Daily Papers

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

Understanding 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.

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.

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.

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/.

Bimanual manipulation is critical to many robotics applications. In contrast to single-arm manipulation, bimanual manipulation tasks are challenging due to higher-dimensional action spaces. Prior works leverage large amounts of data and primitive actions to address this problem, but may suffer from sample inefficiency and limited generalization across various tasks. To this end, we propose VoxAct-B, a language-conditioned, voxel-based method that leverages Vision Language Models (VLMs) to prioritize key regions within the scene and reconstruct a voxel grid. We provide this voxel grid to our bimanual manipulation policy to learn acting and stabilizing actions. This approach enables more efficient policy learning from voxels and is generalizable to different tasks. In simulation, we show that VoxAct-B outperforms strong baselines on fine-grained bimanual manipulation tasks. Furthermore, we demonstrate VoxAct-B on real-world Open Drawer and Open Jar tasks using two UR5s. Code, data, and videos are available at https://voxact-b.github.io.

Comprehending 3D environments is vital for intelligent systems in domains like robotics and autonomous navigation. Voxel grids offer a structured representation of 3D space, but extracting high-level semantic meaning remains challenging. This paper proposes a novel approach utilizing a Vision-Language Model (VLM) to extract "voxel semantics"-object identity, color, and location-from voxel data. Critically, instead of employing complex 3D networks, our method processes the voxel space by systematically slicing it along a primary axis (e.g., the Z-axis, analogous to CT scan slices). These 2D slices are then formatted and sequentially fed into the image encoder of a standard VLM. The model learns to aggregate information across slices and correlate spatial patterns with semantic concepts provided by the language component. This slice-based strategy aims to leverage the power of pre-trained 2D VLMs for efficient 3D semantic understanding directly from voxel representations.

We present X^3 (pronounced XCube), a novel generative model for high-resolution sparse 3D voxel grids with arbitrary attributes. Our model can generate millions of voxels with a finest effective resolution of up to 1024^3 in a feed-forward fashion without time-consuming test-time optimization. To achieve this, we employ a hierarchical voxel latent diffusion model which generates progressively higher resolution grids in a coarse-to-fine manner using a custom framework built on the highly efficient VDB data structure. Apart from generating high-resolution objects, we demonstrate the effectiveness of XCube on large outdoor scenes at scales of 100mtimes100m with a voxel size as small as 10cm. We observe clear qualitative and quantitative improvements over past approaches. In addition to unconditional generation, we show that our model can be used to solve a variety of tasks such as user-guided editing, scene completion from a single scan, and text-to-3D. More results and details can be found at https://research.nvidia.com/labs/toronto-ai/xcube/.

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

Recent advances in sparse voxel representations have significantly improved the quality of 3D content generation, enabling high-resolution modeling with fine-grained geometry. However, existing frameworks suffer from severe computational inefficiencies due to the quadratic complexity of attention mechanisms in their two-stage diffusion pipelines. In this work, we propose Ultra3D, an efficient 3D generation framework that significantly accelerates sparse voxel modeling without compromising quality. Our method leverages the compact VecSet representation to efficiently generate a coarse object layout in the first stage, reducing token count and accelerating voxel coordinate prediction. To refine per-voxel latent features in the second stage, we introduce Part Attention, a geometry-aware localized attention mechanism that restricts attention computation within semantically consistent part regions. This design preserves structural continuity while avoiding unnecessary global attention, achieving up to 6.7x speed-up in latent generation. To support this mechanism, we construct a scalable part annotation pipeline that converts raw meshes into part-labeled sparse voxels. Extensive experiments demonstrate that Ultra3D supports high-resolution 3D generation at 1024 resolution and achieves state-of-the-art performance in both visual fidelity and user preference.

