Daily Papers

A fundamental question in cognitive neuroscience is what shapes visual perception: the external world's structure or the brain's internal architecture. Although some perceptual variability can be traced to individual differences, brain responses to naturalistic stimuli evoke similar activity patterns across individuals, suggesting a convergent representational principle. Here, we test if this stimulus-driven convergence follows a common trajectory across people and deep neural networks (DNNs) during its transformation from sensory to high-level internal representations. We introduce a unified framework that traces representational flow by combining inter-subject similarity with alignment to model hierarchies. Applying this framework to three independent fMRI datasets of visual scene perception, we reveal a cortex-wide network, conserved across individuals, organized into two pathways: a medial-ventral stream for scene structure and a lateral-dorsal stream tuned for social and biological content. This functional organization is captured by the hierarchies of vision DNNs but not language models, reinforcing the specificity of the visual-to-semantic transformation. These findings show a convergent computational solution for visual encoding in both human and artificial vision, driven by the structure of the external world.

How the wiring and functional organization of cortex shape recurrent computation remains a central question in both neuroscience and machine learning. Here, we leverage data released through the Machine Intelligence from Cortical Networks (MICrONS) program--a functional connectomics resource spanning multiple areas of mouse visual cortex, in which dense calcium imaging is co-registered with high-resolution electron microscopy reconstruction from the same animal--to build biologically grounded recurrent neural networks. Using neuronal spatial coordinates, anatomical connectivity, and function-derived relationships from nearly 12,000 coregistered excitatory neurons, we initialize recurrent weights and impose communication-aware spatial constraints during learning. Across three cognitive decision-making tasks, networks constrained by cortical structure and function consistently outperform baseline and partially constrained models. Functional weight initialization provides the largest gain, while real spatial embedding yields robust additional improvements across conditions. These biologically grounded networks also develop low-entropy, modular, and small-world organization, and retain strong performance even when recurrence is restricted to positive weights. Together, our results show that the machinery of cortex--its geometry, wiring, and functional structure--can be harnessed as a powerful inductive basis for building recurrent networks that learn more effectively while converging toward key organizational principles of biological computation.

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.

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.

Networks capture our intuition about relationships in the world. They describe the friendships between Facebook users, interactions in financial markets, and synapses connecting neurons in the brain. These networks are richly structured with cliques of friends, sectors of stocks, and a smorgasbord of cell types that govern how neurons connect. Some networks, like social network friendships, can be directly observed, but in many cases we only have an indirect view of the network through the actions of its constituents and an understanding of how the network mediates that activity. In this work, we focus on the problem of latent network discovery in the case where the observable activity takes the form of a mutually-excitatory point process known as a Hawkes process. We build on previous work that has taken a Bayesian approach to this problem, specifying prior distributions over the latent network structure and a likelihood of observed activity given this network. We extend this work by proposing a discrete-time formulation and developing a computationally efficient stochastic variational inference (SVI) algorithm that allows us to scale the approach to long sequences of observations. We demonstrate our algorithm on the calcium imaging data used in the Chalearn neural connectomics challenge.

We developed a tool for visualizing and analyzing large pre-trained vision models by mapping them onto the brain, thus exposing their hidden inside. Our innovation arises from a surprising usage of brain encoding: predicting brain fMRI measurements in response to images. We report two findings. First, explicit mapping between the brain and deep-network features across dimensions of space, layers, scales, and channels is crucial. This mapping method, FactorTopy, is plug-and-play for any deep-network; with it, one can paint a picture of the network onto the brain (literally!). Second, our visualization shows how different training methods matter: they lead to remarkable differences in hierarchical organization and scaling behavior, growing with more data or network capacity. It also provides insight into fine-tuning: how pre-trained models change when adapting to small datasets. We found brain-like hierarchically organized network suffer less from catastrophic forgetting after fine-tuned.

Despite their success, modern convolutional neural networks (CNNs) exhibit fundamental limitations, including data inefficiency, poor out-of-distribution generalization, and vulnerability to adversarial perturbations. These shortcomings can be traced to a lack of inductive biases that reflect the inherent geometric structure of the visual world. The primate visual system, in contrast, demonstrates superior efficiency and robustness, suggesting that its architectural and computational principles,which evolved to internalize these structures,may offer a blueprint for more capable artificial vision. This paper introduces Visual Cortex Network (VCNet), a novel neural network architecture whose design is informed by the macro-scale organization of the primate visual cortex. VCNet is framed as a geometric framework that emulates key biological mechanisms, including hierarchical processing across distinct cortical areas, dual-stream information segregation for learning disentangled representations, and top-down predictive feedback for representation refinement. We interpret these mechanisms through the lens of geometry and dynamical systems, positing that they guide the learning of structured, low-dimensional neural manifolds. We evaluate VCNet on two specialized benchmarks: the Spots-10 animal pattern dataset, which probes sensitivity to natural textures, and a light field image classification task, which requires processing higher-dimensional visual data. Our results show that VCNet achieves state-of-the-art accuracy of 92.1\% on Spots-10 and 74.4\% on the light field dataset, surpassing contemporary models of comparable size. This work demonstrates that integrating high-level neuroscientific principles, viewed through a geometric lens, can lead to more efficient and robust models, providing a promising direction for addressing long-standing challenges in machine learning.

A biological neural network in the cortex forms a neural field. Neurons in the field have their own receptive fields, and connection weights between two neurons are random but highly correlated when they are in close proximity in receptive fields. In this paper, we investigate such neural fields in a multilayer architecture to investigate the supervised learning of the fields. We empirically compare the performances of our field model with those of randomly connected deep networks. The behavior of a randomly connected network is investigated on the basis of the key idea of the neural tangent kernel regime, a recent development in the machine learning theory of over-parameterized networks; for most randomly connected neural networks, it is shown that global minima always exist in their small neighborhoods. We numerically show that this claim also holds for our neural fields. In more detail, our model has two structures: i) each neuron in a field has a continuously distributed receptive field, and ii) the initial connection weights are random but not independent, having correlations when the positions of neurons are close in each layer. We show that such a multilayer neural field is more robust than conventional models when input patterns are deformed by noise disturbances. Moreover, its generalization ability can be slightly superior to that of conventional models.

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.

Ablation studies have been widely used in the field of neuroscience to tackle complex biological systems such as the extensively studied Drosophila central nervous system, the vertebrate brain and more interestingly and most delicately, the human brain. In the past, these kinds of studies were utilized to uncover structure and organization in the brain, i.e. a mapping of features inherent to external stimuli onto different areas of the neocortex. considering the growth in size and complexity of state-of-the-art artificial neural networks (ANNs) and the corresponding growth in complexity of the tasks that are tackled by these networks, the question arises whether ablation studies may be used to investigate these networks for a similar organization of their inner representations. In this paper, we address this question and performed two ablation studies in two fundamentally different ANNs to investigate their inner representations of two well-known benchmark datasets from the computer vision domain. We found that features distinct to the local and global structure of the data are selectively represented in specific parts of the network. Furthermore, some of these representations are redundant, awarding the network a certain robustness to structural damages. We further determined the importance of specific parts of the network for the classification task solely based on the weight structure of single units. Finally, we examined the ability of damaged networks to recover from the consequences of ablations by means of recovery training. We argue that ablations studies are a feasible method to investigate knowledge representations in ANNs and are especially helpful to examine a networks robustness to structural damages, a feature of ANNs that will become increasingly important for future safety-critical applications.

Deep neural networks trained on Functional Connectivity (FC) networks extracted from functional Magnetic Resonance Imaging (fMRI) data have gained popularity due to the increasing availability of data and advances in model architectures, including Graph Neural Network (GNN). Recent research on the application of GNN to FC suggests that exploiting the time-varying properties of the FC could significantly improve the accuracy and interpretability of the model prediction. However, the high cost of acquiring high-quality fMRI data and corresponding phenotypic labels poses a hurdle to their application in real-world settings, such that a model na\"ively trained in a supervised fashion can suffer from insufficient performance or a lack of generalization on a small number of data. In addition, most Self-Supervised Learning (SSL) approaches for GNNs to date adopt a contrastive strategy, which tends to lose appropriate semantic information when the graph structure is perturbed or does not leverage both spatial and temporal information simultaneously. In light of these challenges, we propose a generative SSL approach that is tailored to effectively harness spatio-temporal information within dynamic FC. Our empirical results, experimented with large-scale (>50,000) fMRI datasets, demonstrate that our approach learns valuable representations and enables the construction of accurate and robust models when fine-tuned for downstream tasks.

Nearby neurons in cortex share similar response profiles, producing systematic spatial organization across sensory and cognitive systems. Recent topographic models reproduce aspects of this structure but remain unimodal and spatially constrain each layer separately, yielding fragmented maps that capture neither the contiguity of cortical processing streams nor their integration across modalities. We introduce Topo-Omni, a topographic multimodal model in which visual, auditory, and language/cognitive processing share a single contiguous in-silico sheet. Built by fine-tuning a pretrained foundation model with a spatial smoothness objective, this architecture develops clusters across modalities that are consistent with human neuroimaging, from sensory to cognitive systems. Driving or suppressing a cluster selectively biases or impairs perception, paralleling human intervention studies. Finally, we use our model to screen for novel clusters in-silico and discover new natural landscape and animal networks which we validate in human data. A single spatial principle thus organizes representations across modalities and processing stages, yielding testable hypotheses about cortical organization.

The whole-brain connectome of a fruit fly comprises over 130K neurons connected with a probability of merely 0.02%, yet achieves an average shortest path of only 4.4 hops. Despite being highly structured at the circuit level, the network's long-range connections are broadly distributed across brain regions, functioning as stochastic shortcuts that enable efficient global communication. Inspired by this observation, we propose Stochastic Attention (SA), a drop-in enhancement for sliding-window attention (SWA) that applies a random permutation to the token sequence before windowed attention and restores the original order afterward. This transforms the fixed local window into a stochastic global one within the same O(nw) per-layer budget. Through depth, independently sampled permutations yield exponentially growing receptive fields, achieving full sequence coverage in O(log_w n) layers versus O(n/w) for SWA. We validate SA in two settings: pre-training language models from scratch, where a gated SA + SWA combination achieves the best average zero-shot accuracy, and training-free inference on Qwen3-8B and Qwen3-30B-A3B, where SA consistently outperforms SWA and matches or exceeds Mixture of Block Attention at comparable compute budgets. These results suggest that connectome-inspired stochastic routing is a practical primitive for improving the expressivity of efficient attention, complementary to existing linear and sparse approaches.

State-of-the-art systems neuroscience experiments yield large-scale multimodal data, and these data sets require new tools for analysis. Inspired by the success of large pretrained models in vision and language domains, we reframe the analysis of large-scale, cellular-resolution neuronal spiking data into an autoregressive spatiotemporal generation problem. Neuroformer is a multimodal, multitask generative pretrained transformer (GPT) model that is specifically designed to handle the intricacies of data in systems neuroscience. It scales linearly with feature size, can process an arbitrary number of modalities, and is adaptable to downstream tasks, such as predicting behavior. We first trained Neuroformer on simulated datasets, and found that it both accurately predicted simulated neuronal circuit activity, and also intrinsically inferred the underlying neural circuit connectivity, including direction. When pretrained to decode neural responses, the model predicted the behavior of a mouse with only few-shot fine-tuning, suggesting that the model begins learning how to do so directly from the neural representations themselves, without any explicit supervision. We used an ablation study to show that joint training on neuronal responses and behavior boosted performance, highlighting the model's ability to associate behavioral and neural representations in an unsupervised manner. These findings show that Neuroformer can analyze neural datasets and their emergent properties, informing the development of models and hypotheses associated with the brain.

