Daily Papers

Facial emotion recognition (FER) models trained only on pixels often fail to generalize across datasets because facial appearance is an indirect and biased proxy for underlying affect. We present NeuroGaze-Distill, a cross-modal distillation framework that transfers brain-informed priors into an image-only FER student via static Valence/Arousal (V/A) prototypes and a depression-inspired geometric prior (D-Geo). A teacher trained on EEG topographic maps from DREAMER (with MAHNOB-HCI as unlabeled support) produces a consolidated 5x5 V/A prototype grid that is frozen and reused; no EEG-face pairing and no non-visual signals at deployment are required. The student (ResNet-18/50) is trained on FERPlus with conventional CE/KD and two lightweight regularizers: (i) Proto-KD (cosine) aligns student features to the static prototypes; (ii) D-Geo softly shapes the embedding geometry in line with affective findings often reported in depression research (e.g., anhedonia-like contraction in high-valence regions). We evaluate both within-domain (FERPlus validation) and cross-dataset protocols (AffectNet-mini; optional CK+), reporting standard 8-way scores alongside present-only Macro-F1 and balanced accuracy to fairly handle label-set mismatch. Ablations attribute consistent gains to prototypes and D-Geo, and favor 5x5 over denser grids for stability. The method is simple, deployable, and improves robustness without architectural complexity.

Recent progress in brain-guided image generation has improved the quality of fMRI-based reconstructions; however, fundamental challenges remain in preserving object-level structure and semantic fidelity. Many existing approaches overlook the spatial arrangement of salient objects, leading to conceptually inconsistent outputs. We propose a saliency-driven decoding framework that employs graph-informed saliency priors to translate structural cues from brain signals into spatial masks. These masks, together with semantic information extracted from embeddings, condition a diffusion model to guide image regeneration, helping preserve object conformity while maintaining natural scene composition. In contrast to pipelines that invoke multiple diffusion stages, our approach relies on a single frozen model, offering a more lightweight yet effective design. Experiments show that this strategy improves both conceptual alignment and structural similarity to the original stimuli, while also introducing a new direction for efficient, interpretable, and structurally grounded brain decoding.

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.

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.

Large language models (LLMs) sometimes fail to respond appropriately to deterministic tasks -- such as counting or forming acronyms -- because the implicit prior distribution they have learned over sequences of tokens influences their responses. In this work, we show that, in at least some cases, LLMs actually compute the information needed to perform these tasks correctly, and we identify some interventions that can allow them to access this information to improve their performance. First, we show that simply prompting the language model to not rely on its prior knowledge leads to dramatic improvements in prior-dominated tasks. We then use mechanistic interpretability techniques to localize the prior within the LLM and manipulate the extent to which that prior influences its responses. Specifically, we show that it is possible to identify layers of the underlying neural network that correlate with the prior probability of a response and that lightweight finetuning of these layers with basic prompts on prior-dominated tasks achieves high performance on held-out answers. These results suggest that the information required to produce a correct response is contained within the representations of the problems formed by the models. Furthermore, we show that this finetuning is significantly more effective for prior-dominated tasks, and that the error after finetuning is no longer correlated with the prior. Our results suggest that it may be possible to define effective methods for manipulating the extent to which LLMs rely upon their priors in solving problems, potentially increasing their performance in settings where LLMs hallucinate for reasons related to the prior probability of token sequences.

Posterior sampling allows the exploitation of prior knowledge of the environment's transition dynamics to improve the sample efficiency of reinforcement learning. The prior is typically specified as a class of parametric distributions, a task that can be cumbersome in practice, often resulting in the choice of uninformative priors. In this work, we propose a novel posterior sampling approach in which the prior is given as a (partial) causal graph over the environment's variables. The latter is often more natural to design, such as listing known causal dependencies between biometric features in a medical treatment study. Specifically, we propose a hierarchical Bayesian procedure, called C-PSRL, simultaneously learning the full causal graph at the higher level and the parameters of the resulting factored dynamics at the lower level. For this procedure, we provide an analysis of its Bayesian regret, which explicitly connects the regret rate with the degree of prior knowledge. Our numerical evaluation conducted in illustrative domains confirms that C-PSRL strongly improves the efficiency of posterior sampling with an uninformative prior while performing close to posterior sampling with the full causal graph.

The Bayesian treatment of neural networks dictates that a prior distribution is specified over their weight and bias parameters. This poses a challenge because modern neural networks are characterized by a large number of parameters, and the choice of these priors has an uncontrolled effect on the induced functional prior, which is the distribution of the functions obtained by sampling the parameters from their prior distribution. We argue that this is a hugely limiting aspect of Bayesian deep learning, and this work tackles this limitation in a practical and effective way. Our proposal is to reason in terms of functional priors, which are easier to elicit, and to "tune" the priors of neural network parameters in a way that they reflect such functional priors. Gaussian processes offer a rigorous framework to define prior distributions over functions, and we propose a novel and robust framework to match their prior with the functional prior of neural networks based on the minimization of their Wasserstein distance. We provide vast experimental evidence that coupling these priors with scalable Markov chain Monte Carlo sampling offers systematically large performance improvements over alternative choices of priors and state-of-the-art approximate Bayesian deep learning approaches. We consider this work a considerable step in the direction of making the long-standing challenge of carrying out a fully Bayesian treatment of neural networks, including convolutional neural networks, a concrete possibility.

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.

We propose NEURONA, a neuro-symbolic framework for fMRI decoding and concept grounding in neural activity. Leveraging image- and video-based fMRI question-answering datasets, NEURONA learns to decode interacting concepts from visual stimuli based on patterns of fMRI responses, integrating symbolic reasoning and compositional execution with fMRI grounding across brain regions. We demonstrate that incorporating structural priors (e.g., compositional predicate-argument dependencies between concepts) into the decoding process significantly improves both decoding accuracy over precise queries, and notably, generalization to unseen queries at test time. With NEURONA, we highlight neuro-symbolic frameworks as promising tools for understanding neural activity.

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.

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

Priors are essential for reconstructing images from noisy and/or incomplete measurements. The choice of the prior determines both the quality and uncertainty of recovered images. We propose turning score-based diffusion models into principled image priors ("score-based priors") for analyzing a posterior of images given measurements. Previously, probabilistic priors were limited to handcrafted regularizers and simple distributions. In this work, we empirically validate the theoretically-proven probability function of a score-based diffusion model. We show how to sample from resulting posteriors by using this probability function for variational inference. Our results, including experiments on denoising, deblurring, and interferometric imaging, suggest that score-based priors enable principled inference with a sophisticated, data-driven image prior.

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.

Can our brain signals faithfully reflect the original visual stimuli, even including high-frequency details? Although human perceptual and cognitive capacities enable us to process and remember visual information, these abilities are constrained by several factors, such as limited attentional resources and the finite capacity of visual memory. When visual stimuli are processed by human visual system into brain signals, some information is inevitably lost, leading to a discrepancy known as the System GAP. Additionally, perceptual and cognitive dynamics, along with technical noise in signal acquisition, degrade the fidelity of brain signals relative to the visual stimuli, known as the Random GAP. When encoded brain representations are directly aligned with the corresponding pretrained image features, the System GAP and Random GAP between paired data challenge the model, requiring it to bridge these gaps. However, in the context of limited paired data, these gaps are difficult for the model to learn, leading to overfitting and poor generalization to new data. To address these GAPs, we propose a simple yet effective approach called the Uncertainty-aware Blur Prior (UBP). It estimates the uncertainty within the paired data, reflecting the mismatch between brain signals and visual stimuli. Based on this uncertainty, UBP dynamically blurs the high-frequency details of the original images, reducing the impact of the mismatch and improving alignment. Our method achieves a top-1 accuracy of 50.9\% and a top-5 accuracy of 79.7\% on the zero-shot brain-to-image retrieval task, surpassing previous state-of-the-art methods by margins of 13.7\% and 9.8\%, respectively. Code is available at https://github.com/HaitaoWuTJU/Uncertainty-aware-Blur-Prior{GitHub}.

Large Vision-Language Models (LVLMs) have demonstrated outstanding performance across various multimodal tasks. However, they suffer from a problem known as language prior, where responses are generated based solely on textual patterns while disregarding image information. Addressing the issue of language prior is crucial, as it can lead to undesirable biases or hallucinations when dealing with images that are out of training distribution. Despite its importance, current methods for accurately measuring language priors in LVLMs are poorly studied. Although existing benchmarks based on counterfactual or out-of-distribution images can partially be used to measure language priors, they fail to disentangle language priors from other confounding factors. To this end, we propose a new benchmark called VLind-Bench, which is the first benchmark specifically designed to measure the language priors, or blindness, of LVLMs. It not only includes tests on counterfactual images to assess language priors but also involves a series of tests to evaluate more basic capabilities such as commonsense knowledge, visual perception, and commonsense biases. For each instance in our benchmark, we ensure that all these basic tests are passed before evaluating the language priors, thereby minimizing the influence of other factors on the assessment. The evaluation and analysis of recent LVLMs in our benchmark reveal that almost all models exhibit a significant reliance on language priors, presenting a strong challenge in the field.