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

Existing automatic 3D image segmentation methods usually fail to meet the clinic use. Many studies have explored an interactive strategy to improve the image segmentation performance by iteratively incorporating user hints. However, the dynamic process for successive interactions is largely ignored. We here propose to model the dynamic process of iterative interactive image segmentation as a Markov decision process (MDP) and solve it with reinforcement learning (RL). Unfortunately, it is intractable to use single-agent RL for voxel-wise prediction due to the large exploration space. To reduce the exploration space to a tractable size, we treat each voxel as an agent with a shared voxel-level behavior strategy so that it can be solved with multi-agent reinforcement learning. An additional advantage of this multi-agent model is to capture the dependency among voxels for segmentation task. Meanwhile, to enrich the information of previous segmentations, we reserve the prediction uncertainty in the state space of MDP and derive an adjustment action space leading to a more precise and finer segmentation. In addition, to improve the efficiency of exploration, we design a relative cross-entropy gain-based reward to update the policy in a constrained direction. Experimental results on various medical datasets have shown that our method significantly outperforms existing state-of-the-art methods, with the advantage of fewer interactions and a faster convergence.

We present VoxelKP, a novel fully sparse network architecture tailored for human keypoint estimation in LiDAR data. The key challenge is that objects are distributed sparsely in 3D space, while human keypoint detection requires detailed local information wherever humans are present. We propose four novel ideas in this paper. First, we propose sparse selective kernels to capture multi-scale context. Second, we introduce sparse box-attention to focus on learning spatial correlations between keypoints within each human instance. Third, we incorporate a spatial encoding to leverage absolute 3D coordinates when projecting 3D voxels to a 2D grid encoding a bird's eye view. Finally, we propose hybrid feature learning to combine the processing of per-voxel features with sparse convolution. We evaluate our method on the Waymo dataset and achieve an improvement of 27% on the MPJPE metric compared to the state-of-the-art, HUM3DIL, trained on the same data, and 12% against the state-of-the-art, GC-KPL, pretrained on a 25times larger dataset. To the best of our knowledge, VoxelKP is the first single-staged, fully sparse network that is specifically designed for addressing the challenging task of 3D keypoint estimation from LiDAR data, achieving state-of-the-art performances. Our code is available at https://github.com/shijianjian/VoxelKP.

Interactive segmentation has recently been explored to effectively and efficiently harvest high-quality segmentation masks by iteratively incorporating user hints. While iterative in nature, most existing interactive segmentation methods tend to ignore the dynamics of successive interactions and take each interaction independently. We here propose to model iterative interactive image segmentation with a Markov decision process (MDP) and solve it with reinforcement learning (RL) where each voxel is treated as an agent. Considering the large exploration space for voxel-wise prediction and the dependence among neighboring voxels for the segmentation tasks, multi-agent reinforcement learning is adopted, where the voxel-level policy is shared among agents. Considering that boundary voxels are more important for segmentation, we further introduce a boundary-aware reward, which consists of a global reward in the form of relative cross-entropy gain, to update the policy in a constrained direction, and a boundary reward in the form of relative weight, to emphasize the correctness of boundary predictions. To combine the advantages of different types of interactions, i.e., simple and efficient for point-clicking, and stable and robust for scribbles, we propose a supervoxel-clicking based interaction design. Experimental results on four benchmark datasets have shown that the proposed method significantly outperforms the state-of-the-arts, with the advantage of fewer interactions, higher accuracy, and enhanced robustness.

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.

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

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

Serialization-based methods, which serialize the 3D voxels and group them into multiple sequences before inputting to Transformers, have demonstrated their effectiveness in 3D object detection. However, serializing 3D voxels into 1D sequences will inevitably sacrifice the voxel spatial proximity. Such an issue is hard to be addressed by enlarging the group size with existing serialization-based methods due to the quadratic complexity of Transformers with feature sizes. Inspired by the recent advances of state space models (SSMs), we present a Voxel SSM, termed as Voxel Mamba, which employs a group-free strategy to serialize the whole space of voxels into a single sequence. The linear complexity of SSMs encourages our group-free design, alleviating the loss of spatial proximity of voxels. To further enhance the spatial proximity, we propose a Dual-scale SSM Block to establish a hierarchical structure, enabling a larger receptive field in the 1D serialization curve, as well as more complete local regions in 3D space. Moreover, we implicitly apply window partition under the group-free framework by positional encoding, which further enhances spatial proximity by encoding voxel positional information. Our experiments on Waymo Open Dataset and nuScenes dataset show that Voxel Mamba not only achieves higher accuracy than state-of-the-art methods, but also demonstrates significant advantages in computational efficiency.

