Daily Papers

Large language models deployed in the wild must adapt to evolving data, user behavior, and task mixtures without erasing previously acquired capabilities. In practice, this remains difficult: sequential updates induce catastrophic forgetting, while many stabilization methods rely on external procedures that are costly, brittle, or difficult to scale. We present TRC^{2} (Thalamically Routed Cortical Columns), a decoder-only architecture that makes continual adaptation a property of the backbone itself. TRC^{2} combines stacked cortical columns with a thalamic modulatory pathway for selective inter-column communication and a hippocampal pathway for event-selective retrieval, delayed surprise-based writing, and replay-driven consolidation. This design localizes fast plasticity while preserving a slower stable computation pathway. We further introduce a causal memory-update scheme and an online replay controller that adjusts consolidation strength from measured forgetting. Across a task-sequential language-modeling stream over C4, WikiText-103, and GSM8K, TRC^{2} consistently improves task-boundary modeling quality and substantially reduces cumulative forgetting relative to Transformer, Mamba, MoE, and DeepSeek baselines trained under the same pipeline. Ablations show that the thalamic and hippocampal components are central to the retention gains, while the full model remains competitive in throughput and training cost.

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.

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.

Within the complex neuroarchitecture of the brain, astrocytes play crucial roles in development, structure, and metabolism. These cells regulate neural activity through tripartite synapses, directly impacting cognitive processes such as learning and memory. Despite the growing recognition of astrocytes' significance, traditional Spiking Neural Network (SNN) models remain predominantly neuron-centric, overlooking the profound influence of astrocytes on neural dynamics. Inspired by these biological insights, we have developed an Astrocyte-Modulated Spiking Unit (AM-SU), an innovative framework that integrates neuron-astrocyte interactions into the computational paradigm, demonstrating wide applicability across various hardware platforms. Our Astrocyte-Modulated Spiking Neural Network (AstroSNN) exhibits exceptional performance in tasks involving memory retention and natural language generation, particularly in handling long-term dependencies and complex linguistic structures. The design of AstroSNN not only enhances its biological authenticity but also introduces novel computational dynamics, enabling more effective processing of complex temporal dependencies. Furthermore, AstroSNN shows low latency, high throughput, and reduced memory usage in practical applications, making it highly suitable for resource-constrained environments. By successfully integrating astrocytic dynamics into intelligent neural networks, our work narrows the gap between biological plausibility and neural modeling, laying the groundwork for future biologically-inspired neural computing research that includes both neurons and astrocytes.

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.

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).

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.

Understanding spatial location and relationships is a fundamental capability for modern artificial intelligence systems. Insights from human spatial cognition provide valuable guidance in this domain. Neuroscientific discoveries have highlighted the role of grid cells as a fundamental neural component for spatial representation, including distance computation, path integration, and scale discernment. In this paper, we introduce a novel positional encoding scheme inspired by Fourier analysis and the latest findings in computational neuroscience regarding grid cells. Assuming that grid cells encode spatial position through a summation of Fourier basis functions, we demonstrate the translational invariance of the grid representation during inner product calculations. Additionally, we derive an optimal grid scale ratio for multi-dimensional Euclidean spaces based on principles of biological efficiency. Utilizing these computational principles, we have developed a Grid-cell inspired Positional Encoding technique, termed GridPE, for encoding locations within high-dimensional spaces. We integrated GridPE into the Pyramid Vision Transformer architecture. Our theoretical analysis shows that GridPE provides a unifying framework for positional encoding in arbitrary high-dimensional spaces. Experimental results demonstrate that GridPE significantly enhances the performance of transformers, underscoring the importance of incorporating neuroscientific insights into the design of artificial intelligence systems.

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.

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.

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

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

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

The brain has computational capabilities that surpass those of modern systems, being able to solve complex problems efficiently in a simple way. Neuromorphic engineering aims to mimic biology in order to develop new systems capable of incorporating such capabilities. Bio-inspired learning systems continue to be a challenge that must be solved, and much work needs to be done in this regard. Among all brain regions, the hippocampus stands out as an autoassociative short-term memory with the capacity to learn and recall memories from any fragment of them. These characteristics make the hippocampus an ideal candidate for developing bio-inspired learning systems that, in addition, resemble content-addressable memories. Therefore, in this work we propose a bio-inspired spiking content-addressable memory model based on the CA3 region of the hippocampus with the ability to learn, forget and recall memories, both orthogonal and non-orthogonal, from any fragment of them. The model was implemented on the SpiNNaker hardware platform using Spiking Neural Networks. A set of experiments based on functional, stress and applicability tests were performed to demonstrate its correct functioning. This work presents the first hardware implementation of a fully-functional bio-inspired spiking hippocampal content-addressable memory model, paving the way for the development of future more complex neuromorphic systems.

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.

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.

We present a novel type of neural fields that uses general radial bases for signal representation. State-of-the-art neural fields typically rely on grid-based representations for storing local neural features and N-dimensional linear kernels for interpolating features at continuous query points. The spatial positions of their neural features are fixed on grid nodes and cannot well adapt to target signals. Our method instead builds upon general radial bases with flexible kernel position and shape, which have higher spatial adaptivity and can more closely fit target signals. To further improve the channel-wise capacity of radial basis functions, we propose to compose them with multi-frequency sinusoid functions. This technique extends a radial basis to multiple Fourier radial bases of different frequency bands without requiring extra parameters, facilitating the representation of details. Moreover, by marrying adaptive radial bases with grid-based ones, our hybrid combination inherits both adaptivity and interpolation smoothness. We carefully designed weighting schemes to let radial bases adapt to different types of signals effectively. Our experiments on 2D image and 3D signed distance field representation demonstrate the higher accuracy and compactness of our method than prior arts. When applied to neural radiance field reconstruction, our method achieves state-of-the-art rendering quality, with small model size and comparable training speed.

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.

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 propose a new neural network design paradigm Reversible Column Network (RevCol). The main body of RevCol is composed of multiple copies of subnetworks, named columns respectively, between which multi-level reversible connections are employed. Such architectural scheme attributes RevCol very different behavior from conventional networks: during forward propagation, features in RevCol are learned to be gradually disentangled when passing through each column, whose total information is maintained rather than compressed or discarded as other network does. Our experiments suggest that CNN-style RevCol models can achieve very competitive performances on multiple computer vision tasks such as image classification, object detection and semantic segmentation, especially with large parameter budget and large dataset. For example, after ImageNet-22K pre-training, RevCol-XL obtains 88.2% ImageNet-1K accuracy. Given more pre-training data, our largest model RevCol-H reaches 90.0% on ImageNet-1K, 63.8% APbox on COCO detection minival set, 61.0% mIoU on ADE20k segmentation. To our knowledge, it is the best COCO detection and ADE20k segmentation result among pure (static) CNN models. Moreover, as a general macro architecture fashion, RevCol can also be introduced into transformers or other neural networks, which is demonstrated to improve the performances in both computer vision and NLP tasks. We release code and models at https://github.com/megvii-research/RevCol

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.

