Daily Papers

Although large language models demonstrate emergent abilities in solving math word problems, there is a challenging task in complex multi-step mathematical reasoning tasks. To improve model performance on mathematical reasoning tasks, previous work has conducted supervised fine-tuning on open-source models by improving the quality and quantity of data. In this paper, we propose a novel approach, named Brain, to imitate human thought processes to enhance mathematical reasoning abilities, using the Frontal Lobe Model to generate plans, and then employing the Parietal Lobe Model to generate code and execute to obtain answers. First, we achieve SOTA performance in comparison with Code LLaMA 7B based models through this method. Secondly, we find that plans can be explicitly extracted from natural language, code, or formal language. Our code and data are publicly available at https://github.com/cyzhh/Brain.

This study reveals an unexpected parallel between instructible vision-language models (VLMs) and human cognitive disorders, specifically constructive apraxia. We tested 25 state-of-the-art VLMs, including GPT-4 Vision, DALL-E 3, and Midjourney v5, on their ability to generate images of the Ponzo illusion, a task that requires basic spatial reasoning and is often used in clinical assessments of constructive apraxia. Remarkably, 24 out of 25 models failed to correctly render two horizontal lines against a perspective background, mirroring the deficits seen in patients with parietal lobe damage. The models consistently misinterpreted spatial instructions, producing tilted or misaligned lines that followed the perspective of the background rather than remaining horizontal. This behavior is strikingly similar to how apraxia patients struggle to copy or construct simple figures despite intact visual perception and motor skills. Our findings suggest that current VLMs, despite their advanced capabilities in other domains, lack fundamental spatial reasoning abilities akin to those impaired in constructive apraxia. This limitation in AI systems provides a novel computational model for studying spatial cognition deficits and highlights a critical area for improvement in VLM architecture and training methodologies.

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

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.

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.

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

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/.

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

Multi-subject fMRI studies are challenging due to the high variability of both brain anatomy and functional brain topographies across participants. An effective way of aggregating multi-subject fMRI data is to extract a shared representation that filters out unwanted variability among subjects. Some recent work has implemented probabilistic models to extract a shared representation in task fMRI. In the present work, we improve upon these models by incorporating temporal information in the common latent structures. We introduce a new model, Shared Gaussian Process Factor Analysis (S-GPFA), that discovers shared latent trajectories and subject-specific functional topographies, while modelling temporal correlation in fMRI data. We demonstrate the efficacy of our model in revealing ground truth latent structures using simulated data, and replicate experimental performance of time-segment matching and inter-subject similarity on the publicly available Raider and Sherlock datasets. We further test the utility of our model by analyzing its learned model parameters in the large multi-site SPINS dataset, on a social cognition task from participants with and without schizophrenia.

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.

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.

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

Working memory (WM), a fundamental cognitive process facilitating the temporary storage, integration, manipulation, and retrieval of information, plays a vital role in reasoning and decision-making tasks. Robust benchmark datasets that capture the multifaceted nature of WM are crucial for the effective development and evaluation of AI WM models. Here, we introduce a comprehensive Working Memory (WorM) benchmark dataset for this purpose. WorM comprises 10 tasks and a total of 1 million trials, assessing 4 functionalities, 3 domains, and 11 behavioral and neural characteristics of WM. We jointly trained and tested state-of-the-art recurrent neural networks and transformers on all these tasks. We also include human behavioral benchmarks as an upper bound for comparison. Our results suggest that AI models replicate some characteristics of WM in the brain, most notably primacy and recency effects, and neural clusters and correlates specialized for different domains and functionalities of WM. In the experiments, we also reveal some limitations in existing models to approximate human behavior. This dataset serves as a valuable resource for communities in cognitive psychology, neuroscience, and AI, offering a standardized framework to compare and enhance WM models, investigate WM's neural underpinnings, and develop WM models with human-like capabilities. Our source code and data are available at https://github.com/ZhangLab-DeepNeuroCogLab/WorM.

Can large language models (LLMs) implement computations of psychopathology? An effective approach to the question hinges on addressing two factors. First, for conceptual validity, we require a general and computational account of psychopathology that is applicable to computational entities without biological embodiment or subjective experience. Second, mechanisms underlying LLM behaviors need to be studied for better methodological validity. Thus, we establish a computational-theoretical framework to provide an account of psychopathology applicable to LLMs. To ground the theory for empirical analysis, we also propose a novel mechanistic interpretability method alongside a tailored empirical analytic framework. Based on the frameworks, we conduct experiments demonstrating three key claims: first, that distinct dysfunctional and problematic representational states are implemented in LLMs; second, that their activations can spread and self-sustain to trap LLMs; and third, that dynamic, cyclic structural causal models encoded in the LLMs underpin these patterns. In concert, the empirical results corroborate our hypothesis that network-theoretic computations of psychopathology have already emerged in LLMs. This suggests that certain LLM behaviors mirroring psychopathology may not be a superficial mimicry but a feature of their internal processing. Thus, our work alludes to the possibility of AI systems with psychopathological behaviors in the near future.

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.

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

Large language models are powerful systems that excel at many tasks, ranging from translation to mathematical reasoning. Yet, at the same time, these models often show unhuman-like characteristics. In the present paper, we address this gap and ask whether large language models can be turned into cognitive models. We find that -- after finetuning them on data from psychological experiments -- these models offer accurate representations of human behavior, even outperforming traditional cognitive models in two decision-making domains. In addition, we show that their representations contain the information necessary to model behavior on the level of individual subjects. Finally, we demonstrate that finetuning on multiple tasks enables large language models to predict human behavior in a previously unseen task. Taken together, these results suggest that large, pre-trained models can be adapted to become generalist cognitive models, thereby opening up new research directions that could transform cognitive psychology and the behavioral sciences as a whole.

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.

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

Establishing a unified theory of cognition has been a major goal of psychology. While there have been previous attempts to instantiate such theories by building computational models, we currently do not have one model that captures the human mind in its entirety. Here we introduce Centaur, a computational model that can predict and simulate human behavior in any experiment expressible in natural language. We derived Centaur by finetuning a state-of-the-art language model on a novel, large-scale data set called Psych-101. Psych-101 reaches an unprecedented scale, covering trial-by-trial data from over 60,000 participants performing over 10,000,000 choices in 160 experiments. Centaur not only captures the behavior of held-out participants better than existing cognitive models, but also generalizes to new cover stories, structural task modifications, and entirely new domains. Furthermore, we find that the model's internal representations become more aligned with human neural activity after finetuning. Taken together, Centaur is the first real candidate for a unified model of human cognition. We anticipate that it will have a disruptive impact on the cognitive sciences, challenging the existing paradigm for developing computational models.

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.

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.

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

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

This paper reports the first brain-inspired large language model (BriLLM). This is a non-Transformer, non-GPT, non-traditional machine learning input-output controlled generative language model. The model is based on the Signal Fully-connected flowing (SiFu) definition on the directed graph in terms of the neural network, and has the interpretability of all nodes on the graph of the whole model, instead of the traditional machine learning model that only has limited interpretability at the input and output ends. In the language model scenario, the token is defined as a node in the graph. A randomly shaped or user-defined signal flow flows between nodes on the principle of "least resistance" along paths. The next token or node to be predicted or generated is the target of the signal flow. As a language model, BriLLM theoretically supports infinitely long n-gram models when the model size is independent of the input and predicted length of the model. The model's working signal flow provides the possibility of recall activation and innate multi-modal support similar to the cognitive patterns of the human brain. At present, we released the first BriLLM version in Chinese, with 4000 tokens, 32-dimensional node width, 16-token long sequence prediction ability, and language model prediction performance comparable to GPT-1. More computing power will help us explore the infinite possibilities depicted above.

Large language models (LLMs) demonstrate impressive performance on a wide variety of tasks, but they often struggle with tasks that require multi-step reasoning or goal-directed planning. To address this, we take inspiration from the human brain, in which planning is accomplished via the recurrent interaction of specialized modules in the prefrontal cortex (PFC). These modules perform functions such as conflict monitoring, state prediction, state evaluation, task decomposition, and task coordination. We find that LLMs are sometimes capable of carrying out these functions in isolation, but struggle to autonomously coordinate them in the service of a goal. Therefore, we propose a black box architecture with multiple LLM-based (GPT-4) modules. The architecture improves planning through the interaction of specialized PFC-inspired modules that break down a larger problem into multiple brief automated calls to the LLM. We evaluate the combined architecture on two challenging planning tasks -- graph traversal and Tower of Hanoi -- finding that it yields significant improvements over standard LLM methods (e.g., zero-shot prompting or in-context learning). These results demonstrate the benefit of utilizing knowledge from cognitive neuroscience to improve planning in LLMs.

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.

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.

With the development in cognitive science and Large Language Models (LLMs), increasing connections have come to light between these two distinct fields. Building upon these connections, we propose a conjecture suggesting the existence of a duality between LLMs and Tulving's theory of memory. We identify a potential correspondence between Tulving's synergistic ecphory model (SEM) of retrieval and the emergent abilities observed in LLMs, serving as supporting evidence for our conjecture. Furthermore, we speculate that consciousness may be considered a form of emergent ability based on this duality. We also discuss how other theories of consciousness intersect with our research.

Language models are increasingly capable, yet still fail at a seemingly simple task of multi-digit multiplication. In this work, we study why, by reverse-engineering a model that successfully learns multiplication via implicit chain-of-thought, and report three findings: (1) Evidence of long-range structure: Logit attributions and linear probes indicate that the model encodes the necessary long-range dependencies for multi-digit multiplication. (2) Mechanism: the model encodes long-range dependencies using attention to construct a directed acyclic graph to ``cache'' and ``retrieve'' pairwise partial products. (3) Geometry: the model implements partial products in attention heads by forming Minkowski sums between pairs of digits, and digits are represented using a Fourier basis, both of which are intuitive and efficient representations that the standard fine-tuning model lacks. With these insights, we revisit the learning dynamics of standard fine-tuning and find that the model converges to a local optimum that lacks the required long-range dependencies. We further validate this understanding by introducing an auxiliary loss that predicts the ``running sum'' via a linear regression probe, which provides an inductive bias that enables the model to successfully learn multi-digit multiplication. In summary, by reverse-engineering the mechanisms of an implicit chain-of-thought model we uncover a pitfall for learning long-range dependencies in Transformers and provide an example of how the correct inductive bias can address this issue.

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.

Brain simulation builds dynamical models to mimic the structure and functions of the brain, while brain-inspired computing (BIC) develops intelligent systems by learning from the structure and functions of the brain. The two fields are intertwined and should share a common programming framework to facilitate each other's development. However, none of the existing software in the fields can achieve this goal, because traditional brain simulators lack differentiability for training, while existing deep learning (DL) frameworks fail to capture the biophysical realism and complexity of brain dynamics. In this paper, we introduce BrainPy, a differentiable brain simulator developed using JAX and XLA, with the aim of bridging the gap between brain simulation and BIC. BrainPy expands upon the functionalities of JAX, a powerful AI framework, by introducing complete capabilities for flexible, efficient, and scalable brain simulation. It offers a range of sparse and event-driven operators for efficient and scalable brain simulation, an abstraction for managing the intricacies of synaptic computations, a modular and flexible interface for constructing multi-scale brain models, and an object-oriented just-in-time compilation approach to handle the memory-intensive nature of brain dynamics. We showcase the efficiency and scalability of BrainPy on benchmark tasks, highlight its differentiable simulation for biologically plausible spiking models, and discuss its potential to support research at the intersection of brain simulation and BIC.

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.

Representations from transformer-based unidirectional language models are known to be effective at predicting brain responses to natural language. However, most studies comparing language models to brains have used GPT-2 or similarly sized language models. Here we tested whether larger open-source models such as those from the OPT and LLaMA families are better at predicting brain responses recorded using fMRI. Mirroring scaling results from other contexts, we found that brain prediction performance scales log-linearly with model size from 125M to 30B parameter models, with ~15% increased encoding performance as measured by correlation with a held-out test set across 3 subjects. Similar log-linear behavior was observed when scaling the size of the fMRI training set. We also characterized scaling for acoustic encoding models that use HuBERT, WavLM, and Whisper, and we found comparable improvements with model size. A noise ceiling analysis of these large, high-performance encoding models showed that performance is nearing the theoretical maximum for brain areas such as the precuneus and higher auditory cortex. These results suggest that increasing scale in both models and data will yield incredibly effective models of language processing in the brain, enabling better scientific understanding as well as applications such as decoding.