Large Language Models (LLMs), despite being trained on text alone, surprisingly develop rich visual priors. These priors allow latent visual capabilities to be unlocked for vision tasks with a relatively small amount of multimodal data, and in some cases, to perform visual tasks without ever having seen an image. Through systematic analysis, we reveal that visual priors-the implicit, emergent knowledge about the visual world acquired during language pre-training-are composed of separable perception and reasoning priors with unique scaling trends and origins. We show that an LLM's latent visual reasoning ability is predominantly developed by pre-training on reasoning-centric data (e.g., code, math, academia) and scales progressively. This reasoning prior acquired from language pre-training is transferable and universally applicable to visual reasoning. In contrast, a perception prior emerges more diffusely from broad corpora, and perception ability is more sensitive to the vision encoder and visual instruction tuning data. In parallel, text describing the visual world proves crucial, though its performance impact saturates rapidly. Leveraging these insights, we propose a data-centric recipe for pre-training vision-aware LLMs and verify it in 1T token scale pre-training. Our findings are grounded in over 100 controlled experiments consuming 500,000 GPU-hours, spanning the full MLLM construction pipeline-from LLM pre-training to visual alignment and supervised multimodal fine-tuning-across five model scales, a wide range of data categories and mixtures, and multiple adaptation setups. Along with our main findings, we propose and investigate several hypotheses, and introduce the Multi-Level Existence Bench (MLE-Bench). Together, this work provides a new way of deliberately cultivating visual priors from language pre-training, paving the way for the next generation of multimodal LLMs.

Currently, it is hard to reap the benefits of deep learning for Bayesian methods, which allow the explicit specification of prior knowledge and accurately capture model uncertainty. We present Prior-Data Fitted Networks (PFNs). PFNs leverage large-scale machine learning techniques to approximate a large set of posteriors. The only requirement for PFNs to work is the ability to sample from a prior distribution over supervised learning tasks (or functions). Our method restates the objective of posterior approximation as a supervised classification problem with a set-valued input: it repeatedly draws a task (or function) from the prior, draws a set of data points and their labels from it, masks one of the labels and learns to make probabilistic predictions for it based on the set-valued input of the rest of the data points. Presented with a set of samples from a new supervised learning task as input, PFNs make probabilistic predictions for arbitrary other data points in a single forward propagation, having learned to approximate Bayesian inference. We demonstrate that PFNs can near-perfectly mimic Gaussian processes and also enable efficient Bayesian inference for intractable problems, with over 200-fold speedups in multiple setups compared to current methods. We obtain strong results in very diverse areas such as Gaussian process regression, Bayesian neural networks, classification for small tabular data sets, and few-shot image classification, demonstrating the generality of PFNs. Code and trained PFNs are released at https://github.com/automl/TransformersCanDoBayesianInference.

We present extensive empirical evidence showing that current Bayesian simulation-based inference algorithms can produce computationally unfaithful posterior approximations. Our results show that all benchmarked algorithms -- (Sequential) Neural Posterior Estimation, (Sequential) Neural Ratio Estimation, Sequential Neural Likelihood and variants of Approximate Bayesian Computation -- can yield overconfident posterior approximations, which makes them unreliable for scientific use cases and falsificationist inquiry. Failing to address this issue may reduce the range of applicability of simulation-based inference. For this reason, we argue that research efforts should be made towards theoretical and methodological developments of conservative approximate inference algorithms and present research directions towards this objective. In this regard, we show empirical evidence that ensembling posterior surrogates provides more reliable approximations and mitigates the issue.

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

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.

Powerful priors allow us to perform inference with insufficient information. In this paper, we propose an autoregressive prior for 3D shapes to solve multimodal 3D tasks such as shape completion, reconstruction, and generation. We model the distribution over 3D shapes as a non-sequential autoregressive distribution over a discretized, low-dimensional, symbolic grid-like latent representation of 3D shapes. This enables us to represent distributions over 3D shapes conditioned on information from an arbitrary set of spatially anchored query locations and thus perform shape completion in such arbitrary settings (e.g., generating a complete chair given only a view of the back leg). We also show that the learned autoregressive prior can be leveraged for conditional tasks such as single-view reconstruction and language-based generation. This is achieved by learning task-specific naive conditionals which can be approximated by light-weight models trained on minimal paired data. We validate the effectiveness of the proposed method using both quantitative and qualitative evaluation and show that the proposed method outperforms the specialized state-of-the-art methods trained for individual tasks. The project page with code and video visualizations can be found at https://yccyenchicheng.github.io/AutoSDF/.

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

We generalize the attention mechanism by viewing it through the lens of Entropic Optimal Transport, revealing that standard attention corresponds to a transport problem regularized by an implicit uniform prior. We introduce Generalized Optimal transport Attention with Trainable priors (GOAT), a new attention mechanism that replaces this naive assumption with a learnable, continuous prior. This prior maintains full compatibility with optimized kernels such as FlashAttention. GOAT also provides an EOT-based explanation of attention sinks and materializes a solution for them, avoiding the representational trade-offs of standard attention. Finally, by absorbing spatial information into the core attention computation, GOAT learns an extrapolatable prior that combines the flexibility of learned positional embeddings with the length generalization of fixed encodings.

Multimodal Large Language Models (MLLMs) perform well on tasks such as visual question answering, but it remains unclear whether their reasoning relies more on memorized world knowledge or on the visual information present in the input image. To investigate this, we introduce Visual CounterFact, a new dataset of visually-realistic counterfactuals that put world knowledge priors (e.g, red strawberry) into direct conflict with visual input (e.g, blue strawberry). Using Visual CounterFact, we show that model predictions initially reflect memorized priors, but shift toward visual evidence in mid-to-late layers. This dynamic reveals a competition between the two modalities, with visual input ultimately overriding priors during evaluation. To control this behavior, we propose Pixels Versus Priors (PvP) steering vectors, a mechanism for controlling model outputs toward either world knowledge or visual input through activation-level interventions. On average, PvP successfully shifts 92.5% of color and 74.6% of size predictions from priors to counterfactuals. Together, these findings offer new tools for interpreting and controlling factual behavior in multimodal models.

Given a stationary state-space model that relates a sequence of hidden states and corresponding measurements or observations, Bayesian filtering provides a principled statistical framework for inferring the posterior distribution of the current state given all measurements up to the present time. For example, the Apollo lunar module implemented a Kalman filter to infer its location from a sequence of earth-based radar measurements and land safely on the moon. To perform Bayesian filtering, we require a measurement model that describes the conditional distribution of each observation given state. The Kalman filter takes this measurement model to be linear, Gaussian. Here we show how a nonlinear, Gaussian approximation to the distribution of state given observation can be used in conjunction with Bayes' rule to build a nonlinear, non-Gaussian measurement model. The resulting approach, called the Discriminative Kalman Filter (DKF), retains fast closed-form updates for the posterior. We argue there are many cases where the distribution of state given measurement is better-approximated as Gaussian, especially when the dimensionality of measurements far exceeds that of states and the Bernstein-von Mises theorem applies. Online neural decoding for brain-computer interfaces provides a motivating example, where filtering incorporates increasingly detailed measurements of neural activity to provide users control over external devices. Within the BrainGate2 clinical trial, the DKF successfully enabled three volunteers with quadriplegia to control an on-screen cursor in real-time using mental imagery alone. Participant "T9" used the DKF to type out messages on a tablet PC.

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

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.

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.

Chain-of-Thought (CoT) prompting improves LLM accuracy on complex tasks but often increases token usage and inference cost. Existing "Budget Forcing" methods reducing cost via fine-tuning with heuristic length penalties, suppress both essential reasoning and redundant filler. We recast efficient reasoning as a lossy compression problem under the Information Bottleneck (IB) principle, and identify a key theoretical gap when applying naive IB to transformers: attention violates the Markov property between prompt, reasoning trace, and response. To resolve this issue, we model CoT generation under the Conditional Information Bottleneck (CIB) principle, where the reasoning trace Z acts as a computational bridge that contains only the information about the response Y that is not directly accessible from the prompt X. This yields a general Reinforcement Learning objective: maximize task reward while compressing completions under a prior over reasoning traces, subsuming common heuristics (e.g., length penalties) as special cases (e.g., uniform priors). In contrast to naive token-counting-based approaches, we introduce a semantic prior that measures token cost by surprisal under a language model prior. Empirically, our CIB objective prunes cognitive bloat while preserving fluency and logic, improving accuracy at moderate compression and enabling aggressive compression with minimal accuracy drop.

Clinical brain-to-text interfaces are designed for paralysed patients who cannot provide extensive training recordings. Pre-training improves data-efficient generalisation by learning statistical priors across subjects, but these priors critically depend on context. While natural speech might unfold gradually over minutes, most methods pre-train with only a few seconds of context. Thus, we propose MEG-XL, a model pre-trained with 2.5 minutes of MEG context per sample, 5-300x longer than prior work, and equivalent to 191k tokens, capturing extended neural context. Fine-tuning on the task of word decoding from brain data, MEG-XL matches supervised performance with a fraction of the data (e.g. 1hr vs 50hrs) and outperforms brain foundation models. We find that models pre-trained with longer contexts learn representations that transfer better to word decoding. Our results indicate that long-context pre-training helps exploit extended neural context that other methods unnecessarily discard. Code, model weights, and instructions are available at https://github.com/neural-processing-lab/MEG-XL .

