Daily Papers

How does the brain predict physical outcomes while acting in the world? Machine learning world models compress visual input into latent spaces, discarding the spatial structure that characterizes sensory cortex. We propose isomorphic world models: architectures preserving sensory topology so that physics prediction becomes geometric propagation rather than abstract state transition. We implement this using neural fields with motor-gated channels, where activity evolves through local lateral connectivity and motor commands multiplicatively modulate specific populations. Three experiments support this approach: (1) local connectivity is sufficient to learn ballistic physics, with predictions traversing intermediate locations rather than "teleporting"; (2) policies trained entirely in imagination transfer to real physics at nearly twice the rate of latent-space alternatives; and (3) motor-gated channels spontaneously develop body-selective encoding through visuomotor prediction alone. These findings suggest intuitive physics and body schema may share a common origin in spatially structured neural dynamics.

We present AROMA (Attentive Reduced Order Model with Attention), a framework designed to enhance the modeling of partial differential equations (PDEs) using local neural fields. Our flexible encoder-decoder architecture can obtain smooth latent representations of spatial physical fields from a variety of data types, including irregular-grid inputs and point clouds. This versatility eliminates the need for patching and allows efficient processing of diverse geometries. The sequential nature of our latent representation can be interpreted spatially and permits the use of a conditional transformer for modeling the temporal dynamics of PDEs. By employing a diffusion-based formulation, we achieve greater stability and enable longer rollouts compared to conventional MSE training. AROMA's superior performance in simulating 1D and 2D equations underscores the efficacy of our approach in capturing complex dynamical behaviors.

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

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

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.

Learning to remember over long timescales is fundamentally challenging for recurrent neural networks (RNNs). While much prior work has explored why RNNs struggle to learn long timescales and how to mitigate this, we still lack a clear understanding of the dynamics involved when RNNs learn long timescales via gradient descent. Here we build a mathematical theory of the learning dynamics of linear RNNs trained to integrate white noise. We show that when the initial recurrent weights are small, the dynamics of learning are described by a low-dimensional system that tracks a single outlier eigenvalue of the recurrent weights. This reveals the precise manner in which the long timescale associated with white noise integration is learned. We extend our analyses to RNNs learning a damped oscillatory filter, and find rich dynamical equations for the evolution of a conjugate pair of outlier eigenvalues. Taken together, our analyses build a rich mathematical framework for studying dynamical learning problems salient for both machine learning and neuroscience.

Seeking high-quality representations with latent variable models (LVMs) to reveal the intrinsic correlation between neural activity and behavior or sensory stimuli has attracted much interest. In the study of the biological visual system, naturalistic visual stimuli are inherently high-dimensional and time-dependent, leading to intricate dynamics within visual neural activity. However, most work on LVMs has not explicitly considered neural temporal relationships. To cope with such conditions, we propose Time-Evolving Visual Dynamical System (TE-ViDS), a sequential LVM that decomposes neural activity into low-dimensional latent representations that evolve over time. To better align the model with the characteristics of visual neural activity, we split latent representations into two parts and apply contrastive learning to shape them. Extensive experiments on synthetic datasets and real neural datasets from the mouse visual cortex demonstrate that TE-ViDS achieves the best decoding performance on naturalistic scenes/movies, extracts interpretable latent trajectories that uncover clear underlying neural dynamics, and provides new insights into differences in visual information processing between subjects and between cortical regions. In summary, TE-ViDS is markedly competent in extracting stimulus-relevant embeddings from visual neural activity and contributes to the understanding of visual processing mechanisms. Our codes are available at https://github.com/Grasshlw/Time-Evolving-Visual-Dynamical-System.

Humans and animals have a rich and flexible understanding of the physical world, which enables them to infer the underlying dynamical trajectories of objects and events, plausible future states, and use that to plan and anticipate the consequences of actions. However, the neural mechanisms underlying these computations are unclear. We combine a goal-driven modeling approach with dense neurophysiological data and high-throughput human behavioral readouts to directly impinge on this question. Specifically, we construct and evaluate several classes of sensory-cognitive networks to predict the future state of rich, ethologically-relevant environments, ranging from self-supervised end-to-end models with pixel-wise or object-centric objectives, to models that future predict in the latent space of purely static image-based or dynamic video-based pretrained foundation models. We find strong differentiation across these model classes in their ability to predict neural and behavioral data both within and across diverse environments. In particular, we find that neural responses are currently best predicted by models trained to predict the future state of their environment in the latent space of pretrained foundation models optimized for dynamic scenes in a self-supervised manner. Notably, models that future predict in the latent space of video foundation models that are optimized to support a diverse range of sensorimotor tasks, reasonably match both human behavioral error patterns and neural dynamics across all environmental scenarios that we were able to test. Overall, these findings suggest that the neural mechanisms and behaviors of primate mental simulation are thus far most consistent with being optimized to future predict on dynamic, reusable visual representations that are useful for embodied AI more generally.

The capabilities of large language models (LLMs) have sparked debate over whether such systems just learn an enormous collection of superficial statistics or a coherent model of the data generating process -- a world model. We find evidence for the latter by analyzing the learned representations of three spatial datasets (world, US, NYC places) and three temporal datasets (historical figures, artworks, news headlines) in the Llama-2 family of models. We discover that LLMs learn linear representations of space and time across multiple scales. These representations are robust to prompting variations and unified across different entity types (e.g. cities and landmarks). In addition, we identify individual ``space neurons'' and ``time neurons'' that reliably encode spatial and temporal coordinates. Our analysis demonstrates that modern LLMs acquire structured knowledge about fundamental dimensions such as space and time, supporting the view that they learn not merely superficial statistics, but literal world 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.

Neural networks transform high-dimensional data into compact, structured representations, often modeled as elements of a lower dimensional latent space. In this paper, we present an alternative interpretation of neural models as dynamical systems acting on the latent manifold. Specifically, we show that autoencoder models implicitly define a latent vector field on the manifold, derived by iteratively applying the encoding-decoding map, without any additional training. We observe that standard training procedures introduce inductive biases that lead to the emergence of attractor points within this vector field. Drawing on this insight, we propose to leverage the vector field as a representation for the network, providing a novel tool to analyze the properties of the model and the data. This representation enables to: (i) analyze the generalization and memorization regimes of neural models, even throughout training; (ii) extract prior knowledge encoded in the network's parameters from the attractors, without requiring any input data; (iii) identify out-of-distribution samples from their trajectories in the vector field. We further validate our approach on vision foundation models, showcasing the applicability and effectiveness of our method in real-world scenarios.

Intelligent systems across physics, language and perception often exhibit factorisable structure, yet are typically modelled by monolithic neural architectures that do not explicitly exploit this structure. The separable neural architecture (SNA) addresses this by formalising a representational class that unifies additive, quadratic and tensor-decomposed neural models. By constraining interaction order and tensor rank, SNAs impose a structural inductive bias that factorises high-dimensional mappings into low-arity components. Separability need not be a property of the system itself: it often emerges in the coordinates or representations through which the system is expressed. Crucially, this coordinate-aware formulation reveals a structural analogy between chaotic spatiotemporal dynamics and linguistic autoregression. By treating continuous physical states as smooth, separable embeddings, SNAs enable distributional modelling of chaotic systems. This approach mitigates the nonphysical drift characteristics of deterministic operators whilst remaining applicable to discrete sequences. The compositional versatility of this approach is demonstrated across four domains: autonomous waypoint navigation via reinforcement learning, inverse generation of multifunctional microstructures, distributional modelling of turbulent flow and neural language modelling. These results establish the separable neural architecture as a domain-agnostic primitive for predictive and generative intelligence, capable of unifying both deterministic and distributional representations.

Recurrent neural networks (RNNs) provide a powerful approach in neuroscience to infer latent dynamics in neural populations and to generate hypotheses about the neural computations underlying behavior. However, past work has focused on relatively simple, input-driven, and largely deterministic behaviors - little is known about the mechanisms that would allow RNNs to generate the richer, spontaneous, and potentially stochastic behaviors observed in natural settings. Modeling with Hidden Markov Models (HMMs) has revealed a segmentation of natural behaviors into discrete latent states with stochastic transitions between them, a type of dynamics that may appear at odds with the continuous state spaces implemented by RNNs. Here we first show that RNNs can replicate HMM emission statistics and then reverse-engineer the trained networks to uncover the mechanisms they implement. In the absence of inputs, the activity of trained RNNs collapses towards a single fixed point. When driven by stochastic input, trajectories instead exhibit noise-sustained dynamics along closed orbits. Rotation along these orbits modulates the emission probabilities and is governed by transitions between regions of slow, noise-driven dynamics connected by fast, deterministic transitions. The trained RNNs develop highly structured connectivity, with a small set of "kick neurons" initiating transitions between these regions. This mechanism emerges during training as the network shifts into a regime of stochastic resonance, enabling it to perform probabilistic computations. Analyses across multiple HMM architectures - fully connected, cyclic, and linear-chain - reveal that this solution generalizes through the modular reuse of the same dynamical motif, suggesting a compositional principle by which RNNs can emulate complex discrete latent dynamics.

Human language processing relies on the brain's capacity for predictive inference. We present a machine learning framework for decoding neural (EEG) responses to dynamic visual language stimuli in Deaf signers. Using coherence between neural signals and optical flow-derived motion features, we construct spatiotemporal representations of predictive neural dynamics. Through entropy-based feature selection, we identify frequency-specific neural signatures that differentiate interpretable linguistic input from linguistically disrupted (time-reversed) stimuli. Our results reveal distributed left-hemispheric and frontal low-frequency coherence as key features in language comprehension, with experience-dependent neural signatures correlating with age. This work demonstrates a novel multimodal approach for probing experience-driven generative models of perception in the brain.