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.

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

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

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 .

As the prevalence of Alzheimer's disease (AD) rises, improving mechanistic insight from non-invasive biomarkers is increasingly critical. Recent work suggests that circuit-level brain alterations manifest as changes in electroencephalography (EEG) spectral features detectable by machine learning. However, conventional deep learning approaches for EEG-based AD detection are computationally intensive and mechanistically opaque. Spiking neural networks (SNNs) offer a biologically plausible and energy-efficient alternative, yet their application to AD diagnosis remains largely unexplored. We propose a neuro-bridge framework that links data-driven learning with minimal, biophysically grounded simulations, enabling bidirectional interpretation between machine learning signatures and circuit-level mechanisms in AD. Using resting-state clinical EEG, we train an SNN classifier that achieves competitive performance (AUC = 0.839) and identifies the aperiodic 1/f slope as a key discriminative marker. The 1/f slope reflects excitation-inhibition balance. To interpret this mechanistically, we construct spiking network simulations in which inhibitory-to-excitatory synaptic ratios are systematically varied to emulate healthy, mild cognitive impairment, and AD-like states. Using both membrane potential-based and synaptic current-based EEG proxies, we reproduce empirical spectral slowing and altered alpha organization. Incorporating empirical functional connectivity priors into multi-subnetwork simulations further enhances spectral differentiation, demonstrating that large-scale network topology constrains EEG signatures more strongly than excitation-inhibition balance alone. Overall, this neuro-bridge approach connects SNN-based classification with interpretable circuit simulations, advancing mechanistic understanding of EEG biomarkers while enabling scalable, explainable AD detection.

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.

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

Understanding how the brain represents visual information is a fundamental challenge in neuroscience and artificial intelligence. While AI-driven decoding of neural data has provided insights into the human visual system, integrating multimodal neuroimaging signals, such as EEG, MEG, and fMRI, remains a critical hurdle due to their inherent spatiotemporal misalignment. Current approaches often analyze these modalities in isolation, limiting a holistic view of neural representation. In this study, we introduce BrainFLORA, a unified framework for integrating cross-modal neuroimaging data to construct a shared neural representation. Our approach leverages multimodal large language models (MLLMs) augmented with modality-specific adapters and task decoders, achieving state-of-the-art performance in joint-subject visual retrieval task and has the potential to extend multitasking. Combining neuroimaging analysis methods, we further reveal how visual concept representations align across neural modalities and with real world object perception. We demonstrate that the brain's structured visual concept representations exhibit an implicit mapping to physical-world stimuli, bridging neuroscience and machine learning from different modalities of neural imaging. Beyond methodological advancements, BrainFLORA offers novel implications for cognitive neuroscience and brain-computer interfaces (BCIs). Our code is available at https://github.com/ncclab-sustech/BrainFLORA.

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 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.

Does structure in representations imply structure in computation? We study how Llama-3.1-8B reasons over cyclic concepts (e.g., "what month is six months after August?"). Even though Llama-3.1-8B's representations for these concepts are circularly structured, we find that instead of directly computing modular addition in the period of the cyclic concept (e.g., 12 for months), the model re-uses a generic addition mechanism across tasks that operates independently of concept-specific geometry. First, it computes the sum of its two inputs using base-10 addition (six + August=14). Then, it maps this sum back to cyclic concept space (14->February). We show that Llama-3.1-8B uses task-agnostic Fourier features to compute these sums--in fact, these features have periods that respect standard base-10 addition, e.g., 2, 5, and 10, rather than the cyclic concept period (e.g., 12 for months). Furthermore, we identify a sparse set of 28 MLP neurons re-used across all tasks (approximately 0.2% of the MLP at layer 18) that can be partitioned into disjoint clusters, each computing the sum for a Fourier feature with a different period. Our work highlights how an interplay between causal abstraction and feature geometry can deepen our mechanistic understanding of LMs.

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.

Why do neurons communicate through spikes? By definition, spikes are all-or-none neural events which occur at continuous times. In other words, spikes are on one side binary, existing or not without further details, and on the other can occur at any asynchronous time, without the need for a centralized clock. This stands in stark contrast to the analog representation of values and the discretized timing classically used in digital processing and at the base of modern-day neural networks. As neural systems almost systematically use this so-called event-based representation in the living world, a better understanding of this phenomenon remains a fundamental challenge in neurobiology in order to better interpret the profusion of recorded data. With the growing need for intelligent embedded systems, it also emerges as a new computing paradigm to enable the efficient operation of a new class of sensors and event-based computers, called neuromorphic, which could enable significant gains in computation time and energy consumption -- a major societal issue in the era of the digital economy and global warming. In this review paper, we provide evidence from biology, theory and engineering that the precise timing of spikes plays a crucial role in our understanding of the efficiency of neural networks.

A key requirement for the development of effective learning representations is their evaluation and comparison to representations we know to be effective. In natural sensory domains, the community has viewed the brain as a source of inspiration and as an implicit benchmark for success. However, it has not been possible to directly test representational learning algorithms directly against the representations contained in neural systems. Here, we propose a new benchmark for visual representations on which we have directly tested the neural representation in multiple visual cortical areas in macaque (utilizing data from [Majaj et al., 2012]), and on which any computer vision algorithm that produces a feature space can be tested. The benchmark measures the effectiveness of the neural or machine representation by computing the classification loss on the ordered eigendecomposition of a kernel matrix [Montavon et al., 2011]. In our analysis we find that the neural representation in visual area IT is superior to visual area V4. In our analysis of representational learning algorithms, we find that three-layer models approach the representational performance of V4 and the algorithm in [Le et al., 2012] surpasses the performance of V4. Impressively, we find that a recent supervised algorithm [Krizhevsky et al., 2012] achieves performance comparable to that of IT for an intermediate level of image variation difficulty, and surpasses IT at a higher difficulty level. We believe this result represents a major milestone: it is the first learning algorithm we have found that exceeds our current estimate of IT representation performance. We hope that this benchmark will assist the community in matching the representational performance of visual cortex and will serve as an initial rallying point for further correspondence between representations derived in brains and machines.