Large Vision-Language Models (LVLMs) demonstrate impressive capabilities in generating detailed and coherent responses from visual inputs. However, they are prone to generate hallucinations due to an over-reliance on language priors. To address this issue, we investigate the language priors in LVLMs and make two key observations: (1) Even when predicting the tokens associated with image-related part-of-speech (POS), models increasingly rely on linguistic priors as the token sequences grow, thereby amplifying hallucinations. (2) Methods that directly calibrate LVLM's output distribution to mitigate language priors can lead to a degradation in text quality or even exacerbate hallucinations. Based on these findings, we propose a novel method, Summary-Guided Decoding (SumGD). This method naturally encourages the model to focus more on image information by reducing the text context through summaries, while controlling only the image-related POS tokens to maintain text quality. Through experiments, we demonstrate that SumGD achieves state-of-the-art performance on object hallucination benchmarks. Furthermore, in terms of the trade-off between precision and recall, SumGD achieves Pareto optimality among the existing methods. Lastly, we observe that although existing methods struggle to balance the reduction of object hallucinations with maintaining text quality, SumGD demonstrates robustness in handling this challenge.

Various stuff and things in visual data possess specific traits, which can be learned by deep neural networks and are implicitly represented as the visual prior, e.g., object location and shape, in the model. Such prior potentially impacts many vision tasks. For example, in conditional image synthesis, spatial conditions failing to adhere to the prior can result in visually inaccurate synthetic results. This work aims to explicitly learn the visual prior and enable the customization of sampling. Inspired by advances in language modeling, we propose to learn Visual prior via Generative Pre-Training, dubbed VisorGPT. By discretizing visual locations of objects, e.g., bounding boxes, human pose, and instance masks, into sequences, \our~can model visual prior through likelihood maximization. Besides, prompt engineering is investigated to unify various visual locations and enable customized sampling of sequential outputs from the learned prior. Experimental results demonstrate that \our~can effectively model the visual prior, which can be employed for many vision tasks, such as customizing accurate human pose for conditional image synthesis models like ControlNet. Code will be released at https://github.com/Sierkinhane/VisorGPT.

Most applications of machine learning to classification assume a closed set of balanced classes. This is at odds with the real world, where class occurrence statistics often follow a long-tailed power-law distribution and it is unlikely that all classes are seen in a single sample. Nonparametric Bayesian models naturally capture this phenomenon, but have significant practical barriers to widespread adoption, namely implementation complexity and computational inefficiency. To address this, we present a method for extracting the inductive bias from a nonparametric Bayesian model and transferring it to an artificial neural network. By simulating data with a nonparametric Bayesian prior, we can metalearn a sequence model that performs inference over an unlimited set of classes. After training, this "neural circuit" has distilled the corresponding inductive bias and can successfully perform sequential inference over an open set of classes. Our experimental results show that the metalearned neural circuit achieves comparable or better performance than particle filter-based methods for inference in these models while being faster and simpler to use than methods that explicitly incorporate Bayesian nonparametric inference.

The field of computer vision is undergoing a paradigm shift toward large-scale foundation model pre-training via self-supervised learning (SSL). Leveraging large volumes of unlabeled brain MRI data, such models can learn anatomical priors that improve few-shot performance in diverse neuroimaging tasks. However, most SSL frameworks are tailored to natural images, and their adaptation to capture multi-modal MRI information remains underexplored. This work proposes a modality-invariant representation learning setup and evaluates its effectiveness in stroke and epilepsy lesion segmentation, following large-scale pre-training. Experimental results suggest that despite successful cross-modality alignment, lesion segmentation primarily benefits from preserving fine-grained modality-specific features. Model checkpoints and code are made publicly available.

Understanding how humans process visual information is one of the crucial steps for unraveling the underlying mechanism of brain activity. Recently, this curiosity has motivated the fMRI-to-image reconstruction task; given the fMRI data from visual stimuli, it aims to reconstruct the corresponding visual stimuli. Surprisingly, leveraging powerful generative models such as the Latent Diffusion Model (LDM) has shown promising results in reconstructing complex visual stimuli such as high-resolution natural images from vision datasets. Despite the impressive structural fidelity of these reconstructions, they often lack details of small objects, ambiguous shapes, and semantic nuances. Consequently, the incorporation of additional semantic knowledge, beyond mere visuals, becomes imperative. In light of this, we exploit how modern LDMs effectively incorporate multi-modal guidance (text guidance, visual guidance, and image layout) for structurally and semantically plausible image generations. Specifically, inspired by the two-streams hypothesis suggesting that perceptual and semantic information are processed in different brain regions, our framework, Brain-Streams, maps fMRI signals from these brain regions to appropriate embeddings. That is, by extracting textual guidance from semantic information regions and visual guidance from perceptual information regions, Brain-Streams provides accurate multi-modal guidance to LDMs. We validate the reconstruction ability of Brain-Streams both quantitatively and qualitatively on a real fMRI dataset comprising natural image stimuli and fMRI data.

Can a diffusion model trained on bedrooms recover human faces? Diffusion models are widely used as priors for inverse problems, but standard approaches usually assume a high-fidelity model trained on data that closely match the unknown signal. In practice, one often must use a mismatched or low-fidelity diffusion prior. Surprisingly, these weak priors often perform nearly as well as full-strength, in-domain baselines. We study when and why inverse solvers are robust to weak diffusion priors. Through extensive experiments, we find that weak priors succeed when measurements are highly informative (e.g., many observed pixels), and we identify regimes where they fail. Our theory, based on Bayesian consistency, gives conditions under which high-dimensional measurements make the posterior concentrate near the true signal. These results provide a principled justification on when weak diffusion priors can be used reliably.

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.

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.

Prior-data fitted networks (PFNs) were recently proposed as a new paradigm for machine learning. Instead of training the network to an observed training set, a fixed model is pre-trained offline on small, simulated training sets from a variety of tasks. The pre-trained model is then used to infer class probabilities in-context on fresh training sets with arbitrary size and distribution. Empirically, PFNs achieve state-of-the-art performance on tasks with similar size to the ones used in pre-training. Surprisingly, their accuracy further improves when passed larger data sets during inference. This article establishes a theoretical foundation for PFNs and illuminates the statistical mechanisms governing their behavior. While PFNs are motivated by Bayesian ideas, a purely frequentistic interpretation of PFNs as pre-tuned, but untrained predictors explains their behavior. A predictor's variance vanishes if its sensitivity to individual training samples does and the bias vanishes only if it is appropriately localized around the test feature. The transformer architecture used in current PFN implementations ensures only the former. These findings shall prove useful for designing architectures with favorable empirical behavior.

Seeing is believing, however, the underlying mechanism of how human visual perceptions are intertwined with our cognitions is still a mystery. Thanks to the recent advances in both neuroscience and artificial intelligence, we have been able to record the visually evoked brain activities and mimic the visual perception ability through computational approaches. In this paper, we pay attention to visual stimuli reconstruction by reconstructing the observed images based on portably accessible brain signals, i.e., electroencephalography (EEG) data. Since EEG signals are dynamic in the time-series format and are notorious to be noisy, processing and extracting useful information requires more dedicated efforts; In this paper, we propose a comprehensive pipeline, named NeuroImagen, for reconstructing visual stimuli images from EEG signals. Specifically, we incorporate a novel multi-level perceptual information decoding to draw multi-grained outputs from the given EEG data. A latent diffusion model will then leverage the extracted information to reconstruct the high-resolution visual stimuli images. The experimental results have illustrated the effectiveness of image reconstruction and superior quantitative performance of our proposed method.

Sequential Bayesian inference can be used for continual learning to prevent catastrophic forgetting of past tasks and provide an informative prior when learning new tasks. We revisit sequential Bayesian inference and test whether having access to the true posterior is guaranteed to prevent catastrophic forgetting in Bayesian neural networks. To do this we perform sequential Bayesian inference using Hamiltonian Monte Carlo. We propagate the posterior as a prior for new tasks by fitting a density estimator on Hamiltonian Monte Carlo samples. We find that this approach fails to prevent catastrophic forgetting demonstrating the difficulty in performing sequential Bayesian inference in neural networks. From there we study simple analytical examples of sequential Bayesian inference and CL and highlight the issue of model misspecification which can lead to sub-optimal continual learning performance despite exact inference. Furthermore, we discuss how task data imbalances can cause forgetting. From these limitations, we argue that we need probabilistic models of the continual learning generative process rather than relying on sequential Bayesian inference over Bayesian neural network weights. In this vein, we also propose a simple baseline called Prototypical Bayesian Continual Learning, which is competitive with state-of-the-art Bayesian continual learning methods on class incremental continual learning vision benchmarks.

Electroencephalography (EEG) captures neural activity across multiple temporal and spectral scales, yielding signals that are rich but complex for representation learning. Recently, EEG foundation models trained to predict masked signal-tokens have shown promise for learning generalizable representations. However, their performance is hindered by their signal tokenization modules. Existing neural tokenizers fail to preserve high-frequency dynamics, limiting their ability to reconstruct EEG signals with high fidelity. We introduce NeuroRVQ, a scalable Large Brainwave Model (LBM) centered on a codebook-based tokenizer. Our tokenizer integrates: (i) multi-scale feature extraction modules that capture the full frequency neural spectrum; (ii) hierarchical residual vector quantization (RVQ) codebooks for high-resolution encoding; and, (iii) an EEG signal phase- and amplitude-aware loss function for efficient training. This design enables efficient EEG compression while supporting accurate reconstruction across all frequency bands, leading to robust generative masked modeling. Our empirical results demonstrate that NeuroRVQ achieves lower reconstruction error and outperforms existing LBMs on a variety of downstream tasks. More broadly, NeuroRVQ tokenizer establishes a strong prior for codebook-based general-purpose brainwave models, enabling advances in neural decoding, generative modeling and multimodal biosignal integration.