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.

Bayesian models of cognition have gained considerable traction in computational neuroscience and psychiatry. Their scopes are now expected to expand rapidly to artificial intelligence, providing general inference frameworks to support embodied, adaptable, and energy-efficient autonomous agents. A central theory in this domain is predictive coding, which posits that learning and behaviour are driven by hierarchical probabilistic inferences about the causes of sensory inputs. Biological realism constrains these networks to rely on simple local computations in the form of precision-weighted predictions and prediction errors. This can make this framework highly efficient, but its implementation comes with unique challenges on the software development side. Embedding such models in standard neural network libraries often becomes limiting, as these libraries' compilation and differentiation backends can force a conceptual separation between optimization algorithms and the systems being optimized. This critically departs from other biological principles such as self-monitoring, self-organisation, cellular growth and functional plasticity. In this paper, we introduce pyhgf: a Python package backed by JAX and Rust for creating, manipulating and sampling dynamic networks for predictive coding. We improve over other frameworks by enclosing the network components as transparent, modular and malleable variables in the message-passing steps. The resulting graphs can implement arbitrary computational complexities as beliefs propagation. But the transparency of core variables can also translate into inference processes that leverage self-organisation principles, and express structure learning, meta-learning or causal discovery as the consequence of network structural adaptation to surprising inputs. The code, tutorials and documentation are hosted at: https://github.com/ilabcode/pyhgf.

Large Language Models (LLMs) have been shown to be effective models of the human language system, with some models predicting most explainable variance of brain activity in current datasets. Even in untrained models, the representations induced by architectural priors can exhibit reasonable alignment to brain data. In this work, we investigate the key architectural components driving the surprising alignment of untrained models. To estimate LLM-to-brain similarity, we first select language-selective units within an LLM, similar to how neuroscientists identify the language network in the human brain. We then benchmark the brain alignment of these LLM units across five different brain recording datasets. By isolating critical components of the Transformer architecture, we identify tokenization strategy and multihead attention as the two major components driving brain alignment. A simple form of recurrence further improves alignment. We further demonstrate this quantitative brain alignment of our model by reproducing landmark studies in the language neuroscience field, showing that localized model units -- just like language voxels measured empirically in the human brain -- discriminate more reliably between lexical than syntactic differences, and exhibit similar response profiles under the same experimental conditions. Finally, we demonstrate the utility of our model's representations for language modeling, achieving improved sample and parameter efficiency over comparable architectures. Our model's estimates of surprisal sets a new state-of-the-art in the behavioral alignment to human reading times. Taken together, we propose a highly brain- and behaviorally-aligned model that conceptualizes the human language system as an untrained shallow feature encoder, with structural priors, combined with a trained decoder to achieve efficient and performant language processing.

Understanding the connections between artificial and biological intelligent systems can reveal fundamental principles underlying general intelligence. While many artificial intelligence (AI) models have a neuroscience counterpart, such connections are largely missing in Transformer models and the self-attention mechanism. Here, we examine the relationship between attention heads and human episodic memory. We focus on the induction heads, which contribute to the in-context learning capabilities of Transformer-based large language models (LLMs). We demonstrate that induction heads are behaviorally, functionally, and mechanistically similar to the contextual maintenance and retrieval (CMR) model of human episodic memory. Our analyses of LLMs pre-trained on extensive text data show that CMR-like heads often emerge in the intermediate model layers and that their behavior qualitatively mirrors the memory biases seen in humans. Our findings uncover a parallel between the computational mechanisms of LLMs and human memory, offering valuable insights into both research fields.

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.

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.

The observed similarities in the behavior of humans and Large Language Models (LLMs) have prompted researchers to consider the potential of using LLMs as models of human cognition. However, several significant challenges must be addressed before LLMs can be legitimately regarded as cognitive models. For instance, LLMs are trained on far more data than humans typically encounter, and may have been directly trained on human data in specific cognitive tasks or aligned with human preferences. Consequently, the origins of these behavioral similarities are not well understood. In this paper, we propose a novel way to enhance the utility of LLMs as cognitive models. This approach involves (i) leveraging computationally equivalent tasks that both an LLM and a rational agent need to master for solving a cognitive problem and (ii) examining the specific task distributions required for an LLM to exhibit human-like behaviors. We apply this approach to decision-making -- specifically risky and intertemporal choice -- where the key computationally equivalent task is the arithmetic of expected value calculations. We show that an LLM pretrained on an ecologically valid arithmetic dataset, which we call Arithmetic-GPT, predicts human behavior better than many traditional cognitive models. Pretraining LLMs on ecologically valid arithmetic datasets is sufficient to produce a strong correspondence between these models and human decision-making. Our results also suggest that LLMs used as cognitive models should be carefully investigated via ablation studies of the pretraining data.

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.

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

Brain decoding, a pivotal field in neuroscience, aims to reconstruct stimuli from acquired brain signals, primarily utilizing functional magnetic resonance imaging (fMRI). Currently, brain decoding is confined to a per-subject-per-model paradigm, limiting its applicability to the same individual for whom the decoding model is trained. This constraint stems from three key challenges: 1) the inherent variability in input dimensions across subjects due to differences in brain size; 2) the unique intrinsic neural patterns, influencing how different individuals perceive and process sensory information; 3) limited data availability for new subjects in real-world scenarios hampers the performance of decoding models. In this paper, we present a novel approach, MindBridge, that achieves cross-subject brain decoding by employing only one model. Our proposed framework establishes a generic paradigm capable of addressing these challenges by introducing biological-inspired aggregation function and novel cyclic fMRI reconstruction mechanism for subject-invariant representation learning. Notably, by cycle reconstruction of fMRI, MindBridge can enable novel fMRI synthesis, which also can serve as pseudo data augmentation. Within the framework, we also devise a novel reset-tuning method for adapting a pretrained model to a new subject. Experimental results demonstrate MindBridge's ability to reconstruct images for multiple subjects, which is competitive with dedicated subject-specific models. Furthermore, with limited data for a new subject, we achieve a high level of decoding accuracy, surpassing that of subject-specific models. This advancement in cross-subject brain decoding suggests promising directions for wider applications in neuroscience and indicates potential for more efficient utilization of limited fMRI data in real-world scenarios. Project page: https://littlepure2333.github.io/MindBridge

A new prior is proposed for learning representations of high-level concepts of the kind we manipulate with language. This prior can be combined with other priors in order to help disentangling abstract factors from each other. It is inspired by cognitive neuroscience theories of consciousness, seen as a bottleneck through which just a few elements, after having been selected by attention from a broader pool, are then broadcast and condition further processing, both in perception and decision-making. The set of recently selected elements one becomes aware of is seen as forming a low-dimensional conscious state. This conscious state is combining the few concepts constituting a conscious thought, i.e., what one is immediately conscious of at a particular moment. We claim that this architectural and information-processing constraint corresponds to assumptions about the joint distribution between high-level concepts. To the extent that these assumptions are generally true (and the form of natural language seems consistent with them), they can form a useful prior for representation learning. A low-dimensional thought or conscious state is analogous to a sentence: it involves only a few variables and yet can make a statement with very high probability of being true. This is consistent with a joint distribution (over high-level concepts) which has the form of a sparse factor graph, i.e., where the dependencies captured by each factor of the factor graph involve only very few variables while creating a strong dip in the overall energy function. The consciousness prior also makes it natural to map conscious states to natural language utterances or to express classical AI knowledge in a form similar to facts and rules, albeit capturing uncertainty as well as efficient search mechanisms implemented by attention mechanisms.

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.

Large language models accumulate vast knowledge during pre-training, yet the dynamics governing this acquisition remain poorly understood. This work investigates the learning dynamics of language models on a synthetic factual recall task, uncovering three key findings: First, language models learn in three phases, exhibiting a performance plateau before acquiring precise factual knowledge. Mechanistically, this plateau coincides with the formation of attention-based circuits that support recall. Second, the training data distribution significantly impacts learning dynamics, as imbalanced distributions lead to shorter plateaus. Finally, hallucinations emerge simultaneously with knowledge, and integrating new knowledge into the model through fine-tuning is challenging, as it quickly corrupts its existing parametric memories. Our results emphasize the importance of data distribution in knowledge acquisition and suggest novel data scheduling strategies to accelerate neural network training.

We analyse perception and memory, using mathematical models for knowledge graphs and tensors, to gain insights into the corresponding functionalities of the human mind. Our discussion is based on the concept of propositional sentences consisting of subject-predicate-object (SPO) triples for expressing elementary facts. SPO sentences are the basis for most natural languages but might also be important for explicit perception and declarative memories, as well as intra-brain communication and the ability to argue and reason. A set of SPO sentences can be described as a knowledge graph, which can be transformed into an adjacency tensor. We introduce tensor models, where concepts have dual representations as indices and associated embeddings, two constructs we believe are essential for the understanding of implicit and explicit perception and memory in the brain. We argue that a biological realization of perception and memory imposes constraints on information processing. In particular, we propose that explicit perception and declarative memories require a semantic decoder, which, in a simple realization, is based on four layers: First, a sensory memory layer, as a buffer for sensory input, second, an index layer representing concepts, third, a memoryless representation layer for the broadcasting of information ---the "blackboard", or the "canvas" of the brain--- and fourth, a working memory layer as a processing center and data buffer. We discuss the operations of the four layers and relate them to the global workspace theory. In a Bayesian brain interpretation, semantic memory defines the prior for observable triple statements. We propose that ---in evolution and during development--- semantic memory, episodic memory, and natural language evolved as emergent properties in agents' process to gain a deeper understanding of sensory information.

Reconstructions of visual perception from brain activity have improved tremendously, but the practical utility of such methods has been limited. This is because such models are trained independently per subject where each subject requires dozens of hours of expensive fMRI training data to attain high-quality results. The present work showcases high-quality reconstructions using only 1 hour of fMRI training data. We pretrain our model across 7 subjects and then fine-tune on minimal data from a new subject. Our novel functional alignment procedure linearly maps all brain data to a shared-subject latent space, followed by a shared non-linear mapping to CLIP image space. We then map from CLIP space to pixel space by fine-tuning Stable Diffusion XL to accept CLIP latents as inputs instead of text. This approach improves out-of-subject generalization with limited training data and also attains state-of-the-art image retrieval and reconstruction metrics compared to single-subject approaches. MindEye2 demonstrates how accurate reconstructions of perception are possible from a single visit to the MRI facility. All code is available on GitHub.

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

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.

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

In this work, we introduce Brain Latent Progression (BrLP), a novel spatiotemporal disease progression model based on latent diffusion. BrLP is designed to predict the evolution of diseases at the individual level on 3D brain MRIs. Existing deep generative models developed for this task are primarily data-driven and face challenges in learning disease progressions. BrLP addresses these challenges by incorporating prior knowledge from disease models to enhance the accuracy of predictions. To implement this, we propose to integrate an auxiliary model that infers volumetric changes in various brain regions. Additionally, we introduce Latent Average Stabilization (LAS), a novel technique to improve spatiotemporal consistency of the predicted progression. BrLP is trained and evaluated on a large dataset comprising 11,730 T1-weighted brain MRIs from 2,805 subjects, collected from three publicly available, longitudinal Alzheimer's Disease (AD) studies. In our experiments, we compare the MRI scans generated by BrLP with the actual follow-up MRIs available from the subjects, in both cross-sectional and longitudinal settings. BrLP demonstrates significant improvements over existing methods, with an increase of 22% in volumetric accuracy across AD-related brain regions and 43% in image similarity to the ground-truth scans. The ability of BrLP to generate conditioned 3D scans at the subject level, along with the novelty of integrating prior knowledge to enhance accuracy, represents a significant advancement in disease progression modeling, opening new avenues for precision medicine. The code of BrLP is available at the following link: https://github.com/LemuelPuglisi/BrLP.

