of-the-art methods in multi-modal metastases and glioma tumor segmentation. The code is available at https://github.com/xq141839/MSM-Seg.