The brain is the perfect place to look for inspiration to develop more efficient neural networks. The inner workings of our synapses and neurons provide a glimpse at what the future of deep learning might look like. This paper serves as a tutorial and perspective showing how to apply the lessons learnt from several decades of research in deep learning, gradient descent, backpropagation and neuroscience to biologically plausible spiking neural neural networks. We also explore the delicate interplay between encoding data as spikes and the learning process; the challenges and solutions of applying gradient-based learning to spiking neural networks (SNNs); the subtle link between temporal backpropagation and spike timing dependent plasticity, and how deep learning might move towards biologically plausible online learning. Some ideas are well accepted and commonly used amongst the neuromorphic engineering community, while others are presented or justified for the first time here. The fields of deep learning and spiking neural networks evolve very rapidly. We endeavour to treat this document as a 'dynamic' manuscript that will continue to be updated as the common practices in training SNNs also change. A series of companion interactive tutorials complementary to this paper using our Python package, snnTorch, are also made available. See https://snntorch.readthedocs.io/en/latest/tutorials/index.html .

Brain MRI underpins a wide range of neuroscientific and clinical applications, yet most learning-based methods remain task-specific and require substantial labeled data. Here we show that a single self-supervised representation can generalize across heterogeneous brain MRI endpoints. We trained BrainDINO, a self-distilled foundation model, on approximately 6.6 million unlabeled axial slices from 20 datasets encompassing broad variation in population, disease, and acquisition setting. Using a frozen encoder with lightweight task heads, BrainDINO supported transfer across tumor segmentation, neurodegenerative and neurodevelopmental conditions classification, brain age estimation, post-stroke temporal prediction, molecular status prediction, MRI sequence classification, and survival modeling. Across tasks and supervision regimes, BrainDINO consistently equaled or exceeded natural-image and MRI-specific self-supervised baselines, with particularly strong advantages under label scarcity. Representation analyses further showed anatomically organized and pathology-sensitive feature structure in the absence of task-specific supervision. Our findings indicate that large-scale slice-wise self-supervised learning can yield a unified brain MRI representation that supports diverse neuroimaging tasks without volumetric pretraining or full-network fine-tuning, establishing a scalable foundation for robust and data-efficient brain imaging analysis.

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.

Humans abstract experiences into structured representations to facilitate pattern inference and knowledge transfer. While the hippocampal-entorhinal (HPC-MEC) circuit is known to represent both spatial and conceptual spaces, the mechanisms for concurrently extracting abstract structures from continuous, high-dimensional dynamics remain poorly understood. We propose a brain-inspired hierarchical model that simultaneously infers latent transitions and constructs a predictive visual world model. Our architecture employs an inverse model for structural extraction alongside an HPC-MEC coupling model that dissociates relational structures (MEC) from integrated episodic scenes (HPC). Using primitive transformation dynamics as a benchmark, we demonstrate the model's capacity for structural abstraction. By leveraging velocity-driven path integration, the framework enables robust prediction and structural reuse across diverse contexts, thereby achieving structural generalization. This work provides a novel computational framework for understanding how brain-inspired, self-supervised learning of world models facilitates the acquisition of reusable abstract knowledge.

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.

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

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.

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

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.

Neural fields are increasingly used as a light-weight, continuous, and differentiable signal representation in (bio)medical imaging. However, unlike discrete signal representations such as voxel grids, neural fields cannot be easily extended. As neural fields are, in essence, neural networks, prior signals represented in a neural field will degrade when the model is presented with new data due to catastrophic forgetting. This work examines the extent to which different neural field approaches suffer from catastrophic forgetting and proposes a strategy to mitigate this issue. We consider the scenario in which data becomes available incrementally, with only the most recent data available for neural field fitting. In a series of experiments on cardiac cine MRI data, we demonstrate how knowledge distillation mitigates catastrophic forgetting when the spatiotemporal domain is enlarged or the dimensionality of the represented signal is increased. We find that the amount of catastrophic forgetting depends, to a large extent, on the neural fields model used, and that distillation could enable continual learning in neural fields.

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.

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.

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.

Artificial neural networks (ANN) were inspired by the architecture and functions of the human brain and have revolutionised the field of artificial intelligence (AI). Inspired by studies on the latent geometry of the brain we posit that an increase in the research and application of hyperbolic geometry in machine learning will lead to increased accuracy, improved feature space representations and more efficient models across a range of tasks. We look at the structure and functions of the human brain, highlighting the alignment between the brain's hierarchical nature and hyperbolic geometry. By examining the brain's complex network of neuron connections and its cognitive processes, we illustrate how hyperbolic geometry plays a pivotal role in human intelligence. Empirical evidence indicates that hyperbolic neural networks outperform Euclidean models for tasks including natural language processing, computer vision and complex network analysis, requiring fewer parameters and exhibiting better generalisation. Despite its nascent adoption, hyperbolic geometry holds promise for improving machine learning models and advancing the field toward AGI.

High-resolution brain imaging can now capture not just synapse locations but their molecular composition, with the cost of such mapping falling exponentially. Yet such ultrastructural data has so far told us little about local neuronal physiology - specifically, the parameters (e.g., synaptic efficacies, local conductances) that govern neural dynamics. We propose to translate molecularly annotated ultrastructure into physiology, introducing the concept of an ultrastructure-to-dynamics compiler: a learned mapping from molecularly annotated ultrastructure to simulator-ready, uncertainty-aware physiological parameters. The requirement is paired training data, with jointly acquired ultrastructure from imaging, and dynamical responses to perturbations from physiological experiments. With this data we can train models that predict local physiology directly from structure. Such a compiler would support biophysical simulations by turning anatomical maps into models of circuit dynamics, shifting structure-to-function from a descriptive program to a predictive one and opening routes to understanding neural computation and forecasting intervention effects.

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.

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.

We present a Cortical Neural Pool (CNP) architecture featuring a high-speed, resource-efficient CORDIC-based Hodgkin Huxley (RCHH) neuron model. Unlike shared CORDIC-based DNN approaches, the proposed neuron leverages modular and performance-optimised CORDIC stages with a latency-area trade-off. The FPGA implementation of the RCHH neuron shows 24.5% LUT reduction and 35.2% improved speed, compared to SoTA designs, with 70% better normalised root mean square error (NRMSE). Furthermore, the CNP exhibits 2.85x higher throughput (12.69 GOPS) compared to a functionally equivalent CORDIC-based DNN engine, with only a 0.35% accuracy drop compared to the DNN counterpart on the MNIST dataset. The overall results indicate that the design shows biologically accurate, low-resource spiking neural network implementations for resource-constrained edge AI applications.

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.