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.

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

A major goal of neuroscience is to understand brain computations during visual processing in naturalistic settings. A dominant approach is to use image-computable deep neural networks trained with different task objectives as a basis for linear encoding models. However, in addition to requiring tuning a large number of parameters, the linear encoding approach ignores the structure of the feature maps both in the brain and the models. Recently proposed alternatives have focused on decomposing the linear mapping to spatial and feature components but focus on finding static receptive fields for units that are applicable only in early visual areas. In this work, we employ the attention mechanism used in the transformer architecture to study how retinotopic visual features can be dynamically routed to category-selective areas in high-level visual processing. We show that this computational motif is significantly more powerful than alternative methods in predicting brain activity during natural scene viewing, across different feature basis models and modalities. We also show that this approach is inherently more interpretable, without the need to create importance maps, by interpreting the attention routing signal for different high-level categorical areas. Our approach proposes a mechanistic model of how visual information from retinotopic maps can be routed based on the relevance of the input content to different category-selective regions.

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

Attending to what is relevant is fundamental to both the mammalian brain and modern machine learning models such as Transformers. Yet, determining relevance remains a core challenge, traditionally offloaded to learning algorithms like backpropagation. Inspired by recent cellular neurobiological evidence linking neocortical pyramidal cells to distinct mental states, this work shows how models (e.g., Transformers) can emulate high-level perceptual processing and awake thought (imagination) states to pre-select relevant information before applying attention. Triadic neuronal-level modulation loops among questions (Q), clues (keys, K), and hypotheses (values, V) enable diverse, deep, parallel reasoning chains at the representation level and allow a rapid shift from initial biases to refined understanding. This leads to orders-of-magnitude faster learning with significantly reduced computational demand (e.g., fewer heads, layers, and tokens), at an approximate cost of O(N), where N is the number of input tokens. Results span reinforcement learning (e.g., CarRacing in a high-dimensional visual setup), computer vision, and natural language question answering.

Understanding 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.

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.

We propose an efficient radiance field rendering algorithm that incorporates a rasterization process on adaptive sparse voxels without neural networks or 3D Gaussians. There are two key contributions coupled with the proposed system. The first is to adaptively and explicitly allocate sparse voxels to different levels of detail within scenes, faithfully reproducing scene details with 65536^3 grid resolution while achieving high rendering frame rates. Second, we customize a rasterizer for efficient adaptive sparse voxels rendering. We render voxels in the correct depth order by using ray direction-dependent Morton ordering, which avoids the well-known popping artifact found in Gaussian splatting. Our method improves the previous neural-free voxel model by over 4db PSNR and more than 10x FPS speedup, achieving state-of-the-art comparable novel-view synthesis results. Additionally, our voxel representation is seamlessly compatible with grid-based 3D processing techniques such as Volume Fusion, Voxel Pooling, and Marching Cubes, enabling a wide range of future extensions and applications.