The utility of a learned neural representation depends on how well its geometry supports performance in downstream tasks. This geometry depends on the structure of the inputs, the structure of the target outputs, and the architecture of the network. By studying the learning dynamics of networks with one hidden layer, we discovered that the network's activation function has an unexpectedly strong impact on the representational geometry: Tanh networks tend to learn representations that reflect the structure of the target outputs, while ReLU networks retain more information about the structure of the raw inputs. This difference is consistently observed across a broad class of parameterized tasks in which we modulated the degree of alignment between the geometry of the task inputs and that of the task labels. We analyzed the learning dynamics in weight space and show how the differences between the networks with Tanh and ReLU nonlinearities arise from the asymmetric asymptotic behavior of ReLU, which leads feature neurons to specialize for different regions of input space. By contrast, feature neurons in Tanh networks tend to inherit the task label structure. Consequently, when the target outputs are low dimensional, Tanh networks generate neural representations that are more disentangled than those obtained with a ReLU nonlinearity. Our findings shed light on the interplay between input-output geometry, nonlinearity, and learned representations in neural networks.

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.

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

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

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.

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

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.

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

We address hallucination detection in Large Language Models (LLMs) and Multimodal Large Language Models (MLLMs) by framing the problem through the lens of dynamical systems stability theory. Rather than treating hallucination as a straightforward classification task, we conceptualize (M)LLMs as dynamical systems, where factual knowledge is represented by stable equilibrium points within the representation space. Our main insight is that hallucinations tend to arise at the boundaries of knowledge-transition regions separating stable and unstable zones. To capture this phenomenon, we propose Lyapunov Probes: lightweight networks trained with derivative-based stability constraints that enforce a monotonic decay in confidence under input perturbations. By performing systematic perturbation analysis and applying a two-stage training process, these probes reliably distinguish between stable factual regions and unstable, hallucination-prone regions. Experiments on diverse datasets and models demonstrate consistent improvements over existing baselines.

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

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.

The predictive learning of spatiotemporal sequences aims to generate future images by learning from the historical context, where the visual dynamics are believed to have modular structures that can be learned with compositional subsystems. This paper models these structures by presenting PredRNN, a new recurrent network, in which a pair of memory cells are explicitly decoupled, operate in nearly independent transition manners, and finally form unified representations of the complex environment. Concretely, besides the original memory cell of LSTM, this network is featured by a zigzag memory flow that propagates in both bottom-up and top-down directions across all layers, enabling the learned visual dynamics at different levels of RNNs to communicate. It also leverages a memory decoupling loss to keep the memory cells from learning redundant features. We further propose a new curriculum learning strategy to force PredRNN to learn long-term dynamics from context frames, which can be generalized to most sequence-to-sequence models. We provide detailed ablation studies to verify the effectiveness of each component. Our approach is shown to obtain highly competitive results on five datasets for both action-free and action-conditioned predictive learning scenarios.

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.

As artificial intelligence models have exploded in scale and capability, understanding of their internal mechanisms remains a critical challenge. Inspired by the success of dynamical systems approaches in neuroscience, here we propose a novel framework for studying computations in deep learning systems. We focus on the residual stream (RS) in transformer models, conceptualizing it as a dynamical system evolving across layers. We find that activations of individual RS units exhibit strong continuity across layers, despite the RS being a non-privileged basis. Activations in the RS accelerate and grow denser over layers, while individual units trace unstable periodic orbits. In reduced-dimensional spaces, the RS follows a curved trajectory with attractor-like dynamics in the lower layers. These insights bridge dynamical systems theory and mechanistic interpretability, establishing a foundation for a "neuroscience of AI" that combines theoretical rigor with large-scale data analysis to advance our understanding of modern neural networks.

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.

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

Transformer models underpin many recent advances in practical machine learning applications, yet understanding their internal behavior continues to elude researchers. Given the size and complexity of these models, forming a comprehensive picture of their inner workings remains a significant challenge. To this end, we set out to understand small transformer models in a more tractable setting: that of solving mazes. In this work, we focus on the abstractions formed by these models and find evidence for the consistent emergence of structured internal representations of maze topology and valid paths. We demonstrate this by showing that the residual stream of only a single token can be linearly decoded to faithfully reconstruct the entire maze. We also find that the learned embeddings of individual tokens have spatial structure. Furthermore, we take steps towards deciphering the circuity of path-following by identifying attention heads (dubbed adjacency heads), which are implicated in finding valid subsequent tokens.

We propose a new class of parameterizations for spatio-temporal point processes which leverage Neural ODEs as a computational method and enable flexible, high-fidelity models of discrete events that are localized in continuous time and space. Central to our approach is a combination of continuous-time neural networks with two novel neural architectures, i.e., Jump and Attentive Continuous-time Normalizing Flows. This approach allows us to learn complex distributions for both the spatial and temporal domain and to condition non-trivially on the observed event history. We validate our models on data sets from a wide variety of contexts such as seismology, epidemiology, urban mobility, and neuroscience.

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.

The brain understands the external world through an internal model that generates predictions and refines them based on prediction errors. A complete prediction specifies what will happen, when it will happen, and with what probability, which we refer to as a "prediction object". Existing models typically capture only what and when, omit probabilities, and rely on biologically-implausible algorithms. Here we show that a single population of spiking neurons can jointly encode the prediction object through a biologically grounded learning mechanism. We implement a heterogeneous Izhikevich spiking reservoir with readouts trained by an error-modulated, attention-gated three-factor Hebbian rule and test it on a novel paradigm that controls both the timing and probability of upcoming stimuli. By integrating real-time learning of "when" with offline consolidation of "what", the model encodes the complete prediction object, firing at the correct times with magnitudes proportional to the probabilities. Critically, it rapidly adapts to changes in both stimulus timing and probability, an ability that global least-squares methods such as FORCE lack without explicit resets. During learning, the model self-organizes its readout weights into near-orthogonal subspaces for "what" and "when," showing that multiplexed encoding arises naturally from generic recurrent dynamics under local, error-gated modulation. These results challenge the view that "what" and "when" predictions require separate modules, suggesting instead that mixed selectivity within shared populations supports flexible predictive cognition. The model also predicts phase-specific neuromodulation and overlapping neural subspaces, offering a parsimonious alternative to hierarchical predictive-coding accounts.

As Vision Transformers (ViTs) become standard vision backbones, a mechanistic account of their computational phenomenology is essential. Despite architectural cues that hint at dynamical structure, there is no settled framework that interprets Transformer depth as a well-characterized flow. In this work, we introduce the Block-Recurrent Hypothesis (BRH), arguing that trained ViTs admit a block-recurrent depth structure such that the computation of the original L blocks can be accurately rewritten using only k ll L distinct blocks applied recurrently. Across diverse ViTs, between-layer representational similarity matrices suggest few contiguous phases. To determine whether these phases reflect genuinely reusable computation, we train block-recurrent surrogates of pretrained ViTs: Recurrent Approximations to Phase-structured TransfORmers (Raptor). In small-scale, we demonstrate that stochastic depth and training promote recurrent structure and subsequently correlate with our ability to accurately fit Raptor. We then provide an empirical existence proof for BRH by training a Raptor model to recover 96% of DINOv2 ImageNet-1k linear probe accuracy in only 2 blocks at equivalent computational cost. Finally, we leverage our hypothesis to develop a program of Dynamical Interpretability. We find i) directional convergence into class-dependent angular basins with self-correcting trajectories under small perturbations, ii) token-specific dynamics, where cls executes sharp late reorientations while patch tokens exhibit strong late-stage coherence toward their mean direction, and iii) a collapse to low rank updates in late depth, consistent with convergence to low-dimensional attractors. Altogether, we find a compact recurrent program emerges along ViT depth, pointing to a low-complexity normative solution that enables these models to be studied through principled dynamical systems analysis.

Neural populations exhibit latent dynamical structures that drive time-evolving spiking activities, motivating the search for models that capture both intrinsic network dynamics and external unobserved influences. In this work, we introduce LangevinFlow, a sequential Variational Auto-Encoder where the time evolution of latent variables is governed by the underdamped Langevin equation. Our approach incorporates physical priors -- such as inertia, damping, a learned potential function, and stochastic forces -- to represent both autonomous and non-autonomous processes in neural systems. Crucially, the potential function is parameterized as a network of locally coupled oscillators, biasing the model toward oscillatory and flow-like behaviors observed in biological neural populations. Our model features a recurrent encoder, a one-layer Transformer decoder, and Langevin dynamics in the latent space. Empirically, our method outperforms state-of-the-art baselines on synthetic neural populations generated by a Lorenz attractor, closely matching ground-truth firing rates. On the Neural Latents Benchmark (NLB), the model achieves superior held-out neuron likelihoods (bits per spike) and forward prediction accuracy across four challenging datasets. It also matches or surpasses alternative methods in decoding behavioral metrics such as hand velocity. Overall, this work introduces a flexible, physics-inspired, high-performing framework for modeling complex neural population dynamics and their unobserved influences.

Brain-to-image decoding has been recently propelled by the progress in generative AI models and the availability of large ultra-high field functional Magnetic Resonance Imaging (fMRI). However, current approaches depend on complicated multi-stage pipelines and preprocessing steps that typically collapse the temporal dimension of brain recordings, thereby limiting time-resolved brain decoders. Here, we introduce Dynadiff (Dynamic Neural Activity Diffusion for Image Reconstruction), a new single-stage diffusion model designed for reconstructing images from dynamically evolving fMRI recordings. Our approach offers three main contributions. First, Dynadiff simplifies training as compared to existing approaches. Second, our model outperforms state-of-the-art models on time-resolved fMRI signals, especially on high-level semantic image reconstruction metrics, while remaining competitive on preprocessed fMRI data that collapse time. Third, this approach allows a precise characterization of the evolution of image representations in brain activity. Overall, this work lays the foundation for time-resolved brain-to-image decoding.