Neuromorphic computing with spiking neural networks is promising for energy-efficient artificial intelligence (AI) applications. However, different from humans who continually learn different tasks in a lifetime, neural network models suffer from catastrophic forgetting. How could neuronal operations solve this problem is an important question for AI and neuroscience. Many previous studies draw inspiration from observed neuroscience phenomena and propose episodic replay or synaptic metaplasticity, but they are not guaranteed to explicitly preserve knowledge for neuron populations. Other works focus on machine learning methods with more mathematical grounding, e.g., orthogonal projection on high dimensional spaces, but there is no neural correspondence for neuromorphic computing. In this work, we develop a new method with neuronal operations based on lateral connections and Hebbian learning, which can protect knowledge by projecting activity traces of neurons into an orthogonal subspace so that synaptic weight update will not interfere with old tasks. We show that Hebbian and anti-Hebbian learning on recurrent lateral connections can effectively extract the principal subspace of neural activities and enable orthogonal projection. This provides new insights into how neural circuits and Hebbian learning can help continual learning, and also how the concept of orthogonal projection can be realized in neuronal systems. Our method is also flexible to utilize arbitrary training methods based on presynaptic activities/traces. Experiments show that our method consistently solves forgetting for spiking neural networks with nearly zero forgetting under various supervised training methods with different error propagation approaches, and outperforms previous approaches under various settings. Our method can pave a solid path for building continual neuromorphic computing systems.

The vastness of the design space created by the combination of a large number of computational mechanisms, including machine learning, is an obstacle to creating an artificial general intelligence (AGI). Brain-inspired AGI development, in other words, cutting down the design space to look more like a biological brain, which is an existing model of a general intelligence, is a promising plan for solving this problem. However, it is difficult for an individual to design a software program that corresponds to the entire brain because the neuroscientific data required to understand the architecture of the brain are extensive and complicated. The whole-brain architecture approach divides the brain-inspired AGI development process into the task of designing the brain reference architecture (BRA) -- the flow of information and the diagram of corresponding components -- and the task of developing each component using the BRA. This is called BRA-driven development. Another difficulty lies in the extraction of the operating principles necessary for reproducing the cognitive-behavioral function of the brain from neuroscience data. Therefore, this study proposes the Structure-constrained Interface Decomposition (SCID) method, which is a hypothesis-building method for creating a hypothetical component diagram consistent with neuroscientific findings. The application of this approach has begun for building various regions of the brain. Moving forward, we will examine methods of evaluating the biological plausibility of brain-inspired software. This evaluation will also be used to prioritize different computational mechanisms, which should be merged, associated with the same regions of the brain.

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

Conventional Computed Tomography (CT) methods require large numbers of noise-free projections for accurate density reconstructions, limiting their applicability to the more complex class of Cone Beam Geometry CT (CBCT) reconstruction. Recently, deep learning methods have been proposed to overcome these limitations, with methods based on neural fields (NF) showing strong performance, by approximating the reconstructed density through a continuous-in-space coordinate based neural network. Our focus is on improving such methods, however, unlike previous work, which requires training an NF from scratch for each new set of projections, we instead propose to leverage anatomical consistencies over different scans by training a single conditional NF on a dataset of projections. We propose a novel conditioning method where local modulations are modeled per patient as a field over the input domain through a Neural Modulation Field (NMF). The resulting Conditional Cone Beam Neural Tomography (CondCBNT) shows improved performance for both high and low numbers of available projections on noise-free and noisy data.

Spiking Transformers have recently emerged as promising architectures for combining the efficiency of spiking neural networks with the representational power of self-attention. However, the lack of standardized implementations, evaluation pipelines, and consistent design choices has hindered fair comparison and principled analysis. In this paper, we introduce STEP, a unified benchmark framework for Spiking Transformers that supports a wide range of tasks, including classification, segmentation, and detection across static, event-based, and sequential datasets. STEP provides modular support for diverse components such as spiking neurons, input encodings, surrogate gradients, and multiple backends (e.g., SpikingJelly, BrainCog). Using STEP, we reproduce and evaluate several representative models, and conduct systematic ablation studies on attention design, neuron types, encoding schemes, and temporal modeling capabilities. We also propose a unified analytical model for energy estimation, accounting for spike sparsity, bitwidth, and memory access, and show that quantized ANNs may offer comparable or better energy efficiency. Our results suggest that current Spiking Transformers rely heavily on convolutional frontends and lack strong temporal modeling, underscoring the need for spike-native architectural innovations. The full code is available at: https://github.com/Fancyssc/STEP

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.

Large language models (LLMs) like GPTs, trained on vast datasets, have demonstrated impressive capabilities in language understanding, reasoning, and planning, achieving human-level performance in various tasks. Most studies focus on enhancing these models by training on ever-larger datasets to build more powerful foundation models. While training stronger models is important, enabling models to evolve during inference is equally crucial, a process we refer to as AI self-evolution. Unlike large-scale training, self-evolution may rely on limited data or interactions. Inspired by the columnar organization of the human cerebral cortex, we hypothesize that AI models could develop cognitive abilities and build internal representations through iterative interactions with their environment. To achieve this, models need long-term memory (LTM) to store and manage processed interaction data. LTM supports self-evolution by representing diverse experiences across environments and agents. In this report, we explore AI self-evolution and its potential to enhance models during inference. We examine LTM's role in lifelong learning, allowing models to evolve based on accumulated interactions. We outline the structure of LTM and the systems needed for effective data retention and representation. We also classify approaches for building personalized models with LTM data and show how these models achieve self-evolution through interaction. Using LTM, our multi-agent framework OMNE achieved first place on the GAIA benchmark, demonstrating LTM's potential for AI self-evolution. Finally, we present a roadmap for future research, emphasizing the importance of LTM for advancing AI technology and its practical applications.

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.

Recent progress in task-optimized neural networks has established encoding models as a powerful tool for predicting brain responses to naturalistic stimuli, yet most existing approaches rely on unimodal representations. The emergence of omni-modal foundation models and rich multimodal neural datasets enables encoding models that jointly integrate visual, auditory, and linguistic information across subjects. We introduce MIRAGE, a brain encoding framework for predicting whole-brain fMRI responses to naturalistic audiovisual stimuli. MIRAGE achieves state-of-the-art performance via a native multimodal backbone and adaptive feature gating across layers. These representations are then combined with a transformer-based brain encoder and a subject-specific linear head over the cortical parcels. Controlled comparisons show that natively multimodal features consistently outperform post-hoc aggregation of independent unimodal features, across architectural levels and backbones. Beyond predictive accuracy, the learned attention weights are directly inspectable to interpret the modality-specific gating profile over the backbone, and each modality traces a distinct anatomical pattern across cortex. Together, these results propose adaptive layer-wise aggregation of natively multimodal features as a generalizable, interpretable, and accurate approach for whole-brain encoding.

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.

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.