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.

The structure of biological neural circuits-modular, hierarchical, and sparsely interconnected-reflects an efficient trade-off between wiring cost, functional specialization, and robustness. These principles offer valuable insights for artificial neural network (ANN) design, especially as networks grow in depth and scale. Sparsity, in particular, has been widely explored for reducing memory and computation, improving speed, and enhancing generalization. Motivated by systems neuroscience findings, we explore how patterns of functional connectivity in the mouse visual cortex-specifically, ensemble-to-ensemble communication, can inform ANN design. We introduce G2GNet, a novel architecture that imposes sparse, modular connectivity across feedforward layers. Despite having significantly fewer parameters than fully connected models, G2GNet achieves superior accuracy on standard vision benchmarks. To our knowledge, this is the first architecture to incorporate biologically observed functional connectivity patterns as a structural bias in ANN design. We complement this static bias with a dynamic sparse training (DST) mechanism that prunes and regrows edges during training. We also propose a Hebbian-inspired rewiring rule based on activation correlations, drawing on principles of biological plasticity. G2GNet achieves up to 75% sparsity while improving accuracy by up to 4.3% on benchmarks, including Fashion-MNIST, CIFAR-10, and CIFAR-100, outperforming dense baselines with far fewer computations.

Understanding what individual neurons encode is a core question in neuroscience. In primary visual cortex (V1), mathematical models (e.g., Gabor functions) capture neural selectivity, but no comparable framework exists for higher areas. We show that natural language can fill this role: across macaque V1 and V4, the selectivity of most neurons is captured by concise, verifiable semantic descriptions. Using digital twins of V1 and V4, we develop a closed-loop framework that translates each neuron's high- and low-activating images into dense captions, generates a semantic hypothesis and synthesized images, and verifies the hypothesis in silico. Descriptions range from oriented edges and spatial frequency in V1 to conjunctions of form, color, and texture in V4. In V4, images generated from activating and suppressing hypotheses drove 96.1% of neurons above the 95th and 97.6% below the 5th percentile of natural-image responses, respectively (vs. ~10% for random images); V1 activation results matched V4, while V1 suppression was less describable in language. Representational similarity analysis reveals partial alignment between neural activity, vision embeddings, and language embeddings, with vision most aligned to neural activity; alignment lost in the text bottleneck is recovered when hypotheses are rendered back into images, showing that linguistic compression is lossy yet semantically faithful. Together, these results show that combining generative models with neural digital twins enables interpretable, testable descriptions of neural function at scale, toward agentic scientific discovery.

The human brain is a complex, dynamic network, which is commonly studied using functional magnetic resonance imaging (fMRI) and modeled as network of Regions of interest (ROIs) for understanding various brain functions. Recent studies utilize deep learning approaches to learn the brain network representation based on functional connectivity (FC) profile, broadly falling into two main categories. The Fixed-FC approaches, utilizing the FC profile which represents the linear temporal relation within the brain network, are limited by failing to capture informative brain temporal dynamics. On the other hand, the Dynamic-FC approaches, modeling the evolving FC profile over time, often exhibit less satisfactory performance due to challenges in handling the inherent noisy nature of fMRI data. To address these challenges, we propose Brain Masked Auto-Encoder (BrainMAE) for learning representations directly from fMRI time-series data. Our approach incorporates two essential components: a region-aware graph attention mechanism designed to capture the relationships between different brain ROIs, and a novel self-supervised masked autoencoding framework for effective model pre-training. These components enable the model to capture rich temporal dynamics of brain activity while maintaining resilience to inherent noise in fMRI data. Our experiments demonstrate that BrainMAE consistently outperforms established baseline methods by significant margins in four distinct downstream tasks. Finally, leveraging the model's inherent interpretability, our analysis of model-generated representations reveals findings that resonate with ongoing research in the field of neuroscience.

Cortical neurons are complex, multi-timescale processors wired into recurrent circuits, shaped by long evolutionary pressure under stringent biological constraints. Mainstream machine learning, by contrast, predominantly builds models from extremely simple units, a default inherited from early neural-network theory. We treat this as a normative architectural question. How should one split a fixed parameter budget P between the number of units N, per-unit effective complexity k_e, and per-unit connectivity k_c? What controls the optimal allocation? This calls for a model in which per-unit complexity can be tuned independently of width and connectivity. Accordingly, we introduce the ELM Network, whose recurrent layer is built from Expressive Leaky Memory (ELM) neurons, chosen to mirror functional components of cortical neurons. The architecture allows for individually adjusting N, k_e, and k_c and trains stably across orders of magnitude in scale. We evaluate the model on two qualitatively different sequence benchmarks: the neuromorphic SHD-Adding task and Enwik8 character-level language modeling. Performance improves monotonically along each of the three axes individually. Under a fixed budget, a clear non-trivial optimum emerges in their tradeoff, and larger budgets favor both more and more complex neurons. A closed-form information-theoretic model captures these tradeoffs and attributes the diminishing returns at two ends to: per-neuron signal-to-noise saturation and across-neuron redundancy. A hyperparameter sweep spanning three orders of magnitude in trainable parameters traces a near-Pareto-frontier scaling law consistent with the framework. This suggests that the simple-unit default in ML is not obviously optimal once this tradeoff surface is probed, and offers a normative lens on cortex's reliance on complex spatio-temporal integrators.

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.

There is a concerted effort to build domain-general artificial intelligence in the form of universal neural network models with sufficient computational flexibility to solve a wide variety of cognitive tasks but without requiring fine-tuning on individual problem spaces and domains. To do this, models need appropriate priors and inductive biases, such that trained models can generalise to out-of-distribution examples and new problem sets. Here we provide an overview of the hallmarks endowing biological neural networks with the functionality needed for flexible cognition, in order to establish which features might also be important to achieve similar functionality in artificial systems. We specifically discuss the role of system-level distribution of network communication and recurrence, in addition to the role of short-term topological changes for efficient local computation. As machine learning models become more complex, these principles may provide valuable directions in an otherwise vast space of possible architectures. In addition, testing these inductive biases within artificial systems may help us to understand the biological principles underlying domain-general cognition.

The deep neural nets of modern artificial intelligence (AI) have not achieved defining features of biological intelligence, including abstraction, causal learning, and energy-efficiency. While scaling to larger models has delivered performance improvements for current applications, more brain-like capacities may demand new theories, models, and methods for designing artificial learning systems. Here, we argue that this opportunity to reassess insights from the brain should stimulate cooperation between AI research and theory-driven computational neuroscience (CN). To motivate a brain basis of neural computation, we present a dynamical view of intelligence from which we elaborate concepts of sparsity in network structure, temporal dynamics, and interactive learning. In particular, we suggest that temporal dynamics, as expressed through neural synchrony, nested oscillations, and flexible sequences, provide a rich computational layer for reading and updating hierarchical models distributed in long-term memory networks. Moreover, embracing agent-centered paradigms in AI and CN will accelerate our understanding of the complex dynamics and behaviors that build useful world models. A convergence of AI/CN theories and objectives will reveal dynamical principles of intelligence for brains and engineered learning systems. This article was inspired by our symposium on dynamical neuroscience and machine learning at the 6th Annual US/NIH BRAIN Initiative Investigators Meeting.

Neural decoding, the process of understanding how brain activity corresponds to different stimuli, has been a primary objective in cognitive sciences. Over the past three decades, advancements in functional Magnetic Resonance Imaging and machine learning have greatly improved our ability to map visual stimuli to brain activity, especially in the visual cortex. Concurrently, research has expanded into decoding more complex processes like language and memory across the whole brain, utilizing techniques to handle greater variability and improve signal accuracy. We argue that "seeing" involves more than just mapping visual stimuli onto the visual cortex; it engages the entire brain, as various emotions and cognitive states can emerge from observing different scenes. In this paper, we develop algorithms to enhance our understanding of visual processes by incorporating whole-brain activation maps while individuals are exposed to visual stimuli. We utilize large-scale fMRI encoders and Image generative models pre-trained on large public datasets, which are then fine-tuned through Image-fMRI contrastive learning. Our models hence can decode visual experience across the entire cerebral cortex, surpassing the traditional confines of the visual cortex. We first compare our method with state-of-the-art approaches to decoding visual processing and show improved predictive semantic accuracy by 43%. A network ablation analysis suggests that beyond the visual cortex, the default mode network contributes most to decoding stimuli, in line with the proposed role of this network in sense-making and semantic processing. Additionally, we implemented zero-shot imagination decoding on an extra validation dataset, achieving a p-value of 0.0206 for mapping the reconstructed images and ground-truth text stimuli, which substantiates the model's capability to capture semantic meanings across various scenarios.

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.

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.

Deep convolutional artificial neural networks (ANNs) are the leading class of candidate models of the mechanisms of visual processing in the primate ventral stream. While initially inspired by brain anatomy, over the past years, these ANNs have evolved from a simple eight-layer architecture in AlexNet to extremely deep and branching architectures, demonstrating increasingly better object categorization performance, yet bringing into question how brain-like they still are. In particular, typical deep models from the machine learning community are often hard to map onto the brain's anatomy due to their vast number of layers and missing biologically-important connections, such as recurrence. Here we demonstrate that better anatomical alignment to the brain and high performance on machine learning as well as neuroscience measures do not have to be in contradiction. We developed CORnet-S, a shallow ANN with four anatomically mapped areas and recurrent connectivity, guided by Brain-Score, a new large-scale composite of neural and behavioral benchmarks for quantifying the functional fidelity of models of the primate ventral visual stream. Despite being significantly shallower than most models, CORnet-S is the top model on Brain-Score and outperforms similarly compact models on ImageNet. Moreover, our extensive analyses of CORnet-S circuitry variants reveal that recurrence is the main predictive factor of both Brain-Score and ImageNet top-1 performance. Finally, we report that the temporal evolution of the CORnet-S "IT" neural population resembles the actual monkey IT population dynamics. Taken together, these results establish CORnet-S, a compact, recurrent ANN, as the current best model of the primate ventral visual stream.

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.

Understanding functional representations within higher visual cortex is a fundamental question in computational neuroscience. While artificial neural networks pretrained on large-scale datasets exhibit striking representational alignment with human neural responses, learning image-computable models of visual cortex relies on individual-level, large-scale fMRI datasets. The necessity for expensive, time-intensive, and often impractical data acquisition limits the generalizability of encoders to new subjects and stimuli. BraInCoRL uses in-context learning to predict voxelwise neural responses from few-shot examples without any additional finetuning for novel subjects and stimuli. We leverage a transformer architecture that can flexibly condition on a variable number of in-context image stimuli, learning an inductive bias over multiple subjects. During training, we explicitly optimize the model for in-context learning. By jointly conditioning on image features and voxel activations, our model learns to directly generate better performing voxelwise models of higher visual cortex. We demonstrate that BraInCoRL consistently outperforms existing voxelwise encoder designs in a low-data regime when evaluated on entirely novel images, while also exhibiting strong test-time scaling behavior. The model also generalizes to an entirely new visual fMRI dataset, which uses different subjects and fMRI data acquisition parameters. Further, BraInCoRL facilitates better interpretability of neural signals in higher visual cortex by attending to semantically relevant stimuli. Finally, we show that our framework enables interpretable mappings from natural language queries to voxel selectivity.