Text-conditioned diffusion models have emerged as a promising tool for neural video generation. However, current models still struggle with intricate spatiotemporal prompts and often generate restricted or incorrect motion (e.g., even lacking the ability to be prompted for objects moving from left to right). To address these limitations, we introduce LLM-grounded Video Diffusion (LVD). Instead of directly generating videos from the text inputs, LVD first leverages a large language model (LLM) to generate dynamic scene layouts based on the text inputs and subsequently uses the generated layouts to guide a diffusion model for video generation. We show that LLMs are able to understand complex spatiotemporal dynamics from text alone and generate layouts that align closely with both the prompts and the object motion patterns typically observed in the real world. We then propose to guide video diffusion models with these layouts by adjusting the attention maps. Our approach is training-free and can be integrated into any video diffusion model that admits classifier guidance. Our results demonstrate that LVD significantly outperforms its base video diffusion model and several strong baseline methods in faithfully generating videos with the desired attributes and motion patterns.

Spatial cognition enables adaptive goal-directed behavior by constructing internal models of space. Robust biological systems consolidate spatial knowledge into three interconnected forms: landmarks for salient cues, route knowledge for movement trajectories, and survey knowledge for map-like representations. While recent advances in multi-modal large language models (MLLMs) have enabled visual-language reasoning in embodied agents, these efforts lack structured spatial memory and instead operate reactively, limiting their generalization and adaptability in complex real-world environments. Here we present Brain-inspired Spatial Cognition for Navigation (BSC-Nav), a unified framework for constructing and leveraging structured spatial memory in embodied agents. BSC-Nav builds allocentric cognitive maps from egocentric trajectories and contextual cues, and dynamically retrieves spatial knowledge aligned with semantic goals. Integrated with powerful MLLMs, BSC-Nav achieves state-of-the-art efficacy and efficiency across diverse navigation tasks, demonstrates strong zero-shot generalization, and supports versatile embodied behaviors in the real physical world, offering a scalable and biologically grounded path toward general-purpose spatial intelligence.

Task-trained recurrent neural networks (RNNs) are widely used in neuroscience and machine learning to model dynamical computations. To gain mechanistic insight into how neural systems solve tasks, prior work often reverse-engineers individual trained networks. However, different RNNs trained on the same task and achieving similar performance can exhibit strikingly different internal solutions, a phenomenon known as solution degeneracy. Here, we develop a unified framework to systematically quantify and control solution degeneracy across three levels: behavior, neural dynamics, and weight space. We apply this framework to 3,400 RNNs trained on four neuroscience-relevant tasks: flip-flop memory, sine wave generation, delayed discrimination, and path integration, while systematically varying task complexity, learning regime, network size, and regularization. We find that higher task complexity and stronger feature learning reduce degeneracy in neural dynamics but increase it in weight space, with mixed effects on behavior. In contrast, larger networks and structural regularization reduce degeneracy at all three levels. These findings empirically validate the Contravariance Principle and provide practical guidance for researchers seeking to tune the variability of RNN solutions, either to uncover shared neural mechanisms or to model the individual variability observed in biological systems. This work provides a principled framework for quantifying and controlling solution degeneracy in task-trained RNNs, offering new tools for building more interpretable and biologically grounded models of neural computation.

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.

Animals ranging from rats to humans can demonstrate cognitive map capabilities. We evolved weights in a biologically plausible recurrent neural network (RNN) using an evolutionary algorithm to replicate the behavior and neural activity observed in rats during a spatial and working memory task in a triple T-maze. The rat was simulated in the Webots robot simulator and used vision, distance and accelerometer sensors to navigate a virtual maze. After evolving weights from sensory inputs to the RNN, within the RNN, and from the RNN to the robot's motors, the Webots agent successfully navigated the space to reach all four reward arms with minimal repeats before time-out. Our current findings suggest that it is the RNN dynamics that are key to performance, and that performance is not dependent on any one sensory type, which suggests that neurons in the RNN are performing mixed selectivity and conjunctive coding. Moreover, the RNN activity resembles spatial information and trajectory-dependent coding observed in the hippocampus. Collectively, the evolved RNN exhibits navigation skills, spatial memory, and working memory. Our method demonstrates how the dynamic activity in evolved RNNs can capture interesting and complex cognitive behavior and may be used to create RNN controllers for robotic applications.

Humans experience the world through constantly changing visual stimuli, where scenes can shift and move, change in appearance, and vary in distance. The dynamic nature of visual perception is a fundamental aspect of our daily lives, yet the large majority of research on object and scene processing, particularly using fMRI, has focused on static stimuli. While studies of static image perception are attractive due to their computational simplicity, they impose a strong non-naturalistic constraint on our investigation of human vision. In contrast, dynamic visual stimuli offer a more ecologically-valid approach but present new challenges due to the interplay between spatial and temporal information, making it difficult to disentangle the representations of stable image features and motion. To overcome this limitation -- given dynamic inputs, we explicitly decouple the modeling of static image representations and motion representations in the human brain. Three results demonstrate the feasibility of this approach. First, we show that visual motion information as optical flow can be predicted (or decoded) from brain activity as measured by fMRI. Second, we show that this predicted motion can be used to realistically animate static images using a motion-conditioned video diffusion model (where the motion is driven by fMRI brain activity). Third, we show prediction in the reverse direction: existing video encoders can be fine-tuned to predict fMRI brain activity from video imagery, and can do so more effectively than image encoders. This foundational work offers a novel, extensible framework for interpreting how the human brain processes dynamic visual information.

Despite the ubiquity of large language models (LLMs) in AI research, the question of embodiment in LLMs remains underexplored, distinguishing them from embodied systems in robotics where sensory perception directly informs physical action. Our investigation navigates the intriguing terrain of whether LLMs, despite their non-embodied nature, effectively capture implicit human intuitions about fundamental, spatial building blocks of language. We employ insights from spatial cognitive foundations developed through early sensorimotor experiences, guiding our exploration through the reproduction of three psycholinguistic experiments. Surprisingly, correlations between model outputs and human responses emerge, revealing adaptability without a tangible connection to embodied experiences. Notable distinctions include polarized language model responses and reduced correlations in vision language models. This research contributes to a nuanced understanding of the interplay between language, spatial experiences, and the computations made by large language models. More at https://cisnlp.github.io/Spatial_Schemas/

Predicting the behavior of complex systems is critical in many scientific and engineering domains, and hinges on the model's ability to capture their underlying dynamics. Existing methods encode the intrinsic dynamics of high-dimensional observations through latent representations and predict autoregressively. However, these latent representations lose the inherent spatial structure of spatiotemporal dynamics, leading to the predictor's inability to effectively model spatial interactions and neglect emerging dynamics during long-term prediction. In this work, we propose SparseDiff, introducing a test-time adaptation strategy to dynamically update the encoding scheme to accommodate emergent spatiotemporal structures during the long-term evolution of the system. Specifically, we first design a codebook-based sparse encoder, which coarsens the continuous spatial domain into a sparse graph topology. Then, we employ a graph neural ordinary differential equation to model the dynamics and guide a diffusion decoder for reconstruction. SparseDiff autoregressively predicts the spatiotemporal evolution and adjust the sparse topological structure to adapt to emergent spatiotemporal patterns by adaptive re-encoding. Extensive evaluations on representative systems demonstrate that SparseDiff achieves an average prediction error reduction of 49.99\% compared to baselines, requiring only 1\% of the spatial resolution.

We introduce NerVE, a unified eigenspectral framework for understanding how feed-forward networks (FFNs) in large language models (LLMs) organize and regulate information flow in high-dimensional latent space. Despite FFNs dominating the parameter budget, their high-dimensional dynamics remain poorly understood. NerVE addresses this gap through lightweight, memory-efficient tracking of eigenspectrum dynamics via four complementary metrics: Spectral Entropy (dispersion), Participation Ratio (effective dimensionality), Eigenvalue Early Enrichment (top-heaviness), and Jensen-Shannon divergence (distributional shifts). Our key insight is that FFN nonlinearities reinject variance across eigenmodes, fundamentally governing latent dimension utilization, and that optimizer geometry strongly modulates the extent of this variance reinjection. We validate NerVE across model scales, and diverse architectural and optimizer configurations, each uniquely shaping FFN dynamics: normalization schemes controlling variance flow; FFN weight geometries constraining latent space; positional encoding and activation functions regulating information flow; and optimizer choices redistributing effective capacity across depth. Across these settings, NerVE consistently recovers stable spectral signatures that correlate with model's generalization ability and respond predictably to design choices, generalizing beyond transformer to MLP-Mixer architectures, providing actionable insights for architectural and optimizer choices beyond trial-and-error.

This paper studies the emergence of interpretable categorical features within large language models (LLMs), analyzing their behavior across training checkpoints (time), transformer layers (space), and varying model sizes (scale). Using sparse autoencoders for mechanistic interpretability, we identify when and where specific semantic concepts emerge within neural activations. Results indicate clear temporal and scale-specific thresholds for feature emergence across multiple domains. Notably, spatial analysis reveals unexpected semantic reactivation, with early-layer features re-emerging at later layers, challenging standard assumptions about representational dynamics in transformer models.