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

Although native speech and music envelope following responses (EFRs) play a crucial role in auditory processing and cognition, their frequency profile, such as the dominating frequency and spectral coherence, is largely unknown. We have assumed that the auditory pathway - which transmits envelope components of speech and music to the scalp through time-varying neurophysiological processes - is a linear time-varying system, with the envelope and the multi-channel EEG responses as excitation and response, respectively. This paper investigates the transfer function of this system through two analytical techniques - time-averaged spectral responses and cross-spectral density - in the frequency domain at four different positions of the human scalp. Our findings suggest that alpha (8-11 Hz), lower gamma (53-56 Hz), and higher gamma (78-81 Hz) bands are the peak responses of the system. These frequently appearing dominant frequency responses may be the key components of familiar speech perception, maintaining attention, binding acoustic features, and memory processing. The cross-spectral density, which reflects the spatial neural coherence of the human brain, shows that 10-13 Hz, 27-29 Hz, and 62-64 Hz are common for all channel pairs. As neural coherences are frequently observed in these frequencies among native participants, we suggest that these distributed neural processes are also dominant in native speech and music perception.

We propose a novel algorithm called Backpropagation Neural Tree (BNeuralT), which is a stochastic computational dendritic tree. BNeuralT takes random repeated inputs through its leaves and imposes dendritic nonlinearities through its internal connections like a biological dendritic tree would do. Considering the dendritic-tree like plausible biological properties, BNeuralT is a single neuron neural tree model with its internal sub-trees resembling dendritic nonlinearities. BNeuralT algorithm produces an ad hoc neural tree which is trained using a stochastic gradient descent optimizer like gradient descent (GD), momentum GD, Nesterov accelerated GD, Adagrad, RMSprop, or Adam. BNeuralT training has two phases, each computed in a depth-first search manner: the forward pass computes neural tree's output in a post-order traversal, while the error backpropagation during the backward pass is performed recursively in a pre-order traversal. A BNeuralT model can be considered a minimal subset of a neural network (NN), meaning it is a "thinned" NN whose complexity is lower than an ordinary NN. Our algorithm produces high-performing and parsimonious models balancing the complexity with descriptive ability on a wide variety of machine learning problems: classification, regression, and pattern recognition.

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

Existing deep-learning approaches to semantic column type annotation (CTA) have important shortcomings: they rely on semantic types which are fixed at training time; require a large number of training samples per type and incur large run-time inference costs; and their performance can degrade when evaluated on novel datasets, even when types remain constant. Large language models have exhibited strong zero-shot classification performance on a wide range of tasks and in this paper we explore their use for CTA. We introduce ArcheType, a simple, practical method for context sampling, prompt serialization, model querying, and label remapping, which enables large language models to solve CTA problems in a fully zero-shot manner. We ablate each component of our method separately, and establish that improvements to context sampling and label remapping provide the most consistent gains. ArcheType establishes a new state-of-the-art performance on zero-shot CTA benchmarks (including three new domain-specific benchmarks which we release along with this paper), and when used in conjunction with classical CTA techniques, it outperforms a SOTA DoDuo model on the fine-tuned SOTAB benchmark. Our code is available at https://github.com/penfever/ArcheType.

Decoding language from brain activity is a long-awaited goal in both healthcare and neuroscience. Major milestones have recently been reached thanks to intracranial devices: subject-specific pipelines trained on invasive brain responses to basic language tasks now start to efficiently decode interpretable features (e.g. letters, words, spectrograms). However, scaling this approach to natural speech and non-invasive brain recordings remains a major challenge. Here, we propose a single end-to-end architecture trained with contrastive learning across a large cohort of individuals to predict self-supervised representations of natural speech. We evaluate our model on four public datasets, encompassing 169 volunteers recorded with magneto- or electro-encephalography (M/EEG), while they listened to natural speech. The results show that our model can identify, from 3s of MEG signals, the corresponding speech segment with up to 72.5% top-10 accuracy out of 1,594 distinct segments (and 44% top-1 accuracy), and up to 19.1% out of 2,604 segments for EEG recordings -- hence allowing the decoding of phrases absent from the training set. Model comparison and ablation analyses show that these performances directly benefit from our original design choices, namely the use of (i) a contrastive objective, (ii) pretrained representations of speech and (iii) a common convolutional architecture simultaneously trained across several participants. Together, these results delineate a promising path to decode natural language processing in real time from non-invasive recordings of brain activity.

Electroencephalography (EEG) is a non-invasive technique to measure and record brain electrical activity, widely used in various BCI and healthcare applications. Early EEG decoding methods rely on supervised learning, limited by specific tasks and datasets, hindering model performance and generalizability. With the success of large language models, there is a growing body of studies focusing on EEG foundation models. However, these studies still leave challenges: Firstly, most of existing EEG foundation models employ full EEG modeling strategy. It models the spatial and temporal dependencies between all EEG patches together, but ignores that the spatial and temporal dependencies are heterogeneous due to the unique structural characteristics of EEG signals. Secondly, existing EEG foundation models have limited generalizability on a wide range of downstream BCI tasks due to varying formats of EEG data, making it challenging to adapt to. To address these challenges, we propose a novel foundation model called CBraMod. Specifically, we devise a criss-cross transformer as the backbone to thoroughly leverage the structural characteristics of EEG signals, which can model spatial and temporal dependencies separately through two parallel attention mechanisms. And we utilize an asymmetric conditional positional encoding scheme which can encode positional information of EEG patches and be easily adapted to the EEG with diverse formats. CBraMod is pre-trained on a very large corpus of EEG through patch-based masked EEG reconstruction. We evaluate CBraMod on up to 10 downstream BCI tasks (12 public datasets). CBraMod achieves the state-of-the-art performance across the wide range of tasks, proving its strong capability and generalizability. The source code is publicly available at https://github.com/wjq-learning/CBraMod.

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.

Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are only selective for a small number of linear projections of a potentially high-dimensional input. Here we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g. naturalistic) stimulus distribution, we review several inference methods, focussing in particular on two information-theory-based approaches (maximization of stimulus energy or of noise entropy) and a likelihood-based approach (Bayesian spike-triggered covariance, extensions of generalized linear models). We analyze the formal connection between the likelihood-based and information-based approaches to show how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus.

The Strong Platonic Representation Hypothesis suggests that representational convergence in artificial neural networks can be harnessed constructively: embeddings can be translated across models through a universal latent space without paired data. We ask whether an analogous geometry can be recovered across human brains. Using fMRI data from the Natural Scenes Dataset, we propose a self-supervised encoder that learns subject-specific embeddings from brain data alone by exploiting repeated stimulus presentations. We show that these independently learned spaces can be translated across subjects using unsupervised orthogonal rotations, without paired cross-subject samples or intermediate model representations. Synchronizing pairwise rotations into a single shared latent space further improves cross-subject retrieval, indicating that subject-specific spaces are mutually compatible with a common coordinate system. These results provide evidence for a shared neural geometry in the human visual cortex: subject-specific fMRI representations are approximately isometric across individuals and can be translated through purely geometric transformations.