Recent voxel-wise multimodal brain encoding studies have shown that multimodal large language models (MLLMs) exhibit a higher degree of brain alignment compared to unimodal models in both unimodal and multimodal stimulus settings. More recently, instruction-tuned multimodal models have shown to generate task-specific representations that align strongly with brain activity. However, prior work evaluating the brain alignment of MLLMs has primarily focused on unimodal settings or relied on non-instruction-tuned multimodal models for multimodal stimuli. To address this gap, we investigated brain alignment, that is, measuring the degree of predictivity of neural activity recorded while participants were watching naturalistic movies (video along with audio) with representations derived from MLLMs. We utilized instruction-specific embeddings from six video and two audio instruction-tuned MLLMs. Experiments with 13 video task-specific instructions show that instruction-tuned video MLLMs significantly outperform non-instruction-tuned multimodal (by 15%) and unimodal models (by 20%). Our evaluation of MLLMs for both video and audio tasks using language-guided instructions shows clear disentanglement in task-specific representations from MLLMs, leading to precise differentiation of multimodal functional processing in the brain. We also find that MLLM layers align hierarchically with the brain, with early sensory areas showing strong alignment with early layers, while higher-level visual and language regions align more with middle to late layers. These findings provide clear evidence for the role of task-specific instructions in improving the alignment between brain activity and MLLMs, and open new avenues for mapping joint information processing in both the systems. We make the code publicly available [https://github.com/subbareddy248/mllm_videos].

Integrated Information Theory (IIT) provides a quantitative framework for explaining consciousness phenomenon, positing that conscious systems comprise elements integrated through causal properties. We apply IIT 3.0 and 4.0 -- the latest iterations of this framework -- to sequences of Large Language Model (LLM) representations, analyzing data derived from existing Theory of Mind (ToM) test results. Our study systematically investigates whether the differences of ToM test performances, when presented in the LLM representations, can be revealed by IIT estimates, i.e., Phi^{max} (IIT 3.0), Phi (IIT 4.0), Conceptual Information (IIT 3.0), and Phi-structure (IIT 4.0). Furthermore, we compare these metrics with the Span Representations independent of any estimate for consciousness. This additional effort aims to differentiate between potential "consciousness" phenomena and inherent separations within LLM representational space. We conduct comprehensive experiments examining variations across LLM transformer layers and linguistic spans from stimuli. Our results suggest that sequences of contemporary Transformer-based LLM representations lack statistically significant indicators of observed "consciousness" phenomena but exhibit intriguing patterns under spatio-permutational analyses. The Appendix and code are available as Supplementary Materials at: https://doi.org/10.1016/j.nlp.2025.100163.

This paper describes a novel nonparametric model for modeling diffusion MRI signals in q-space. In q-space, diffusion MRI signal is measured for a sequence of magnetic strengths (b-values) and magnetic gradient directions (b-vectors). We propose a Poly-RBF model, which employs a bidirectional framework with polynomial bases to model the signal along the b-value direction and Gaussian radial bases across the b-vectors. The model can accommodate sparse data on b-values and moderately dense data on b-vectors. The utility of Poly-RBF is inspected for two applications: 1) prediction of the dMRI signal, and 2) harmonization of dMRI data collected under different acquisition protocols with different scanners. Our results indicate that the proposed Poly-RBF model can more accurately predict the unmeasured diffusion signal than its competitors such as the Gaussian process model in {\tt Eddy} of FSL. Applying it to harmonizing the diffusion signal can significantly improve the reproducibility of derived white matter microstructure measures.

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.

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.

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

We propose a novel nonlinear bidirectionally coupled heterogeneous chain network whose dynamics evolve in discrete time. The backbone of the model is a pair of popular map-based neuron models, the Chialvo and the Rulkov maps. This model is assumed to proximate the intricate dynamical properties of neurons in the widely complex nervous system. The model is first realized via various nonlinear analysis techniques: fixed point analysis, phase portraits, Jacobian matrix, and bifurcation diagrams. We observe the coexistence of chaotic and period-4 attractors. Various codimension-1 and -2 patterns for example saddle-node, period-doubling, Neimark-Sacker, double Neimark-Sacker, flip- and fold-Neimark Sacker, and 1:1 and 1:2 resonance are also explored. Furthermore, the study employs two synchronization measures to quantify how the oscillators in the network behave in tandem with each other over a long number of iterations. Finally, a time series analysis of the model is performed to investigate its complexity in terms of sample entropy.

While electroencephalogram (EEG) has been a crucial tool for monitoring the brain and diagnosing neurological disorders (e.g., epilepsy), learning meaningful representations from raw EEG signals remains challenging due to limited annotations and high signal variability. Recently, EEG foundation models (FMs) have shown promising potential by adopting transformer architectures and self-supervised pre-training methods from large language models (e.g., masked prediction) to learn representations from diverse EEG data, followed by fine-tuning on specific EEG tasks. Nonetheless, these large models often incurred high computational costs during both training and inference, with only marginal performance improvements as model size increases. In this work, we proposed EEG representation learning framework building upon Generative Diffusion Model (EEGDM). Specifically, we developed structured state-space model for diffusion pretraining (SSMDP) to better capture the temporal dynamics of EEG signals and trained the architecture using a Denoising Diffusion Probabilistic Model. The resulting latent EEG representations were then used for downstream classification tasks via our proposed latent fusion transformer (LFT). To evaluate our method, we used the multi-event Temple University EEG Event Corpus and compared EEGDM with current state-of-the-art approaches, including EEG FMs. Empirical results showed that our method outperformed existing methods while being approximately 19x more lightweight. These findings suggested that EEGDM offered a promising alternative to current FMs. Our code is available at: https://github.com/jhpuah/EEGDM.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. Here we introduce BrainFM, a modality-agnostic, multi-task vision foundation model for human brain imaging. With the proposed "mild-to-severe" intra-subject generation and "real-synth" mix-up training strategy, BrainFM is resilient to the appearance of acquired images (e.g., modality, contrast, deformation, resolution, artifacts), and can be directly applied to five fundamental brain imaging tasks, including image synthesis for CT and T1w/T2w/FLAIR MRI, anatomy segmentation, scalp-to-cortical distance, bias field estimation, and registration. We evaluate the efficacy of BrainFM on eleven public datasets, and demonstrate its robustness and effectiveness across all tasks and input modalities. Code is available at https://github.com/jhuldr/BrainFM.

Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging. Methods: We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP). Results: We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity. Conclusion: Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics. Significance: Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

Large Language Models (LLMs) do not differentially represent numbers, which are pervasive in text. In contrast, neuroscience research has identified distinct neural representations for numbers and words. In this work, we investigate how well popular LLMs capture the magnitudes of numbers (e.g., that 4 < 5) from a behavioral lens. Prior research on the representational capabilities of LLMs evaluates whether they show human-level performance, for instance, high overall accuracy on standard benchmarks. Here, we ask a different question, one inspired by cognitive science: How closely do the number representations of LLMscorrespond to those of human language users, who typically demonstrate the distance, size, and ratio effects? We depend on a linking hypothesis to map the similarities among the model embeddings of number words and digits to human response times. The results reveal surprisingly human-like representations across language models of different architectures, despite the absence of the neural circuitry that directly supports these representations in the human brain. This research shows the utility of understanding LLMs using behavioral benchmarks and points the way to future work on the number representations of LLMs and their cognitive plausibility.

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.

Diffusion models are a class of generative models that learn to synthesize samples by inverting a diffusion process that gradually maps data into noise. While these models have enjoyed great success recently, a full theoretical understanding of their observed properties is still lacking, in particular, their weak sensitivity to the choice of noise family and the role of adequate scheduling of noise levels for good synthesis. By identifying a correspondence between diffusion models and a well-known paradigm in cognitive science known as serial reproduction, whereby human agents iteratively observe and reproduce stimuli from memory, we show how the aforementioned properties of diffusion models can be explained as a natural consequence of this correspondence. We then complement our theoretical analysis with simulations that exhibit these key features. Our work highlights how classic paradigms in cognitive science can shed light on state-of-the-art machine learning problems.

To handle the scarcity and heterogeneity of electroencephalography (EEG) data for Brain-Computer Interface (BCI) tasks, and to harness the power of large publicly available data sets, we propose Neuro-GPT, a foundation model consisting of an EEG encoder and a GPT model. The foundation model is pre-trained on a large-scale data set using a self-supervised task that learns how to reconstruct masked EEG segments. We then fine-tune the model on a Motor Imagery Classification task to validate its performance in a low-data regime (9 subjects). Our experiments demonstrate that applying a foundation model can significantly improve classification performance compared to a model trained from scratch, which provides evidence for the generalizability of the foundation model and its ability to address challenges of data scarcity and heterogeneity in EEG. The code is publicly available at github.com/wenhui0206/NeuroGPT.

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

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.

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

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

The Mamba layer offers an efficient selective state space model (SSM) that is highly effective in modeling multiple domains including NLP, long-range sequences processing, and computer vision. Selective SSMs are viewed as dual models, in which one trains in parallel on the entire sequence via IO-aware parallel scan, and deploys in an autoregressive manner. We add a third view and show that such models can be viewed as attention-driven models. This new perspective enables us to compare the underlying mechanisms to that of the self-attention layers in transformers and allows us to peer inside the inner workings of the Mamba model with explainability methods. Our code is publicly available.

We present MindEye, a novel fMRI-to-image approach to retrieve and reconstruct viewed images from brain activity. Our model comprises two parallel submodules that are specialized for retrieval (using contrastive learning) and reconstruction (using a diffusion prior). MindEye can map fMRI brain activity to any high dimensional multimodal latent space, like CLIP image space, enabling image reconstruction using generative models that accept embeddings from this latent space. We comprehensively compare our approach with other existing methods, using both qualitative side-by-side comparisons and quantitative evaluations, and show that MindEye achieves state-of-the-art performance in both reconstruction and retrieval tasks. In particular, MindEye can retrieve the exact original image even among highly similar candidates indicating that its brain embeddings retain fine-grained image-specific information. This allows us to accurately retrieve images even from large-scale databases like LAION-5B. We demonstrate through ablations that MindEye's performance improvements over previous methods result from specialized submodules for retrieval and reconstruction, improved training techniques, and training models with orders of magnitude more parameters. Furthermore, we show that MindEye can better preserve low-level image features in the reconstructions by using img2img, with outputs from a separate autoencoder. All code is available on GitHub.

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

Understanding memorisation in language models has practical and societal implications, e.g., studying models' training dynamics or preventing copyright infringements. Prior work defines memorisation as the causal effect of training with an instance on the model's ability to predict that instance. This definition relies on a counterfactual: the ability to observe what would have happened had the model not seen that instance. Existing methods struggle to provide computationally efficient and accurate estimates of this counterfactual. Further, they often estimate memorisation for a model architecture rather than for a specific model instance. This paper fills an important gap in the literature, proposing a new, principled, and efficient method to estimate memorisation based on the difference-in-differences design from econometrics. Using this method, we characterise a model's memorisation profile--its memorisation trends across training--by only observing its behaviour on a small set of instances throughout training. In experiments with the Pythia model suite, we find that memorisation (i) is stronger and more persistent in larger models, (ii) is determined by data order and learning rate, and (iii) has stable trends across model sizes, thus making memorisation in larger models predictable from smaller ones.

While Attention has come to be an important mechanism in deep learning, there remains limited intuition for why it works so well. Here, we show that Transformer Attention can be closely related under certain data conditions to Kanerva's Sparse Distributed Memory (SDM), a biologically plausible associative memory model. We confirm that these conditions are satisfied in pre-trained GPT2 Transformer models. We discuss the implications of the Attention-SDM map and provide new computational and biological interpretations of Attention.

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.