Growing evidence indicates that only a sparse subset from a pool of sensory neurons is active for the encoding of visual stimuli at any instant in time. Traditionally, to replicate such biological sparsity, generative models have been using the ell_1 norm as a penalty due to its convexity, which makes it amenable to fast and simple algorithmic solvers. In this work, we use biological vision as a test-bed and show that the soft thresholding operation associated to the use of the ell_1 norm is highly suboptimal compared to other functions suited to approximating ell_q with 0 leq q < 1 (including recently proposed Continuous Exact relaxations), both in terms of performance and in the production of features that are akin to signatures of the primary visual cortex. We show that ell_1 sparsity produces a denser code or employs a pool with more neurons, i.e. has a higher degree of overcompleteness, in order to maintain the same reconstruction error as the other methods considered. For all the penalty functions tested, a subset of the neurons develop orientation selectivity similarly to V1 neurons. When their code is sparse enough, the methods also develop receptive fields with varying functionalities, another signature of V1. Compared to other methods, soft thresholding achieves this level of sparsity at the expense of much degraded reconstruction performance, that more likely than not is not acceptable in biological vision. Our results indicate that V1 uses a sparsity inducing regularization that is closer to the ell_0 pseudo-norm rather than to the ell_1 norm.

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

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.

Recent advances in 3D X-ray Computed Tomographic (CT) sensors have stimulated research efforts to unveil the extremely complex micro-scale processes that control the activity of soil microorganisms. Voxel-based description (up to hundreds millions voxels) of the pore space can be extracted, from grey level 3D CT scanner images, by means of simple image processing tools. Classical methods for numerical simulation of biological dynamics using mesh of voxels, such as Lattice Boltzmann Model (LBM), are too much time consuming. Thus, the use of more compact and reliable geometrical representations of pore space can drastically decrease the computational cost of the simulations. Several recent works propose basic analytic volume primitives (e.g. spheres, generalized cylinders, ellipsoids) to define a piece-wise approximation of pore space for numerical simulation of draining, diffusion and microbial decomposition. Such approaches work well but the drawback is that it generates approximation errors. In the present work, we study another alternative where pore space is described by means of geometrically relevant connected subsets of voxels (regions) computed from the curvilinear skeleton. Indeed, many works use the curvilinear skeleton (3D medial axis) for analyzing and partitioning 3D shapes within various domains (medicine, material sciences, petroleum engineering, etc.) but only a few ones in soil sciences. Within the context of soil sciences, most studies dealing with 3D medial axis focus on the determination of pore throats. Here, we segment pore space using curvilinear skeleton in order to achieve numerical simulation of microbial decomposition (including diffusion processes). We validate simulation outputs by comparison with other methods using different pore space geometrical representations (balls, voxels).

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.

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.

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

Part-based 3D generation holds great potential for various applications. Previous part generators that represent parts using implicit vector-set tokens often suffer from insufficient geometric details. Another line of work adopts an explicit voxel representation but shares a global voxel grid among all parts; this often causes small parts to occupy too few voxels, leading to degraded quality. In this paper, we propose FullPart, a novel framework that combines both implicit and explicit paradigms. It first derives the bounding box layout through an implicit box vector-set diffusion process, a task that implicit diffusion handles effectively since box tokens contain little geometric detail. Then, it generates detailed parts, each within its own fixed full-resolution voxel grid. Instead of sharing a global low-resolution space, each part in our method - even small ones - is generated at full resolution, enabling the synthesis of intricate details. We further introduce a center-point encoding strategy to address the misalignment issue when exchanging information between parts of different actual sizes, thereby maintaining global coherence. Moreover, to tackle the scarcity of reliable part data, we present PartVerse-XL, the largest human-annotated 3D part dataset to date with 40K objects and 320K parts. Extensive experiments demonstrate that FullPart achieves state-of-the-art results in 3D part generation. We will release all code, data, and model to benefit future research in 3D part generation.

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.

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

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/.