A Neural Process (NP) estimates a stochastic process implicitly defined with neural networks given a stream of data, rather than pre-specifying priors already known, such as Gaussian processes. An ideal NP would learn everything from data without any inductive biases, but in practice, we often restrict the class of stochastic processes for the ease of estimation. One such restriction is the use of a finite-dimensional latent variable accounting for the uncertainty in the functions drawn from NPs. Some recent works show that this can be improved with more "data-driven" source of uncertainty such as bootstrapping. In this work, we take a different approach based on the martingale posterior, a recently developed alternative to Bayesian inference. For the martingale posterior, instead of specifying prior-likelihood pairs, a predictive distribution for future data is specified. Under specific conditions on the predictive distribution, it can be shown that the uncertainty in the generated future data actually corresponds to the uncertainty of the implicitly defined Bayesian posteriors. Based on this result, instead of assuming any form of the latent variables, we equip a NP with a predictive distribution implicitly defined with neural networks and use the corresponding martingale posteriors as the source of uncertainty. The resulting model, which we name as Martingale Posterior Neural Process (MPNP), is demonstrated to outperform baselines on various tasks.

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

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.

Recent work has demonstrated that complex visual stimuli can be decoded from human brain activity using deep generative models, offering new ways to probe how the brain represents real-world scenes. However, many existing approaches first map brain signals into intermediate image or text feature spaces before guiding the generative process, which obscures the contributions of different brain areas to the final reconstruction output. In this work, we propose NeuroAdapter, a visual decoding framework that directly conditions a latent diffusion model on brain representations, bypassing the need for intermediate feature spaces. Our method demonstrates competitive visual reconstruction quality on public fMRI datasets compared to prior work, while providing greater transparency into how brain signals drive visual reconstruction. To this end, we introduce an Image-Brain BI-directional interpretability framework (IBBI) that analyzes cross-attention patterns across diffusion denoising steps to reveal how different cortical areas influence the unfolding generative trajectory. Our work highlights the potential of end-to-end brain-to-image reconstruction and establishes a path for interpretable neural decoding.

Pretrained generative models have opened new frontiers in brain decoding by enabling the synthesis of realistic texts and images from non-invasive brain recordings. However, the reliability of such outputs remains questionable--whether they truly reflect semantic activation in the brain, or are merely hallucinated by the powerful generative models. In this paper, we focus on EEG-to-text decoding and address its hallucination issue through the lens of posterior collapse. Acknowledging the underlying mismatch in information capacity between EEG and text, we reframe the decoding task as semantic summarization of core meanings rather than previously verbatim reconstruction of stimulus texts. To this end, we propose the Generative Language Inspection Model (GLIM), which emphasizes learning informative and interpretable EEG representations to improve semantic grounding under heterogeneous and small-scale data conditions. Experiments on the public ZuCo dataset demonstrate that GLIM consistently generates fluent, EEG-grounded sentences without teacher forcing. Moreover, it supports more robust evaluation beyond text similarity, through EEG-text retrieval and zero-shot semantic classification across sentiment categories, relation types, and corpus topics. Together, our architecture and evaluation protocols lay the foundation for reliable and scalable benchmarking in generative brain decoding.

In medical imaging, anomaly detection is a vital element of healthcare diagnostics, especially for neurological conditions which can be life-threatening. Conventional deterministic methods often fall short when it comes to capturing the inherent uncertainty of anomaly detection tasks. This paper introduces a Bayesian Variational Autoencoder (VAE) equipped with multi-head attention mechanisms for detecting anomalies in brain magnetic resonance imaging (MRI). For the purpose of improving anomaly detection performance, we incorporate both epistemic and aleatoric uncertainty estimation through Bayesian inference. The model was tested on the BraTS2020 dataset, and the findings were a 0.83 ROC AUC and a 0.83 PR AUC. The data in our paper suggests that modeling uncertainty is an essential component of anomaly detection, enhancing both performance and interpretability and providing confidence estimates, as well as anomaly predictions, for clinicians to leverage in making medical decisions.

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.

Unsupervised learning of hierarchical representations has been one of the most vibrant research directions in deep learning during recent years. In this work we study biologically inspired unsupervised strategies in neural networks based on local Hebbian learning. We propose new mechanisms to extend the Bayesian Confidence Propagating Neural Network (BCPNN) architecture, and demonstrate their capability for unsupervised learning of salient hidden representations when tested on the MNIST dataset.

In neural decoding research, one of the most intriguing topics is the reconstruction of perceived natural images based on fMRI signals. Previous studies have succeeded in re-creating different aspects of the visuals, such as low-level properties (shape, texture, layout) or high-level features (category of objects, descriptive semantics of scenes) but have typically failed to reconstruct these properties together for complex scene images. Generative AI has recently made a leap forward with latent diffusion models capable of generating high-complexity images. Here, we investigate how to take advantage of this innovative technology for brain decoding. We present a two-stage scene reconstruction framework called ``Brain-Diffuser''. In the first stage, starting from fMRI signals, we reconstruct images that capture low-level properties and overall layout using a VDVAE (Very Deep Variational Autoencoder) model. In the second stage, we use the image-to-image framework of a latent diffusion model (Versatile Diffusion) conditioned on predicted multimodal (text and visual) features, to generate final reconstructed images. On the publicly available Natural Scenes Dataset benchmark, our method outperforms previous models both qualitatively and quantitatively. When applied to synthetic fMRI patterns generated from individual ROI (region-of-interest) masks, our trained model creates compelling ``ROI-optimal'' scenes consistent with neuroscientific knowledge. Thus, the proposed methodology can have an impact on both applied (e.g. brain-computer interface) and fundamental neuroscience.

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/.

Treatment effect estimation in continuous time is crucial for personalized medicine. However, existing methods for this task are limited to point estimates of the potential outcomes, whereas uncertainty estimates have been ignored. Needless to say, uncertainty quantification is crucial for reliable decision-making in medical applications. To fill this gap, we propose a novel Bayesian neural controlled differential equation (BNCDE) for treatment effect estimation in continuous time. In our BNCDE, the time dimension is modeled through a coupled system of neural controlled differential equations and neural stochastic differential equations, where the neural stochastic differential equations allow for tractable variational Bayesian inference. Thereby, for an assigned sequence of treatments, our BNCDE provides meaningful posterior predictive distributions of the potential outcomes. To the best of our knowledge, ours is the first tailored neural method to provide uncertainty estimates of treatment effects in continuous time. As such, our method is of direct practical value for promoting reliable decision-making in medicine.

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

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/

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

As the global burden of Alzheimer's disease (AD) continues to grow, early and accurate detection has become increasingly critical, especially in regions with limited access to advanced diagnostic tools. We propose BRAINS (Biomedical Retrieval-Augmented Intelligence for Neurodegeneration Screening) to address this challenge. This novel system harnesses the powerful reasoning capabilities of Large Language Models (LLMs) for Alzheimer's detection and monitoring. BRAINS features a dual-module architecture: a cognitive diagnostic module and a case-retrieval module. The Diagnostic Module utilizes LLMs fine-tuned on cognitive and neuroimaging datasets -- including MMSE, CDR scores, and brain volume metrics -- to perform structured assessments of Alzheimer's risk. Meanwhile, the Case Retrieval Module encodes patient profiles into latent representations and retrieves similar cases from a curated knowledge base. These auxiliary cases are fused with the input profile via a Case Fusion Layer to enhance contextual understanding. The combined representation is then processed with clinical prompts for inference. Evaluations on real-world datasets demonstrate BRAINS effectiveness in classifying disease severity and identifying early signs of cognitive decline. This system not only shows strong potential as an assistive tool for scalable, explainable, and early-stage Alzheimer's disease detection, but also offers hope for future applications in the field.

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

We consider concept generalization at a large scale in the diverse and natural visual spectrum. Established computational modes (i.e., rule-based or similarity-based) are primarily studied isolated and focus on confined and abstract problem spaces. In this work, we study these two modes when the problem space scales up, and the complexity of concepts becomes diverse. Specifically, at the representational level, we seek to answer how the complexity varies when a visual concept is mapped to the representation space. Prior psychology literature has shown that two types of complexities (i.e., subjective complexity and visual complexity) (Griffiths and Tenenbaum, 2003) build an inverted-U relation (Donderi, 2006; Sun and Firestone, 2021). Leveraging Representativeness of Attribute (RoA), we computationally confirm the following observation: Models use attributes with high RoA to describe visual concepts, and the description length falls in an inverted-U relation with the increment in visual complexity. At the computational level, we aim to answer how the complexity of representation affects the shift between the rule- and similarity-based generalization. We hypothesize that category-conditioned visual modeling estimates the co-occurrence frequency between visual and categorical attributes, thus potentially serving as the prior for the natural visual world. Experimental results show that representations with relatively high subjective complexity outperform those with relatively low subjective complexity in the rule-based generalization, while the trend is the opposite in the similarity-based generalization.

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.

Following the success of Proximal Policy Optimization (PPO) for Reinforcement Learning from Human Feedback (RLHF), new techniques such as Sequence Likelihood Calibration (SLiC) and Direct Policy Optimization (DPO) have been proposed that are offline in nature and use rewards in an indirect manner. These techniques, in particular DPO, have recently become the tools of choice for LLM alignment due to their scalability and performance. However, they leave behind important features of the PPO approach. Methods such as SLiC or RRHF make use of the Reward Model (RM) only for ranking/preference, losing fine-grained information and ignoring the parametric form of the RM (eg., Bradley-Terry, Plackett-Luce), while methods such as DPO do not use even a separate reward model. In this work, we propose a novel approach, named BRAIn, that re-introduces the RM as part of a distribution matching approach.BRAIn considers the LLM distribution conditioned on the assumption of output goodness and applies Bayes theorem to derive an intractable posterior distribution where the RM is explicitly represented. BRAIn then distills this posterior into an amortized inference network through self-normalized importance sampling, leading to a scalable offline algorithm that significantly outperforms prior art in summarization and AntropicHH tasks. BRAIn also has interesting connections to PPO and DPO for specific RM choices.