Despite their impressive capabilities, multimodal large language models (MLLMs) are prone to hallucinations, i.e., the generated content that is nonsensical or unfaithful to input sources. Unlike in LLMs, hallucinations in MLLMs often stem from the sensitivity of text decoder to visual tokens, leading to a phenomenon akin to "amnesia" about visual information. To address this issue, we propose MemVR, a novel decoding paradigm inspired by common cognition: when the memory of an image seen the moment before is forgotten, people will look at it again for factual answers. Following this principle, we treat visual tokens as supplementary evidence, re-injecting them into the MLLM through Feed Forward Network (FFN) as "key-value memory" at the middle trigger layer. This "look-twice" mechanism occurs when the model exhibits high uncertainty during inference, effectively enhancing factual alignment. Comprehensive experimental evaluations demonstrate that MemVR significantly mitigates hallucination across various MLLMs and excels in general benchmarks without incurring additional time overhead. The implementation is available from https://github.com/1zhou-Wang/MemVR

Instruction-tuning is a widely adopted method of finetuning that enables large language models (LLMs) to generate output that more closely resembles human responses to natural language queries, in many cases leading to human-level performance on diverse testbeds. However, it remains unclear whether instruction-tuning truly makes LLMs more similar to how humans process language. We investigate the effect of instruction-tuning on LLM-human similarity in two ways: (1) brain alignment, the similarity of LLM internal representations to neural activity in the human language system, and (2) behavioral alignment, the similarity of LLM and human behavior on a reading task. We assess 25 vanilla and instruction-tuned LLMs across three datasets involving humans reading naturalistic stories and sentences. We discover that instruction-tuning generally enhances brain alignment by an average of 6%, but does not have a similar effect on behavioral alignment. To identify the factors underlying LLM-brain alignment, we compute correlations between the brain alignment of LLMs and various model properties, such as model size, various problem-solving abilities, and performance on tasks requiring world knowledge spanning various domains. Notably, we find a strong positive correlation between brain alignment and model size (r = 0.95), as well as performance on tasks requiring world knowledge (r = 0.81). Our results demonstrate that instruction-tuning LLMs improves both world knowledge representations and brain alignment, suggesting that mechanisms that encode world knowledge in LLMs also improve representational alignment to the human brain.

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.

In this work, we present a computing platform named digital twin brain (DTB) that can simulate spiking neuronal networks of the whole human brain scale and more importantly, a personalized biological brain structure. In comparison to most brain simulations with a homogeneous global structure, we highlight that the sparseness, couplingness and heterogeneity in the sMRI, DTI and PET data of the brain has an essential impact on the efficiency of brain simulation, which is proved from the scaling experiments that the DTB of human brain simulation is communication-intensive and memory-access intensive computing systems rather than computation-intensive. We utilize a number of optimization techniques to balance and integrate the computation loads and communication traffics from the heterogeneous biological structure to the general GPU-based HPC and achieve leading simulation performance for the whole human brain-scaled spiking neuronal networks. On the other hand, the biological structure, equipped with a mesoscopic data assimilation, enables the DTB to investigate brain cognitive function by a reverse-engineering method, which is demonstrated by a digital experiment of visual evaluation on the DTB. Furthermore, we believe that the developing DTB will be a promising powerful platform for a large of research orients including brain-inspiredintelligence, rain disease medicine and brain-machine interface.

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.

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.

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.

Language models show a surprising range of capabilities, but the source of their apparent competence is unclear. Do these networks just memorize a collection of surface statistics, or do they rely on internal representations of the process that generates the sequences they see? We investigate this question by applying a variant of the GPT model to the task of predicting legal moves in a simple board game, Othello. Although the network has no a priori knowledge of the game or its rules, we uncover evidence of an emergent nonlinear internal representation of the board state. Interventional experiments indicate this representation can be used to control the output of the network and create "latent saliency maps" that can help explain predictions in human terms.

Do machines and humans process language in similar ways? A recent line of research has hinted in the affirmative, demonstrating that human brain signals can be effectively predicted using the internal representations of language models (LMs). This is thought to reflect shared computational principles between LMs and human language processing. However, there are also clear differences in how LMs and humans acquire and use language, even if the final task they are performing is the same. Despite this, there is little work exploring systematic differences between human and machine language processing using brain data. To address this question, we examine the differences between LM representations and the human brain's responses to language, specifically by examining a dataset of Magnetoencephalography (MEG) responses to a written narrative. In doing so we identify three phenomena that, in prior work, LMs have been found to not capture well: emotional understanding, figurative language processing, and physical commonsense. By fine-tuning LMs on datasets related to these phenomena, we observe that fine-tuned LMs show improved alignment with human brain responses across these tasks. Our study implies that the observed divergences between LMs and human brains may stem from LMs' inadequate representation of these specific types of knowledge.

We put forward the dynamical study of a novel higher-order small network of Chialvo neurons arranged in a ring-star topology, with the neurons interacting via linear diffusive couplings. This model is perceived to imitate the nonlinear dynamical properties exhibited by a realistic nervous system where the neurons transfer information through higher-order multi-body interactions. We first analyze our model using the tools from nonlinear dynamics literature: fixed point analysis, Jacobian matrix, and bifurcation patterns. We observe the coexistence of chaotic attractors, and also an intriguing route to chaos starting from a fixed point, to period-doubling, to cyclic quasiperiodic closed invariant curves, to ultimately chaos. We numerically observe the existence of codimension-1 bifurcation patterns: saddle-node, period-doubling, and Neimark Sacker. We also qualitatively study the typical phase portraits of the system and numerically quantify chaos and complexity using the 0-1 test and sample entropy measure respectively. Finally, we study the collective behavior of the neurons in terms of two synchronization measures: the cross-correlation coefficient, and the Kuramoto order parameter.

Adaptive behavior often requires predicting future events. The theory of reinforcement learning prescribes what kinds of predictive representations are useful and how to compute them. This paper integrates these theoretical ideas with work on cognition and neuroscience. We pay special attention to the successor representation (SR) and its generalizations, which have been widely applied both as engineering tools and models of brain function. This convergence suggests that particular kinds of predictive representations may function as versatile building blocks of intelligence.

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.

Humans are highly adaptable, swiftly switching between different modes to progressively handle different tasks, situations and contexts. In Human-object interaction (HOI) activities, these modes can be attributed to two mechanisms: (1) the large-scale consistent plan for the whole activity and (2) the small-scale children interactive actions that start and end along the timeline. While neuroscience and cognitive science have confirmed this multi-mechanism nature of human behavior, machine modeling approaches for human motion are trailing behind. While attempted to use gradually morphing structures (e.g., graph attention networks) to model the dynamic HOI patterns, they miss the expeditious and discrete mode-switching nature of the human motion. To bridge that gap, this work proposes to model two concurrent mechanisms that jointly control human motion: the Persistent process that runs continually on the global scale, and the Transient sub-processes that operate intermittently on the local context of the human while interacting with objects. These two mechanisms form an interactive Persistent-Transient Duality that synergistically governs the activity sequences. We model this conceptual duality by a parent-child neural network of Persistent and Transient channels with a dedicated neural module for dynamic mechanism switching. The framework is trialed on HOI motion forecasting. On two rich datasets and a wide variety of settings, the model consistently delivers superior performances, proving its suitability for the challenge.

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.

This position paper explores the rapid development of Foundation Models (FMs) in AI and their implications for intelligence and reasoning. It examines the characteristics of FMs, including their training on vast datasets and use of embedding spaces to capture semantic relationships. The paper discusses recent advancements in FMs' reasoning abilities which we argue cannot be attributed to increased model size but to novel training techniques which yield learning phenomena like grokking. It also addresses the challenges in benchmarking FMs and compares their structure to the human brain. We argue that while FMs show promising developments in reasoning and knowledge representation, understanding their inner workings remains a significant challenge, similar to ongoing efforts in neuroscience to comprehend human brain function. Despite having some similarities, fundamental differences between FMs and the structure of human brain warn us against making direct comparisons or expecting neuroscience to provide immediate insights into FM function.

It is desirable for statistical models to detect signals of interest independently of their position. If the data is generated by some smooth process, this additional structure should be taken into account. We introduce a new class of neural networks that are shift invariant and preserve smoothness of the data: functional neural networks (FNNs). For this, we use methods from functional data analysis (FDA) to extend multi-layer perceptrons and convolutional neural networks to functional data. We propose different model architectures, show that the models outperform a benchmark model from FDA in terms of accuracy and successfully use FNNs to classify electroencephalography (EEG) data.

Recent fMRI-to-image approaches mainly focused on associating fMRI signals with specific conditions of pre-trained diffusion models. These approaches, while producing high-quality images, capture only a limited aspect of the complex information in fMRI signals and offer little detailed control over image creation. In contrast, this paper proposes to directly modulate the generation process of diffusion models using fMRI signals. Our approach, NeuroPictor, divides the fMRI-to-image process into three steps: i) fMRI calibrated-encoding, to tackle multi-individual pre-training for a shared latent space to minimize individual difference and enable the subsequent cross-subject training; ii) fMRI-to-image cross-subject pre-training, perceptually learning to guide diffusion model with high- and low-level conditions across different individuals; iii) fMRI-to-image single-subject refining, similar with step ii but focus on adapting to particular individual. NeuroPictor extracts high-level semantic features from fMRI signals that characterizing the visual stimulus and incrementally fine-tunes the diffusion model with a low-level manipulation network to provide precise structural instructions. By training with over 60,000 fMRI-image pairs from various individuals, our model enjoys superior fMRI-to-image decoding capacity, particularly in the within-subject setting, as evidenced in benchmark datasets. Project page: https://jingyanghuo.github.io/neuropictor/.

Recent advances in large language models (LLMs) provide a new opportunity to address the long-standing question of how concepts are represented and organized in the mind, which is central to unravelling the nature of human cognition. Here, we reframed the classic reverse dictionary task to simulate human concept inference in context and investigated the emergence of human-like conceptual representations within LLMs. We found that LLMs were able to infer concepts from definitional descriptions and construct representation spaces that converge towards a shared, context-independent structure. These representations effectively predicted human behavioural judgments and aligned well with neural activity patterns in the human brain, offering evidence for biological plausibility. These findings demonstrate that human-like conceptual representations and organization can naturally emerge from language prediction, even without real-world grounding. Our work supports the view that LLMs serve as valuable tools for understanding complex human cognition and paves the way for better alignment between artificial and human intelligence.

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.

This article addresses the challenge of modeling the amplitude of spatially indexed low frequency fluctuations (ALFF) in resting state functional MRI as a function of cortical structural features and a multi-task coactivation network in the Adolescent Brain Cognitive Development (ABCD) Study. It proposes a generative model that integrates effects of spatially-varying inputs and a network-valued input using deep neural networks to capture complex non-linear and spatial associations with the output. The method models spatial smoothness, accounts for subject heterogeneity and complex associations between network and spatial images at different scales, enables accurate inference of each images effect on the output image, and allows prediction with uncertainty quantification via Monte Carlo dropout, contributing to one of the first Explainable AI (XAI) frameworks for heterogeneous imaging data. The model is highly scalable to high-resolution data without the heavy pre-processing or summarization often required by Bayesian methods. Empirical results demonstrate its strong performance compared to existing statistical and deep learning methods. We applied the XAI model to the ABCD data which revealed associations between cortical features and ALFF throughout the entire brain. Our model performed comparably to existing methods in predictive accuracy but provided superior uncertainty quantification and faster computation, demonstrating its effectiveness for large-scale neuroimaging analysis. Open-source software in Python for XAI is available.

Artificial neural networks are being proposed as models of parts of the brain. The networks are compared to recordings of biological neurons, and good performance in reproducing neural responses is considered to support the model's validity. A key question is how much this system identification approach tells us about brain computation. Does it validate one model architecture over another? We evaluate the most commonly used comparison techniques, such as a linear encoding model and centered kernel alignment, to correctly identify a model by replacing brain recordings with known ground truth models. System identification performance is quite variable; it also depends significantly on factors independent of the ground truth architecture, such as stimuli images. In addition, we show the limitations of using functional similarity scores in identifying higher-level architectural motifs.