Softmax attention is the principle backbone of foundation models for various artificial intelligence applications, yet its quadratic complexity in sequence length can limit its inference throughput in long-context settings. To address this challenge, alternative architectures such as linear attention, State Space Models (SSMs), and Recurrent Neural Networks (RNNs) have been considered as more efficient alternatives. While connections between these approaches exist, such models are commonly developed in isolation and there is a lack of theoretical understanding of the shared principles underpinning these architectures and their subtle differences, greatly influencing performance and scalability. In this paper, we introduce the Dynamical Systems Framework (DSF), which allows a principled investigation of all these architectures in a common representation. Our framework facilitates rigorous comparisons, providing new insights on the distinctive characteristics of each model class. For instance, we compare linear attention and selective SSMs, detailing their differences and conditions under which both are equivalent. We also provide principled comparisons between softmax attention and other model classes, discussing the theoretical conditions under which softmax attention can be approximated. Additionally, we substantiate these new insights with empirical validations and mathematical arguments. This shows the DSF's potential to guide the systematic development of future more efficient and scalable foundation models.

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

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.

We introduce a novel approach for analyzing the training dynamics of ReLU networks by examining the characteristic activation boundaries of individual ReLU neurons. Our proposed analysis reveals a critical instability in common neural network parameterizations and normalizations during stochastic optimization, which impedes fast convergence and hurts generalization performance. Addressing this, we propose Geometric Parameterization (GmP), a novel neural network parameterization technique that effectively separates the radial and angular components of weights in the hyperspherical coordinate system. We show theoretically that GmP resolves the aforementioned instability issue. We report empirical results on various models and benchmarks to verify GmP's theoretical advantages of optimization stability, convergence speed and generalization performance.

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

Training recurrent neural networks (RNNs) is a high-dimensional process that requires updating numerous parameters. Therefore, it is often difficult to pinpoint the underlying learning mechanisms. To address this challenge, we propose to gain mechanistic insights into the phenomenon of abrupt learning by studying RNNs trained to perform diverse short-term memory tasks. In these tasks, RNN training begins with an initial search phase. Following a long period of plateau in accuracy, the values of the loss function suddenly drop, indicating abrupt learning. Analyzing the neural computation performed by these RNNs reveals geometric restructuring (GR) in their phase spaces prior to the drop. To promote these GR events, we introduce a temporal consistency regularization that accelerates (bioplausible) training, facilitates attractor formation, and enables efficient learning in strongly connected networks. Our findings offer testable predictions for neuroscientists and emphasize the need for goal-agnostic secondary mechanisms to facilitate learning in biological and artificial networks.

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.

Motivated by the celebrated discrete-time model of nervous activity outlined by McCulloch and Pitts in 1943, we propose a novel continuous-time model, the McCulloch-Pitts network (MPN), for sequence learning in spiking neural networks. Our model has a local learning rule, such that the synaptic weight updates depend only on the information directly accessible by the synapse. By exploiting asymmetry in the connections between binary neurons, we show that MPN can be trained to robustly memorize multiple spatiotemporal patterns of binary vectors, generalizing the ability of the symmetric Hopfield network to memorize static spatial patterns. In addition, we demonstrate that the model can efficiently learn sequences of binary pictures as well as generative models for experimental neural spike-train data. Our learning rule is consistent with spike-timing-dependent plasticity (STDP), thus providing a theoretical ground for the systematic design of biologically inspired networks with large and robust long-range sequence storage capacity.

Modelling the complex spatiotemporal patterns of large-scale brain dynamics is crucial for neuroscience, but traditional methods fail to capture the rich structure in modalities such as magnetoencephalography (MEG). Recent advances in deep learning have enabled significant progress in other domains, such as language and vision, by using foundation models at scale. Here, we introduce MEG-GPT, a transformer based foundation model that uses time-attention and next time-point prediction. To facilitate this, we also introduce a novel data-driven tokeniser for continuous MEG data, which preserves the high temporal resolution of continuous MEG signals without lossy transformations. We trained MEG-GPT on tokenised brain region time-courses extracted from a large-scale MEG dataset (N=612, eyes-closed rest, Cam-CAN data), and show that the learnt model can generate data with realistic spatio-spectral properties, including transient events and population variability. Critically, it performs well in downstream decoding tasks, improving downstream supervised prediction task, showing improved zero-shot generalisation across sessions (improving accuracy from 0.54 to 0.59) and subjects (improving accuracy from 0.41 to 0.49) compared to a baseline methods. Furthermore, we show the model can be efficiently fine-tuned on a smaller labelled dataset to boost performance in cross-subject decoding scenarios. This work establishes a powerful foundation model for electrophysiological data, paving the way for applications in computational neuroscience and neural decoding.

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

Current controllable diffusion models typically rely on fixed architectures that modify intermediate activations to inject guidance conditioned on a new modality. This approach uses a static conditioning strategy for a dynamic, multi-stage denoising process, limiting the model's ability to adapt its response as the generation evolves from coarse structure to fine detail. We introduce TC-LoRA (Temporally Modulated Conditional LoRA), a new paradigm that enables dynamic, context-aware control by conditioning the model's weights directly. Our framework uses a hypernetwork to generate LoRA adapters on-the-fly, tailoring weight modifications for the frozen backbone at each diffusion step based on time and the user's condition. This mechanism enables the model to learn and execute an explicit, adaptive strategy for applying conditional guidance throughout the entire generation process. Through experiments on various data domains, we demonstrate that this dynamic, parametric control significantly enhances generative fidelity and adherence to spatial conditions compared to static, activation-based methods. TC-LoRA establishes an alternative approach in which the model's conditioning strategy is modified through a deeper functional adaptation of its weights, allowing control to align with the dynamic demands of the task and generative stage.

Humans inhabit a physical 4D world where geometric structure and semantic content evolve over time, constituting a dynamic 4D reality (spatial with temporal dimension). While current Multimodal Large Language Models (MLLMs) excel in static visual understanding, can they also be adept at "thinking in dynamics", i.e., perceive, track and reason about spatio-temporal dynamics in evolving scenes? To systematically assess their spatio-temporal reasoning and localized dynamics perception capabilities, we introduce Dyn-Bench, a large-scale benchmark built from diverse real-world and synthetic video datasets, enabling robust and scalable evaluation of spatio-temporal understanding. Through multi-stage filtering from massive 2D and 4D data sources, Dyn-Bench provides a high-quality collection of dynamic scenes, comprising 1k videos, 7k visual question answering (VQA) pairs, and 3k dynamic object grounding pairs. We probe general, spatial and region-level MLLMs to express how they think in dynamics both linguistically and visually, and find that existing models cannot simultaneously maintain strong performance in both spatio-temporal reasoning and dynamic object grounding, often producing inconsistent interpretations of motion and interaction. Notably, conventional prompting strategies (e.g., chain-of-thought or caption-based hints) provide limited improvement, whereas structured integration approaches, including Mask-Guided Fusion and Spatio-Temporal Textual Cognitive Map (ST-TCM), significantly enhance MLLMs' dynamics perception and spatio-temporal reasoning in the physical 4D world. Code and benchmark are available at https://dyn-bench.github.io/.

As Large Language Models (LLMs) continue to advance, they exhibit certain cognitive patterns similar to those of humans that are not directly specified in training data. This study investigates this phenomenon by focusing on temporal cognition in LLMs. Leveraging the similarity judgment task, we find that larger models spontaneously establish a subjective temporal reference point and adhere to the Weber-Fechner law, whereby the perceived distance logarithmically compresses as years recede from this reference point. To uncover the mechanisms behind this behavior, we conducted multiple analyses across neuronal, representational, and informational levels. We first identify a set of temporal-preferential neurons and find that this group exhibits minimal activation at the subjective reference point and implements a logarithmic coding scheme convergently found in biological systems. Probing representations of years reveals a hierarchical construction process, where years evolve from basic numerical values in shallow layers to abstract temporal orientation in deep layers. Finally, using pre-trained embedding models, we found that the training corpus itself possesses an inherent, non-linear temporal structure, which provides the raw material for the model's internal construction. In discussion, we propose an experientialist perspective for understanding these findings, where the LLMs' cognition is viewed as a subjective construction of the external world by its internal representational system. This nuanced perspective implies the potential emergence of alien cognitive frameworks that humans cannot intuitively predict, pointing toward a direction for AI alignment that focuses on guiding internal constructions. Our code is available at https://TheOtherMind.github.io.

Despite rapid adoption and deployment of large language models (LLMs), the internal computations of these models remain opaque and poorly understood. In this work, we seek to understand how high-level human-interpretable features are represented within the internal neuron activations of LLMs. We train k-sparse linear classifiers (probes) on these internal activations to predict the presence of features in the input; by varying the value of k we study the sparsity of learned representations and how this varies with model scale. With k=1, we localize individual neurons which are highly relevant for a particular feature, and perform a number of case studies to illustrate general properties of LLMs. In particular, we show that early layers make use of sparse combinations of neurons to represent many features in superposition, that middle layers have seemingly dedicated neurons to represent higher-level contextual features, and that increasing scale causes representational sparsity to increase on average, but there are multiple types of scaling dynamics. In all, we probe for over 100 unique features comprising 10 different categories in 7 different models spanning 70 million to 6.9 billion parameters.

Transformer architectures have revolutionized artificial intelligence (AI) through their attention mechanisms, yet the computational principles underlying their success remain opaque. We present a novel theoretical framework that reinterprets the core computation of attention as Pavlovian conditioning. Our model finds a direct mathematical analogue in linear attention, which simplifies the analysis of the underlying associative process. We demonstrate that attention's queries, keys, and values can be mapped to the three elements of classical conditioning: test stimuli that probe associations, conditional stimuli (CS) that serve as retrieval cues, and unconditional stimuli (US) that contain response information. Through this lens, we suggest that each attention operation constructs a transient associative memory via a Hebbian rule, where CS-US pairs form dynamic associations that test stimuli can later retrieve. Our framework yields several theoretical insights grounded in this linearized model: (1) a capacity theorem showing that attention heads can store O(d_k) associations before interference degrades retrieval; (2) an error propagation analysis revealing fundamental architectural trade-offs of balancing model depth, width, and head redundancy to maintain reliability; and (3) an understanding of how biologically plausible learning rules could enhance transformer architectures. By establishing this deep connection, we suggest that the success of modern AI may stem not from architectural novelty alone, but from implementing computational principles that biology optimized over millions of years of evolution.