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.

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.

Neuroscience employs diverse neuroimaging techniques, each offering distinct insights into brain activity, from electrophysiological recordings such as EEG, which have high temporal resolution, to hemodynamic modalities such as fMRI, which have increased spatial precision. However, integrating these heterogeneous data sources remains a challenge, which limits a comprehensive understanding of brain function. We present the Spatiotemporal Alignment of Multimodal Brain Activity (SAMBA) framework, which bridges the spatial and temporal resolution gaps across modalities by learning a unified latent space free of modality-specific biases. SAMBA introduces a novel attention-based wavelet decomposition for spectral filtering of electrophysiological recordings, graph attention networks to model functional connectivity between functional brain units, and recurrent layers to capture temporal autocorrelations in brain signal. We show that the training of SAMBA, aside from achieving translation, also learns a rich representation of brain information processing. We showcase this classify external stimuli driving brain activity from the representation learned in hidden layers of SAMBA, paving the way for broad downstream applications in neuroscience research and clinical contexts.

Learning and decision making in the brain are key processes critical to survival, and yet are processes implemented by non-ideal biological building blocks which can impose significant error. We explore quantitatively how the brain might cope with this inherent source of error by taking advantage of two ubiquitous mechanisms, redundancy and synchronization. In particular we consider a neural process whose goal is to learn a decision function by implementing a nonlinear gradient dynamics. The dynamics, however, are assumed to be corrupted by perturbations modeling the error which might be incurred due to limitations of the biology, intrinsic neuronal noise, and imperfect measurements. We show that error, and the associated uncertainty surrounding a learned solution, can be controlled in large part by trading off synchronization strength among multiple redundant neural systems against the noise amplitude. The impact of the coupling between such redundant systems is quantified by the spectrum of the network Laplacian, and we discuss the role of network topology in synchronization and in reducing the effect of noise. A range of situations in which the mechanisms we model arise in brain science are discussed, and we draw attention to experimental evidence suggesting that cortical circuits capable of implementing the computations of interest here can be found on several scales. Finally, simulations comparing theoretical bounds to the relevant empirical quantities show that the theoretical estimates we derive can be tight.

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.

We study the intriguing connection between visual data, deep networks, and the brain. Our method creates a universal channel alignment by using brain voxel fMRI response prediction as the training objective. We discover that deep networks, trained with different objectives, share common feature channels across various models. These channels can be clustered into recurring sets, corresponding to distinct brain regions, indicating the formation of visual concepts. Tracing the clusters of channel responses onto the images, we see semantically meaningful object segments emerge, even without any supervised decoder. Furthermore, the universal feature alignment and the clustering of channels produce a picture and quantification of how visual information is processed through the different network layers, which produces precise comparisons between the networks.

Biological neural networks define the brain function and intelligence of humans and other mammals, and form ultra-large, spatial, structured graphs. Their neuronal organization is closely interconnected with the spatial organization of the brain's microvasculature, which supplies oxygen to the neurons and builds a complementary spatial graph. This vasculature (or the vessel structure) plays an important role in neuroscience; for example, the organization of (and changes to) vessel structure can represent early signs of various pathologies, e.g. Alzheimer's disease or stroke. Recently, advances in tissue clearing have enabled whole brain imaging and segmentation of the entirety of the mouse brain's vasculature. Building on these advances in imaging, we are presenting an extendable dataset of whole-brain vessel graphs based on specific imaging protocols. Specifically, we extract vascular graphs using a refined graph extraction scheme leveraging the volume rendering engine Voreen and provide them in an accessible and adaptable form through the OGB and PyTorch Geometric dataloaders. Moreover, we benchmark numerous state-of-the-art graph learning algorithms on the biologically relevant tasks of vessel prediction and vessel classification using the introduced vessel graph dataset. Our work paves a path towards advancing graph learning research into the field of neuroscience. Complementarily, the presented dataset raises challenging graph learning research questions for the machine learning community, in terms of incorporating biological priors into learning algorithms, or in scaling these algorithms to handle sparse,spatial graphs with millions of nodes and edges. All datasets and code are available for download at https://github.com/jocpae/VesselGraph .

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.

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.

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.

Functional brain network (FBN) modeling often relies on local pairwise interactions, whose limitation in capturing high-order dependencies is theoretically analyzed in this paper. Meanwhile, the computational burden and heuristic nature of current hypergraph modeling approaches hinder end-to-end learning of FBN structures directly from data distributions. To address this, we propose to extract high-order FBN structures under global constraints, and implement this as a Global Constraints oriented Multi-resolution (GCM) FBN structure learning framework. It incorporates 4 types of global constraint (signal synchronization, subject identity, expected edge numbers, and data labels) to enable learning FBN structures for 4 distinct levels (sample/subject/group/project) of modeling resolution. Experimental results demonstrate that GCM achieves up to a 30.6% improvement in relative accuracy and a 96.3% reduction in computational time across 5 datasets and 2 task settings, compared to 9 baselines and 10 state-of-the-art methods. Extensive experiments validate the contributions of individual components and highlight the interpretability of GCM. This work offers a novel perspective on FBN structure learning and provides a foundation for interdisciplinary applications in cognitive neuroscience. Code is publicly available on https://github.com/lzhan94swu/GCM.

Graph Neural Networks (GNN) can capture the geometric properties of neural representations in EEG data. Here we utilise those to study how reinforcement-based motor learning affects neural activity patterns during motor planning, leveraging the inherent graph structure of EEG channels to capture the spatial relationships in brain activity. By exploiting task-specific symmetries, we define different pretraining strategies that not only improve model performance across all participant groups but also validate the robustness of the geometric representations. Explainability analysis based on the graph structures reveals consistent group-specific neural signatures that persist across pretraining conditions, suggesting stable geometric structures in the neural representations associated with motor learning and feedback processing. These geometric patterns exhibit partial invariance to certain task space transformations, indicating symmetries that enable generalisation across conditions while maintaining specificity to individual learning strategies. This work demonstrates how GNNs can uncover the effects of previous outcomes on motor planning, in a complex real-world task, providing insights into the geometric principles governing neural representations. Our experimental design bridges the gap between controlled experiments and ecologically valid scenarios, offering new insights into the organisation of neural representations during naturalistic motor learning, which may open avenues for exploring fundamental principles governing brain activity in complex tasks.

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.

Vision-language models (VLMs) achieve strong multimodal performance, yet how computation is organized across populations of neurons remains poorly understood. In this work, we study VLMs through the lens of neural topology, representing each layer as a within-layer correlation graph derived from neuron-neuron co-activations. This view allows us to ask whether population-level structure is behaviorally meaningful, how it changes across modalities and depth, and whether it identifies causally influential internal components under intervention. We show that correlation topology carries recoverable behavioral signal; moreover, cross-modal structure progressively consolidates with depth around a compact set of recurrent hub neurons, whose targeted perturbation substantially alters model output. Neural topology thus emerges as a meaningful intermediate scale for VLM interpretability: richer than local attribution, more tractable than full circuit recovery, and empirically tied to multimodal behavior. Code is publicly available at https://github.com/he-h/vlm-graph-probing.

Graph Convolutional Networks (GCNs) achieve an impressive performance due to the remarkable representation ability in learning the graph information. However, GCNs, when implemented on a deep network, require expensive computation power, making them difficult to be deployed on battery-powered devices. In contrast, Spiking Neural Networks (SNNs), which perform a bio-fidelity inference process, offer an energy-efficient neural architecture. In this work, we propose SpikingGCN, an end-to-end framework that aims to integrate the embedding of GCNs with the biofidelity characteristics of SNNs. The original graph data are encoded into spike trains based on the incorporation of graph convolution. We further model biological information processing by utilizing a fully connected layer combined with neuron nodes. In a wide range of scenarios (e.g. citation networks, image graph classification, and recommender systems), our experimental results show that the proposed method could gain competitive performance against state-of-the-art approaches. Furthermore, we show that SpikingGCN on a neuromorphic chip can bring a clear advantage of energy efficiency into graph data analysis, which demonstrates its great potential to construct environment-friendly machine learning models.

Biological cortical neurons are remarkably sophisticated computational devices, temporally integrating their vast synaptic input over an intricate dendritic tree, subject to complex, nonlinearly interacting internal biological processes. A recent study proposed to characterize this complexity by fitting accurate surrogate models to replicate the input-output relationship of a detailed biophysical cortical pyramidal neuron model and discovered it needed temporal convolutional networks (TCN) with millions of parameters. Requiring these many parameters, however, could stem from a misalignment between the inductive biases of the TCN and cortical neuron's computations. In light of this, and to explore the computational implications of leaky memory units and nonlinear dendritic processing, we introduce the Expressive Leaky Memory (ELM) neuron model, a biologically inspired phenomenological model of a cortical neuron. Remarkably, by exploiting such slowly decaying memory-like hidden states and two-layered nonlinear integration of synaptic input, our ELM neuron can accurately match the aforementioned input-output relationship with under ten thousand trainable parameters. To further assess the computational ramifications of our neuron design, we evaluate it on various tasks with demanding temporal structures, including the Long Range Arena (LRA) datasets, as well as a novel neuromorphic dataset based on the Spiking Heidelberg Digits dataset (SHD-Adding). Leveraging a larger number of memory units with sufficiently long timescales, and correspondingly sophisticated synaptic integration, the ELM neuron displays substantial long-range processing capabilities, reliably outperforming the classic Transformer or Chrono-LSTM architectures on LRA, and even solving the Pathfinder-X task with over 70% accuracy (16k context length).

Spatial and temporal resource constraints are critical for both biological and artificial intelligent systems. Here we define differentiable cost terms for breadth, depth, and time within a recurrent convolutional neural network conceived as a finite subset of an infinite lattice. We optimize these costs jointly with task errors via backpropagation. We set different pressures on breadth, depth, and time, which leads to diverse computational graphs emerging organically through training. We find that all three resources can be traded off against each other to achieve a given level of accuracy. Networks grow in all three dimensions with task complexity and spontaneously take more recurrent steps when inputs are occluded. Surprisingly, time used by the model correlates with human reaction times in an object recognition task. Our framework provides a normative account of how resource constraints shape neural architectures, connecting to questions about brain design in neuroscience, and may help illuminate the diversity of neural solutions found in nature.

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.

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.