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.

Data scarcity in the brain-computer interface field can be alleviated through the use of generative models, specifically diffusion models. While diffusion models have previously been successfully applied to electroencephalogram (EEG) data, existing models lack flexibility w.r.t.~sampling or require alternative representations of the EEG data. To overcome these limitations, we introduce a novel approach to conditional diffusion models that utilizes classifier-free guidance to directly generate subject-, session-, and class-specific EEG data. In addition to commonly used metrics, domain-specific metrics are employed to evaluate the specificity of the generated samples. The results indicate that the proposed model can generate EEG data that resembles real data for each subject, session, and class.

While prior work has explored whether large language models (LLMs) possess a "theory of mind" (ToM) - the ability to attribute mental states to oneself and others - there has been little work testing whether LLMs can implicitly apply such knowledge to predict behavior, or to judge whether an observed behavior is rational. Such skills are critical for appropriate interaction in social environments. We create a new dataset, SimpleTom, containing concise, diverse stories (e.g., "The can of Pringles has moldy chips in it. Mary picks up the can in the supermarket and walks to the cashier."), each with three questions that test different degrees of ToM reasoning, asking models to predict (a) mental state ("Is Mary aware of the mold?"), (b) behavior ("Will Mary pay for the chips or report the mold?"), and (c) judgment ("Mary paid for the chips. Was that reasonable?"). To our knowledge, SimpleToM is the first dataset to systematically explore downstream reasoning requiring knowledge of mental states in realistic scenarios. Our experimental results are intriguing: While most models can reliably predict mental state on our dataset (a), they often fail to correctly predict the behavior (b), and fare even worse at judging whether given behaviors are reasonable (c), despite being correctly aware of the protagonist's mental state should make such secondary predictions obvious. We further show that we can help models do better at (b) and (c) via interventions such as reminding the model of its earlier mental state answer and mental-state-specific chain-of-thought prompting, raising the action prediction accuracies (e.g., from 49.5% to 93.5% for GPT-4o) and judgment accuracies (e.g., from 15.3% to 94.7% in GPT-4o). While this shows that models can be coaxed to perform well, it requires task-specific interventions, and the natural model performances remain low, a cautionary tale for LLM deployment.

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

Colloquially speaking, image generation models based upon diffusion processes are frequently said to exhibit "hallucinations," samples that could never occur in the training data. But where do such hallucinations come from? In this paper, we study a particular failure mode in diffusion models, which we term mode interpolation. Specifically, we find that diffusion models smoothly "interpolate" between nearby data modes in the training set, to generate samples that are completely outside the support of the original training distribution; this phenomenon leads diffusion models to generate artifacts that never existed in real data (i.e., hallucinations). We systematically study the reasons for, and the manifestation of this phenomenon. Through experiments on 1D and 2D Gaussians, we show how a discontinuous loss landscape in the diffusion model's decoder leads to a region where any smooth approximation will cause such hallucinations. Through experiments on artificial datasets with various shapes, we show how hallucination leads to the generation of combinations of shapes that never existed. Finally, we show that diffusion models in fact know when they go out of support and hallucinate. This is captured by the high variance in the trajectory of the generated sample towards the final few backward sampling process. Using a simple metric to capture this variance, we can remove over 95% of hallucinations at generation time while retaining 96% of in-support samples. We conclude our exploration by showing the implications of such hallucination (and its removal) on the collapse (and stabilization) of recursive training on synthetic data with experiments on MNIST and 2D Gaussians dataset. We release our code at https://github.com/locuslab/diffusion-model-hallucination.

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

Availability of large and diverse medical datasets is often challenged by privacy and data sharing restrictions. For successful application of machine learning techniques for disease diagnosis, prognosis, and precision medicine, large amounts of data are necessary for model building and optimization. To help overcome such limitations in the context of brain MRI, we present NeuroSynth: a collection of generative models of normative regional volumetric features derived from structural brain imaging. NeuroSynth models are trained on real brain imaging regional volumetric measures from the iSTAGING consortium, which encompasses over 40,000 MRI scans across 13 studies, incorporating covariates such as age, sex, and race. Leveraging NeuroSynth, we produce and offer 18,000 synthetic samples spanning the adult lifespan (ages 22-90 years), alongside the model's capability to generate unlimited data. Experimental results indicate that samples generated from NeuroSynth agree with the distributions obtained from real data. Most importantly, the generated normative data significantly enhance the accuracy of downstream machine learning models on tasks such as disease classification. Data and models are available at: https://huggingface.co/spaces/rongguangw/neuro-synth.

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

Visual search is a ubiquitous and often challenging daily task, exemplified by looking for the car keys at home or a friend in a crowd. An intriguing property of some classical search tasks is an asymmetry such that finding a target A among distractors B can be easier than finding B among A. To elucidate the mechanisms responsible for asymmetry in visual search, we propose a computational model that takes a target and a search image as inputs and produces a sequence of eye movements until the target is found. The model integrates eccentricity-dependent visual recognition with target-dependent top-down cues. We compared the model against human behavior in six paradigmatic search tasks that show asymmetry in humans. Without prior exposure to the stimuli or task-specific training, the model provides a plausible mechanism for search asymmetry. We hypothesized that the polarity of search asymmetry arises from experience with the natural environment. We tested this hypothesis by training the model on augmented versions of ImageNet where the biases of natural images were either removed or reversed. The polarity of search asymmetry disappeared or was altered depending on the training protocol. This study highlights how classical perceptual properties can emerge in neural network models, without the need for task-specific training, but rather as a consequence of the statistical properties of the developmental diet fed to the model. All source code and data are publicly available at https://github.com/kreimanlab/VisualSearchAsymmetry.

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

We aim to understand grokking, a phenomenon where models generalize long after overfitting their training set. We present both a microscopic analysis anchored by an effective theory and a macroscopic analysis of phase diagrams describing learning performance across hyperparameters. We find that generalization originates from structured representations whose training dynamics and dependence on training set size can be predicted by our effective theory in a toy setting. We observe empirically the presence of four learning phases: comprehension, grokking, memorization, and confusion. We find representation learning to occur only in a "Goldilocks zone" (including comprehension and grokking) between memorization and confusion. We find on transformers the grokking phase stays closer to the memorization phase (compared to the comprehension phase), leading to delayed generalization. The Goldilocks phase is reminiscent of "intelligence from starvation" in Darwinian evolution, where resource limitations drive discovery of more efficient solutions. This study not only provides intuitive explanations of the origin of grokking, but also highlights the usefulness of physics-inspired tools, e.g., effective theories and phase diagrams, for understanding deep learning.

Mathematical reasoning is an increasingly important indicator of large language model (LLM) capabilities, yet we lack understanding of how LLMs process even simple mathematical tasks. To address this, we reverse engineer how three mid-sized LLMs compute addition. We first discover that numbers are represented in these LLMs as a generalized helix, which is strongly causally implicated for the tasks of addition and subtraction, and is also causally relevant for integer division, multiplication, and modular arithmetic. We then propose that LLMs compute addition by manipulating this generalized helix using the "Clock" algorithm: to solve a+b, the helices for a and b are manipulated to produce the a+b answer helix which is then read out to model logits. We model influential MLP outputs, attention head outputs, and even individual neuron preactivations with these helices and verify our understanding with causal interventions. By demonstrating that LLMs represent numbers on a helix and manipulate this helix to perform addition, we present the first representation-level explanation of an LLM's mathematical capability.

Work in psychology has highlighted that the geometric model of similarity standard in deep learning is not psychologically plausible because its metric properties such as symmetry do not align with human perception. In contrast, Tversky (1977) proposed an axiomatic theory of similarity based on a representation of objects as sets of features, and their similarity as a function of common and distinctive features. However, this model has not been used in deep learning before, partly due to the challenge of incorporating discrete set operations. We develop a differentiable parameterization of Tversky's similarity that is learnable through gradient descent, and derive neural network building blocks such as the Tversky projection layer, which unlike the linear projection layer can model non-linear functions such as XOR. Through experiments with image recognition and language modeling, we show that the Tversky projection layer is a beneficial replacement for the linear projection layer, which employs geometric similarity. On the NABirds image classification task, a frozen ResNet-50 adapted with a Tversky projection layer achieves a 24.7% relative accuracy improvement over the linear layer adapter baseline. With Tversky projection layers, GPT-2's perplexity on PTB decreases by 7.5%, and its parameter count by 34.8%. Finally, we propose a unified interpretation of both projection layers as computing similarities of input stimuli to learned prototypes, for which we also propose a novel visualization technique highlighting the interpretability of Tversky projection layers. Our work offers a new paradigm for thinking about the similarity model implicit in deep learning, and designing networks that are interpretable under an established theory of psychological similarity.

Understanding how humans conceptualize and categorize natural objects offers critical insights into perception and cognition. With the advent of Large Language Models (LLMs), a key question arises: can these models develop human-like object representations from linguistic and multimodal data? In this study, we combined behavioral and neuroimaging analyses to explore the relationship between object concept representations in LLMs and human cognition. We collected 4.7 million triplet judgments from LLMs and Multimodal LLMs (MLLMs) to derive low-dimensional embeddings that capture the similarity structure of 1,854 natural objects. The resulting 66-dimensional embeddings were stable, predictive, and exhibited semantic clustering similar to human mental representations. Remarkably, the dimensions underlying these embeddings were interpretable, suggesting that LLMs and MLLMs develop human-like conceptual representations of objects. Further analysis showed strong alignment between model embeddings and neural activity patterns in brain regions such as EBA, PPA, RSC, and FFA. This provides compelling evidence that the object representations in LLMs, while not identical to human ones, share fundamental similarities that reflect key aspects of human conceptual knowledge. Our findings advance the understanding of machine intelligence and inform the development of more human-like artificial cognitive systems.

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.

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

Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel results better than human experts. To evaluate this possibility, we created BrainBench, a forward-looking benchmark for predicting neuroscience results. We find that LLMs surpass experts in predicting experimental outcomes. BrainGPT, an LLM we tuned on the neuroscience literature, performed better yet. Like human experts, when LLMs were confident in their predictions, they were more likely to be correct, which presages a future where humans and LLMs team together to make discoveries. Our approach is not neuroscience-specific and is transferable to other knowledge-intensive endeavors.

Understanding how language model performance varies with scale is critical to benchmark and algorithm development. Scaling laws are one approach to building this understanding, but the requirement of training models across many different scales has limited their use. We propose an alternative, observational approach that bypasses model training and instead builds scaling laws from ~80 publically available models. Building a single scaling law from multiple model families is challenging due to large variations in their training compute efficiencies and capabilities. However, we show that these variations are consistent with a simple, generalized scaling law where language model performance is a function of a low-dimensional capability space, and model families only vary in their efficiency in converting training compute to capabilities. Using this approach, we show the surprising predictability of complex scaling phenomena: we show that several emergent phenomena follow a smooth, sigmoidal behavior and are predictable from small models; we show that the agent performance of models such as GPT-4 can be precisely predicted from simpler non-agentic benchmarks; and we show how to predict the impact of post-training interventions like Chain-of-Thought and Self-Consistency as language model capabilities continue to improve.

A brain tumour is a mass or cluster of abnormal cells in the brain, which has the possibility of becoming life-threatening because of its ability to invade neighbouring tissues and also form metastases. An accurate diagnosis is essential for successful treatment planning and magnetic resonance imaging is the principal imaging modality for diagnostic of brain tumours and their extent. Deep Learning methods in computer vision applications have shown significant improvement in recent years, most of which can be credited to the fact that a sizeable amount of data is available to train models on, and the improvements in the model architectures yielding better approximations in a supervised setting. Classifying tumours using such deep learning methods has made significant progress with the availability of open datasets with reliable annotations. Typically those methods are either 3D models, which use 3D volumetric MRIs or even 2D models considering each slice separately. However, by treating the slice spatial dimension separately, spatiotemporal models can be employed as spatiospatial models for this task. These models have the capabilities of learning specific spatial and temporal relationship, while reducing computational costs. This paper uses two spatiotemporal models, ResNet (2+1)D and ResNet Mixed Convolution, to classify different types of brain tumours. It was observed that both these models performed superior to the pure 3D convolutional model, ResNet18. Furthermore, it was also observed that pre-training the models on a different, even unrelated dataset before training them for the task of tumour classification improves the performance. Finally, Pre-trained ResNet Mixed Convolution was observed to be the best model in these experiments, achieving a macro F1-score of 0.93 and a test accuracy of 96.98\%, while at the same time being the model with the least computational cost.