Attention Model has now become an important concept in neural networks that has been researched within diverse application domains. This survey provides a structured and comprehensive overview of the developments in modeling attention. In particular, we propose a taxonomy which groups existing techniques into coherent categories. We review salient neural architectures in which attention has been incorporated, and discuss applications in which modeling attention has shown a significant impact. We also describe how attention has been used to improve the interpretability of neural networks. Finally, we discuss some future research directions in attention. We hope this survey will provide a succinct introduction to attention models and guide practitioners while developing approaches for their applications.

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.

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

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.

Quantifying similarity between neural representations -- e.g. hidden layer activation vectors -- is a perennial problem in deep learning and neuroscience research. Existing methods compare deterministic responses (e.g. artificial networks that lack stochastic layers) or averaged responses (e.g., trial-averaged firing rates in biological data). However, these measures of _deterministic_ representational similarity ignore the scale and geometric structure of noise, both of which play important roles in neural computation. To rectify this, we generalize previously proposed shape metrics (Williams et al. 2021) to quantify differences in _stochastic_ representations. These new distances satisfy the triangle inequality, and thus can be used as a rigorous basis for many supervised and unsupervised analyses. Leveraging this novel framework, we find that the stochastic geometries of neurobiological representations of oriented visual gratings and naturalistic scenes respectively resemble untrained and trained deep network representations. Further, we are able to more accurately predict certain network attributes (e.g. training hyperparameters) from its position in stochastic (versus deterministic) shape space.

The development of foundation models for functional magnetic resonance imaging (fMRI) time series holds significant promise for predicting phenotypes related to disease and cognition. Current models, however, are often trained using a mask-and-reconstruct objective on small brain regions. This focus on low-level information leads to representations that are sensitive to noise and temporal fluctuations, necessitating extensive fine-tuning for downstream tasks. We introduce Brain-Semantoks, a self-supervised framework designed specifically to learn abstract representations of brain dynamics. Its architecture is built on two core innovations: a semantic tokenizer that aggregates noisy regional signals into robust tokens representing functional networks, and a self-distillation objective that enforces representational stability across time. We show that this objective is stabilized through a novel training curriculum, ensuring the model robustly learns meaningful features from low signal-to-noise time series. We demonstrate that learned representations enable strong performance on a variety of downstream tasks even when only using a linear probe. Furthermore, we provide comprehensive scaling analyses indicating more unlabeled data reliably results in out-of-distribution performance gains without domain adaptation.

Although learned representations underlie neural networks' success, their fundamental properties remain poorly understood. A striking example is the emergence of simple geometric structures in LLM representations: for example, calendar months organize into a circle, years form a smooth one-dimensional manifold, and cities' latitudes and longitudes can be decoded by a linear probe. We show that the statistics of language exhibit a translation symmetry -- e.g., the co-occurrence probability of two months depends only on the time interval between them -- and we prove that the latter governs the aforementioned geometric structures in high-dimensional word embedding models. Moreover, we find that these structures persist even when the co-occurrence statistics are strongly perturbed (for example, by removing all sentences in which two months appear together) and at moderate embedding dimension. We show that this robustness naturally emerges if the co-occurrence statistics are collectively controlled by an underlying continuous latent variable. We empirically validate this theoretical framework in word embedding models, text embedding models, and large language models.

Traffic forecasting represents a crucial problem within intelligent transportation systems. In recent research, Large Language Models (LLMs) have emerged as a promising method, but their intrinsic design, tailored primarily for sequential token processing, introduces notable challenges in effectively capturing spatial dependencies. Specifically, the inherent limitations of LLMs in modeling spatial relationships and their architectural incompatibility with graph-structured spatial data remain largely unaddressed. To overcome these limitations, we introduce ST-LINK, a novel framework that enhances the capability of Large Language Models to capture spatio-temporal dependencies. Its key components are Spatially-Enhanced Attention (SE-Attention) and the Memory Retrieval Feed-Forward Network (MRFFN). SE-Attention extends rotary position embeddings to integrate spatial correlations as direct rotational transformations within the attention mechanism. This approach maximizes spatial learning while preserving the LLM's inherent sequential processing structure. Meanwhile, MRFFN dynamically retrieves and utilizes key historical patterns to capture complex temporal dependencies and improve the stability of long-term forecasting. Comprehensive experiments on benchmark datasets demonstrate that ST-LINK surpasses conventional deep learning and LLM approaches, and effectively captures both regular traffic patterns and abrupt changes.

Not yet. We present SPACE, a benchmark that systematically evaluates spatial cognition in frontier models. Our benchmark builds on decades of research in cognitive science. It evaluates large-scale mapping abilities that are brought to bear when an organism traverses physical environments, smaller-scale reasoning about object shapes and layouts, and cognitive infrastructure such as spatial attention and memory. For many tasks, we instantiate parallel presentations via text and images, allowing us to benchmark both large language models and large multimodal models. Results suggest that contemporary frontier models fall short of the spatial intelligence of animals, performing near chance level on a number of classic tests of animal cognition.

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.

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

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.

Most existing spatial reasoning benchmarks focus on static or globally observable environments, failing to capture the challenges of long-horizon reasoning and memory utilization under partial observability and dynamic changes. We introduce two dynamic spatial benchmarks, locally observable maze navigation and match-2 elimination that systematically evaluate models' abilities in spatial understanding and adaptive planning when local perception, environment feedback, and global objectives are tightly coupled. Each action triggers structural changes in the environment, requiring continuous update of cognition and strategy. We further propose a subjective experience-based memory mechanism for cross-task experience transfer and validation. Experiments show that our benchmarks reveal key limitations of mainstream models in dynamic spatial reasoning and long-term memory, providing a comprehensive platform for future methodological advances. Our code and data are available at https://anonymous.4open.science/r/EvoEmpirBench-143C/.

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.

Sequence modeling has produced diverse architectures -- from classical recurrent neural networks to modern Transformers and state space models (SSMs) -- yet a unified theoretical understanding of expressivity and trainability trade-offs remains limited. We introduce a unified framework that represents a broad class of sequence maps via an input-dependent effective interaction operator W_{ij}(X), making explicit two recurring construction patterns: (i) the Unified Factorized Framework (Explicit) (attention-style mixing), in which W_{ij}(X) varies through scalar coefficients applied to shared value maps, and (ii) Structured Dynamics (Implicit) (state-space recurrences), in which W_{ij} is induced by a latent dynamical system. Using this framework, we derive three theoretical results. First, we establish the Interaction Rank Gap: models in the Unified Factorized Framework, such as single-head attention, are constrained to a low-dimensional operator span and cannot represent certain structured dynamical maps. Second, we prove an Equivalence (Head-Count) Theorem showing that, within our multi-head factorized class, representing a linear SSM whose lag operators span a k-dimensional subspace on length-n sequences requires and is achievable with H=k heads. Third, we prove a Gradient Highway Result, showing that attention layers admit inputs with distance-independent gradient paths, whereas stable linear dynamics exhibit distance-dependent gradient attenuation. Together, these results formalize a fundamental trade-off between algebraic expressivity (interaction/operator span) and long-range gradient propagation, providing theoretical grounding for modern sequence architecture design.

We introduce Brain-JEPA, a brain dynamics foundation model with the Joint-Embedding Predictive Architecture (JEPA). This pioneering model achieves state-of-the-art performance in demographic prediction, disease diagnosis/prognosis, and trait prediction through fine-tuning. Furthermore, it excels in off-the-shelf evaluations (e.g., linear probing) and demonstrates superior generalizability across different ethnic groups, surpassing the previous large model for brain activity significantly. Brain-JEPA incorporates two innovative techniques: Brain Gradient Positioning and Spatiotemporal Masking. Brain Gradient Positioning introduces a functional coordinate system for brain functional parcellation, enhancing the positional encoding of different Regions of Interest (ROIs). Spatiotemporal Masking, tailored to the unique characteristics of fMRI data, addresses the challenge of heterogeneous time-series patches. These methodologies enhance model performance and advance our understanding of the neural circuits underlying cognition. Overall, Brain-JEPA is paving the way to address pivotal questions of building brain functional coordinate system and masking brain activity at the AI-neuroscience interface, and setting a potentially new paradigm in brain activity analysis through downstream adaptation.

Spatial cognition is fundamental to real-world multimodal intelligence, allowing models to effectively interact with the physical environment. While multimodal large language models (MLLMs) have made significant strides, existing benchmarks often oversimplify spatial cognition, reducing it to a single-dimensional metric, which fails to capture the hierarchical structure and interdependence of spatial abilities. To address this gap, we propose a hierarchical spatial cognition framework that decomposes spatial intelligence into five progressively complex levels from basic observation to high-level planning. Building upon this taxonomy, we construct SpatialBench, a large-scale, fine-grained benchmark covering 15 tasks aligned with these cognitive levels. To provide a unified evaluation across heterogeneous tasks, we further introduce a high-level capability-oriented metric that reliably assesses a model's overall spatial reasoning ability. Extensive experiments over massive MLLMs reveal distinct performance stratification across cognitive levels: models exhibit strong perceptual grounding yet remain limited in symbolic reasoning, causal inference, and planning. Additional human tests demonstrate that humans perform selective, goal-directed abstraction, while MLLMs tend to over-attend to surface details without coherent spatial intent. Our work establishes the first systematic framework for measuring hierarchical spatial cognition in MLLMs, laying the foundation for future spatially intelligent systems.