Multimodal functional neuroimaging enables systematic analysis of brain mechanisms and provides discriminative representations for brain-computer interface (BCI) decoding. However, its acquisition is constrained by high costs and feasibility limitations. Moreover, underrepresentation of specific groups undermines fairness of BCI decoding model. To address these challenges, we propose a unified representation framework for multimodal functional neuroimaging via generative artificial intelligence (AI). By mapping multimodal functional neuroimaging into a unified representation space, the proposed framework is capable of generating data for acquisition-constrained modalities and underrepresented groups. Experiments show that the framework can generate data consistent with real brain activity patterns, provide insights into brain mechanisms, and improve performance on downstream tasks. More importantly, it can enhance model fairness by augmenting data for underrepresented groups. Overall, the framework offers a new paradigm for decreasing the cost of acquiring multimodal functional neuroimages and enhancing the fairness of BCI decoding models.

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.

Diffusion models recently proved to be remarkable priors for Bayesian inverse problems. However, training these models typically requires access to large amounts of clean data, which could prove difficult in some settings. In this work, we present a novel method based on the expectation-maximization algorithm for training diffusion models from incomplete and noisy observations only. Unlike previous works, our method leads to proper diffusion models, which is crucial for downstream tasks. As part of our method, we propose and motivate an improved posterior sampling scheme for unconditional diffusion models. We present empirical evidence supporting the effectiveness of our method.

In standard large vision-language models (LVLMs) pre-training, the model typically maximizes the joint probability of the caption conditioned on the image via next-token prediction (NTP); however, since only a small subset of caption tokens directly relates to the visual content, this naive NTP unintentionally fits the model to noise and increases the risk of hallucination. We present PRIOR, a simple vision-language pre-training approach that addresses this issue by prioritizing image-related tokens through differential weighting in the NTP loss, drawing from the importance sampling framework. PRIOR introduces a reference model-a text-only large language model (LLM) trained on the captions without image inputs, to weight each token based on its probability for LVLMs training. Intuitively, tokens that are directly related to the visual inputs are harder to predict without the image and thus receive lower probabilities from the text-only reference LLM. During training, we implement a token-specific re-weighting term based on the importance scores to adjust each token's loss. We implement PRIOR in two distinct settings: LVLMs with visual encoders and LVLMs without visual encoders. We observe 19% and 8% average relative improvement, respectively, on several vision-language benchmarks compared to NTP. In addition, PRIOR exhibits superior scaling properties, as demonstrated by significantly higher scaling coefficients, indicating greater potential for performance gains compared to NTP given increasing compute and data.

A growing body of work makes use of probing to investigate the working of neural models, often considered black boxes. Recently, an ongoing debate emerged surrounding the limitations of the probing paradigm. In this work, we point out the inability to infer behavioral conclusions from probing results and offer an alternative method that focuses on how the information is being used, rather than on what information is encoded. Our method, Amnesic Probing, follows the intuition that the utility of a property for a given task can be assessed by measuring the influence of a causal intervention that removes it from the representation. Equipped with this new analysis tool, we can ask questions that were not possible before, e.g. is part-of-speech information important for word prediction? We perform a series of analyses on BERT to answer these types of questions. Our findings demonstrate that conventional probing performance is not correlated to task importance, and we call for increased scrutiny of claims that draw behavioral or causal conclusions from probing results.

Bayesian inference usually requires running potentially costly inference procedures separately for every new observation. In contrast, the idea of amortized Bayesian inference is to initially invest computational cost in training an inference network on simulated data, which can subsequently be used to rapidly perform inference (i.e., to return estimates of posterior distributions) for new observations. This approach has been applied to many real-world models in the sciences and engineering, but it is unclear how robust the approach is to adversarial perturbations in the observed data. Here, we study the adversarial robustness of amortized Bayesian inference, focusing on simulation-based estimation of multi-dimensional posterior distributions. We show that almost unrecognizable, targeted perturbations of the observations can lead to drastic changes in the predicted posterior and highly unrealistic posterior predictive samples, across several benchmark tasks and a real-world example from neuroscience. We propose a computationally efficient regularization scheme based on penalizing the Fisher information of the conditional density estimator, and show how it improves the adversarial robustness of amortized Bayesian inference.

Human-interpretable predictions are essential for deploying AI in medical imaging, yet most interpretable-by-design (IBD) frameworks require concept annotations for training data, which are costly and impractical to obtain in clinical contexts. Recent attempts to bypass annotation, such as zero-shot vision-language models or concept-generation frameworks, struggle to capture domain-specific medical features, leading to poor reliability. In this paper, we propose a novel Prior-guided Concept Predictor (PCP), a weakly supervised framework that enables concept answer prediction without explicit supervision or reliance on language models. PCP leverages class-level concept priors as weak supervision and incorporates a refinement mechanism with KL divergence and entropy regularization to align predictions with clinical reasoning. Experiments on PH2 (dermoscopy) and WBCatt (hematology) show that PCP improves concept-level F1-score by over 33% compared to zero-shot baselines, while delivering competitive classification performance on four medical datasets (PH2, WBCatt, HAM10000, and CXR4) relative to fully supervised concept bottleneck models (CBMs) and V-IP.

The success of machine learning algorithms generally depends on data representation, and we hypothesize that this is because different representations can entangle and hide more or less the different explanatory factors of variation behind the data. Although specific domain knowledge can be used to help design representations, learning with generic priors can also be used, and the quest for AI is motivating the design of more powerful representation-learning algorithms implementing such priors. This paper reviews recent work in the area of unsupervised feature learning and deep learning, covering advances in probabilistic models, auto-encoders, manifold learning, and deep networks. This motivates longer-term unanswered questions about the appropriate objectives for learning good representations, for computing representations (i.e., inference), and the geometrical connections between representation learning, density estimation and manifold learning.

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

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.

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.

Typically, children start to learn their first words between 6 and 9 months, linking spoken utterances to their visual referents. Without prior knowledge, a word encountered for the first time can be interpreted in countless ways; it might refer to any of the objects in the environment, their components, or attributes. Using longitudinal, egocentric, and ecologically valid data from the experience of one child, in this work, we propose a self-supervised and biologically plausible strategy to learn strong visual representations. Our masked autoencoder-based visual backbone incorporates knowledge about the blind spot in human eyes to define a novel masking strategy. This mask and reconstruct approach attempts to mimic the way the human brain fills the gaps in the eyes' field of view. This represents a significant shift from standard random masking strategies, which are difficult to justify from a biological perspective. The pretrained encoder is utilized in a contrastive learning-based video-text model capable of acquiring word-referent mappings. Extensive evaluation suggests that the proposed biologically plausible masking strategy is at least as effective as random masking for learning word-referent mappings from cross-situational and temporally extended episodes.

We present TabPFN, a trained Transformer that can do supervised classification for small tabular datasets in less than a second, needs no hyperparameter tuning and is competitive with state-of-the-art classification methods. TabPFN performs in-context learning (ICL), it learns to make predictions using sequences of labeled examples (x, f(x)) given in the input, without requiring further parameter updates. TabPFN is fully entailed in the weights of our network, which accepts training and test samples as a set-valued input and yields predictions for the entire test set in a single forward pass. TabPFN is a Prior-Data Fitted Network (PFN) and is trained offline once, to approximate Bayesian inference on synthetic datasets drawn from our prior. This prior incorporates ideas from causal reasoning: It entails a large space of structural causal models with a preference for simple structures. On the 18 datasets in the OpenML-CC18 suite that contain up to 1 000 training data points, up to 100 purely numerical features without missing values, and up to 10 classes, we show that our method clearly outperforms boosted trees and performs on par with complex state-of-the-art AutoML systems with up to 230times speedup. This increases to a 5 700times speedup when using a GPU. We also validate these results on an additional 67 small numerical datasets from OpenML. We provide all our code, the trained TabPFN, an interactive browser demo and a Colab notebook at https://github.com/automl/TabPFN.

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

Recent works have suggested that finite Bayesian neural networks may sometimes outperform their infinite cousins because finite networks can flexibly adapt their internal representations. However, our theoretical understanding of how the learned hidden layer representations of finite networks differ from the fixed representations of infinite networks remains incomplete. Perturbative finite-width corrections to the network prior and posterior have been studied, but the asymptotics of learned features have not been fully characterized. Here, we argue that the leading finite-width corrections to the average feature kernels for any Bayesian network with linear readout and Gaussian likelihood have a largely universal form. We illustrate this explicitly for three tractable network architectures: deep linear fully-connected and convolutional networks, and networks with a single nonlinear hidden layer. Our results begin to elucidate how task-relevant learning signals shape the hidden layer representations of wide Bayesian neural networks.