Brain signal visualization has emerged as an active research area, serving as a critical interface between the human visual system and computer vision models. Although diffusion models have shown promise in analyzing functional magnetic resonance imaging (fMRI) data, including reconstructing high-quality images consistent with original visual stimuli, their accuracy in extracting semantic and silhouette information from brain signals remains limited. In this regard, we propose a novel approach, referred to as Controllable Mind Visual Diffusion Model (CMVDM). CMVDM extracts semantic and silhouette information from fMRI data using attribute alignment and assistant networks. Additionally, a residual block is incorporated to capture information beyond semantic and silhouette features. We then leverage a control model to fully exploit the extracted information for image synthesis, resulting in generated images that closely resemble the visual stimuli in terms of semantics and silhouette. Through extensive experimentation, we demonstrate that CMVDM outperforms existing state-of-the-art methods both qualitatively and quantitatively.

Temporal context is essential for robotic manipulation because such tasks are inherently non-Markovian, yet mainstream VLA models typically overlook it and struggle with long-horizon, temporally dependent tasks. Cognitive science suggests that humans rely on working memory to buffer short-lived representations for immediate control, while the hippocampal system preserves verbatim episodic details and semantic gist of past experience for long-term memory. Inspired by these mechanisms, we propose MemoryVLA, a Cognition-Memory-Action framework for long-horizon robotic manipulation. A pretrained VLM encodes the observation into perceptual and cognitive tokens that form working memory, while a Perceptual-Cognitive Memory Bank stores low-level details and high-level semantics consolidated from it. Working memory retrieves decision-relevant entries from the bank, adaptively fuses them with current tokens, and updates the bank by merging redundancies. Using these tokens, a memory-conditioned diffusion action expert yields temporally aware action sequences. We evaluate MemoryVLA on 150+ simulation and real-world tasks across three robots. On SimplerEnv-Bridge, Fractal, and LIBERO-5 suites, it achieves 71.9%, 72.7%, and 96.5% success rates, respectively, all outperforming state-of-the-art baselines CogACT and pi-0, with a notable +14.6 gain on Bridge. On 12 real-world tasks spanning general skills and long-horizon temporal dependencies, MemoryVLA achieves 84.0% success rate, with long-horizon tasks showing a +26 improvement over state-of-the-art baseline. Project Page: https://shihao1895.github.io/MemoryVLA

Large language model (LLM)-based decision-making agents have shown the ability to generalize across multiple tasks. However, their performance relies on massive data and compute. We argue that this inefficiency stems from the forgetting phenomenon, in which a model memorizes its behaviors in parameters throughout training. As a result, training on a new task may deteriorate the model's performance on previous tasks. In contrast to LLMs' implicit memory mechanism, the human brain utilizes distributed memory storage, which helps manage and organize multiple skills efficiently, mitigating the forgetting phenomenon. Thus inspired, we propose an internal working memory module to store, blend, and retrieve information for different downstream tasks. Evaluation results show that the proposed method improves training efficiency and generalization in both Atari games and meta-world object manipulation tasks. Moreover, we demonstrate that memory fine-tuning further enhances the adaptability of the proposed architecture.

Large Language Models (LLMs) are prone to hallucination, the generation of plausible yet factually incorrect statements. This work investigates the intrinsic, architectural origins of this failure mode through three primary contributions.First, to enable the reliable tracing of internal semantic failures, we propose Distributional Semantics Tracing (DST), a unified framework that integrates established interpretability techniques to produce a causal map of a model's reasoning, treating meaning as a function of context (distributional semantics). Second, we pinpoint the model's layer at which a hallucination becomes inevitable, identifying a specific commitment layer where a model's internal representations irreversibly diverge from factuality. Third, we identify the underlying mechanism for these failures. We observe a conflict between distinct computational pathways, which we interpret using the lens of dual-process theory: a fast, heuristic associative pathway (akin to System 1) and a slow, deliberate contextual pathway (akin to System 2), leading to predictable failure modes such as Reasoning Shortcut Hijacks. Our framework's ability to quantify the coherence of the contextual pathway reveals a strong negative correlation (rho = -0.863) with hallucination rates, implying that these failures are predictable consequences of internal semantic weakness. The result is a mechanistic account of how, when, and why hallucinations occur within the Transformer architecture.

Do large language models (LLMs) solve reasoning tasks by learning robust generalizable algorithms, or do they memorize training data? To investigate this question, we use arithmetic reasoning as a representative task. Using causal analysis, we identify a subset of the model (a circuit) that explains most of the model's behavior for basic arithmetic logic and examine its functionality. By zooming in on the level of individual circuit neurons, we discover a sparse set of important neurons that implement simple heuristics. Each heuristic identifies a numerical input pattern and outputs corresponding answers. We hypothesize that the combination of these heuristic neurons is the mechanism used to produce correct arithmetic answers. To test this, we categorize each neuron into several heuristic types-such as neurons that activate when an operand falls within a certain range-and find that the unordered combination of these heuristic types is the mechanism that explains most of the model's accuracy on arithmetic prompts. Finally, we demonstrate that this mechanism appears as the main source of arithmetic accuracy early in training. Overall, our experimental results across several LLMs show that LLMs perform arithmetic using neither robust algorithms nor memorization; rather, they rely on a "bag of heuristics".

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.

Temporal point processes (TPP) are a natural tool for modeling event-based data. Among all TPP models, Hawkes processes have proven to be the most widely used, mainly due to their adequate modeling for various applications, particularly when considering exponential or non-parametric kernels. Although non-parametric kernels are an option, such models require large datasets. While exponential kernels are more data efficient and relevant for specific applications where events immediately trigger more events, they are ill-suited for applications where latencies need to be estimated, such as in neuroscience. This work aims to offer an efficient solution to TPP inference using general parametric kernels with finite support. The developed solution consists of a fast ell_2 gradient-based solver leveraging a discretized version of the events. After theoretically supporting the use of discretization, the statistical and computational efficiency of the novel approach is demonstrated through various numerical experiments. Finally, the method's effectiveness is evaluated by modeling the occurrence of stimuli-induced patterns from brain signals recorded with magnetoencephalography (MEG). Given the use of general parametric kernels, results show that the proposed approach leads to an improved estimation of pattern latency than the state-of-the-art.

Over more than a decade there has been an extensive research effort on how to effectively utilize recurrent models and attention. While recurrent models aim to compress the data into a fixed-size memory (called hidden state), attention allows attending to the entire context window, capturing the direct dependencies of all tokens. This more accurate modeling of dependencies, however, comes with a quadratic cost, limiting the model to a fixed-length context. We present a new neural long-term memory module that learns to memorize historical context and helps attention to attend to the current context while utilizing long past information. We show that this neural memory has the advantage of fast parallelizable training while maintaining a fast inference. From a memory perspective, we argue that attention due to its limited context but accurate dependency modeling performs as a short-term memory, while neural memory due to its ability to memorize the data, acts as a long-term, more persistent, memory. Based on these two modules, we introduce a new family of architectures, called Titans, and present three variants to address how one can effectively incorporate memory into this architecture. Our experimental results on language modeling, common-sense reasoning, genomics, and time series tasks show that Titans are more effective than Transformers and recent modern linear recurrent models. They further can effectively scale to larger than 2M context window size with higher accuracy in needle-in-haystack tasks compared to baselines.

Despite their recent successes, Transformer-based large language models show surprising failure modes. A well-known example of such failure modes is their inability to length-generalize: solving problem instances at inference time that are longer than those seen during training. In this work, we further explore the root cause of this failure by performing a detailed analysis of model behaviors on the simple parity task. Our analysis suggests that length generalization failures are intricately related to a model's inability to perform random memory accesses within its context window. We present supporting evidence for this hypothesis by demonstrating the effectiveness of methodologies that circumvent the need for indexing or that enable random token access indirectly, through content-based addressing. We further show where and how the failure to perform random memory access manifests through attention map visualizations.

This study introduces a parameter-efficient Hierarchical Spatial Temporal Network (HiSTN) specifically designed for the task of emotion classification using multi-channel electroencephalogram data. The network incorporates a graph hierarchy constructed from bottom-up at various abstraction levels, offering the dual advantages of enhanced task-relevant deep feature extraction and a lightweight design. The model's effectiveness is further amplified when used in conjunction with a proposed unique label smoothing method. Comprehensive benchmark experiments reveal that this combined approach yields high, balanced performance in terms of both quantitative and qualitative predictions. HiSTN, which has approximately 1,000 parameters, achieves mean F1 scores of 96.82% (valence) and 95.62% (arousal) in subject-dependent tests on the rarely-utilized 5-classification task problem from the DREAMER dataset. In the subject-independent settings, the same model yields mean F1 scores of 78.34% for valence and 81.59% for arousal. The adoption of the Sequential Top-2 Hit Rate (Seq2HR) metric highlights the significant enhancements in terms of the balance between model's quantitative and qualitative for predictions achieved through our approach when compared to training with regular one-hot labels. These improvements surpass 50% in subject-dependent tasks and 30% in subject-independent tasks. The study also includes relevant ablation studies and case explorations to further elucidate the workings of the proposed model and enhance its interpretability.

Increasing the number of parameters in language models is a common strategy to enhance their performance. However, smaller language models remain valuable due to their lower operational costs. Despite their advantages, smaller models frequently underperform compared to their larger counterparts, even when provided with equivalent data and computational resources. Specifically, their performance tends to degrade in the late pretraining phase. This is anecdotally attributed to their reduced representational capacity. Yet, the exact causes of this performance degradation remain unclear. We use the Pythia model suite to analyse the training dynamics that underlie this phenomenon. Across different model sizes, we investigate the convergence of the Attention and MLP activations to their final state and examine how the effective rank of their parameters influences this process. We find that nearly all layers in larger models stabilise early in training - within the first 20% - whereas layers in smaller models exhibit slower and less stable convergence, especially when their parameters have lower effective rank. By linking the convergence of layers' activations to their parameters' effective rank, our analyses can guide future work to address inefficiencies in the learning dynamics of small models.

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

Recent work has proposed the linear representation hypothesis: that language models perform computation by manipulating one-dimensional representations of concepts ("features") in activation space. In contrast, we explore whether some language model representations may be inherently multi-dimensional. We begin by developing a rigorous definition of irreducible multi-dimensional features based on whether they can be decomposed into either independent or non-co-occurring lower-dimensional features. Motivated by these definitions, we design a scalable method that uses sparse autoencoders to automatically find multi-dimensional features in GPT-2 and Mistral 7B. These auto-discovered features include strikingly interpretable examples, e.g. circular features representing days of the week and months of the year. We identify tasks where these exact circles are used to solve computational problems involving modular arithmetic in days of the week and months of the year. Finally, we provide evidence that these circular features are indeed the fundamental unit of computation in these tasks with intervention experiments on Mistral 7B and Llama 3 8B, and we find further circular representations by breaking down the hidden states for these tasks into interpretable components.

This study introduces BrainTransformers, an innovative Large Language Model (LLM) implemented using Spiking Neural Networks (SNN). Our key contributions include: (1) designing SNN-compatible Transformer components such as SNNMatmul, SNNSoftmax, and SNNSiLU; (2) implementing an SNN approximation of the SiLU activation function; and (3) developing a Synapsis module to simulate synaptic plasticity. Our 3-billion parameter model, BrainTransformers-3B-Chat, demonstrates competitive performance across various benchmarks, including MMLU (63.2), BBH (54.1), ARC-C (54.3), and GSM8K (76.3), while potentially offering improved energy efficiency and biological plausibility. The model employs a three-stage training approach, including SNN-specific neuronal synaptic plasticity training. This research opens new avenues for brain-like AI systems in natural language processing and neuromorphic computing. Future work will focus on hardware optimization, developing specialized SNN fine-tuning tools, and exploring practical applications in energy-efficient computing environments.