Spiking Neural Networks (SNNs) are well known as a promising energy-efficient alternative to conventional artificial neural networks. Subject to the preconceived impression that SNNs are sparse firing, the analysis and optimization of inherent redundancy in SNNs have been largely overlooked, thus the potential advantages of spike-based neuromorphic computing in accuracy and energy efficiency are interfered. In this work, we pose and focus on three key questions regarding the inherent redundancy in SNNs. We argue that the redundancy is induced by the spatio-temporal invariance of SNNs, which enhances the efficiency of parameter utilization but also invites lots of noise spikes. Further, we analyze the effect of spatio-temporal invariance on the spatio-temporal dynamics and spike firing of SNNs. Then, motivated by these analyses, we propose an Advance Spatial Attention (ASA) module to harness SNNs' redundancy, which can adaptively optimize their membrane potential distribution by a pair of individual spatial attention sub-modules. In this way, noise spike features are accurately regulated. Experimental results demonstrate that the proposed method can significantly drop the spike firing with better performance than state-of-the-art SNN baselines. Our code is available in https://github.com/BICLab/ASA-SNN.

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

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/.

We create a reusable Transformer, BrainBERT, for intracranial recordings bringing modern representation learning approaches to neuroscience. Much like in NLP and speech recognition, this Transformer enables classifying complex concepts, i.e., decoding neural data, with higher accuracy and with much less data by being pretrained in an unsupervised manner on a large corpus of unannotated neural recordings. Our approach generalizes to new subjects with electrodes in new positions and to unrelated tasks showing that the representations robustly disentangle the neural signal. Just like in NLP where one can study language by investigating what a language model learns, this approach opens the door to investigating the brain by what a model of the brain learns. As a first step along this path, we demonstrate a new analysis of the intrinsic dimensionality of the computations in different areas of the brain. To construct these representations, we combine a technique for producing super-resolution spectrograms of neural data with an approach designed for generating contextual representations of audio by masking. In the future, far more concepts will be decodable from neural recordings by using representation learning, potentially unlocking the brain like language models unlocked language.

Forecasting epileptic seizures from multivariate EEG signals represents a critical challenge in healthcare time series prediction, requiring high sensitivity, low false alarm rates, and subject-specific adaptability. We present STAN, an Adversarial Spatio-Temporal Attention Network that jointly models spatial brain connectivity and temporal neural dynamics through cascaded attention blocks with alternating spatial and temporal modules. Unlike existing approaches that assume fixed preictal durations or separately process spatial and temporal features, STAN captures bidirectional dependencies between spatial and temporal patterns through a unified cascaded architecture. Adversarial training with gradient penalty enables robust discrimination between interictal and preictal states learned from clearly defined 15-minute preictal windows. Continuous 90-minute pre-seizure monitoring reveals that the learned spatio-temporal attention patterns enable early detection: reliable alarms trigger at subject-specific times (typically 15-45 minutes before onset), reflecting the model's capacity to capture subtle preictal dynamics without requiring individualized training. Experiments on two benchmark EEG datasets (CHB-MIT scalp: 8 subjects, 46 events; MSSM intracranial: 4 subjects, 14 events) demonstrate state-of-the-art performance: 96.6% sensitivity with 0.011 false detections per hour and 94.2% sensitivity with 0.063 false detections per hour, respectively, while maintaining computational efficiency (2.3M parameters, 45 ms latency, 180 MB memory) for real-time edge deployment. Beyond epilepsy, the proposed framework provides a general paradigm for spatio-temporal forecasting in healthcare and other time series domains where individual heterogeneity and interpretability are crucial.

We tackle the challenge of rapidly adapting an agent's behavior to solve spatiotemporally continuous problems in novel settings. Animals exhibit extraordinary abilities to adapt to new contexts, a capacity unmatched by artificial systems. Instead of focusing on generalization through deep reinforcement learning, we propose viewing behavior as the physical manifestation of a search procedure, where robust problem-solving emerges from an exhaustive search across all possible behaviors. Surprisingly, this can be done efficiently using online modification of a cognitive graph that guides action, challenging the predominant view that exhaustive search in continuous spaces is impractical. We describe an algorithm that implicitly enumerates behaviors by regulating the tight feedback loop between execution of behaviors and mutation of the graph, and provide a neural implementation based on Hebbian learning and a novel high-dimensional harmonic representation inspired by entorhinal cortex. By framing behavior as search, we provide a mathematically simple and biologically plausible model for real-time behavioral adaptation, successfully solving a variety of continuous state-space navigation problems. This framework not only offers a flexible neural substrate for other applications but also presents a powerful paradigm for understanding adaptive behavior. Our results suggest potential advancements in developmental learning and unsupervised skill acquisition, paving the way for autonomous robots to master complex skills in data-sparse environments demanding flexibility.

We report the presence of a simple neural mechanism that represents an input-output function as a vector within autoregressive transformer language models (LMs). Using causal mediation analysis on a diverse range of in-context-learning (ICL) tasks, we find that a small number attention heads transport a compact representation of the demonstrated task, which we call a function vector (FV). FVs are robust to changes in context, i.e., they trigger execution of the task on inputs such as zero-shot and natural text settings that do not resemble the ICL contexts from which they are collected. We test FVs across a range of tasks, models, and layers and find strong causal effects across settings in middle layers. We investigate the internal structure of FVs and find while that they often contain information that encodes the output space of the function, this information alone is not sufficient to reconstruct an FV. Finally, we test semantic vector composition in FVs, and find that to some extent they can be summed to create vectors that trigger new complex tasks. Taken together, our findings suggest that LLMs contain internal abstractions of general-purpose functions that can be invoked in a variety of contexts.

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

Prior studies on the emergence in large models have primarily focused on how the functional capabilities of large language models (LLMs) scale with model size. Our research, however, transcends this traditional paradigm, aiming to deepen our understanding of the emergence within LLMs by placing a special emphasis not just on the model size but more significantly on the complex behavior of neuron interactions during the training process. By introducing the concepts of "self-organization" and "multifractal analysis," we explore how neuron interactions dynamically evolve during training, leading to "emergence," mirroring the phenomenon in natural systems where simple micro-level interactions give rise to complex macro-level behaviors. To quantitatively analyze the continuously evolving interactions among neurons in large models during training, we propose the Neuron-based Multifractal Analysis (NeuroMFA). Utilizing NeuroMFA, we conduct a comprehensive examination of the emergent behavior in LLMs through the lens of both model size and training process, paving new avenues for research into the emergence in large models.

Large Language Models (LLMs) have reshaped our world with significant advancements in science, engineering, and society through applications ranging from scientific discoveries and medical diagnostics to Chatbots. Despite their ubiquity and utility, the underlying mechanisms of LLM remain concealed within billions of parameters and complex structures, making their inner architecture and cognitive processes challenging to comprehend. We address this gap by adopting approaches to understanding emerging cognition in biology and developing a network-based framework that links cognitive skills, LLM architectures, and datasets, ushering in a paradigm shift in foundation model analysis. The skill distribution in the module communities demonstrates that while LLMs do not strictly parallel the focalized specialization observed in specific biological systems, they exhibit unique communities of modules whose emergent skill patterns partially mirror the distributed yet interconnected cognitive organization seen in avian and small mammalian brains. Our numerical results highlight a key divergence from biological systems to LLMs, where skill acquisition benefits substantially from dynamic, cross-regional interactions and neural plasticity. By integrating cognitive science principles with machine learning, our framework provides new insights into LLM interpretability and suggests that effective fine-tuning strategies should leverage distributed learning dynamics rather than rigid modular interventions.

Spiking Neural Networks (SNNs) offer energy-efficient, biologically plausible computation but suffer from non-differentiable spike generation, necessitating reliance on heuristic surrogate gradients. This paper introduces UltraLIF, a principled framework that replaces surrogate gradients with ultradiscretization, a mathematical formalism from tropical geometry providing continuous relaxations of discrete dynamics. The central insight is that the max-plus semiring underlying ultradiscretization naturally models neural threshold dynamics: the log-sum-exp function serves as a differentiable soft-maximum that converges to hard thresholding as a learnable temperature parameter eps to 0. Two neuron models are derived from distinct dynamical systems: UltraLIF from the LIF ordinary differential equation (temporal dynamics) and UltraDLIF from the diffusion equation modeling gap junction coupling across neuronal populations (spatial dynamics). Both yield fully differentiable SNNs trainable via standard backpropagation with no forward-backward mismatch. Theoretical analysis establishes pointwise convergence to classical LIF dynamics with quantitative error bounds and bounded non-vanishing gradients. Experiments on six benchmarks spanning static images, neuromorphic vision, and audio demonstrate improvements over surrogate gradient baselines, with gains most pronounced in single-timestep (T{=}1) settings on neuromorphic and temporal datasets. An optional sparsity penalty enables significant energy reduction while maintaining competitive accuracy.

Recent advances in mechanistic interpretability have revealed that large language models (LLMs) develop internal representations corresponding not only to concrete entities but also distinct, human-understandable abstract concepts and behaviour. Moreover, these hidden features can be directly manipulated to steer model behaviour. However, it remains an open question whether this phenomenon is unique to models trained on inherently structured data (ie. language, images) or if it is a general property of foundation models. In this work, we investigate the internal representations of a large physics-focused foundation model. Inspired by recent work identifying single directions in activation space for complex behaviours in LLMs, we extract activation vectors from the model during forward passes over simulation datasets for different physical regimes. We then compute "delta" representations between the two regimes. These delta tensors act as concept directions in activation space, encoding specific physical features. By injecting these concept directions back into the model during inference, we can steer its predictions, demonstrating causal control over physical behaviours, such as inducing or removing some particular physical feature from a simulation. These results suggest that scientific foundation models learn generalised representations of physical principles. They do not merely rely on superficial correlations and patterns in the simulations. Our findings open new avenues for understanding and controlling scientific foundation models and has implications for AI-enabled scientific discovery.