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/.

Vital to primary visual processing, retinal circuitry shows many similar structures across a very broad array of species, both vertebrate and non-vertebrate, especially functional components such as lateral inhibition. This surprisingly conservative pattern raises a question of how evolution leads to it, and whether there is any alternative that can also prompt helpful preprocessing. Here we design a method using genetic algorithm that, with many degrees of freedom, leads to architectures whose functions are similar to biological retina, as well as effective alternatives that are different in structures and functions. We compare this model to natural evolution and discuss how our framework can come into goal-driven search and sustainable enhancement of neural network models in machine learning.

This study examines the integration of Contrastive Predictive Coding (CPC) with Spiking Neural Networks (SNN). While CPC learns the predictive structure of data to generate meaningful representations, SNN mimics the computational processes of biological neural systems over time. In this study, the goal is to develop a predictive coding model with greater biological plausibility by processing inputs and outputs in a spike-based system. The proposed model was tested on the MNIST dataset and achieved a high classification rate in distinguishing positive sequential samples from non-sequential negative samples. The study demonstrates that CPC can be effectively combined with SNN, showing that an SNN trained for classification tasks can also function as an encoding mechanism. Project codes and detailed results can be accessed on our GitHub page: https://github.com/vnd-ogrenme/ongorusel-kodlama/tree/main/CPC_SNN

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

In living organisms, homeostasis is the natural regulation of internal states aimed at maintaining conditions compatible with life. Typical artificial systems are not equipped with comparable regulatory features. Here, we introduce an artificial neural network that incorporates homeostatic features. Its own computing substrate is placed in a needful and vulnerable relation to the very objects over which it computes. For example, artificial neurons performing classification of MNIST digits or Fashion-MNIST articles of clothing may receive excitatory or inhibitory effects, which alter their own learning rate as a direct result of perceiving and classifying the digits. In this scenario, accurate recognition is desirable to the agent itself because it guides decisions to regulate its vulnerable internal states and functionality. Counterintuitively, the addition of vulnerability to a learner does not necessarily impair its performance. On the contrary, self-regulation in response to vulnerability confers benefits under certain conditions. We show that homeostatic design confers increased adaptability under concept shift, in which the relationships between labels and data change over time, and that the greatest advantages are obtained under the highest rates of shift. This necessitates the rapid un-learning of past associations and the re-learning of new ones. We also demonstrate the superior abilities of homeostatic learners in environments with dynamically changing rates of concept shift. Our homeostatic design exposes the artificial neural network's thinking machinery to the consequences of its own "thoughts", illustrating the advantage of putting one's own "skin in the game" to improve fluid intelligence.

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.

Attractor dynamics are a fundamental computational motif in neural circuits, supporting diverse cognitive functions through stable, self-sustaining patterns of neural activity. In these lecture notes, we review four key examples that demonstrate how autoassociative neural network models can elucidate the computational mechanisms underlying attractor-based information processing in biological neural systems performing cognitive functions. Drawing on empirical evidence, we explore hippocampal spatial representations, visual classification in the inferotemporal cortex, perceptual adaptation and priming, and working-memory biases shaped by sensory history. Across these domains, attractor network models reveal common computational principles and provide analytical insights into how experience shapes neural activity and behavior. Our synthesis underscores the value of attractor models as powerful tools for probing the neural basis of cognition and behavior.

Regeneration of the nervous system after injury remains an important therapeutic objective, especially in the central nervous system (CNS), in which regeneration is restricted by both neuronal limitations as well as adverse extracellular environments. Conversely, the peripheral nervous system (PNS) displays enhanced regenerative capability in the presence of supportive Schwann cells (SC) and pro-growth stimuli. While the structure and molecular mechanisms are thoroughly understood, functional biomarkers that can non-invasively monitor regeneration in real time are limited. In this review, we discuss the promise of electroencephalography (EEG) as well as electromyography (EMG) as real-time, non-invasive biomarkers to monitor damage to nerves and regeneration in both CNS and PNS contexts. First, we contrast biological and electrophysiological indicators of CNS/PNS injury, showing how EEG signs, including oscillatory power, connectivity, and evoked potential changes, reflect dysfunction due to injury as well as neuroplastic reorganization. Also, EMG provides direct insight into muscle activation and peripheral output, providing useful EEG complementation in neuromuscular pathway integrity and reactivation. In CNS injuries (e.g., stroke, spinal cord injury (SCI)), EEG typically shows global slowing, disrupted interhemispheric coherence, and partial recovery of higher frequencies. For PNS injuries, EEG can capture cortical remapping and return of somatosensory evoked responses with re-establishment of the peripheries' connectivity. EMG, in turn, enables monitoring of reinnervation and restoration of functional motor output. This review presents a dual-system perspective, positioning EEG and EMG not only as diagnostic tools but also as functional biomarkers of neural regeneration, thereby bridging electrophysiology, plasticity, and clinical recovery.

Nowadays, neural networks act as a synonym for artificial intelligence. Present neural network models, although remarkably powerful, are inefficient both in terms of data and energy. Several alternative forms of neural networks have been proposed to address some of these problems. Specifically, spiking neural networks are suitable for efficient hardware implementations. However, effective learning algorithms for spiking networks remain elusive, although it is suspected that effective plasticity mechanisms could alleviate the problem of data efficiency. Here, we present a new framework for spiking neural networks - Spark - built upon the idea of modular design, from simple components to entire models. The aim of this framework is to provide an efficient and streamlined pipeline for spiking neural networks. We showcase this framework by solving the sparse-reward cartpole problem with simple plasticity mechanisms. We hope that a framework compatible with traditional ML pipelines may accelerate research in the area, specifically for continuous and unbatched learning, akin to the one animals exhibit.

The burgeoning field of brain health research increasingly leverages artificial intelligence (AI) to interpret and analyze neurological data. This study introduces a novel approach towards the creation of medical foundation models by integrating a large-scale multi-modal magnetic resonance imaging (MRI) dataset derived from 41,400 participants in its own. Our method involves a novel two-stage pretraining approach using vision transformers. The first stage is dedicated to encoding anatomical structures in generally healthy brains, identifying key features such as shapes and sizes of different brain regions. The second stage concentrates on spatial information, encompassing aspects like location and the relative positioning of brain structures. We rigorously evaluate our model, BrainFounder, using the Brain Tumor Segmentation (BraTS) challenge and Anatomical Tracings of Lesions After Stroke v2.0 (ATLAS v2.0) datasets. BrainFounder demonstrates a significant performance gain, surpassing the achievements of the previous winning solutions using fully supervised learning. Our findings underscore the impact of scaling up both the complexity of the model and the volume of unlabeled training data derived from generally healthy brains, which enhances the accuracy and predictive capabilities of the model in complex neuroimaging tasks with MRI. The implications of this research provide transformative insights and practical applications in healthcare and make substantial steps towards the creation of foundation models for Medical AI. Our pretrained models and training code can be found at https://github.com/lab-smile/GatorBrain.