Modeling spatiotemporal brain dynamics from high-dimensional data, such as functional Magnetic Resonance Imaging (fMRI), is a formidable task in neuroscience. Existing approaches for fMRI analysis utilize hand-crafted features, but the process of feature extraction risks losing essential information in fMRI scans. To address this challenge, we present SwiFT (Swin 4D fMRI Transformer), a Swin Transformer architecture that can learn brain dynamics directly from fMRI volumes in a memory and computation-efficient manner. SwiFT achieves this by implementing a 4D window multi-head self-attention mechanism and absolute positional embeddings. We evaluate SwiFT using multiple large-scale resting-state fMRI datasets, including the Human Connectome Project (HCP), Adolescent Brain Cognitive Development (ABCD), and UK Biobank (UKB) datasets, to predict sex, age, and cognitive intelligence. Our experimental outcomes reveal that SwiFT consistently outperforms recent state-of-the-art models. Furthermore, by leveraging its end-to-end learning capability, we show that contrastive loss-based self-supervised pre-training of SwiFT can enhance performance on downstream tasks. Additionally, we employ an explainable AI method to identify the brain regions associated with sex classification. To our knowledge, SwiFT is the first Swin Transformer architecture to process dimensional spatiotemporal brain functional data in an end-to-end fashion. Our work holds substantial potential in facilitating scalable learning of functional brain imaging in neuroscience research by reducing the hurdles associated with applying Transformer models to high-dimensional fMRI.

Current approaches to automated code generation often rely on monolithic models that lack real-time adaptability and scalability. This limitation is particularly evident in complex programming tasks that require dynamic adjustment and efficiency. The integration of neuroscience principles into Natural Language Processing (NLP) has the potential to revolutionize automated code generation. This paper presents CortexCompile, a novel modular system inspired by the specialized functions of the human brain's cortical regions. By emulating the distinct roles of the Prefrontal Cortex, Parietal Cortex, Temporal Lobe, and Motor Cortex, CortexCompile achieves significant advancements in scalability, efficiency, and adaptability compared to traditional monolithic models like GPT-4o. The system's architecture features a Task Orchestration Agent that manages dynamic task delegation and parallel processing, facilitating the generation of highly accurate and optimized code across increasingly complex programming tasks. Experimental evaluations demonstrate that CortexCompile consistently outperforms GPT-4o in development time, accuracy, and user satisfaction, particularly in tasks involving real-time strategy games and first-person shooters. These findings underscore the viability of neuroscience-inspired architectures in addressing the limitations of current NLP models, paving the way for more efficient and human-like AI systems.

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.

Human cognition emerges from coordinated spiking dynamics in distributed neural circuits, where information is encoded via both firing rates and precise spike timing determined by brain rhythms. Inspired by this notion, we propose a brain-inspired learning primitive in which cognition-level neural synchrony emerges through iterative bottom-up and top-down interactions between micro-scale dynamics of spiking neurons and a macro-scale mechanism of oscillatory synchronization. Specifically, we model each parcel (e.g., a cortical region or an image pixel) in the target system as a spiking neuron embedded in a predefined connectivity scaffold. Low-level information is encoded in a spatiotemporal domain, where neurons are selectively grouped and fire spontaneously over time through self-organized dynamics. In the bottom-up route, oscillatory synchronization is formed from past spiking activity accumulated over a finite memory window. Since brain dynamics operate in a regime of partial and transient synchronization rather than global phase locking, we model oscillatory coordination using a time-delayed synchronization formulation, which enables a top-down modulation of heterogeneous neural spiking for a large-scale distributed system. Together, we devise a spiking-by-synchronization neural network (S2-Net) that uses rhythmic timing as a control mechanism for efficient information processing. Promising results have been achieved across a broad range of tasks, including neural activity decoding, energy-efficient signal processing, temporal binding and semantic reasoning.

Recurrent neural networks (RNNs) are widely used throughout neuroscience as models of local neural activity. Many properties of single RNNs are well characterized theoretically, but experimental neuroscience has moved in the direction of studying multiple interacting areas, and RNN theory needs to be likewise extended. We take a constructive approach towards this problem, leveraging tools from nonlinear control theory and machine learning to characterize when combinations of stable RNNs will themselves be stable. Importantly, we derive conditions which allow for massive feedback connections between interacting RNNs. We parameterize these conditions for easy optimization using gradient-based techniques, and show that stability-constrained "networks of networks" can perform well on challenging sequential-processing benchmark tasks. Altogether, our results provide a principled approach towards understanding distributed, modular function in the brain.

We propose a novel deep network structure called "Network In Network" (NIN) to enhance model discriminability for local patches within the receptive field. The conventional convolutional layer uses linear filters followed by a nonlinear activation function to scan the input. Instead, we build micro neural networks with more complex structures to abstract the data within the receptive field. We instantiate the micro neural network with a multilayer perceptron, which is a potent function approximator. The feature maps are obtained by sliding the micro networks over the input in a similar manner as CNN; they are then fed into the next layer. Deep NIN can be implemented by stacking mutiple of the above described structure. With enhanced local modeling via the micro network, we are able to utilize global average pooling over feature maps in the classification layer, which is easier to interpret and less prone to overfitting than traditional fully connected layers. We demonstrated the state-of-the-art classification performances with NIN on CIFAR-10 and CIFAR-100, and reasonable performances on SVHN and MNIST datasets.

Understanding the inner workings of neural networks is essential for enhancing model performance and interpretability. Current research predominantly focuses on examining the connection between individual neurons and the model's final predictions. Which suffers from challenges in interpreting the internal workings of the model, particularly when neurons encode multiple unrelated features. In this paper, we propose a novel framework that transitions the focus from analyzing individual neurons to investigating groups of neurons, shifting the emphasis from neuron-output relationships to functional interaction between neurons. Our automated framework, NeurFlow, first identifies core neurons and clusters them into groups based on shared functional relationships, enabling a more coherent and interpretable view of the network's internal processes. This approach facilitates the construction of a hierarchical circuit representing neuron interactions across layers, thus improving interpretability while reducing computational costs. Our extensive empirical studies validate the fidelity of our proposed NeurFlow. Additionally, we showcase its utility in practical applications such as image debugging and automatic concept labeling, thereby highlighting its potential to advance the field of neural network explainability.

Traditional methods of computer vision and machine learning cannot match human performance on tasks such as the recognition of handwritten digits or traffic signs. Our biologically plausible deep artificial neural network architectures can. Small (often minimal) receptive fields of convolutional winner-take-all neurons yield large network depth, resulting in roughly as many sparsely connected neural layers as found in mammals between retina and visual cortex. Only winner neurons are trained. Several deep neural columns become experts on inputs preprocessed in different ways; their predictions are averaged. Graphics cards allow for fast training. On the very competitive MNIST handwriting benchmark, our method is the first to achieve near-human performance. On a traffic sign recognition benchmark it outperforms humans by a factor of two. We also improve the state-of-the-art on a plethora of common image classification benchmarks.

The brain solves the credit assignment problem remarkably well. For credit to be assigned across neural networks they must, in principle, wait for specific neural computations to finish. How the brain deals with this inherent locking problem has remained unclear. Deep learning methods suffer from similar locking constraints both on the forward and feedback phase. Recently, decoupled neural interfaces (DNIs) were introduced as a solution to the forward and feedback locking problems in deep networks. Here we propose that a specialised brain region, the cerebellum, helps the cerebral cortex solve similar locking problems akin to DNIs. To demonstrate the potential of this framework we introduce a systems-level model in which a recurrent cortical network receives online temporal feedback predictions from a cerebellar module. We test this cortico-cerebellar recurrent neural network (ccRNN) model on a number of sensorimotor (line and digit drawing) and cognitive tasks (pattern recognition and caption generation) that have been shown to be cerebellar-dependent. In all tasks, we observe that ccRNNs facilitates learning while reducing ataxia-like behaviours, consistent with classical experimental observations. Moreover, our model also explains recent behavioural and neuronal observations while making several testable predictions across multiple levels. Overall, our work offers a novel perspective on the cerebellum as a brain-wide decoupling machine for efficient credit assignment and opens a new avenue between deep learning and neuroscience.

Large language models (LLMs) frequently generate hallucinations -- plausible but factually incorrect outputs -- undermining their reliability. While prior work has examined hallucinations from macroscopic perspectives such as training data and objectives, the underlying neuron-level mechanisms remain largely unexplored. In this paper, we conduct a systematic investigation into hallucination-associated neurons (H-Neurons) in LLMs from three perspectives: identification, behavioral impact, and origins. Regarding their identification, we demonstrate that a remarkably sparse subset of neurons (less than 0.1% of total neurons) can reliably predict hallucination occurrences, with strong generalization across diverse scenarios. In terms of behavioral impact, controlled interventions reveal that these neurons are causally linked to over-compliance behaviors. Concerning their origins, we trace these neurons back to the pre-trained base models and find that these neurons remain predictive for hallucination detection, indicating they emerge during pre-training. Our findings bridge macroscopic behavioral patterns with microscopic neural mechanisms, offering insights for developing more reliable LLMs.

Connectivity structure shapes neural computation, but inferring this structure from population recordings is degenerate: multiple connectivity structures can generate identical dynamics. Recent work uses low-rank recurrent neural networks (lrRNNs) to infer low-dimensional latent dynamics and connectivity from observed activity, enabling a mechanistic interpretation of the dynamics. However, standard approaches for training lrRNNs can recover spurious structures irrelevant to the underlying dynamics. We first characterize the identifiability of connectivity structures in lrRNNs and determine conditions under which a unique solution exists. To find such solutions, we develop an inference framework based on maximum entropy and continuous normalizing flows (CNFs), trained via flow matching. Instead of estimating a single connectivity matrix, our method learns a distribution over connection weights that is maximally unbiased over unidentifiable components while matching the observed dynamics. This approach captures complex yet necessary distributions such as heavy-tailed connectivity found in empirical data. We validate our method on synthetic datasets with connectivity structures that generate multistable attractors, limit cycles, and ring attractors, and demonstrate its applicability in recordings from rat frontal cortex during decision-making. Our framework shifts circuit inference from recovering connectivity to identifying which connectivity structures are computationally required, and which are artifacts of underconstrained inference.

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.

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.

Finding a code to unravel the population of neural responses that leads to a distinct animal behavior has been a long-standing question in the field of neuroscience. With the recent advances in machine learning, it is shown that the hierarchically Deep Neural Networks (DNNs) perform optimally in decoding unique features out of complex datasets. In this study, we utilize the power of a DNN to explore the computational principles in the mammalian brain by exploiting the Neuropixel data from Allen Brain Institute. We decode the neural responses from mouse visual cortex to predict the presented stimuli to the animal for natural (bear, trees, cheetah, etc.) and artificial (drifted gratings, orientated bars, etc.) classes. Our results indicate that neurons in mouse visual cortex encode the features of natural and artificial objects in a distinct manner, and such neural code is consistent across animals. We investigate this by applying transfer learning to train a DNN on the neural responses of a single animal and test its generalized performance across multiple animals. Within a single animal, DNN is able to decode the neural responses with as much as 100% classification accuracy. Across animals, this accuracy is reduced to 91%. This study demonstrates the potential of utilizing the DNN models as a computational framework to understand the neural coding principles in the mammalian brain.

We study the problem of training self-supervised foundation models for functional MRI. Our main contributions are: (1) we introduce a new model family (CortexMAE) trained using the masked autoencoder framework on 2.1K hours of open fMRI data, and (2) we release the first open evaluation suite (Brainmarks) for fMRI foundation models. Our core innovation is simple: we adapt the Vision Transformer to fMRI by first converting each 3D fMRI volume to a 2D map using a cortical flat map projection. We directly compare flat maps to both parcellation and volume-based representations. While each has its advantages, flat maps generally perform best. We perform the first systematic scaling analysis for fMRI and observe strict power law scaling, albeit with limits. Finally, we use Brainmarks to do controlled benchmark comparisons. On subject-level trait prediction, we report a challenging null result: no single model achieves clear state-of-the-art performance. Moreover, all models struggle to outperform a simple functional connectivity baseline. On cognitive state decoding, we observe more robust performance, and in this setting our CortexMAE family outperforms prior models by a large margin. Code, models, and datasets are available at https://github.com/MedARC-AI/CortexMAE and https://github.com/MedARC-AI/Brainmarks.