Dynamic graph representation learning requires capturing both structural relationships and temporal evolution, yet existing approaches face a fundamental trade-off: attention-based methods achieve expressiveness at O(T^2) complexity, while recurrent architectures suffer from gradient pathologies and dense state storage. Spiking neural networks offer event-driven efficiency but remain limited by sequential propagation, binary information loss, and local aggregation that misses global context. We propose ChronoSpike, an adaptive spiking graph neural network that integrates learnable LIF neurons with per-channel membrane dynamics, multi-head attentive spatial aggregation on continuous features, and a lightweight Transformer temporal encoder, enabling both fine-grained local modeling and long-range dependency capture with linear memory complexity O(T cdot d). On three large-scale benchmarks, ChronoSpike outperforms twelve state-of-the-art baselines by 2.0% Macro-F1 and 2.4% Micro-F1 while achieving 3-10times faster training than recurrent methods with a constant 105K-parameter budget independent of graph size. We provide theoretical guarantees for membrane potential boundedness, gradient flow stability under contraction factor ρ< 1, and BIBO stability; interpretability analyses reveal heterogeneous temporal receptive fields and a learned primacy effect with 83-88% sparsity.

Modeling the dynamics of deformable objects is challenging due to their diverse physical properties and the difficulty of estimating states from limited visual information. We address these challenges with a neural dynamics framework that combines object particles and spatial grids in a hybrid representation. Our particle-grid model captures global shape and motion information while predicting dense particle movements, enabling the modeling of objects with varied shapes and materials. Particles represent object shapes, while the spatial grid discretizes the 3D space to ensure spatial continuity and enhance learning efficiency. Coupled with Gaussian Splattings for visual rendering, our framework achieves a fully learning-based digital twin of deformable objects and generates 3D action-conditioned videos. Through experiments, we demonstrate that our model learns the dynamics of diverse objects -- such as ropes, cloths, stuffed animals, and paper bags -- from sparse-view RGB-D recordings of robot-object interactions, while also generalizing at the category level to unseen instances. Our approach outperforms state-of-the-art learning-based and physics-based simulators, particularly in scenarios with limited camera views. Furthermore, we showcase the utility of our learned models in model-based planning, enabling goal-conditioned object manipulation across a range of tasks. The project page is available at https://kywind.github.io/pgnd .

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.

Attention guides our gaze to fixate the proper location of the scene and holds it in that location for the deserved amount of time given current processing demands, before shifting to the next one. As such, gaze deployment crucially is a temporal process. Existing computational models have made significant strides in predicting spatial aspects of observer's visual scanpaths (where to look), while often putting on the background the temporal facet of attention dynamics (when). In this paper we present TPP-Gaze, a novel and principled approach to model scanpath dynamics based on Neural Temporal Point Process (TPP), that jointly learns the temporal dynamics of fixations position and duration, integrating deep learning methodologies with point process theory. We conduct extensive experiments across five publicly available datasets. Our results show the overall superior performance of the proposed model compared to state-of-the-art approaches. Source code and trained models are publicly available at: https://github.com/phuselab/tppgaze.

Biological brains demonstrate complex neural activity, where the timing and interplay between neurons is critical to how brains process information. Most deep learning architectures simplify neural activity by abstracting away temporal dynamics. In this paper we challenge that paradigm. By incorporating neuron-level processing and synchronization, we can effectively reintroduce neural timing as a foundational element. We present the Continuous Thought Machine (CTM), a model designed to leverage neural dynamics as its core representation. The CTM has two core innovations: (1) neuron-level temporal processing, where each neuron uses unique weight parameters to process a history of incoming signals; and (2) neural synchronization employed as a latent representation. The CTM aims to strike a balance between oversimplified neuron abstractions that improve computational efficiency, and biological realism. It operates at a level of abstraction that effectively captures essential temporal dynamics while remaining computationally tractable for deep learning. We demonstrate the CTM's strong performance and versatility across a range of challenging tasks, including ImageNet-1K classification, solving 2D mazes, sorting, parity computation, question-answering, and RL tasks. Beyond displaying rich internal representations and offering a natural avenue for interpretation owing to its internal process, the CTM is able to perform tasks that require complex sequential reasoning. The CTM can also leverage adaptive compute, where it can stop earlier for simpler tasks, or keep computing when faced with more challenging instances. The goal of this work is to share the CTM and its associated innovations, rather than pushing for new state-of-the-art results. To that end, we believe the CTM represents a significant step toward developing more biologically plausible and powerful artificial intelligence systems.

Self-supervised models have revolutionized speech processing, achieving new levels of performance in a wide variety of tasks with limited resources. However, the inner workings of these models are still opaque. In this paper, we aim to analyze the encoded contextual representation of these foundation models based on their inter- and intra-model similarity, independent of any external annotation and task-specific constraint. We examine different SSL models varying their training paradigm -- Contrastive (Wav2Vec2.0) and Predictive models (HuBERT); and model sizes (base and large). We explore these models on different levels of localization/distributivity of information including (i) individual neurons; (ii) layer representation; (iii) attention weights and (iv) compare the representations with their finetuned counterparts.Our results highlight that these models converge to similar representation subspaces but not to similar neuron-localized concepts\footnote{A concept represents a coherent fragment of knowledge, such as ``a class containing certain objects as elements, where the objects have certain properties. We made the code publicly available for facilitating further research, we publicly released our code.

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.

Recent advances in Large Multimodal Models (LMMs) lead to significant breakthroughs in both academia and industry. One question that arises is how we, as humans, can understand their internal neural representations. This paper takes an initial step towards addressing this question by presenting a versatile framework to identify and interpret the semantics within LMMs. Specifically, 1) we first apply a Sparse Autoencoder(SAE) to disentangle the representations into human understandable features. 2) We then present an automatic interpretation framework to interpreted the open-semantic features learned in SAE by the LMMs themselves. We employ this framework to analyze the LLaVA-NeXT-8B model using the LLaVA-OV-72B model, demonstrating that these features can effectively steer the model's behavior. Our results contribute to a deeper understanding of why LMMs excel in specific tasks, including EQ tests, and illuminate the nature of their mistakes along with potential strategies for their rectification. These findings offer new insights into the internal mechanisms of LMMs and suggest parallels with the cognitive processes of the human brain.

Scenes are complex, yet structured collections of parts, including objects and surfaces, that exhibit spatial and semantic relations to one another. An effective visual system therefore needs unified scene representations that relate scene parts to their location and their co-occurrence. We hypothesize that this structure can be learned self-supervised from natural experience by exploiting the temporal regularities of active vision: each fixation reveals a locally-detailed glimpse that is statistically related to the previous one via co-occurrence and saccade-conditioned spatial regularities. We instantiate this idea with Glimpse Prediction Networks (GPNs) -- recurrent models trained to predict the feature embedding of the next glimpse along human-like scanpaths over natural scenes. GPNs successfully learn co-occurrence structure and, when given relative saccade location vectors, show sensitivity to spatial arrangement. Furthermore, recurrent variants of GPNs were able to integrate information across glimpses into a unified scene representation. Notably, these scene representations align strongly with human fMRI responses during natural-scene viewing across mid/high-level visual cortex. Critically, GPNs outperform architecture- and dataset-matched controls trained with explicit semantic objectives, and match or exceed strong modern vision baselines, leaving little unique variance for those alternatives. These results establish next-glimpse prediction during active vision as a biologically plausible, self-supervised route to brain-aligned scene representations learned from natural visual experience.

While Large Language Models (LLMs) excel at generalized reasoning, standard retrieval-augmented approaches fail to address the disconnected nature of long-term agentic memory. To bridge this gap, we introduce Synapse (Synergistic Associative Processing Semantic Encoding), a unified memory architecture that transcends static vector similarity. Drawing from cognitive science, Synapse models memory as a dynamic graph where relevance emerges from spreading activation rather than pre-computed links. By integrating lateral inhibition and temporal decay, the system dynamically highlights relevant sub-graphs while filtering interference. We implement a Triple Hybrid Retrieval strategy that fuses geometric embeddings with activation-based graph traversal. Comprehensive evaluations on the LoCoMo benchmark show that Synapse significantly outperforms state-of-the-art methods in complex temporal and multi-hop reasoning tasks, offering a robust solution to the "Contextual Tunneling" problem. Our code and data will be made publicly available upon acceptance.

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

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

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.

Recent studies in interpretability have explored the inner workings of transformer models trained on tasks across various domains, often discovering that these networks naturally develop highly structured representations. When such representations comprehensively reflect the task domain's structure, they are commonly referred to as "World Models" (WMs). In this work, we identify WMs in transformers trained on maze-solving tasks. By using Sparse Autoencoders (SAEs) and analyzing attention patterns, we examine the construction of WMs and demonstrate consistency between SAE feature-based and circuit-based analyses. By subsequently intervening on isolated features to confirm their causal role, we find that it is easier to activate features than to suppress them. Furthermore, we find that models can reason about mazes involving more simultaneously active features than they encountered during training; however, when these same mazes (with greater numbers of connections) are provided to models via input tokens instead, the models fail. Finally, we demonstrate that positional encoding schemes appear to influence how World Models are structured within the model's residual stream.

Attention mechanisms are a central property of cognitive systems allowing them to selectively deploy cognitive resources in a flexible manner. Attention has been long studied in the neurosciences and there are numerous phenomenological models that try to capture its core properties. Recently attentional mechanisms have become a dominating architectural choice of machine learning and are the central innovation of Transformers. The dominant intuition and formalism underlying their development has drawn on ideas of keys and queries in database management systems. In this work, we propose an alternative Bayesian foundation for attentional mechanisms and show how this unifies different attentional architectures in machine learning. This formulation allows to to identify commonality across different attention ML architectures as well as suggest a bridge to those developed in neuroscience. We hope this work will guide more sophisticated intuitions into the key properties of attention architectures and suggest new ones.