Active learning, a label-efficient paradigm, empowers models to interactively query an oracle for labeling new data. In the realm of LiDAR semantic segmentation, the challenges stem from the sheer volume of point clouds, rendering annotation labor-intensive and cost-prohibitive. This paper presents Annotator, a general and efficient active learning baseline, in which a voxel-centric online selection strategy is tailored to efficiently probe and annotate the salient and exemplar voxel girds within each LiDAR scan, even under distribution shift. Concretely, we first execute an in-depth analysis of several common selection strategies such as Random, Entropy, Margin, and then develop voxel confusion degree (VCD) to exploit the local topology relations and structures of point clouds. Annotator excels in diverse settings, with a particular focus on active learning (AL), active source-free domain adaptation (ASFDA), and active domain adaptation (ADA). It consistently delivers exceptional performance across LiDAR semantic segmentation benchmarks, spanning both simulation-to-real and real-to-real scenarios. Surprisingly, Annotator exhibits remarkable efficiency, requiring significantly fewer annotations, e.g., just labeling five voxels per scan in the SynLiDAR-to-SemanticKITTI task. This results in impressive performance, achieving 87.8% fully-supervised performance under AL, 88.5% under ASFDA, and 94.4% under ADA. We envision that Annotator will offer a simple, general, and efficient solution for label-efficient 3D applications. Project page: https://binhuixie.github.io/annotator-web

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.

Voxel art is a distinctive stylization widely used in games and digital media, yet automated generation from 3D meshes remains challenging due to conflicting requirements of geometric abstraction, semantic preservation, and discrete color coherence. Existing methods either over-simplify geometry or fail to achieve the pixel-precise, palette-constrained aesthetics of voxel art. We introduce Voxify3D, a differentiable two-stage framework bridging 3D mesh optimization with 2D pixel art supervision. Our core innovation lies in the synergistic integration of three components: (1) orthographic pixel art supervision that eliminates perspective distortion for precise voxel-pixel alignment; (2) patch-based CLIP alignment that preserves semantics across discretization levels; (3) palette-constrained Gumbel-Softmax quantization enabling differentiable optimization over discrete color spaces with controllable palette strategies. This integration addresses fundamental challenges: semantic preservation under extreme discretization, pixel-art aesthetics through volumetric rendering, and end-to-end discrete optimization. Experiments show superior performance (37.12 CLIP-IQA, 77.90\% user preference) across diverse characters and controllable abstraction (2-8 colors, 20x-50x resolutions). Project page: https://yichuanh.github.io/Voxify-3D/

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

Human's perception of the visual world is shaped by the stereo processing of 3D information. Understanding how the brain perceives and processes 3D visual stimuli in the real world has been a longstanding endeavor in neuroscience. Towards this goal, we introduce a new neuroscience task: decoding 3D visual perception from EEG signals, a neuroimaging technique that enables real-time monitoring of neural dynamics enriched with complex visual cues. To provide the essential benchmark, we first present EEG-3D, a pioneering dataset featuring multimodal analysis data and extensive EEG recordings from 12 subjects viewing 72 categories of 3D objects rendered in both videos and images. Furthermore, we propose Neuro-3D, a 3D visual decoding framework based on EEG signals. This framework adaptively integrates EEG features derived from static and dynamic stimuli to learn complementary and robust neural representations, which are subsequently utilized to recover both the shape and color of 3D objects through the proposed diffusion-based colored point cloud decoder. To the best of our knowledge, we are the first to explore EEG-based 3D visual decoding. Experiments indicate that Neuro-3D not only reconstructs colored 3D objects with high fidelity, but also learns effective neural representations that enable insightful brain region analysis. The dataset and associated code will be made publicly available.

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

Identifying which brain regions represent a visual concept in the human brain is a central challenge in neuroscience. Existing approaches have localized coarse functional regions (e.g., faces, places) through activation maximization, identifying regions that activate strongly for a target concept relative to other concepts. Yet strong activation alone does not establish that a region represents the concept itself, as responses may instead be driven by correlated visual or semantic cues. We introduce BrainCause, an automated framework that combines generative and brain models to synthesize controlled stimuli and validate neural representations through targeted causal testing. Given a query specifying a concept of interest, our framework constructs targeted stimulus sets comprising concept images, counterfactual edits that remove the target concept while preserving other image content, and images with candidate correlated distractors. It then uses an image-to-fMRI encoding model to predict brain responses and searches for representations that respond specifically to the target concept over correlated alternatives. BrainCause returns validated candidate representations and proposes follow-up fMRI experiments to further test or extend its discoveries. Our approach successfully recovers known functional localizations and identifies new candidate representations across dozens of concepts, validated on both predicted and measured fMRI data. Critically, we show that without causal validation, a large fraction of localizations would be false positives, confirming that activation alone is insufficient evidence of representation.