Artificial Neural Networks (ANN) have gained significant popularity thanks to their ability to learn using the well-known backpropagation algorithm. Conversely, Spiking Neural Networks (SNNs), despite having broader capabilities than ANNs, have always posed challenges in the training phase. This paper shows a new method to perform supervised learning on SNNs, using Spike Timing Dependent Plasticity (STDP) and homeostasis, aiming at training the network to identify spatial patterns. Spatial patterns refer to spike patterns without a time component, where all spike events occur simultaneously. The method is tested using the SpiNNaker digital architecture. A SNN is trained to recognise one or multiple patterns and performance metrics are extracted to measure the performance of the network. Some considerations are drawn from the results showing that, in the case of a single trained pattern, the network behaves as the ideal detector, with 100% accuracy in detecting the trained pattern. However, as the number of trained patterns on a single network increases, the accuracy of identification is linked to the similarities between these patterns. This method of training an SNN to detect spatial patterns may be applied to pattern recognition in static images or traffic analysis in computer networks, where each network packet represents a spatial pattern. It will be stipulated that the homeostatic factor may enable the network to detect patterns with some degree of similarity, rather than only perfectly matching patterns.The principles outlined in this article serve as the fundamental building blocks for more complex systems that utilise both spatial and temporal patterns by converting specific features of input signals into spikes.One example of such a system is a computer network packet classifier, tasked with real-time identification of packet streams based on features within the packet content

Our ability to use deep learning approaches to decipher neural activity would likely benefit from greater scale, in terms of both model size and datasets. However, the integration of many neural recordings into one unified model is challenging, as each recording contains the activity of different neurons from different individual animals. In this paper, we introduce a training framework and architecture designed to model the population dynamics of neural activity across diverse, large-scale neural recordings. Our method first tokenizes individual spikes within the dataset to build an efficient representation of neural events that captures the fine temporal structure of neural activity. We then employ cross-attention and a PerceiverIO backbone to further construct a latent tokenization of neural population activities. Utilizing this architecture and training framework, we construct a large-scale multi-session model trained on large datasets from seven nonhuman primates, spanning over 158 different sessions of recording from over 27,373 neural units and over 100 hours of recordings. In a number of different tasks, we demonstrate that our pretrained model can be rapidly adapted to new, unseen sessions with unspecified neuron correspondence, enabling few-shot performance with minimal labels. This work presents a powerful new approach for building deep learning tools to analyze neural data and stakes out a clear path to training at scale.

Recent breakthroughs in synaptic-resolution network connectomics have revealed that brain circuits feature fine-scale structural connectivity, such as pairs of correlated synaptic couplings known as second-order motifs. Large-scale recordings of neuronal activity in networks containing nonlinear neurons reveal macroscopic heterogeneous population dynamics throughout the brain. These findings rekindle the inquiry into this intriguing question: Can microscale synaptic structures contribute to macroscopic heterogeneous dynamics and computations in ways that canonical brain circuit models cannot? To answer this question, we create random RNNs with various cell types, nonlinear non-negative neural responses, and arbitrary marginal and second-order correlated synaptic statistics. We derive mean-field low-rank equations for P-population networks in which the pre- and postsynaptic neuronal population identities determine the synaptic and motif strengths. Our framework requires 2P latent dynamic variables with P variables describing mean population activity and P variables capturing within-population variability. Theoretical and simulational results demonstrate that chain motifs induce correlations in synaptic variability, enabling microscopic fluctuations to be integrated and influence mesoscopic mean population dynamics. We apply this framework to reverse engineer network connectivity that recapitulates the heterogeneous activity across the population in the mouse primary visual cortex. By bridging the gap between synaptic organization and nonlinear heterogeneous population dynamics, our results offer a principled approach and testable predictions regarding the relationship between fine-scale connectivity, heterogeneous dynamics, and functional computations.

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.

In standard Convolutional Neural Networks (CNNs), the receptive fields of artificial neurons in each layer are designed to share the same size. It is well-known in the neuroscience community that the receptive field size of visual cortical neurons are modulated by the stimulus, which has been rarely considered in constructing CNNs. We propose a dynamic selection mechanism in CNNs that allows each neuron to adaptively adjust its receptive field size based on multiple scales of input information. A building block called Selective Kernel (SK) unit is designed, in which multiple branches with different kernel sizes are fused using softmax attention that is guided by the information in these branches. Different attentions on these branches yield different sizes of the effective receptive fields of neurons in the fusion layer. Multiple SK units are stacked to a deep network termed Selective Kernel Networks (SKNets). On the ImageNet and CIFAR benchmarks, we empirically show that SKNet outperforms the existing state-of-the-art architectures with lower model complexity. Detailed analyses show that the neurons in SKNet can capture target objects with different scales, which verifies the capability of neurons for adaptively adjusting their receptive field sizes according to the input. The code and models are available at https://github.com/implus/SKNet.

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.

Recurrent Neural Networks (RNNs) are popular models of brain function. The typical training strategy is to adjust their input-output behavior so that it matches that of the biological circuit of interest. Even though this strategy ensures that the biological and artificial networks perform the same computational task, it does not guarantee that their internal activity dynamics match. This suggests that the trained RNNs might end up performing the task employing a different internal computational mechanism, which would make them a suboptimal model of the biological circuit. In this work, we introduce a novel training strategy that allows learning not only the input-output behavior of an RNN but also its internal network dynamics, based on sparse neural recordings. We test the proposed method by training an RNN to simultaneously reproduce internal dynamics and output signals of a physiologically-inspired neural model. Specifically, this model generates the multiphasic muscle-like activity patterns typically observed during the execution of reaching movements, based on the oscillatory activation patterns concurrently observed in the motor cortex. Remarkably, we show that the reproduction of the internal dynamics is successful even when the training algorithm relies on the activities of a small subset of neurons sampled from the biological network. Furthermore, we show that training the RNNs with this method significantly improves their generalization performance. Overall, our results suggest that the proposed method is suitable for building powerful functional RNN models, which automatically capture important computational properties of the biological circuit of interest from sparse neural recordings.

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.

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.

The Backpropagation algorithm has often been criticised for its lack of biological realism. In an attempt to find a more biologically plausible alternative, the recently introduced Forward-Forward algorithm replaces the forward and backward passes of Backpropagation with two forward passes. In this work, we show that the internal representations obtained by the Forward-Forward algorithm can organise into category-specific ensembles exhibiting high sparsity -- composed of a low number of active units. This situation is reminiscent of what has been observed in cortical sensory areas, where neuronal ensembles are suggested to serve as the functional building blocks for perception and action. Interestingly, while this sparse pattern does not typically arise in models trained with standard Backpropagation, it can emerge in networks trained with Backpropagation on the same objective proposed for the Forward-Forward algorithm.

Graph Transformers have recently been successful in various graph representation learning tasks, providing a number of advantages over message-passing Graph Neural Networks. Utilizing Graph Transformers for learning the representation of the brain functional connectivity network is also gaining interest. However, studies to date have underlooked the temporal dynamics of functional connectivity, which fluctuates over time. Here, we propose a method for learning the representation of dynamic functional connectivity with Graph Transformers. Specifically, we define the connectome embedding, which holds the position, structure, and time information of the functional connectivity graph, and use Transformers to learn its representation across time. We perform experiments with over 50,000 resting-state fMRI samples obtained from three datasets, which is the largest number of fMRI data used in studies by far. The experimental results show that our proposed method outperforms other competitive baselines in gender classification and age regression tasks based on the functional connectivity extracted from the fMRI data.

Spiking Neural Networks (SNNs) have garnered significant attention as a central paradigm in neuromorphic computing, owing to their energy efficiency and biological plausibility. However, training deep SNNs has critically depended on explicit normalization schemes, leading to a trade-off between performance and biological realism. To resolve this conflict, we propose a normalization-free learning framework that incorporates lateral inhibition inspired by cortical circuits. Our framework replaces the traditional feedforward SNN layer with distinct excitatory (E) and inhibitory (I) neuronal populations that capture the key features of the cortical E-I interaction. The E-I circuit dynamically regulates neuronal activity through subtractive and divisive inhibition, which respectively control the excitability and gain of neurons. To stabilize end-to-end training of the biologically constrained SNNs, we propose two key techniques: E-I Init and E-I Prop. E-I Init is a dynamic parameter initialization scheme that balances excitatory and inhibitory inputs while performing gain control. E-I Prop decouples the backpropagation of the circuit from the forward pass, regulating gradient flow. Experiments across multiple datasets and network architectures demonstrate that our framework enables stable training of deep normalization-free SNNs with biological realism, achieving competitive performance. Therefore, our work not only provides a solution to training deep SNNs but also serves as a computational platform for further exploring the functions of E-I interaction in large-scale cortical computation. Code is available at https://github.com/vwOvOwv/DeepEISNN.

Spiking Neural Networks (SNNs) are computational models inspired by the structure and dynamics of biological neuronal networks. Their event-driven nature enables them to achieve high energy efficiency, particularly when deployed on neuromorphic hardware platforms. Unlike conventional Artificial Neural Networks (ANNs), which primarily rely on layered architectures, SNNs naturally support a wide range of connectivity patterns, from traditional layered structures to small-world graphs characterized by locally dense and globally sparse connections. In this work, we introduce NeuroCoreX, an FPGA-based emulator designed for the flexible co-design and testing of SNNs. NeuroCoreX supports all-to-all connectivity, providing the capability to implement diverse network topologies without architectural restrictions. It features a biologically motivated local learning mechanism based on Spike-Timing-Dependent Plasticity (STDP). The neuron model implemented within NeuroCoreX is the Leaky Integrate-and-Fire (LIF) model, with current-based synapses facilitating spike integration and transmission . A Universal Asynchronous Receiver-Transmitter (UART) interface is provided for programming and configuring the network parameters, including neuron, synapse, and learning rule settings. Users interact with the emulator through a simple Python-based interface, streamlining SNN deployment from model design to hardware execution. NeuroCoreX is released as an open-source framework, aiming to accelerate research and development in energy-efficient, biologically inspired computing.

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.