In the present research, we delve into the intricate realm of electroencephalogram (EEG) data analysis, focusing on sequence-to-sequence prediction of data across 32 EEG channels. The study harmoniously fuses the principles of applied chaos theory and dynamical systems theory to engender a novel feature set, enriching the representational capacity of our deep learning model. The endeavour's cornerstone is a transformer-based sequence-to-sequence architecture, calibrated meticulously to capture the non-linear and high-dimensional temporal dependencies inherent in EEG sequences. Through judicious architecture design, parameter initialisation strategies, and optimisation techniques, we have navigated the intricate balance between computational expediency and predictive performance. Our model stands as a vanguard in EEG data sequence prediction, demonstrating remarkable generalisability and robustness. The findings not only extend our understanding of EEG data dynamics but also unveil a potent analytical framework that can be adapted to diverse temporal sequence prediction tasks in neuroscience and beyond.

The memory of contemporary Large Language Models is bound by a physical paradox: as they learn, they fill up. The linear accumulation (O(N)) of Key-Value states treats context as a warehouse of static artifacts, eventually forcing a destructive choice between amnesia and latency. We challenge this discrete orthodoxy, proposing that long-term memory is not the storage of items, but the persistence of a trajectory. We introduce Phonetic Trajectory Memory (PTM), a neuro-symbolic architecture that encodes language not as a sequence of tensors, but as a continuous path on an ergodic manifold governed by irrational rotation matrices. By decoupling the navigation (an invariant O(1) geometric signal) from the reconstruction (a probabilistic generative act), PTM achieves a compression magnitude of greater than 3,000x relative to dense caches. We demonstrate that retrieval becomes a process of resonance: the phonetic trace stabilizes the model against hallucination via "Signal Consensus" mechanism, securing up to approximately 92% factual accuracy. While this aggressive abstraction alters generative texture, it unlocks immediate access latency (approximately 34ms) independent of depth. Our results suggest that infinite context does not require infinite silicon; it requires treating memory not as data to be stored, but as a reconstructive process acting on a conserved, undying physical signal.

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.

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.

State space models (SSMs) have shown remarkable empirical performance on many long sequence modeling tasks, but a theoretical understanding of these models is still lacking. In this work, we study the learning dynamics of linear SSMs to understand how covariance structure in data, latent state size, and initialization affect the evolution of parameters throughout learning with gradient descent. We show that focusing on the learning dynamics in the frequency domain affords analytical solutions under mild assumptions, and we establish a link between one-dimensional SSMs and the dynamics of deep linear feed-forward networks. Finally, we analyze how latent state over-parameterization affects convergence time and describe future work in extending our results to the study of deep SSMs with nonlinear connections. This work is a step toward a theory of learning dynamics in deep state space models.

Machine learning architectures, including transformers and recurrent neural networks (RNNs) have revolutionized forecasting in applications ranging from text processing to extreme weather. Notably, advanced network architectures, tuned for applications such as natural language processing, are transferable to other tasks such as spatiotemporal forecasting tasks. However, there is a scarcity of ablation studies to illustrate the key components that enable this forecasting accuracy. The absence of such studies, although explainable due to the associated computational cost, intensifies the belief that these models ought to be considered as black boxes. In this work, we decompose the key architectural components of the most powerful neural architectures, namely gating and recurrence in RNNs, and attention mechanisms in transformers. Then, we synthesize and build novel hybrid architectures from the standard blocks, performing ablation studies to identify which mechanisms are effective for each task. The importance of considering these components as hyper-parameters that can augment the standard architectures is exhibited on various forecasting datasets, from the spatiotemporal chaotic dynamics of the multiscale Lorenz 96 system, the Kuramoto-Sivashinsky equation, as well as standard real world time-series benchmarks. A key finding is that neural gating and attention improves the performance of all standard RNNs in most tasks, while the addition of a notion of recurrence in transformers is detrimental. Furthermore, our study reveals that a novel, sparsely used, architecture which integrates Recurrent Highway Networks with neural gating and attention mechanisms, emerges as the best performing architecture in high-dimensional spatiotemporal forecasting of dynamical systems.

This study introduces a novel approach by replacing the traditional perceptron neuron model with a biologically inspired probabilistic meta neuron, where the internal neuron parameters are jointly learned, leading to improved classification accuracy of spiking neural networks (SNNs). To validate this innovation, we implement and compare two SNN architectures: one based on standard leaky integrate-and-fire (LIF) neurons and another utilizing the proposed probabilistic meta neuron model. As a second key contribution, we present a new biologically inspired classification framework that uniquely integrates SNNs with Lempel-Ziv complexity (LZC) a measure closely related to entropy rate. By combining the temporal precision and biological plausibility of SNNs with the capacity of LZC to capture structural regularity, the proposed approach enables efficient and interpretable classification of spatiotemporal neural data, an aspect not addressed in existing works. We consider learning algorithms such as backpropagation, spike-timing-dependent plasticity (STDP), and the Tempotron learning rule. To explore neural dynamics, we use Poisson processes to model neuronal spike trains, a well-established method for simulating the stochastic firing behavior of biological neurons. Our results reveal that depending on the training method, the classifier's efficiency can improve by up to 11.00%, highlighting the advantage of learning additional neuron parameters beyond the traditional focus on weighted inputs alone.

Reconstructing human dynamic vision from brain activity is a challenging task with great scientific significance. The difficulty stems from two primary issues: (1) vision-processing mechanisms in the brain are highly intricate and not fully revealed, making it challenging to directly learn a mapping between fMRI and video; (2) the temporal resolution of fMRI is significantly lower than that of natural videos. To overcome these issues, this paper propose a two-stage model named Mind-Animator, which achieves state-of-the-art performance on three public datasets. Specifically, during the fMRI-to-feature stage, we decouple semantic, structural, and motion features from fMRI through fMRI-vision-language tri-modal contrastive learning and sparse causal attention. In the feature-to-video stage, these features are merged to videos by an inflated Stable Diffusion. We substantiate that the reconstructed video dynamics are indeed derived from fMRI, rather than hallucinations of the generative model, through permutation tests. Additionally, the visualization of voxel-wise and ROI-wise importance maps confirms the neurobiological interpretability of our model.

Large language models (LLMs) have complicated internal dynamics, but induce representations of words and phrases whose geometry we can study. Human language processing is also opaque, but neural response measurements can provide (noisy) recordings of activation during listening or reading, from which we can extract similar representations of words and phrases. Here we study the extent to which the geometries induced by these representations, share similarities in the context of brain decoding. We find that the larger neural language models get, the more their representations are structurally similar to neural response measurements from brain imaging. Code is available at https://github.com/coastalcph/brainlm.

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

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.

The brain is a noisy system subject to energy constraints. These facts are rarely taken into account when modelling artificial neural networks. In this paper, we are interested in demonstrating that those factors can actually lead to the appearance of robust associative memories. We first propose a simplified model of noise in the brain, taking into account synaptic noise and interference from neurons external to the network. When coarsely quantized, we show that this noise can be reduced to insertions and erasures. We take a neural network with recurrent modifiable connections, and subject it to noisy external inputs. We introduce an energy usage limitation principle in the network as well as consolidated Hebbian learning, resulting in an incremental processing of inputs. We show that the connections naturally formed correspond to state-of-the-art binary sparse associative memories.

The abilities to perceive, learn, and use generalities, similarities, classes, i.e., semantic memory (SM), is central to cognition. Machine learning (ML), neural network, and AI research has been primarily driven by tasks requiring such abilities. However, another central facet of cognition, single-trial formation of permanent memories of experiences, i.e., episodic memory (EM), has had relatively little focus. Only recently has EM-like functionality been added to Deep Learning (DL) models, e.g., Neural Turing Machine, Memory Networks. However, in these cases: a) EM is implemented as a separate module, which entails substantial data movement (and so, time and power) between the DL net itself and EM; and b) individual items are stored localistically within the EM, precluding realizing the exponential representational efficiency of distributed over localist coding. We describe Sparsey, an unsupervised, hierarchical, spatial/spatiotemporal associative memory model differing fundamentally from mainstream ML models, most crucially, in its use of sparse distributed representations (SDRs), or, cell assemblies, which admits an extremely efficient, single-trial learning algorithm that maps input similarity into code space similarity (measured as intersection). SDRs of individual inputs are stored in superposition and because similarity is preserved, the patterns of intersections over the assigned codes reflect the similarity, i.e., statistical, structure, of all orders, not simply pairwise, over the inputs. Thus, SM, i.e., a generative model, is built as a computationally free side effect of the act of storing episodic memory traces of individual inputs, either spatial patterns or sequences. We report initial results on MNIST and on the Weizmann video event recognition benchmarks. While we have not yet attained SOTA class accuracy, learning takes only minutes on a single CPU.

Chaotic systems are intrinsically sensitive to small errors, challenging efforts to construct predictive data-driven models of real-world dynamical systems such as fluid flows or neuronal activity. Prior efforts comprise either specialized models trained separately on individual time series, or foundation models trained on vast time series databases with little underlying dynamical structure. Motivated by dynamical systems theory, we present Panda, Patched Attention for Nonlinear DynAmics. We train Panda on a novel synthetic, extensible dataset of 2 times 10^4 chaotic dynamical systems that we discover using an evolutionary algorithm. Trained purely on simulated data, Panda exhibits emergent properties: zero-shot forecasting of unseen real world chaotic systems, and nonlinear resonance patterns in cross-channel attention heads. Despite having been trained only on low-dimensional ordinary differential equations, Panda spontaneously develops the ability to predict partial differential equations without retraining. We demonstrate a neural scaling law for differential equations, underscoring the potential of pretrained models for probing abstract mathematical domains like nonlinear dynamics.