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.

The liquid state machine (LSM) combines low training complexity and biological plausibility, which has made it an attractive machine learning framework for edge and neuromorphic computing paradigms. Originally proposed as a model of brain computation, the LSM tunes its internal weights without backpropagation of gradients, which results in lower performance compared to multi-layer neural networks. Recent findings in neuroscience suggest that astrocytes, a long-neglected non-neuronal brain cell, modulate synaptic plasticity and brain dynamics, tuning brain networks to the vicinity of the computationally optimal critical phase transition between order and chaos. Inspired by this disruptive understanding of how brain networks self-tune, we propose the neuron-astrocyte liquid state machine (NALSM) that addresses under-performance through self-organized near-critical dynamics. Similar to its biological counterpart, the astrocyte model integrates neuronal activity and provides global feedback to spike-timing-dependent plasticity (STDP), which self-organizes NALSM dynamics around a critical branching factor that is associated with the edge-of-chaos. We demonstrate that NALSM achieves state-of-the-art accuracy versus comparable LSM methods, without the need for data-specific hand-tuning. With a top accuracy of 97.61% on MNIST, 97.51% on N-MNIST, and 85.84% on Fashion-MNIST, NALSM achieved comparable performance to current fully-connected multi-layer spiking neural networks trained via backpropagation. Our findings suggest that the further development of brain-inspired machine learning methods has the potential to reach the performance of deep learning, with the added benefits of supporting robust and energy-efficient neuromorphic computing on the edge.

Electroencephalography (EEG) foundation models have recently emerged as a promising paradigm for brain-computer interfaces (BCIs), aiming to learn transferable neural representations from large-scale heterogeneous recordings. Despite rapid progresses, there lacks fair and comprehensive comparisons of existing EEG foundation models, due to inconsistent pre-training objectives, preprocessing choices, and downstream evaluation protocols. This paper fills this gap. We first review 50 representative models and organize their design choices into a unified taxonomic framework including data standardization, model architectures, and self-supervised pre-training strategies. We then evaluate 12 open-source foundation models and competitive specialist baselines across 13 EEG datasets spanning nine BCI paradigms. Emphasizing real-world deployments, we consider both cross-subject generalization under a leave-one-subject-out protocol and rapid calibration under a within-subject few-shot setting. We further compare full-parameter fine-tuning with linear probing to assess the transferability of pre-trained representations, and examine the relationship between model scale and downstream performance. Our results indicate that: 1) linear probing is frequently insufficient; 2) specialist models trained from scratch remain competitive across many tasks; and, 3) larger foundation models do not necessarily yield better generalization performance under current data regimes and training practices.

Every day, the human brain processes an immense volume of visual information, relying on intricate neural mechanisms to perceive and interpret these stimuli. Recent breakthroughs in functional magnetic resonance imaging (fMRI) have enabled scientists to extract visual information from human brain activity patterns. In this study, we present an innovative method for decoding brain activity into meaningful images and captions, with a specific focus on brain captioning due to its enhanced flexibility as compared to brain decoding into images. Our approach takes advantage of cutting-edge image captioning models and incorporates a unique image reconstruction pipeline that utilizes latent diffusion models and depth estimation. We utilized the Natural Scenes Dataset, a comprehensive fMRI dataset from eight subjects who viewed images from the COCO dataset. We employed the Generative Image-to-text Transformer (GIT) as our backbone for captioning and propose a new image reconstruction pipeline based on latent diffusion models. The method involves training regularized linear regression models between brain activity and extracted features. Additionally, we incorporated depth maps from the ControlNet model to further guide the reconstruction process. We evaluate our methods using quantitative metrics for both generated captions and images. Our brain captioning approach outperforms existing methods, while our image reconstruction pipeline generates plausible images with improved spatial relationships. In conclusion, we demonstrate significant progress in brain decoding, showcasing the enormous potential of integrating vision and language to better understand human cognition. Our approach provides a flexible platform for future research, with potential applications in various fields, including neural art, style transfer, and portable devices.

In the past five years, the use of generative and foundational AI systems has greatly improved the decoding of brain activity. Visual perception, in particular, can now be decoded from functional Magnetic Resonance Imaging (fMRI) with remarkable fidelity. This neuroimaging technique, however, suffers from a limited temporal resolution (approx0.5 Hz) and thus fundamentally constrains its real-time usage. Here, we propose an alternative approach based on magnetoencephalography (MEG), a neuroimaging device capable of measuring brain activity with high temporal resolution (approx5,000 Hz). For this, we develop an MEG decoding model trained with both contrastive and regression objectives and consisting of three modules: i) pretrained embeddings obtained from the image, ii) an MEG module trained end-to-end and iii) a pretrained image generator. Our results are threefold: Firstly, our MEG decoder shows a 7X improvement of image-retrieval over classic linear decoders. Second, late brain responses to images are best decoded with DINOv2, a recent foundational image model. Third, image retrievals and generations both suggest that high-level visual features can be decoded from MEG signals, although the same approach applied to 7T fMRI also recovers better low-level features. Overall, these results, while preliminary, provide an important step towards the decoding -- in real-time -- of the visual processes continuously unfolding within the human brain.

Neural fields, mapping low-dimensional input coordinates to corresponding signals, have shown promising results in representing various signals. Numerous methodologies have been proposed, and techniques employing MLPs and grid representations have achieved substantial success. MLPs allow compact and high expressibility, yet often suffer from spectral bias and slow convergence speed. On the other hand, methods using grids are free from spectral bias and achieve fast training speed, however, at the expense of high spatial complexity. In this work, we propose a novel way for exploiting both MLPs and grid representations in neural fields. Unlike the prevalent methods that combine them sequentially (extract features from the grids first and feed them to the MLP), we inject spectral bias-free grid representations into the intermediate features in the MLP. More specifically, we suggest a Coordinate-Aware Modulation (CAM), which modulates the intermediate features using scale and shift parameters extracted from the grid representations. This can maintain the strengths of MLPs while mitigating any remaining potential biases, facilitating the rapid learning of high-frequency components. In addition, we empirically found that the feature normalizations, which have not been successful in neural filed literature, proved to be effective when applied in conjunction with the proposed CAM. Experimental results demonstrate that CAM enhances the performance of neural representation and improves learning stability across a range of signals. Especially in the novel view synthesis task, we achieved state-of-the-art performance with the least number of parameters and fast training speed for dynamic scenes and the best performance under 1MB memory for static scenes. CAM also outperforms the best-performing video compression methods using neural fields by a large margin.