Electroencephalography (EEG) and magnetoencephalography (MEG) measure neural activity non-invasively by capturing electromagnetic fields generated by dendritic currents. Although rooted in the same biophysics, EEG and MEG exhibit distinct signal patterns, further complicated by variations in sensor configurations across modalities and recording devices. Existing approaches typically rely on separate, modality- and dataset-specific models, which limits the performance and cross-domain scalability. This paper proposes BrainOmni, the first brain foundation model that generalises across heterogeneous EEG and MEG recordings. To unify diverse data sources, we introduce BrainTokenizer,the first tokenizer that quantises spatiotemporal brain activity into discrete representations. Central to BrainTokenizer is a novel Sensor Encoder that encodes sensor properties such as spatial layout, orientation, and type, enabling compatibility across devices and modalities. Building upon the discrete representations, BrainOmni learns unified semantic embeddings of brain signals by self-supervised pretraining. To the best of our knowledge, it is the first foundation model to support both EEG and MEG signals, as well as the first to incorporate large-scale MEG pretraining. A total of 1,997 hours of EEG and 656 hours of MEG data are curated and standardised from publicly available sources for pretraining. Experiments show that BrainOmni outperforms both existing foundation models and state-of-the-art task-specific models on a range of downstream tasks. It also demonstrates strong generalisation to unseen EEG and MEG devices. Further analysis reveals that joint EEG-MEG (EMEG) training yields consistent improvements across both modalities. Code and model checkpoints will be released upon acceptance.

The human brain processes dynamic visual input through hierarchically organized, functionally specialized regions. While recent in silico brain encoding models can synthesize optimal stimuli to probe selectivity in different brain regions, prior work has been largely limited to static images, leaving dynamic visual processing underexplored. We introduce a novel neural-guided video synthesis framework that generates stimuli optimized for target brain regions across visual cortex. Our method performs evolutionary search over a structured prompt space, guided by a dynamic encoding model that predicts voxel-level responses to video inputs. By maximizing predicted activity for a target ROI, the framework efficiently discovers hyper-activating dynamic stimuli that consistently surpass handcrafted localizer videos. The synthesized videos recover known selectivities across ventral, dorsal, and lateral pathways, and further reveal systematic differences in sensitivity to temporal dynamics. A searchlight analysis provides new insight into the progression toward increasingly complex social-dynamic features along the lateral stream, further supported by probing with synthesized abstract, non-naturalistic stimuli. Taken together, our framework enables in silico exploration of dynamic visual selectivity, with new predictions for in vivo experiments

Human brains respond to semantic features of presented stimuli with different neurons. It is then curious whether modern deep neural networks admit a similar behavior pattern. Specifically, this paper finds a small cluster of neurons in a diffusion model corresponding to a particular subject. We call those neurons the concept neurons. They can be identified by statistics of network gradients to a stimulation connected with the given subject. The concept neurons demonstrate magnetic properties in interpreting and manipulating generation results. Shutting them can directly yield the related subject contextualized in different scenes. Concatenating multiple clusters of concept neurons can vividly generate all related concepts in a single image. A few steps of further fine-tuning can enhance the multi-concept capability, which may be the first to manage to generate up to four different subjects in a single image. For large-scale applications, the concept neurons are environmentally friendly as we only need to store a sparse cluster of int index instead of dense float32 values of the parameters, which reduces storage consumption by 90\% compared with previous subject-driven generation methods. Extensive qualitative and quantitative studies on diverse scenarios show the superiority of our method in interpreting and manipulating diffusion models.

Uncovering the fundamental neural correlates of biological intelligence, developing mathematical models, and conducting computational simulations are critical for advancing new paradigms in artificial intelligence (AI). In this study, we implemented a comprehensive visual decision-making model that spans from visual input to behavioral output, using a neural dynamics modeling approach. Drawing inspiration from the key components of the dorsal visual pathway in primates, our model not only aligns closely with human behavior but also reflects neural activities in primates, and achieving accuracy comparable to convolutional neural networks (CNNs). Moreover, magnetic resonance imaging (MRI) identified key neuroimaging features such as structural connections and functional connectivity that are associated with performance in perceptual decision-making tasks. A neuroimaging-informed fine-tuning approach was introduced and applied to the model, leading to performance improvements that paralleled the behavioral variations observed among subjects. Compared to classical deep learning models, our model more accurately replicates the behavioral performance of biological intelligence, relying on the structural characteristics of biological neural networks rather than extensive training data, and demonstrating enhanced resilience to perturbation.

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/.

Advances in neural recording present increasing opportunities to study neural activity in unprecedented detail. Latent variable models (LVMs) are promising tools for analyzing this rich activity across diverse neural systems and behaviors, as LVMs do not depend on known relationships between the activity and external experimental variables. However, progress with LVMs for neuronal population activity is currently impeded by a lack of standardization, resulting in methods being developed and compared in an ad hoc manner. To coordinate these modeling efforts, we introduce a benchmark suite for latent variable modeling of neural population activity. We curate four datasets of neural spiking activity from cognitive, sensory, and motor areas to promote models that apply to the wide variety of activity seen across these areas. We identify unsupervised evaluation as a common framework for evaluating models across datasets, and apply several baselines that demonstrate benchmark diversity. We release this benchmark through EvalAI. http://neurallatents.github.io

Deep Learning has revolutionized various fields, including Computer Vision, Natural Language Processing, as well as Biomedical research. Within the field of neuroscience, specifically in electrophysiological neuroimaging, researchers are starting to explore leveraging deep learning to make predictions on their data without extensive feature engineering. The availability of large-scale datasets is a crucial aspect of allowing the experimentation of Deep Learning models. We are publishing the first large-scale clinical EEG dataset that simplifies data access and management for Deep Learning. This dataset contains eyes-closed EEG data prepared from a collection of 1,574 juvenile participants from the Healthy Brain Network. We demonstrate a use case integrating this framework, and discuss why providing such neuroinformatics infrastructure to the community is critical for future scientific discoveries.

Understanding how complex cognitive functions are organized within artificial systems is central to interpreting large language models (LLMs) and relating them to biological cognition. Yet although LLMs exhibit broad cognitive-like behaviours, it remains unclear whether their internal representations form reproducible functional systems that explain behaviour, failure and links to human cognition. Here we present NeuroCogMap, a cognitive neuroscience-inspired framework that organizes internal features of LLMs into functional parcels and links them to interpretable functions, cognitive capabilities and a cognitive hierarchy. These parcels form a stable and semantically coherent organization that is partly conserved across models and functionally linked to model outputs. Within this organization, major LLM failures, including hallucination, bias, refusal failure and sycophancy, correspond to distinct disruptions in representational and behavioural-control systems, yielding internal signatures for mechanism-guided detection and targeted intervention. Beyond model behaviour, NeuroCogMap improves prediction of human cortical responses during naturalistic language comprehension, with the strongest correspondence in higher-order association cortex. At the cognitive level, its internal signatures expose latent strategies that guide refinements of classical models of human decision-making. Together, these findings establish NeuroCogMap as a system-level framework for mapping functional organization in artificial systems and for relating this organization to human cortical function and cognitive behaviour.

Electroencephalography (EEG) foundation models hold significant promise for universal Brain-Computer Interfaces (BCIs). However, existing approaches often rely on end-to-end fine-tuning and exhibit limited efficacy under frozen-probing protocols, lacking the intrinsic universality required for broad generalization. This limitation stems from adapting general-purpose sequence architectures that overlook the biophysical and dynamical principles of neural activity. To bridge this gap, we propose DeeperBrain, a neuro-grounded foundation model integrating domain-specific inductive biases into its model design and learning objectives. Architecturally, DeeperBrain incorporates a volume conduction-aware channel encoding to model spatial mixing via 3D geometry, and a neurodynamics-aware temporal encoding capturing slow adaptations using oscillatory and exponential bases. For pretraining, we introduce a dual-objective strategy combining Masked EEG Reconstruction (MER) for local fidelity and Neurodynamics Statistics Prediction (NSP). NSP enforces alignment with macroscopic brain states by predicting interpretable order parameters, including spectral power, functional connectivity, cross-frequency coupling, and dynamic complexity. Extensive experiments demonstrate that DeeperBrain achieves state-of-the-art or highly competitive performance under end-to-end fine-tuning. Crucially, it maintains superior efficacy under a rigorous frozen-probing protocol, verifying that embedding neuroscientific first principles endows learned representations with the intrinsic universality essential for universal BCI. The code will be publicly available.

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.

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.

Recurrent connectivity in the visual cortex is believed to aid object recognition for challenging conditions such as occlusion. Here we investigate if and how artificial neural networks also benefit from recurrence. We compare architectures composed of bottom-up, lateral and top-down connections and evaluate their performance using two novel stereoscopic occluded object datasets. We find that classification accuracy is significantly higher for recurrent models when compared to feedforward models of matched parametric complexity. Additionally we show that for challenging stimuli, the recurrent feedback is able to correctly revise the initial feedforward guess.

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.

Deciphering brain function through non-invasive recordings requires synthesizing complementary high-frequency electromagnetic (EEG/MEG) and low-frequency metabolic (fMRI) signals. However, despite their shared neural origins, extreme discrepancies have traditionally confined these modalities to isolated analysis pipelines, hindering a holistic interpretation of brain activity. To bridge this fragmentation, we introduce NOBEL, a neuro-omni-modal brain-encoding large language model (LLM) that unifies these heterogeneous signals within the LLM's semantic embedding space. Our architecture integrates a unified encoder for EEG and MEG with a novel dual-path strategy for fMRI, aligning non-invasive brain signals and external sensory stimuli into a shared token space, then leverages an LLM as a universal backbone. Extensive evaluations demonstrate that NOBEL serves as a robust generalist across standard single-modal tasks. We also show that the synergistic fusion of electromagnetic and metabolic signals yields higher decoding accuracy than unimodal baselines, validating the complementary nature of multiple neural modalities. Furthermore, NOBEL exhibits strong capabilities in stimulus-aware decoding, effectively interpreting visual semantics from multi-subject fMRI data on the NSD and HAD datasets while uniquely leveraging direct stimulus inputs to verify causal links between sensory signals and neural responses. NOBEL thus takes a step towards unifying non-invasive brain decoding, demonstrating the promising potential of omni-modal brain understanding.

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.

Emergence of deep neural networks (DNNs) has raised enormous attention towards artificial neural networks (ANNs) once again. They have become the state-of-the-art models and have won different machine learning challenges. Although these networks are inspired by the brain, they lack biological plausibility, and they have structural differences compared to the brain. Spiking neural networks (SNNs) have been around for a long time, and they have been investigated to understand the dynamics of the brain. However, their application in real-world and complicated machine learning tasks were limited. Recently, they have shown great potential in solving such tasks. Due to their energy efficiency and temporal dynamics there are many promises in their future development. In this work, we reviewed the structures and performances of SNNs on image classification tasks. The comparisons illustrate that these networks show great capabilities for more complicated problems. Furthermore, the simple learning rules developed for SNNs, such as STDP and R-STDP, can be a potential alternative to replace the backpropagation algorithm used in DNNs.

Current AI systems achieve impressive performance on many tasks, yet they lack core attributes of biological intelligence, including rapid, continual learning, representations grounded in sensorimotor interactions, and structured knowledge that enables efficient generalization. Neuroscience theory suggests that mammals evolved flexible intelligence through the replication of a semi-independent, sensorimotor module, a functional unit known as a cortical column. To address the disparity between biological and artificial intelligence, thousand-brains systems were proposed as a means of mirroring the architecture of cortical columns and their interactions. In the current work, we evaluate the unique properties of Monty, the first implementation of a thousand-brains system. We focus on 3D object perception, and in particular, the combined task of object recognition and pose estimation. Utilizing the YCB dataset of household objects, we first assess Monty's use of sensorimotor learning to build structured representations, finding that these enable robust generalization. These representations include an emphasis on classifying objects by their global shape, as well as a natural ability to detect object symmetries. We then explore Monty's use of model-free and model-based policies to enable rapid inference by supporting principled movements. We find that such policies complement Monty's modular architecture, a design that can accommodate communication between modules to further accelerate inference speed via a novel `voting' algorithm. Finally, we examine Monty's use of associative, Hebbian-like binding to enable rapid, continual, and computationally efficient learning, properties that compare favorably to current deep learning architectures. While Monty is still in a nascent stage of development, these findings support thousand-brains systems as a powerful and promising new approach to AI.