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

Interpreting individual neurons or directions in activations space is an important component of mechanistic interpretability. As such, many algorithms have been proposed to automatically produce neuron explanations, but it is often not clear how reliable these explanations are, or which methods produce the best explanations. This can be measured via crowd-sourced evaluations, but they can often be noisy and expensive, leading to unreliable results. In this paper, we carefully analyze the evaluation pipeline and develop a cost-effective and highly accurate crowdsourced evaluation strategy. In contrast to previous human studies that only rate whether the explanation matches the most highly activating inputs, we estimate whether the explanation describes neuron activations across all inputs. To estimate this effectively, we introduce a novel application of importance sampling to determine which inputs are the most valuable to show to raters, leading to around 30x cost reduction compared to uniform sampling. We also analyze the label noise present in crowd-sourced evaluations and propose a Bayesian method to aggregate multiple ratings leading to a further ~5x reduction in number of ratings required for the same accuracy. Finally, we use these methods to conduct a large-scale study comparing the quality of neuron explanations produced by the most popular methods for two different vision models.

Foundation models have transformed AI by reducing reliance on task-specific data through large-scale pretraining. While successful in language and vision, their adoption in EEG has lagged due to the heterogeneity of public datasets, which are collected under varying protocols, devices, and electrode configurations. Existing EEG foundation models struggle to generalize across these variations, often restricting pretraining to a single setup, resulting in suboptimal performance, in particular under linear probing. We present REVE (Representation for EEG with Versatile Embeddings), a pretrained model explicitly designed to generalize across diverse EEG signals. REVE introduces a novel 4D positional encoding scheme that enables it to process signals of arbitrary length and electrode arrangement. Using a masked autoencoding objective, we pretrain REVE on over 60,000 hours of EEG data from 92 datasets spanning 25,000 subjects, representing the largest EEG pretraining effort to date. REVE achieves state-of-the-art results on 10 downstream EEG tasks, including motor imagery classification, seizure detection, sleep staging, cognitive load estimation, and emotion recognition. With little to no fine-tuning, it demonstrates strong generalization, and nuanced spatio-temporal modeling. We release code, pretrained weights, and tutorials to support standardized EEG research and accelerate progress in clinical neuroscience.

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.

Large vision-language models (LVLMs) achieve strong performance on multimodal tasks, yet they often default to their language prior (LP) -- memorized textual patterns from pre-training while under-utilizing visual evidence. Prior analyses of LP mostly rely on input-output probing, which fails to reveal the internal mechanisms governing when and how vision influences model behavior. To address this gap, we present the first systematic analysis of language prior through the lens of chain-of-embedding, which examines the layer-wise representation dynamics within LVLMs. Our analysis reveals a universal phenomenon: each model exhibits a Visual Integration Point (VIP), a critical layer at which visual information begins to meaningfully reshape hidden representations and influence decoding. Building on this observation, we introduce the Total Visual Integration (TVI) estimator, which aggregates representation distance beyond the VIP to quantify how strongly visual query influences response generation. Across 54 model-dataset combinations spanning 9 contemporary LVLMs and 6 benchmarks, we demonstrate that VIP consistently emerges, and that TVI reliably predicts the strength of language prior. This offers a principled toolkit for diagnosing and understanding language prior in LVLMs.

Latent Gaussian process (GP) models are widely used in neuroscience to uncover hidden state evolutions from sequential observations, mainly in neural activity recordings. While latent GP models provide a principled and powerful solution in theory, the intractable posterior in non-conjugate settings necessitates approximate inference schemes, which may lack scalability. In this work, we propose cvHM, a general inference framework for latent GP models leveraging Hida-Mat\'ern kernels and conjugate computation variational inference (CVI). With cvHM, we are able to perform variational inference of latent neural trajectories with linear time complexity for arbitrary likelihoods. The reparameterization of stationary kernels using Hida-Mat\'ern GPs helps us connect the latent variable models that encode prior assumptions through dynamical systems to those that encode trajectory assumptions through GPs. In contrast to previous work, we use bidirectional information filtering, leading to a more concise implementation. Furthermore, we employ the Whittle approximate likelihood to achieve highly efficient hyperparameter learning.

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.

Incorporating domain-specific priors in search and navigation tasks has shown promising results in improving generalization and sample complexity over end-to-end trained policies. In this work, we study how object embeddings that capture spatial semantic priors can guide search and navigation tasks in a structured environment. We know that humans can search for an object like a book, or a plate in an unseen house, based on the spatial semantics of bigger objects detected. For example, a book is likely to be on a bookshelf or a table, whereas a plate is likely to be in a cupboard or dishwasher. We propose a method to incorporate such spatial semantic awareness in robots by leveraging pre-trained language models and multi-relational knowledge bases as object embeddings. We demonstrate using these object embeddings to search a query object in an unseen indoor environment. We measure the performance of these embeddings in an indoor simulator (AI2Thor). We further evaluate different pre-trained embedding onSuccess Rate(SR) and success weighted by Path Length(SPL).

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.

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

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.

Why do brains have inhibitory connections? Why do deep networks have negative weights? We propose an answer from the perspective of representation capacity. We believe representing functions is the primary role of both (i) the brain in natural intelligence, and (ii) deep networks in artificial intelligence. Our answer to why there are inhibitory/negative weights is: to learn more functions. We prove that, in the absence of negative weights, neural networks with non-decreasing activation functions are not universal approximators. While this may be an intuitive result to some, to the best of our knowledge, there is no formal theory, in either machine learning or neuroscience, that demonstrates why negative weights are crucial in the context of representation capacity. Further, we provide insights on the geometric properties of the representation space that non-negative deep networks cannot represent. We expect these insights will yield a deeper understanding of more sophisticated inductive priors imposed on the distribution of weights that lead to more efficient biological and machine learning.

Solving ill-posed inverse problems requires careful formulation of prior beliefs over the signals of interest and an accurate description of their manifestation into noisy measurements. Handcrafted signal priors based on e.g. sparsity are increasingly replaced by data-driven deep generative models, and several groups have recently shown that state-of-the-art score-based diffusion models yield particularly strong performance and flexibility. In this paper, we show that the powerful paradigm of posterior sampling with diffusion models can be extended to include rich, structured, noise models. To that end, we propose a joint conditional reverse diffusion process with learned scores for the noise and signal-generating distribution. We demonstrate strong performance gains across various inverse problems with structured noise, outperforming competitive baselines that use normalizing flows and adversarial networks. This opens up new opportunities and relevant practical applications of diffusion modeling for inverse problems in the context of non-Gaussian measurement models.

Recent research has demonstrated that feature attribution methods for deep networks can themselves be incorporated into training; these attribution priors optimize for a model whose attributions have certain desirable properties -- most frequently, that particular features are important or unimportant. These attribution priors are often based on attribution methods that are not guaranteed to satisfy desirable interpretability axioms, such as completeness and implementation invariance. Here, we introduce attribution priors to optimize for higher-level properties of explanations, such as smoothness and sparsity, enabled by a fast new attribution method formulation called expected gradients that satisfies many important interpretability axioms. This improves model performance on many real-world tasks where previous attribution priors fail. Our experiments show that the gains from combining higher-level attribution priors with expected gradients attributions are consistent across image, gene expression, and health care data sets. We believe this work motivates and provides the necessary tools to support the widespread adoption of axiomatic attribution priors in many areas of applied machine learning. The implementations and our results have been made freely available to academic communities.

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

To make deliberate progress towards more intelligent and more human-like artificial systems, we need to be following an appropriate feedback signal: we need to be able to define and evaluate intelligence in a way that enables comparisons between two systems, as well as comparisons with humans. Over the past hundred years, there has been an abundance of attempts to define and measure intelligence, across both the fields of psychology and AI. We summarize and critically assess these definitions and evaluation approaches, while making apparent the two historical conceptions of intelligence that have implicitly guided them. We note that in practice, the contemporary AI community still gravitates towards benchmarking intelligence by comparing the skill exhibited by AIs and humans at specific tasks such as board games and video games. We argue that solely measuring skill at any given task falls short of measuring intelligence, because skill is heavily modulated by prior knowledge and experience: unlimited priors or unlimited training data allow experimenters to "buy" arbitrary levels of skills for a system, in a way that masks the system's own generalization power. We then articulate a new formal definition of intelligence based on Algorithmic Information Theory, describing intelligence as skill-acquisition efficiency and highlighting the concepts of scope, generalization difficulty, priors, and experience. Using this definition, we propose a set of guidelines for what a general AI benchmark should look like. Finally, we present a benchmark closely following these guidelines, the Abstraction and Reasoning Corpus (ARC), built upon an explicit set of priors designed to be as close as possible to innate human priors. We argue that ARC can be used to measure a human-like form of general fluid intelligence and that it enables fair general intelligence comparisons between AI systems and humans.

We marry ideas from deep neural networks and approximate Bayesian inference to derive a generalised class of deep, directed generative models, endowed with a new algorithm for scalable inference and learning. Our algorithm introduces a recognition model to represent approximate posterior distributions, and that acts as a stochastic encoder of the data. We develop stochastic back-propagation -- rules for back-propagation through stochastic variables -- and use this to develop an algorithm that allows for joint optimisation of the parameters of both the generative and recognition model. We demonstrate on several real-world data sets that the model generates realistic samples, provides accurate imputations of missing data and is a useful tool for high-dimensional data visualisation.