Predictive Coding (PC) is a theoretical framework in cognitive science suggesting that the human brain processes cognition through spatiotemporal prediction of the visual world. Existing studies have developed spatiotemporal prediction neural networks based on the PC theory, emulating its two core mechanisms: Correcting predictions from residuals and hierarchical learning. However, these models do not show the enhancement of prediction skills on real-world forecasting tasks and ignore the Precision Weighting mechanism of PC theory. The precision weighting mechanism posits that the brain allocates more attention to signals with lower precision, contributing to the cognitive ability of human brains. This work introduces the Cognitive Diffusion Probabilistic Models (CogDPM), which demonstrate the connection between diffusion probabilistic models and PC theory. CogDPM features a precision estimation method based on the hierarchical sampling capabilities of diffusion models and weight the guidance with precision weights estimated by the inherent property of diffusion models. We experimentally show that the precision weights effectively estimate the data predictability. We apply CogDPM to real-world prediction tasks using the United Kindom precipitation and ERA surface wind datasets. Our results demonstrate that CogDPM outperforms both existing domain-specific operational models and general deep prediction models by providing more proficient forecasting.

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.

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.

Large language models perform near-Bayesian inference yet violate permutation invariance on exchangeable data. We resolve this by showing transformers minimize expected conditional description length (cross-entropy) over orderings, E_pi[ell(Y mid Gamma_pi(X))], which admits a Kolmogorov-complexity interpretation up to additive constants, rather than the permutation-invariant description length ell(Y mid X). This makes them Bayesian in expectation, not in realization. We derive (i) a Quantified Martingale Violation bound showing order-induced deviations scale as O(log n) with constants; (ii) the Expectation-level Decompression Law linking information budgets to reliability for Bernoulli predicates; and (iii) deployable planners (B2T/RoH/ISR) for answer/abstain decisions. Empirically, permutation dispersion follows a+bln n (Qwen2-7B b approx 0.377, Llama-3.1-8B b approx 0.147); permutation mixtures improve ground-truth likelihood/accuracy; and randomized dose-response shows hallucinations drop by sim 0.13 per additional nat. A pre-specified audit with a fixed ISR=1.0 achieves near-0\% hallucinations via calibrated refusal at 24\% abstention. The framework turns hallucinations into predictable compression failures and enables principled information budgeting.

Large-scale pretrained language models (LMs) are said to ``lack the ability to connect utterances to the world'' (Bender and Koller, 2020), because they do not have ``mental models of the world' '(Mitchell and Krakauer, 2023). If so, one would expect LM representations to be unrelated to representations induced by vision models. We present an empirical evaluation across four families of LMs (BERT, GPT-2, OPT and LLaMA-2) and three vision model architectures (ResNet, SegFormer, and MAE). Our experiments show that LMs partially converge towards representations isomorphic to those of vision models, subject to dispersion, polysemy and frequency. This has important implications for both multi-modal processing and the LM understanding debate (Mitchell and Krakauer, 2023).

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

We investigate in-context temporal biases in attention heads and transformer outputs. Using cognitive science methodologies, we analyze attention scores and outputs of the GPT-2 models of varying sizes. Across attention heads, we observe effects characteristic of human episodic memory, including temporal contiguity, primacy and recency. Transformer outputs demonstrate a tendency toward in-context serial recall. Importantly, this effect is eliminated after the ablation of the induction heads, which are the driving force behind the contiguity effect. Our findings offer insights into how transformers organize information temporally during in-context learning, shedding light on their similarities and differences with human memory and learning.

Memory is fundamental to intelligence, enabling learning, reasoning, and adaptability across biological and artificial systems. While Transformer architectures excel at sequence modeling, they face critical limitations in long-range context retention, continual learning, and knowledge integration. This review presents a unified framework bridging neuroscience principles, including dynamic multi-timescale memory, selective attention, and consolidation, with engineering advances in Memory-Augmented Transformers. We organize recent progress through three taxonomic dimensions: functional objectives (context extension, reasoning, knowledge integration, adaptation), memory representations (parameter-encoded, state-based, explicit, hybrid), and integration mechanisms (attention fusion, gated control, associative retrieval). Our analysis of core memory operations (reading, writing, forgetting, and capacity management) reveals a shift from static caches toward adaptive, test-time learning systems. We identify persistent challenges in scalability and interference, alongside emerging solutions including hierarchical buffering and surprise-gated updates. This synthesis provides a roadmap toward cognitively-inspired, lifelong-learning Transformer architectures.

Large Language Models (LLMs) and Large Multi-modality Models (LMMs) have demonstrated remarkable decision masking capabilities on a variety of tasks. However, they inherently operate planning within the language space, lacking the vision and spatial imagination ability. In contrast, humans utilize both left and right hemispheres of the brain for language and visual planning during the thinking process. Therefore, we introduce a novel vision-language planning framework in this work to perform concurrent visual and language planning for tasks with inputs of any form. Our framework incorporates visual planning to capture intricate environmental details, while language planning enhances the logical coherence of the overall system. We evaluate the effectiveness of our framework across vision-language tasks, vision-only tasks, and language-only tasks. The results demonstrate the superior performance of our approach, indicating that the integration of visual and language planning yields better contextually aware task execution.

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

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

This paper discusses a simple and explicit toy-model example of the categorical Hopfield equations introduced in previous work of Manin and the author. These describe dynamical assignments of resources to networks, where resources are objects in unital symmetric monoidal categories and assignments are realized by summing functors. The special case discussed here is based on computational resources (computational models of neurons) as objects in a category of DNNs, with a simple choice of the endofunctors defining the Hopfield equations that reproduce the usual updating of the weights in DNNs by gradient descent.

Reconstructing human vision from brain activities has been an appealing task that helps to understand our cognitive process. Even though recent research has seen great success in reconstructing static images from non-invasive brain recordings, work on recovering continuous visual experiences in the form of videos is limited. In this work, we propose Mind-Video that learns spatiotemporal information from continuous fMRI data of the cerebral cortex progressively through masked brain modeling, multimodal contrastive learning with spatiotemporal attention, and co-training with an augmented Stable Diffusion model that incorporates network temporal inflation. We show that high-quality videos of arbitrary frame rates can be reconstructed with Mind-Video using adversarial guidance. The recovered videos were evaluated with various semantic and pixel-level metrics. We achieved an average accuracy of 85% in semantic classification tasks and 0.19 in structural similarity index (SSIM), outperforming the previous state-of-the-art by 45%. We also show that our model is biologically plausible and interpretable, reflecting established physiological processes.

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.

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

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.

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

Characterizing the relationship between neural population activity and behavioral data is a central goal of neuroscience. While latent variable models (LVMs) are successful in describing high-dimensional time-series data, they are typically only designed for a single type of data, making it difficult to identify structure shared across different experimental data modalities. Here, we address this shortcoming by proposing an unsupervised LVM which extracts temporally evolving shared and independent latents for distinct, simultaneously recorded experimental modalities. We do this by combining Gaussian Process Factor Analysis (GPFA), an interpretable LVM for neural spiking data with temporally smooth latent space, with Gaussian Process Variational Autoencoders (GP-VAEs), which similarly use a GP prior to characterize correlations in a latent space, but admit rich expressivity due to a deep neural network mapping to observations. We achieve interpretability in our model by partitioning latent variability into components that are either shared between or independent to each modality. We parameterize the latents of our model in the Fourier domain, and show improved latent identification using this approach over standard GP-VAE methods. We validate our model on simulated multi-modal data consisting of Poisson spike counts and MNIST images that scale and rotate smoothly over time. We show that the multi-modal GP-VAE (MM-GPVAE) is able to not only identify the shared and independent latent structure across modalities accurately, but provides good reconstructions of both images and neural rates on held-out trials. Finally, we demonstrate our framework on two real world multi-modal experimental settings: Drosophila whole-brain calcium imaging alongside tracked limb positions, and Manduca sexta spike train measurements from ten wing muscles as the animal tracks a visual stimulus.

Sequence modeling plays a vital role across various domains, with recurrent neural networks being historically the predominant method of performing these tasks. However, the emergence of transformers has altered this paradigm due to their superior performance. Built upon these advances, transformers have conjoined CNNs as two leading foundational models for learning visual representations. However, transformers are hindered by the O(N^2) complexity of their attention mechanisms, while CNNs lack global receptive fields and dynamic weight allocation. State Space Models (SSMs), specifically the \textbf{Mamba} model with selection mechanisms and hardware-aware architecture, have garnered immense interest lately in sequential modeling and visual representation learning, challenging the dominance of transformers by providing infinite context lengths and offering substantial efficiency maintaining linear complexity in the input sequence. Capitalizing on the advances in computer vision, medical imaging has heralded a new epoch with Mamba models. Intending to help researchers navigate the surge, this survey seeks to offer an encyclopedic review of Mamba models in medical imaging. Specifically, we start with a comprehensive theoretical review forming the basis of SSMs, including Mamba architecture and its alternatives for sequence modeling paradigms in this context. Next, we offer a structured classification of Mamba models in the medical field and introduce a diverse categorization scheme based on their application, imaging modalities, and targeted organs. Finally, we summarize key challenges, discuss different future research directions of the SSMs in the medical domain, and propose several directions to fulfill the demands of this field. In addition, we have compiled the studies discussed in this paper along with their open-source implementations on our GitHub repository.

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

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.

Test-time Scaling (TTS) has been demonstrated to significantly enhance the reasoning capabilities of Large Language Models (LLMs) during the inference phase without altering model parameters. However, existing TTS methods are largely independent, implying that LLMs have not yet evolved to progressively learn how to scale more effectively. With the objective of evolving LLMs to learn ``how to scale test-time computation,'' we propose LatentEvolve, a self-evolving latent TTS framework inspired by the complementary learning system (CLS) theory. Analogous to the human brain's dual system of a fast-recall hippocampus and a slow-consolidating neocortex, LatentEvolve comprises two evolutionary components: daytime scaling, which rapidly retrieves historical latent representations to better guide current LLM reasoning; and nighttime scaling, which integrates past latent optimizations in a manner akin to the human brain's consolidation of experiences during sleep. The alternation of daytime and nighttime processes facilitates a fast and slow evolution of LLM TTS, mirroring human cognitive dynamics in a fully unsupervised manner. Extensive experiments across eight benchmarks and five model backbones demonstrate that our LatentEvolve surpasses state-of-the-art TTS methods such as LatentSeek and TTRL by up to 13.33% and exhibits exceptional cross-domain and cross-backbone generalization.

Speech language models align with human brain responses to natural language to an impressive degree. However, current models rely heavily on low-level speech features, indicating they lack brain-relevant semantics which limits their utility as model organisms of semantic processing in the brain. In this work, we address this limitation by inducing brain-relevant bias directly into the models via fine-tuning with fMRI recordings of people listening to natural stories, a process we name brain-tuning. After testing it on 3 different pretrained model families, we show that brain-tuning not only improves overall alignment with new brain recordings in semantic language regions, but also reduces the reliance on low-level speech features for this alignment. Excitingly, we further show that brain-tuning leads to 1) consistent improvements in performance on a range of downstream tasks and 2) a representational space with increased semantic preference. Our results provide converging evidence, for the first time, that incorporating brain signals into the training of language models improves the models' semantic understanding.