Electroencephalography (EEG) signals provide critical insights for applications in disease diagnosis and healthcare. However, the scarcity of labeled EEG data poses a significant challenge. Foundation models offer a promising solution by leveraging large-scale unlabeled data through pre-training, enabling strong performance across diverse tasks. While both temporal dynamics and inter-channel relationships are vital for understanding EEG signals, existing EEG foundation models primarily focus on the former, overlooking the latter. To address this limitation, we propose Graph-Enhanced EEG Foundation Model (GEFM), a novel foundation model for EEG that integrates both temporal and inter-channel information. Our architecture combines Graph Neural Networks (GNNs), which effectively capture relational structures, with a masked autoencoder to enable efficient pre-training. We evaluated our approach using three downstream tasks and experimented with various GNN architectures. The results demonstrate that our proposed model, particularly when employing the GCN architecture with optimized configurations, consistently outperformed baseline methods across all tasks. These findings suggest that our model serves as a robust foundation model for EEG analysis.

Training a unified multilingual model promotes knowledge transfer but inevitably introduces negative interference. Language-specific modeling methods show promise in reducing interference. However, they often rely on heuristics to distribute capacity and struggle to foster cross-lingual transfer via isolated modules. In this paper, we explore intrinsic task modularity within multilingual networks and leverage these observations to circumvent interference under multilingual translation. We show that neurons in the feed-forward layers tend to be activated in a language-specific manner. Meanwhile, these specialized neurons exhibit structural overlaps that reflect language proximity, which progress across layers. Based on these findings, we propose Neuron Specialization, an approach that identifies specialized neurons to modularize feed-forward layers and then continuously updates them through sparse networks. Extensive experiments show that our approach achieves consistent performance gains over strong baselines with additional analyses demonstrating reduced interference and increased knowledge transfer.

It has long been known in both neuroscience and AI that ``binding'' between neurons leads to a form of competitive learning where representations are compressed in order to represent more abstract concepts in deeper layers of the network. More recently, it was also hypothesized that dynamic (spatiotemporal) representations play an important role in both neuroscience and AI. Building on these ideas, we introduce Artificial Kuramoto Oscillatory Neurons (AKOrN) as a dynamical alternative to threshold units, which can be combined with arbitrary connectivity designs such as fully connected, convolutional, or attentive mechanisms. Our generalized Kuramoto updates bind neurons together through their synchronization dynamics. We show that this idea provides performance improvements across a wide spectrum of tasks such as unsupervised object discovery, adversarial robustness, calibrated uncertainty quantification, and reasoning. We believe that these empirical results show the importance of rethinking our assumptions at the most basic neuronal level of neural representation, and in particular show the importance of dynamical representations.

A basic question within the emerging field of mechanistic interpretability is the degree to which neural networks learn the same underlying mechanisms. In other words, are neural mechanisms universal across different models? In this work, we study the universality of individual neurons across GPT2 models trained from different initial random seeds, motivated by the hypothesis that universal neurons are likely to be interpretable. In particular, we compute pairwise correlations of neuron activations over 100 million tokens for every neuron pair across five different seeds and find that 1-5\% of neurons are universal, that is, pairs of neurons which consistently activate on the same inputs. We then study these universal neurons in detail, finding that they usually have clear interpretations and taxonomize them into a small number of neuron families. We conclude by studying patterns in neuron weights to establish several universal functional roles of neurons in simple circuits: deactivating attention heads, changing the entropy of the next token distribution, and predicting the next token to (not) be within a particular set.

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.

Spiking Neural Networks (SNNs) provide a promising framework for energy-efficient and biologically grounded computation; however, scalable learning in deep recurrent architectures with sparse connectivity remains a major challenge. In this work, we propose a structured multi-layer recurrent SNN architecture composed of locally dense recurrent layers augmented with sparse small-world long-range projections to a readout population. The long-range connectivity is largely fixed, preserving routing efficiency and hardware scalability, while synaptic adaptation is performed using strictly local plasticity mechanisms. To enable supervised learning without backpropagation or surrogate gradients, we introduce a biologically motivated learning framework that combines: (i) population-based winner-take-all (WTA) teaching signals at the output layer, (ii) fixed random broadcast alignment feedback pathways, and (iii) low-dimensional modulatory neuron populations that gate synaptic updates through three-factor learning rules with eligibility traces. This design supports deep recurrent computation with sparse global communication and purely local synaptic updates. We analyze the algorithmic properties, computational complexity, and hardware feasibility of the proposed approach, and demonstrate stable learning and competitive performance on benchmark classification tasks. The results highlight the potential of structured recurrence and neuromodulatory learning to enable scalable, hardware-compatible SNN training beyond gradient-based methods.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

We present (Experience-Modulated Biologically-inspired Emergent Reasoning), a hybrid cognitive architecture that reorganises the relationship between large language models (LLMs) and memory: rather than augmenting an LLM with retrieval tools, we place the LLM as a replaceable reasoning engine within a persistent, biologically-grounded associative substrate. The architecture centres on a 220,000-neuron spiking neural network (SNN) with spike-timing-dependent plasticity (STDP), four-layer hierarchical organisation (sensory/concept/category/meta-pattern), inhibitory E/I balance, and reward-modulated learning. Text embeddings are encoded into the SNN via a novel z-score standardised top-k population code that is dimension-independent by construction, achieving 82.2\% discrimination retention across embedding dimensionalities. We show that STDP lateral propagation during idle operation can trigger and shape LLM actions without external prompting or scripted triggers: the SNN determines when to act and what associations to surface, while the LLM selects the action type and generates content. In one instance, the system autonomously initiated contact with a user after learned person-topic associations fired laterally during an 8-hour idle period. From a clean start with zero learned weights, the first SNN-triggered action occurred after only 7 conversational exchanges (14 messages).

Meaningful and simplified representations of neural activity can yield insights into how and what information is being processed within a neural circuit. However, without labels, finding representations that reveal the link between the brain and behavior can be challenging. Here, we introduce a novel unsupervised approach for learning disentangled representations of neural activity called Swap-VAE. Our approach combines a generative modeling framework with an instance-specific alignment loss that tries to maximize the representational similarity between transformed views of the input (brain state). These transformed (or augmented) views are created by dropping out neurons and jittering samples in time, which intuitively should lead the network to a representation that maintains both temporal consistency and invariance to the specific neurons used to represent the neural state. Through evaluations on both synthetic data and neural recordings from hundreds of neurons in different primate brains, we show that it is possible to build representations that disentangle neural datasets along relevant latent dimensions linked to behavior.

Visual decoding from brain signals is a key challenge at the intersection of computer vision and neuroscience, requiring methods that bridge neural representations and computational models of vision. A field-wide goal is to achieve generalizable, cross-subject models. A major obstacle towards this goal is the substantial variability in neural representations across individuals, which has so far required training bespoke models or fine-tuning separately for each subject. To address this challenge, we introduce a meta-optimized approach for semantic visual decoding from fMRI that generalizes to novel subjects without any fine-tuning. By simply conditioning on a small set of image-brain activation examples from the new individual, our model rapidly infers their unique neural encoding patterns to facilitate robust and efficient visual decoding. Our approach is explicitly optimized for in-context learning of the new subject's encoding model and performs decoding by hierarchical inference, inverting the encoder. First, for multiple brain regions, we estimate the per-voxel visual response encoder parameters by constructing a context over multiple stimuli and responses. Second, we construct a context consisting of encoder parameters and response values over multiple voxels to perform aggregated functional inversion. We demonstrate strong cross-subject and cross-scanner generalization across diverse visual backbones without retraining or fine-tuning. Moreover, our approach requires neither anatomical alignment nor stimulus overlap. This work is a critical step towards a generalizable foundation model for non-invasive brain decoding.

Recent findings in neuroscience suggest that the human brain represents information in a geometric structure (for instance, through conceptual spaces). In order to communicate, we flatten the complex representation of entities and their attributes into a single word or a sentence. In this paper we use graph convolutional networks to support the evolution of language and cooperation in multi-agent systems. Motivated by an image-based referential game, we propose a graph referential game with varying degrees of complexity, and we provide strong baseline models that exhibit desirable properties in terms of language emergence and cooperation. We show that the emerged communication protocol is robust, that the agents uncover the true factors of variation in the game, and that they learn to generalize beyond the samples encountered during training.

Neurons in the brain are organized such that nearby cells tend to share similar functions. AI models lack this organization, and past efforts to introduce topography have often led to trade-offs between topography and task performance. In this work, we present TopoLoss, a new loss function that promotes spatially organized topographic representations in AI models without significantly sacrificing task performance. TopoLoss is highly adaptable and can be seamlessly integrated into the training of leading model architectures. We validate our method on both vision (ResNet-18, ResNet-50, ViT) and language models (GPT-Neo-125M, NanoGPT), collectively TopoNets. TopoNets are the highest-performing supervised topographic models to date, exhibiting brain-like properties such as localized feature processing, lower dimensionality, and increased efficiency. TopoNets also predict responses in the brain and replicate the key topographic signatures observed in the brain's visual and language cortices. Together, this work establishes a robust and generalizable framework for integrating topography into leading model architectures, advancing the development of high-performing models that more closely emulate the computational strategies of the human brain.

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.

Originally inspired by neurobiology, deep neural network models have become a powerful tool of machine learning and artificial intelligence, where they are used to approximate functions and dynamics by learning from examples. Here we give a brief introduction to neural network models and deep learning for biologists. We introduce feedforward and recurrent networks and explain the expressive power of this modeling framework and the backpropagation algorithm for setting the parameters. Finally, we consider how deep neural networks might help us understand the brain's computations.

This position and survey paper identifies the emerging convergence of neuroscience, artificial general intelligence (AGI), and neuromorphic computing toward a unified research paradigm. Using a framework grounded in brain physiology, we highlight how synaptic plasticity, sparse spike-based communication, and multimodal association provide design principles for next-generation AGI systems that potentially combine both human and machine intelligences. The review traces this evolution from early connectionist models to state-of-the-art large language models, demonstrating how key innovations like transformer attention, foundation-model pre-training, and multi-agent architectures mirror neurobiological processes like cortical mechanisms, working memory, and episodic consolidation. We then discuss emerging physical substrates capable of breaking the von Neumann bottleneck to achieve brain-scale efficiency in silicon: memristive crossbars, in-memory compute arrays, and emerging quantum and photonic devices. There are four critical challenges at this intersection: 1) integrating spiking dynamics with foundation models, 2) maintaining lifelong plasticity without catastrophic forgetting, 3) unifying language with sensorimotor learning in embodied agents, and 4) enforcing ethical safeguards in advanced neuromorphic autonomous systems. This combined perspective across neuroscience, computation, and hardware offers an integrative agenda for in each of these fields.