How to decode human vision through neural signals has attracted a long-standing interest in neuroscience and machine learning. Modern contrastive learning and generative models improved the performance of fMRI-based visual decoding and reconstruction. However, the high cost and low temporal resolution of fMRI limit their applications in brain-computer interfaces (BCIs), prompting a high need for EEG-based visual reconstruction. In this study, we present an EEG-based visual reconstruction framework. It consists of a plug-and-play EEG encoder called the Adaptive Thinking Mapper (ATM), which is aligned with image embeddings, and a two-stage EEG guidance image generator that first transforms EEG features into image priors and then reconstructs the visual stimuli with a pre-trained image generator. Our approach allows EEG embeddings to achieve superior performance in image classification and retrieval tasks. Our two-stage image generation strategy vividly reconstructs images seen by humans. Furthermore, we analyzed the impact of signals from different time windows and brain regions on decoding and reconstruction. The versatility of our framework is demonstrated in the magnetoencephalogram (MEG) data modality. We report that EEG-based visual decoding achieves SOTA performance, highlighting the portability, low cost, and high temporal resolution of EEG, enabling a wide range of BCI applications. The code of ATM is available at https://github.com/dongyangli-del/EEG_Image_decode.

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-based language models rely on positional encoding (PE) to handle token order and support context length extrapolation. However, existing PE methods lack theoretical clarity and rely on limited evaluation metrics to substantiate their extrapolation claims. We propose the Bayesian Attention Mechanism (BAM), a theoretical framework that formulates positional encoding as a prior within a probabilistic model. BAM unifies existing methods (e.g., NoPE and ALiBi) and motivates a new Generalized Gaussian positional prior that substantially improves long-context generalization. Empirically, BAM enables accurate information retrieval at 500times the training context length, outperforming previous state-of-the-art context length generalization in long context retrieval accuracy while maintaining comparable perplexity and introducing minimal additional parameters.

Despite extensive standardization, diagnostic interviews for mental health disorders encompass substantial subjective judgment. Previous studies have demonstrated that EEG-based neural measures can function as reliable objective correlates of depression, or even predictors of depression and its course. However, their clinical utility has not been fully realized because of 1) the lack of automated ways to deal with the inherent noise associated with EEG data at scale, and 2) the lack of knowledge of which aspects of the EEG signal may be markers of a clinical disorder. Here we adapt an unsupervised pipeline from the recent deep representation learning literature to address these problems by 1) learning a disentangled representation using beta-VAE to denoise the signal, and 2) extracting interpretable features associated with a sparse set of clinical labels using a Symbol-Concept Association Network (SCAN). We demonstrate that our method is able to outperform the canonical hand-engineered baseline classification method on a number of factors, including participant age and depression diagnosis. Furthermore, our method recovers a representation that can be used to automatically extract denoised Event Related Potentials (ERPs) from novel, single EEG trajectories, and supports fast supervised re-mapping to various clinical labels, allowing clinicians to re-use a single EEG representation regardless of updates to the standardized diagnostic system. Finally, single factors of the learned disentangled representations often correspond to meaningful markers of clinical factors, as automatically detected by SCAN, allowing for human interpretability and post-hoc expert analysis of the recommendations made by the model.

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.

Autoencoders and their variants are among the most widely used models in representation learning and generative modeling. However, autoencoder-based models usually assume that the learned representations are i.i.d. and fail to capture the correlations between the data samples. To address this issue, we propose a novel Sparse Gaussian Process Bayesian Autoencoder (SGPBAE) model in which we impose fully Bayesian sparse Gaussian Process priors on the latent space of a Bayesian Autoencoder. We perform posterior estimation for this model via stochastic gradient Hamiltonian Monte Carlo. We evaluate our approach qualitatively and quantitatively on a wide range of representation learning and generative modeling tasks and show that our approach consistently outperforms multiple alternatives relying on Variational Autoencoders.

In this paper, we introduce fastHDMI, a Python package designed for efficient variable screening in high-dimensional datasets, particularly neuroimaging data. This work pioneers the application of three mutual information estimation methods for neuroimaging variable selection, a novel approach implemented via fastHDMI. These advancements enhance our ability to analyze the complex structures of neuroimaging datasets, providing improved tools for variable selection in high-dimensional spaces. Using the preprocessed ABIDE dataset, we evaluate the performance of these methods through extensive simulations. The tests cover a range of conditions, including linear and nonlinear associations, as well as continuous and binary outcomes. Our results highlight the superiority of the FFTKDE-based mutual information estimation for feature screening in continuous nonlinear outcomes, while binning-based methods outperform others for binary outcomes with nonlinear probability preimages. For linear simulations, both Pearson correlation and FFTKDE-based methods show comparable performance for continuous outcomes, while Pearson excels in binary outcomes with linear probability preimages. A comprehensive case study using the ABIDE dataset further demonstrates fastHDMI's practical utility, showcasing the predictive power of models built from variables selected using our screening techniques. This research affirms the computational efficiency and methodological strength of fastHDMI, significantly enriching the toolkit available for neuroimaging analysis.

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.

Text-to-3D generation by distilling pretrained large-scale text-to-image diffusion models has shown great promise but still suffers from inconsistent 3D geometric structures (Janus problems) and severe artifacts. The aforementioned problems mainly stem from 2D diffusion models lacking 3D awareness during the lifting. In this work, we present GeoDream, a novel method that incorporates explicit generalized 3D priors with 2D diffusion priors to enhance the capability of obtaining unambiguous 3D consistent geometric structures without sacrificing diversity or fidelity. Specifically, we first utilize a multi-view diffusion model to generate posed images and then construct cost volume from the predicted image, which serves as native 3D geometric priors, ensuring spatial consistency in 3D space. Subsequently, we further propose to harness 3D geometric priors to unlock the great potential of 3D awareness in 2D diffusion priors via a disentangled design. Notably, disentangling 2D and 3D priors allows us to refine 3D geometric priors further. We justify that the refined 3D geometric priors aid in the 3D-aware capability of 2D diffusion priors, which in turn provides superior guidance for the refinement of 3D geometric priors. Our numerical and visual comparisons demonstrate that GeoDream generates more 3D consistent textured meshes with high-resolution realistic renderings (i.e., 1024 times 1024) and adheres more closely to semantic coherence.

Generating images from brain waves is gaining increasing attention due to its potential to advance brain-computer interface (BCI) systems by understanding how brain signals encode visual cues. Most of the literature has focused on fMRI-to-Image tasks as fMRI is characterized by high spatial resolution. However, fMRI is an expensive neuroimaging modality and does not allow for real-time BCI. On the other hand, electroencephalography (EEG) is a low-cost, non-invasive, and portable neuroimaging technique, making it an attractive option for future real-time applications. Nevertheless, EEG presents inherent challenges due to its low spatial resolution and susceptibility to noise and artifacts, which makes generating images from EEG more difficult. In this paper, we address these problems with a streamlined framework based on the ControlNet adapter for conditioning a latent diffusion model (LDM) through EEG signals. We conduct experiments and ablation studies on popular benchmarks to demonstrate that the proposed method beats other state-of-the-art models. Unlike these methods, which often require extensive preprocessing, pretraining, different losses, and captioning models, our approach is efficient and straightforward, requiring only minimal preprocessing and a few components. Code will be available after publication.

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

We propose EEG-SimpleConv, a straightforward 1D convolutional neural network for Motor Imagery decoding in BCI. Our main motivation is to propose a simple and performing baseline to compare to, using only very standard ingredients from the literature. We evaluate its performance on four EEG Motor Imagery datasets, including simulated online setups, and compare it to recent Deep Learning and Machine Learning approaches. EEG-SimpleConv is at least as good or far more efficient than other approaches, showing strong knowledge-transfer capabilities across subjects, at the cost of a low inference time. We advocate that using off-the-shelf ingredients rather than coming with ad-hoc solutions can significantly help the adoption of Deep Learning approaches for BCI. We make the code of the models and the experiments accessible.

In visual decision making, high-level features, such as object categories, have a strong influence on choice. However, the impact of low-level features on behavior is less understood partly due to the high correlation between high- and low-level features in the stimuli presented (e.g., objects of the same category are more likely to share low-level features). To disentangle these effects, we propose a method that de-correlates low- and high-level visual properties in a novel set of stimuli. Our method uses two Convolutional Neural Networks (CNNs) as candidate models of the ventral visual stream: the CORnet-S that has high neural predictivity in high-level, IT-like responses and the VGG-16 that has high neural predictivity in low-level responses. Triplets (root, image1, image2) of stimuli are parametrized by the level of low- and high-level similarity of images extracted from the different layers. These stimuli are then used in a decision-making task where participants are tasked to choose the most similar-to-the-root image. We found that different networks show differing abilities to predict the effects of low-versus-high-level similarity: while CORnet-S outperforms VGG-16 in explaining human choices based on high-level similarity, VGG-16 outperforms CORnet-S in explaining human choices based on low-level similarity. Using Brain-Score, we observed that the behavioral prediction abilities of different layers of these networks qualitatively corresponded to their ability to explain neural activity at different levels of the visual hierarchy. In summary, our algorithm for stimulus set generation enables the study of how different representations in the visual stream affect high-level cognitive behaviors.

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/.

Interpreting the inner function of neural networks is crucial for the trustworthy development and deployment of these black-box models. Prior interpretability methods focus on correlation-based measures to attribute model decisions to individual examples. However, these measures are susceptible to noise and spurious correlations encoded in the model during the training phase (e.g., biased inputs, model overfitting, or misspecification). Moreover, this process has proven to result in noisy and unstable attributions that prevent any transparent understanding of the model's behavior. In this paper, we develop a robust interventional-based method grounded by causal analysis to capture cause-effect mechanisms in pre-trained neural networks and their relation to the prediction. Our novel approach relies on path interventions to infer the causal mechanisms within hidden layers and isolate relevant and necessary information (to model prediction), avoiding noisy ones. The result is task-specific causal explanatory graphs that can audit model behavior and express the actual causes underlying its performance. We apply our method to vision models trained on classification tasks. On image classification tasks, we provide extensive quantitative experiments to show that our approach can capture more stable and faithful explanations than standard attribution-based methods. Furthermore, the underlying causal graphs reveal the neural interactions in the model, making it a valuable tool in other applications (e.g., model repair).