Recent advancements in large language models (LLMs) with billions of parameters have improved performance in various applications, but their inference processes demand significant energy and computational resources. In contrast, the human brain, with approximately 86 billion neurons, is much more energy-efficient than LLMs with similar parameters. Inspired by this, we redesign 7sim70 billion parameter LLMs using bio-plausible spiking mechanisms, emulating the efficient behavior of the human brain. We propose the first spiking large language model, SpikeLLM. Coupled with the proposed model, two essential approaches are proposed to improve spike training efficiency: Generalized Integrate-and-Fire (GIF) neurons to compress spike length from T to T{L} log_2 L bits, and an Optimal Brain Spiking framework to divide outlier channels and allocate different T for GIF neurons, which further compresses spike length to approximate log_2T bits. The necessity of spike-driven LLM is proved by comparison with quantized LLMs with similar operations. In the OmniQuant pipeline, SpikeLLM reduces 11.01% WikiText2 perplexity and improves 2.55% accuracy of common scene reasoning on a LLAMA-7B W4A4 model. In the GPTQ pipeline, SpikeLLM achieves direct additive in linear layers, significantly exceeding PB-LLMs.

Inspired by the Many-Worlds Interpretation (MWI), this work introduces a novel neural network architecture that splits the same input signal into parallel branches at each layer, utilizing a Hyper Rectified Activation, referred to as ANDHRA. The branched layers do not merge and form separate network paths, leading to multiple network heads for output prediction. For a network with a branching factor of 2 at three levels, the total number of heads is 2^3 = 8 . The individual heads are jointly trained by combining their respective loss values. However, the proposed architecture requires additional parameters and memory during training due to the additional branches. During inference, the experimental results on CIFAR-10/100 demonstrate that there exists one individual head that outperforms the baseline accuracy, achieving statistically significant improvement with equal parameters and computational cost.

We consider the solvable neural scaling model with three parameters: data complexity, target complexity, and model-parameter-count. We use this neural scaling model to derive new predictions about the compute-limited, infinite-data scaling law regime. To train the neural scaling model, we run one-pass stochastic gradient descent on a mean-squared loss. We derive a representation of the loss curves which holds over all iteration counts and improves in accuracy as the model parameter count grows. We then analyze the compute-optimal model-parameter-count, and identify 4 phases (+3 subphases) in the data-complexity/target-complexity phase-plane. The phase boundaries are determined by the relative importance of model capacity, optimizer noise, and embedding of the features. We furthermore derive, with mathematical proof and extensive numerical evidence, the scaling-law exponents in all of these phases, in particular computing the optimal model-parameter-count as a function of floating point operation budget.

Learning arguably involves the discovery and memorization of abstract rules. The aim of this paper is to study associative memory mechanisms. Our model is based on high-dimensional matrices consisting of outer products of embeddings, which relates to the inner layers of transformer language models. We derive precise scaling laws with respect to sample size and parameter size, and discuss the statistical efficiency of different estimators, including optimization-based algorithms. We provide extensive numerical experiments to validate and interpret theoretical results, including fine-grained visualizations of the stored memory associations.

Can Vision Language Models (VLMs) imagine the full scene from just a few views, like humans do? Humans form spatial mental models, internal representations of unseen space, to reason about layout, perspective, and motion. Our new MindCube benchmark with 21,154 questions across 3,268 images exposes this critical gap, where existing VLMs exhibit near-random performance. Using MindCube, we systematically evaluate how well VLMs build robust spatial mental models through representing positions (cognitive mapping), orientations (perspective-taking), and dynamics (mental simulation for "what-if" movements). We then explore three approaches to help VLMs approximate spatial mental models, including unseen intermediate views, natural language reasoning chains, and cognitive maps. The significant improvement comes from a synergistic approach, "map-then-reason", that jointly trains the model to first generate a cognitive map and then reason upon it. By training models to reason over these internal maps, we boosted accuracy from 37.8% to 60.8% (+23.0%). Adding reinforcement learning pushed performance even further to 70.7% (+32.9%). Our key insight is that such scaffolding of spatial mental models, actively constructing and utilizing internal structured spatial representations with flexible reasoning processes, significantly improves understanding of unobservable space.

Objective: Electroencephalography signals are recorded as a multidimensional dataset. We propose a new framework based on the augmented covariance extracted from an autoregressive model to improve motor imagery classification. Methods: From the autoregressive model can be derived the Yule-Walker equations, which show the emergence of a symmetric positive definite matrix: the augmented covariance matrix. The state-of the art for classifying covariance matrices is based on Riemannian Geometry. A fairly natural idea is therefore to extend the standard approach using these augmented covariance matrices. The methodology for creating the augmented covariance matrix shows a natural connection with the delay embedding theorem proposed by Takens for dynamical systems. Such an embedding method is based on the knowledge of two parameters: the delay and the embedding dimension, respectively related to the lag and the order of the autoregressive model. This approach provides new methods to compute the hyper-parameters in addition to standard grid search. Results: The augmented covariance matrix performed noticeably better than any state-of-the-art methods. We will test our approach on several datasets and several subjects using the MOABB framework, using both within-session and cross-session evaluation. Conclusion: The improvement in results is due to the fact that the augmented covariance matrix incorporates not only spatial but also temporal information, incorporating nonlinear components of the signal through an embedding procedure, which allows the leveraging of dynamical systems algorithms. Significance: These results extend the concepts and the results of the Riemannian distance based classification algorithm.

Large language models (LLMs) can sometimes report the strategies they actually use to solve tasks, but they can also fail to do so. This suggests some degree of metacognition -- the capacity to monitor one's own cognitive processes for subsequent reporting and self-control. Metacognitive abilities enhance AI capabilities but raise safety concerns, as models might obscure their internal processes to evade neural-activation-based oversight mechanisms designed to detect harmful behaviors. Given society's increased reliance on these models, it is critical that we understand the limits of their metacognitive abilities, particularly their ability to monitor their internal activations. To address this, we introduce a neuroscience-inspired neurofeedback paradigm designed to quantify the ability of LLMs to explicitly report and control their activation patterns. By presenting models with sentence-label pairs where labels correspond to sentence-elicited internal activations along specific directions in the neural representation space, we demonstrate that LLMs can learn to report and control these activations. The performance varies with several factors: the number of example pairs provided, the semantic interpretability of the target neural direction, and the variance explained by that direction. These results reveal a "metacognitive space" with dimensionality much lower than the model's neural space, suggesting LLMs can monitor only a subset of their neural mechanisms. Our findings provide empirical evidence quantifying metacognitive capabilities in LLMs, with significant implications for AI safety.

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

Transformer-based language models excel at both recall (retrieving memorized facts) and reasoning (performing multi-step inference), but whether these abilities rely on distinct internal mechanisms remains unclear. Distinguishing recall from reasoning is crucial for predicting model generalization, designing targeted evaluations, and building safer interventions that affect one ability without disrupting the other.We approach this question through mechanistic interpretability, using controlled datasets of synthetic linguistic puzzles to probe transformer models at the layer, head, and neuron level. Our pipeline combines activation patching and structured ablations to causally measure component contributions to each task type. Across two model families (Qwen and LLaMA), we find that interventions on distinct layers and attention heads lead to selective impairments: disabling identified "recall circuits" reduces fact-retrieval accuracy by up to 15\% while leaving reasoning intact, whereas disabling "reasoning circuits" reduces multi-step inference by a comparable margin. At the neuron level, we observe task-specific firing patterns, though these effects are less robust, consistent with neuronal polysemanticity.Our results provide the first causal evidence that recall and reasoning rely on separable but interacting circuits in transformer models. These findings advance mechanistic interpretability by linking circuit-level structure to functional specialization and demonstrate how controlled datasets and causal interventions can yield mechanistic insights into model cognition, informing safer deployment of large language models.

Mainstream Transformer-based large language models face major efficiency bottlenecks: training computation scales quadratically with sequence length, and inference memory grows linearly, limiting long-context processing. Building large models on non-NVIDIA platforms also poses challenges for stable and efficient training. To address this, we introduce SpikingBrain, a family of brain-inspired models designed for efficient long-context training and inference. SpikingBrain leverages the MetaX GPU cluster and focuses on three aspects: (1) Model Architecture: linear and hybrid-linear attention architectures with adaptive spiking neurons; (2) Algorithmic Optimizations: an efficient, conversion-based training pipeline and a dedicated spike coding framework; (3) System Engineering: customized training frameworks, operator libraries, and parallelism strategies tailored to MetaX hardware. Using these techniques, we develop two models: SpikingBrain-7B, a linear LLM, and SpikingBrain-76B, a hybrid-linear MoE LLM. These models demonstrate the feasibility of large-scale LLM development on non-NVIDIA platforms. SpikingBrain achieves performance comparable to open-source Transformer baselines while using only about 150B tokens for continual pre-training. Our models significantly improve long-sequence training efficiency and deliver inference with (partially) constant memory and event-driven spiking behavior. For example, SpikingBrain-7B attains over 100x speedup in Time to First Token for 4M-token sequences. Training remains stable for weeks on hundreds of MetaX C550 GPUs, with the 7B model reaching a Model FLOPs Utilization of 23.4 percent. The proposed spiking scheme achieves 69.15 percent sparsity, enabling low-power operation. Overall, this work demonstrates the potential of brain-inspired mechanisms to drive the next generation of efficient and scalable large model design.

Multimodal large language models (MLLMs) face an inherent trade-off between faithfulness and creativity, as different tasks require varying degrees of associative reasoning. However, existing methods lack the flexibility to modulate this reasoning strength, limiting MLLMs' adaptability across factual and creative scenarios. To bridge this gap, we propose equipping MLLMs with mechanisms that enable flexible control over associative reasoning. We begin by investigating the internal mechanisms underlying associative behavior in MLLMs and find that: (1) middle layers play a pivotal role in shaping model's associative tendencies, (2) modifying representations in these layers effectively regulates associative reasoning strength, and (3) hallucinations can be exploited to derive steering vectors that guide this modulation. Building on these findings, we introduce Flexible Association Control (FlexAC), a lightweight and training-free framework for modulating associative behavior in MLLMs. FlexAC first induces hallucination-guided intermediate representations to encode associative directions. Then, it selects high-association instances to construct effective associative steering vectors, whose strengths are adaptively calibrated to balance creative guidance with output stability. Finally, recognizing the multi-dimensional nature of associative reasoning, FlexAC incorporates task-specific associative vectors derived from a forward pass on a few target-domain samples, enabling models to follow diverse associative directions and better adapt to creative tasks. Notably, our method achieves up to a 5.8x improvement in creativity on Creation-MMBench and a 29% reduction in hallucination rate on CHAIR, surpassing existing baselines and demonstrating its effectiveness in enabling flexible control over associative reasoning in MLLMs. Our code is available at https://github.com/ylhz/FlexAC.

Electroencephalography (EEG) offers a non-invasive lens into human brain activity, but building large-scale models is hampered by topological heterogeneity: each public EEG data defines its own electrode layout, limiting generalization. We introduce LUNA (Latent Unified Network Architecture), a self-supervised foundation model that reconciles disparate electrode geometries while scaling linearly -- not quadratically -- with channel count. LUNA compresses multi-channel EEG into a fixed-size, topology-agnostic latent space via learned queries and cross-attention. Downstream transformer blocks then operate exclusively on this latent representation using patch-wise temporal self-attention, decoupling computation from electrode count. Pre-trained on TUEG and Siena (over 21,000 hours of raw EEG across diverse montages) using a masked-patch reconstruction objective, LUNA transfers effectively to four downstream tasks: abnormality detection, artifact rejection, slowing classification, and emotion recognition. It demonstrates highly competitive performance across several benchmarks, achieving state-of-the-art results on TUAR and TUSL, e.g., 0.921 AUROC on TUAR, while reducing FLOPs by 300x and trimming GPU memory use by up to 10x. Critically, these gains are consistent across all evaluated electrode configurations. Code is available at https://github.com/pulp-bio/BioFoundation

Memorization in language models is typically treated as a homogenous phenomenon, neglecting the specifics of the memorized data. We instead model memorization as the effect of a set of complex factors that describe each sample and relate it to the model and corpus. To build intuition around these factors, we break memorization down into a taxonomy: recitation of highly duplicated sequences, reconstruction of inherently predictable sequences, and recollection of sequences that are neither. We demonstrate the usefulness of our taxonomy by using it to construct a predictive model for memorization. By analyzing dependencies and inspecting the weights of the predictive model, we find that different factors influence the likelihood of memorization differently depending on the taxonomic category.

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