A growing literature in computational neuroscience leverages gradient descent and learning algorithms that approximate it to study synaptic plasticity in the brain. However, the vast majority of this work ignores a critical underlying assumption: the choice of distance for synaptic changes - i.e. the geometry of synaptic plasticity. Gradient descent assumes that the distance is Euclidean, but many other distances are possible, and there is no reason that biology necessarily uses Euclidean geometry. Here, using the theoretical tools provided by mirror descent, we show that the distribution of synaptic weights will depend on the geometry of synaptic plasticity. We use these results to show that experimentally-observed log-normal weight distributions found in several brain areas are not consistent with standard gradient descent (i.e. a Euclidean geometry), but rather with non-Euclidean distances. Finally, we show that it should be possible to experimentally test for different synaptic geometries by comparing synaptic weight distributions before and after learning. Overall, our work shows that the current paradigm in theoretical work on synaptic plasticity that assumes Euclidean synaptic geometry may be misguided and that it should be possible to experimentally determine the true geometry of synaptic plasticity in the brain.

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

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.

Classical models of memory in psychology and neuroscience rely on similarity-based retrieval of stored patterns, where similarity is a function of retrieval cues and the stored patterns. While parsimonious, these models do not allow distinct representations for storage and retrieval, despite their distinct computational demands. Key-value memory systems, in contrast, distinguish representations used for storage (values) and those used for retrieval (keys). This allows key-value memory systems to optimize simultaneously for fidelity in storage and discriminability in retrieval. We review the computational foundations of key-value memory, its role in modern machine learning systems, related ideas from psychology and neuroscience, applications to a number of empirical puzzles, and possible biological implementations.

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.

Brain Signals, such as Electroencephalography (EEG), and human languages have been widely explored independently for many downstream tasks, however, the connection between them has not been well explored. In this study, we explore the relationship and dependency between EEG and language. To study at the representation level, we introduced MTAM, a Multimodal Transformer Alignment Model, to observe coordinated representations between the two modalities. We used various relationship alignment-seeking techniques, such as Canonical Correlation Analysis and Wasserstein Distance, as loss functions to transfigure features. On downstream applications, sentiment analysis and relation detection, we achieved new state-of-the-art results on two datasets, ZuCo and K-EmoCon. Our method achieved an F1-score improvement of 1.7% on K-EmoCon and 9.3% on Zuco datasets for sentiment analysis, and 7.4% on ZuCo for relation detection. In addition, we provide interpretations of the performance improvement: (1) feature distribution shows the effectiveness of the alignment module for discovering and encoding the relationship between EEG and language; (2) alignment weights show the influence of different language semantics as well as EEG frequency features; (3) brain topographical maps provide an intuitive demonstration of the connectivity in the brain regions. Our code is available at https://github.com/Jason-Qiu/EEG_Language_Alignment.

Enabling effective brain-computer interfaces requires understanding how the human brain encodes stimuli across modalities such as visual, language (or text), etc. Brain encoding aims at constructing fMRI brain activity given a stimulus. There exists a plethora of neural encoding models which study brain encoding for single mode stimuli: visual (pretrained CNNs) or text (pretrained language models). Few recent papers have also obtained separate visual and text representation models and performed late-fusion using simple heuristics. However, previous work has failed to explore: (a) the effectiveness of image Transformer models for encoding visual stimuli, and (b) co-attentive multi-modal modeling for visual and text reasoning. In this paper, we systematically explore the efficacy of image Transformers (ViT, DEiT, and BEiT) and multi-modal Transformers (VisualBERT, LXMERT, and CLIP) for brain encoding. Extensive experiments on two popular datasets, BOLD5000 and Pereira, provide the following insights. (1) To the best of our knowledge, we are the first to investigate the effectiveness of image and multi-modal Transformers for brain encoding. (2) We find that VisualBERT, a multi-modal Transformer, significantly outperforms previously proposed single-mode CNNs, image Transformers as well as other previously proposed multi-modal models, thereby establishing new state-of-the-art. The supremacy of visio-linguistic models raises the question of whether the responses elicited in the visual regions are affected implicitly by linguistic processing even when passively viewing images. Future fMRI tasks can verify this computational insight in an appropriate experimental setting.

Artificial neural networks for motor control usually adopt generic architectures like fully connected MLPs. While general, these tabula rasa architectures rely on large amounts of experience to learn, are not easily transferable to new bodies, and have internal dynamics that are difficult to interpret. In nature, animals are born with highly structured connectivity in their nervous systems shaped by evolution; this innate circuitry acts synergistically with learning mechanisms to provide inductive biases that enable most animals to function well soon after birth and learn efficiently. Convolutional networks inspired by visual circuitry have encoded useful biases for vision. However, it is unknown the extent to which ANN architectures inspired by neural circuitry can yield useful biases for other AI domains. In this work, we ask what advantages biologically inspired ANN architecture can provide in the domain of motor control. Specifically, we translate C. elegans locomotion circuits into an ANN model controlling a simulated Swimmer agent. On a locomotion task, our architecture achieves good initial performance and asymptotic performance comparable with MLPs, while dramatically improving data efficiency and requiring orders of magnitude fewer parameters. Our architecture is interpretable and transfers to new body designs. An ablation analysis shows that constrained excitation/inhibition is crucial for learning, while weight initialization contributes to good initial performance. Our work demonstrates several advantages of biologically inspired ANN architecture and encourages future work in more complex embodied control.

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

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.

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.

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.

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.

There is an analogy that is often made between deep neural networks and actual brains, suggested by the nomenclature itself: the "neurons" in deep neural networks should correspond to neurons (or nerve cells, to avoid confusion) in the brain. We claim, however, that this analogy doesn't even type check: it is structurally flawed. In agreement with the slightly glib summary of Hebbian learning as "cells that fire together wire together", this article makes the case that the analogy should be different. Since the "neurons" in deep neural networks are managing the changing weights, they are more akin to the synapses in the brain; instead, it is the wires in deep neural networks that are more like nerve cells, in that they are what cause the information to flow. An intuition that nerve cells seem like more than mere wires is exactly right, and is justified by a precise category-theoretic analogy which we will explore in this article. Throughout, we will continue to highlight the error in equating artificial neurons with nerve cells by leaving "neuron" in quotes or by calling them artificial neurons. We will first explain how to view deep neural networks as nested dynamical systems with a very restricted sort of interaction pattern, and then explain a more general sort of interaction for dynamical systems that is useful throughout engineering, but which fails to adapt to changing circumstances. As mentioned, an analogy is then forced upon us by the mathematical formalism in which they are both embedded. We call the resulting encompassing generalization deeply interacting learning systems: they have complex interaction as in control theory, but adaptation to circumstances as in deep neural networks.