Does the relationship between learning rules and brain alignment generalize across species? We extend our prior finding that untrained CNNs match backpropagation at human V1 by testing the same five learning rules against macaque electrophysiology. The rules are backpropagation (BP), feedback alignment (FA), predictive coding (PC), spike-timing-dependent plasticity (STDP), and an untrained random-weights baseline. The macaque data come from two datasets: MajajHong2015 (V4/IT, 3,200 stimulus presentations, 88/168 neurons) and FreemanZiemba2013 (V1/V2, 135 stimuli, 102/103 neurons). Using RSA with identical model weights from our human study, we find: (1) all models achieve higher alignment with macaque early visual cortex (rho = 0.15-0.30 at V1/V2) than with human fMRI (rho = 0.01-0.08), consistent with the higher signal-to-noise ratio of electrophysiology; (2) STDP and PC produce the highest macaque V1/V2 alignment (rho ~ 0.30 and 0.28), consistent with their leading position among trained rules in human V1; (3) at IT, learning rule rankings show no detectable correlation across species (Kendall's tau = 0.00, p = 1.00), though this null result is expected given that n = 5 provides power only at tau = +/-1.0, and is further confounded by stimulus set differences; (4) a pretrained ResNet-50 (ImageNet) achieves rho = 0.25 at macaque IT, substantially above all custom CNN conditions (rho = 0.07-0.14), suggesting IT alignment is limited by model capacity and training data rather than by the learning rule. Noise ceilings, multi-seed variability (5 seeds), and a stimulus-control analysis are reported. These results demonstrate that early visual alignment is robust across species, while higher-area alignment is modulated by model capacity and stimulus domain.

A hallmark of intelligence is the ability to autonomously learn new flexible, cognitive behaviors - that is, behaviors where the appropriate action depends not just on immediate stimuli (as in simple reflexive stimulus-response associations), but on contextual information that must be adequately acquired, stored and processed. While many meta-learning algorithms can design agents that autonomously learn new tasks, cognitive tasks adds another level of learning and memory to typical ``learning-to-learn'' problems. Here we evolve neural networks, endowed with plastic connections and neuromodulation, over a sizable set of simple cognitive tasks adapted from a computational neuroscience framework. The resulting evolved networks can automatically modify their own connectivity to acquire a novel simple cognitive task, never seen during evolution, from stimuli and rewards alone, through the spontaneous operation of their evolved neural organization and plasticity system. Our results emphasize the importance of carefully considering the multiple learning loops involved in the emergence of intelligent behavior.

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.

Image-to-fMRI encoding is important for both neuroscience research and practical applications. However, such "Brain-Encoders" have been typically trained per-subject and per fMRI-dataset, thus restricted to very limited training data. In this paper we propose a Universal Brain-Encoder, which can be trained jointly on data from many different subjects/datasets/machines. What makes this possible is our new voxel-centric Encoder architecture, which learns a unique "voxel-embedding" per brain-voxel. Our Encoder trains to predict the response of each brain-voxel on every image, by directly computing the cross-attention between the brain-voxel embedding and multi-level deep image features. This voxel-centric architecture allows the functional role of each brain-voxel to naturally emerge from the voxel-image cross-attention. We show the power of this approach to (i) combine data from multiple different subjects (a "Crowd of Brains") to improve each individual brain-encoding, (ii) quick & effective Transfer-Learning across subjects, datasets, and machines (e.g., 3-Tesla, 7-Tesla), with few training examples, and (iii) use the learned voxel-embeddings as a powerful tool to explore brain functionality (e.g., what is encoded where in the brain).

State-of-the-art methods for self-supervised learning (SSL) build representations by maximizing the similarity between different transformed "views" of a sample. Without sufficient diversity in the transformations used to create views, however, it can be difficult to overcome nuisance variables in the data and build rich representations. This motivates the use of the dataset itself to find similar, yet distinct, samples to serve as views for one another. In this paper, we introduce Mine Your Own vieW (MYOW), a new approach for self-supervised learning that looks within the dataset to define diverse targets for prediction. The idea behind our approach is to actively mine views, finding samples that are neighbors in the representation space of the network, and then predict, from one sample's latent representation, the representation of a nearby sample. After showing the promise of MYOW on benchmarks used in computer vision, we highlight the power of this idea in a novel application in neuroscience where SSL has yet to be applied. When tested on multi-unit neural recordings, we find that MYOW outperforms other self-supervised approaches in all examples (in some cases by more than 10%), and often surpasses the supervised baseline. With MYOW, we show that it is possible to harness the diversity of the data to build rich views and leverage self-supervision in new domains where augmentations are limited or unknown.

Some neurons in deep networks specialize in recognizing highly specific perceptual, structural, or semantic features of inputs. In computer vision, techniques exist for identifying neurons that respond to individual concept categories like colors, textures, and object classes. But these techniques are limited in scope, labeling only a small subset of neurons and behaviors in any network. Is a richer characterization of neuron-level computation possible? We introduce a procedure (called MILAN, for mutual-information-guided linguistic annotation of neurons) that automatically labels neurons with open-ended, compositional, natural language descriptions. Given a neuron, MILAN generates a description by searching for a natural language string that maximizes pointwise mutual information with the image regions in which the neuron is active. MILAN produces fine-grained descriptions that capture categorical, relational, and logical structure in learned features. These descriptions obtain high agreement with human-generated feature descriptions across a diverse set of model architectures and tasks, and can aid in understanding and controlling learned models. We highlight three applications of natural language neuron descriptions. First, we use MILAN for analysis, characterizing the distribution and importance of neurons selective for attribute, category, and relational information in vision models. Second, we use MILAN for auditing, surfacing neurons sensitive to human faces in datasets designed to obscure them. Finally, we use MILAN for editing, improving robustness in an image classifier by deleting neurons sensitive to text features spuriously correlated with class labels.

This work introduces a new computational theory of mind grounded in set theory and hyperdimensional computing. Whereas traditional neural networks rely on continuous weights and matrix multiplication, this framework works with sparse binary data. It represents information as discrete sets, directly modeling biological neural population codes. I demonstrate that associative memory emerges naturally from network topologies featuring a combinatorially expanded hidden layer. Learning is driven by topological plasticity rather than scalar weight adjustments. This architecture unifies auto-associative and hetero-associative learning under a single core algorithm: information retrieval via subset pattern matching and exact nearest-neighbor search. Operating with constant-time complexity, these mechanisms bridge perceptual data (sparse distributed representations) and symbols (sparse holographic representations) without continuous bottlenecks. Mapping this framework to neuroanatomy, I propose that both the cerebellum and the neocortex implement variants of this algorithm, making subset pattern matching the fundamental engine of cognition. Because it relies on discrete logic rather than matrix arithmetic, this algorithm translates directly into in-memory hardware. This opens a new route toward synthetic intelligence with human-level energy efficiency.

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.

Neuronal morphology encodes critical information about circuit function, development, and disease, yet current methods analyze topology or graph structure in isolation. We introduce GraPHFormer, a multimodal architecture that unifies these complementary views through CLIP-style contrastive learning. Our vision branch processes a novel three-channel persistence image encoding unweighted, persistence-weighted, and radius-weighted topological densities via DINOv2-ViT-S. In parallel, a TreeLSTM encoder captures geometric and radial attributes from skeleton graphs. Both project to a shared embedding space trained with symmetric InfoNCE loss, augmented by persistence-space transformations that preserve topological semantics. Evaluated on six benchmarks (BIL-6, ACT-4, JML-4, N7, M1-Cell, M1-REG) spanning self-supervised and supervised settings, GraPHFormer achieves state-of-the-art performance on five benchmarks, significantly outperforming topology-only, graph-only, and morphometrics baselines. We demonstrate practical utility by discriminating glial morphologies across cortical regions and species, and detecting signatures of developmental and degenerative processes. Code: https://github.com/Uzshah/GraPHFormer

Surface analysis of the cortex is ubiquitous in human neuroimaging with MRI, e.g., for cortical registration, parcellation, or thickness estimation. The convoluted cortical geometry requires isotropic scans (e.g., 1mm MPRAGEs) and good gray-white matter contrast for 3D reconstruction. This precludes the analysis of most brain MRI scans acquired for clinical purposes. Analyzing such scans would enable neuroimaging studies with sample sizes that cannot be achieved with current research datasets, particularly for underrepresented populations and rare diseases. Here we present the first method for cortical reconstruction, registration, parcellation, and thickness estimation for clinical brain MRI scans of any resolution and pulse sequence. The methods has a learning component and a classical optimization module. The former uses domain randomization to train a CNN that predicts an implicit representation of the white matter and pial surfaces (a signed distance function) at 1mm isotropic resolution, independently of the pulse sequence and resolution of the input. The latter uses geometry processing to place the surfaces while accurately satisfying topological and geometric constraints, thus enabling subsequent parcellation and thickness estimation with existing methods. We present results on 5mm axial FLAIR scans from ADNI and on a highly heterogeneous clinical dataset with 5,000 scans. Code and data are publicly available at https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all-clinical

Backpropagation algorithm has driven the remarkable success of deep neural networks, but its lack of biological plausibility and high computational costs have motivated the ongoing search for alternative training methods. Hebbian learning has attracted considerable interest as a biologically plausible alternative to backpropagation. Nevertheless, its exclusive reliance on local information, without consideration of global task objectives, fundamentally limits its scalability. Inspired by the biological synergy between neuromodulators and local plasticity, we introduce a novel model-agnostic Global-guided Hebbian Learning (GHL) framework, which seamlessly integrates local and global information to scale up across diverse networks and tasks. In specific, the local component employs Oja's rule with competitive learning to ensure stable and effective local updates. Meanwhile, the global component introduces a sign-based signal that guides the direction of local Hebbian plasticity updates. Extensive experiments demonstrate that our method consistently outperforms existing Hebbian approaches. Notably, on large-scale network and complex datasets like ImageNet, our framework achieves the competitive results and significantly narrows the gap with standard backpropagation.

Cortical surface registration plays a crucial role in aligning cortical functional and anatomical features across individuals. However, conventional registration algorithms are computationally inefficient. Recently, learning-based registration algorithms have emerged as a promising solution, significantly improving processing efficiency. Nonetheless, there remains a gap in the development of a learning-based method that exceeds the state-of-the-art conventional methods simultaneously in computational efficiency, registration accuracy, and distortion control, despite the theoretically greater representational capabilities of deep learning approaches. To address the challenge, we present SUGAR, a unified unsupervised deep-learning framework for both rigid and non-rigid registration. SUGAR incorporates a U-Net-based spherical graph attention network and leverages the Euler angle representation for deformation. In addition to the similarity loss, we introduce fold and multiple distortion losses, to preserve topology and minimize various types of distortions. Furthermore, we propose a data augmentation strategy specifically tailored for spherical surface registration, enhancing the registration performance. Through extensive evaluation involving over 10,000 scans from 7 diverse datasets, we showed that our framework exhibits comparable or superior registration performance in accuracy, distortion, and test-retest reliability compared to conventional and learning-based methods. Additionally, SUGAR achieves remarkable sub-second processing times, offering a notable speed-up of approximately 12,000 times in registering 9,000 subjects from the UK Biobank dataset in just 32 minutes. This combination of high registration performance and accelerated processing time may greatly benefit large-scale neuroimaging studies.