We address prevailing challenges of the brain-powered research, departing from the observation that the literature hardly recover accurate spatial information and require subject-specific models. To address these challenges, we propose UMBRAE, a unified multimodal decoding of brain signals. First, to extract instance-level conceptual and spatial details from neural signals, we introduce an efficient universal brain encoder for multimodal-brain alignment and recover object descriptions at multiple levels of granularity from subsequent multimodal large language model (MLLM). Second, we introduce a cross-subject training strategy mapping subject-specific features to a common feature space. This allows a model to be trained on multiple subjects without extra resources, even yielding superior results compared to subject-specific models. Further, we demonstrate this supports weakly-supervised adaptation to new subjects, with only a fraction of the total training data. Experiments demonstrate that UMBRAE not only achieves superior results in the newly introduced tasks but also outperforms methods in well established tasks. To assess our method, we construct and share with the community a comprehensive brain understanding benchmark BrainHub. Our code and benchmark are available at https://weihaox.github.io/UMBRAE.

Large language models demonstrate remarkable in-context learning capabilities, adapting to new tasks without parameter updates. While this phenomenon has been successfully modeled as implicit Bayesian inference, recent empirical findings reveal a fundamental contradiction: transformers systematically violate the martingale property, a cornerstone requirement of Bayesian updating on exchangeable data. This violation challenges the theoretical foundations underlying uncertainty quantification in critical applications. Our theoretical analysis establishes four key results: (1) positional encodings induce martingale violations of order Theta(log n / n); (2) transformers achieve information-theoretic optimality with excess risk O(n^{-1/2}) in expectation over orderings; (3) the implicit posterior representation converges to the true Bayesian posterior in the space of sufficient statistics; and (4) we derive the optimal chain-of-thought length as k^* = Theta(nlog(1/varepsilon)) with explicit constants, providing a principled approach to reduce inference costs while maintaining performance. Empirical validation on GPT-3 confirms predictions (1)-(3), with transformers reaching 99\% of theoretical entropy limits within 20 examples. Our framework provides practical methods for extracting calibrated uncertainty estimates from position-aware architectures and optimizing computational efficiency in deployment.

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.

Conditional Neural Processes (CNPs) are a class of metalearning models popular for combining the runtime efficiency of amortized inference with reliable uncertainty quantification. Many relevant machine learning tasks, such as in spatio-temporal modeling, Bayesian Optimization and continuous control, inherently contain equivariances -- for example to translation -- which the model can exploit for maximal performance. However, prior attempts to include equivariances in CNPs do not scale effectively beyond two input dimensions. In this work, we propose Relational Conditional Neural Processes (RCNPs), an effective approach to incorporate equivariances into any neural process model. Our proposed method extends the applicability and impact of equivariant neural processes to higher dimensions. We empirically demonstrate the competitive performance of RCNPs on a large array of tasks naturally containing equivariances.

Recent research developing neural network architectures with external memory have often used the benchmark bAbI question and answering dataset which provides a challenging number of tasks requiring reasoning. Here we employed a classic associative inference task from the memory-based reasoning neuroscience literature in order to more carefully probe the reasoning capacity of existing memory-augmented architectures. This task is thought to capture the essence of reasoning -- the appreciation of distant relationships among elements distributed across multiple facts or memories. Surprisingly, we found that current architectures struggle to reason over long distance associations. Similar results were obtained on a more complex task involving finding the shortest path between nodes in a path. We therefore developed MEMO, an architecture endowed with the capacity to reason over longer distances. This was accomplished with the addition of two novel components. First, it introduces a separation between memories (facts) stored in external memory and the items that comprise these facts in external memory. Second, it makes use of an adaptive retrieval mechanism, allowing a variable number of "memory hops" before the answer is produced. MEMO is capable of solving our novel reasoning tasks, as well as match state of the art results in bAbI.

Reinforcement Learning with Verifiable Rewards (RLVR) for large language models (LLMs) has achieved remarkable progress in enhancing LLMs' reasoning capabilities on tasks with clear correctness criteria, such as mathematical reasoning tasks. Several training metrics, such as entropy or response length, have been observed to correlate with different reasoning behaviors in reinforcement learning. Prior approaches incorporate such priors through reward or advantage shaping, which often relies on hand-crafted penalties and preferences (e.g., higher-is-better or lower-is-better). However, without careful hyperparameter tuning, these directional priors can be overly biased and may lead to failure. To this end, we introduce Conditional advANtage estimatiON (CANON), amplifying the impact of the target metric without presuming its direction. Specifically, CANON regroups the sampled responses into two groups based on the higher or lower value of a target metric, measures which metric trend contributes to better performance through inter-group comparison, and identifies the better response within the same group. In summary, CANON based on entropy consistently outperforms prior methods across three LLMs on both math reasoning and high-complexity logic tasks. When applied to response length, CANON further improves token efficiency, yielding a more favorable Pareto frontier in the performance-cost trade-off.

Event-related potential (ERP), a specialized paradigm of electroencephalographic (EEG), reflects neurological responses to external stimuli or events, generally associated with the brain's processing of specific cognitive tasks. ERP plays a critical role in cognitive analysis, the detection of neurological diseases, and the assessment of psychological states. Recent years have seen substantial advances in deep learning-based methods for spontaneous EEG and other non-time-locked task-related EEG signals. However, their effectiveness on ERP data remains underexplored, and many existing ERP studies still rely heavily on manually extracted features. In this paper, we conduct a comprehensive benchmark study that systematically compares traditional manual features (followed by a linear classifier), deep learning models, and pre-trained EEG foundation models for ERP analysis. We establish a unified data preprocessing and training pipeline and evaluate these approaches on two representative tasks, ERP stimulus classification and ERP-based brain disease detection, across 12 publicly available datasets. Furthermore, we investigate various patch-embedding strategies within advanced Transformer architectures to identify embedding designs that better suit ERP data. Our study provides a landmark framework to guide method selection and tailored model design for future ERP analysis. The code is available at https://github.com/DL4mHealth/ERP-Benchmark.

Deciphering visual content from functional Magnetic Resonance Imaging (fMRI) helps illuminate the human vision system. However, the scarcity of fMRI data and noise hamper brain decoding model performance. Previous approaches primarily employ subject-specific models, sensitive to training sample size. In this paper, we explore a straightforward but overlooked solution to address data scarcity. We propose shallow subject-specific adapters to map cross-subject fMRI data into unified representations. Subsequently, a shared deeper decoding model decodes cross-subject features into the target feature space. During training, we leverage both visual and textual supervision for multi-modal brain decoding. Our model integrates a high-level perception decoding pipeline and a pixel-wise reconstruction pipeline guided by high-level perceptions, simulating bottom-up and top-down processes in neuroscience. Empirical experiments demonstrate robust neural representation learning across subjects for both pipelines. Moreover, merging high-level and low-level information improves both low-level and high-level reconstruction metrics. Additionally, we successfully transfer learned general knowledge to new subjects by training new adapters with limited training data. Compared to previous state-of-the-art methods, notably pre-training-based methods (Mind-Vis and fMRI-PTE), our approach achieves comparable or superior results across diverse tasks, showing promise as an alternative method for cross-subject fMRI data pre-training. Our code and pre-trained weights will be publicly released at https://github.com/YulongBonjour/See_Through_Their_Minds.

In this paper, we introduce CineBrain, the first large-scale dataset featuring simultaneous EEG and fMRI recordings during dynamic audiovisual stimulation. Recognizing the complementary strengths of EEG's high temporal resolution and fMRI's deep-brain spatial coverage, CineBrain provides approximately six hours of narrative-driven content from the popular television series The Big Bang Theory for each of six participants. Building upon this unique dataset, we propose CineSync, an innovative multimodal decoding framework integrates a Multi-Modal Fusion Encoder with a diffusion-based Neural Latent Decoder. Our approach effectively fuses EEG and fMRI signals, significantly improving the reconstruction quality of complex audiovisual stimuli. To facilitate rigorous evaluation, we introduce Cine-Benchmark, a comprehensive evaluation protocol that assesses reconstructions across semantic and perceptual dimensions. Experimental results demonstrate that CineSync achieves state-of-the-art video reconstruction performance and highlight our initial success in combining fMRI and EEG for reconstructing both video and audio stimuli. Project Page: https://jianxgao.github.io/CineBrain.

Neural Posterior Estimation methods for simulation-based inference can be ill-suited for dealing with posterior distributions obtained by conditioning on multiple observations, as they tend to require a large number of simulator calls to learn accurate approximations. In contrast, Neural Likelihood Estimation methods can handle multiple observations at inference time after learning from individual observations, but they rely on standard inference methods, such as MCMC or variational inference, which come with certain performance drawbacks. We introduce a new method based on conditional score modeling that enjoys the benefits of both approaches. We model the scores of the (diffused) posterior distributions induced by individual observations, and introduce a way of combining the learned scores to approximately sample from the target posterior distribution. Our approach is sample-efficient, can naturally aggregate multiple observations at inference time, and avoids the drawbacks of standard inference methods.

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

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