Modeling long-range spatiotemporal dynamics in functional Magnetic Resonance Imaging (fMRI) remains a key challenge due to the high dimensionality of the four-dimensional signals. Prior voxel-based models, although demonstrating excellent performance and interpretation capabilities, are constrained by prohibitive memory demands and thus can only capture limited temporal windows. To address this, we propose TABLeT (Two-dimensionally Autoencoded Brain Latent Transformer), a novel approach that tokenizes fMRI volumes using a pre-trained 2D natural image autoencoder. Each 3D fMRI volume is compressed into a compact set of continuous tokens, enabling long-sequence modeling with a simple Transformer encoder with limited VRAM. Across large-scale benchmarks including the UK-Biobank (UKB), Human Connectome Project (HCP), and ADHD-200 datasets, TABLeT outperforms existing models in multiple tasks, while demonstrating substantial gains in computational and memory efficiency over the state-of-the-art voxel-based method given the same input. Furthermore, we develop a self-supervised masked token modeling approach to pre-train TABLeT, which improves the model's performance for various downstream tasks. Our findings suggest a promising approach for scalable and interpretable spatiotemporal modeling of brain activity. Our code is available at https://github.com/beotborry/TABLeT.

Neural representations carry rich geometric structure; but does that structure causally shape behavior? To address this question, we intervene along paths through activation space defined by different geometries, and measure the behavioral trajectories they induce. In particular, we test whether interventions that respect the geometry of activation space will yield behaviors close to those the model exhibits naturally. Concretely, we first fit an activation manifold M_h to representations and a behavior manifold M_y to output probability distributions. We then test the link M_h leftrightarrow M_y via interventions: we find that steering along M_h, which we term manifold steering, yields behavioral trajectories that follow M_y, while linear steering -- which assumes a Euclidean geometry -- cuts through off-manifold regions and hence produces unnatural outputs. Moreover, optimizing interventions in activation space to produce paths along M_y recovers activation trajectories that trace the curvature of M_h. We demonstrate this bidirectional relationship between the geometry of representation and behavior across tasks and modalities. In language models, we use reasoning tasks with cyclic and sequential geometries as well as in-context learning tasks with more complex graph geometries. In a video world model, we use a task with geometry corresponding to physical dynamics. Overall, our work shows that geometry in neural representation is not merely incidental, but is in fact the proper object for enabling principled control via intervention on internals. This recasts the core problem of steering from finding the right direction to finding the right geometry.

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.

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

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.

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

Magnetic resonance imaging (MRI) is the standard modality to understand human brain structure and function in vivo (antemortem). Decades of research in human neuroimaging has led to the widespread development of methods and tools to provide automated volume-based segmentations and surface-based parcellations which help localize brain functions to specialized anatomical regions. Recently ex vivo (postmortem) imaging of the brain has opened-up avenues to study brain structure at sub-millimeter ultra high-resolution revealing details not possible to observe with in vivo MRI. Unfortunately, there has been limited methodological development in ex vivo MRI primarily due to lack of datasets and limited centers with such imaging resources. Therefore, in this work, we present one-of-its-kind dataset of 82 ex vivo T2w whole brain hemispheres MRI at 0.3 mm isotropic resolution spanning Alzheimer's disease and related dementias. We adapted and developed a fast and easy-to-use automated surface-based pipeline to parcellate, for the first time, ultra high-resolution ex vivo brain tissue at the native subject space resolution using the Desikan-Killiany-Tourville (DKT) brain atlas. This allows us to perform vertex-wise analysis in the template space and thereby link morphometry measures with pathology measurements derived from histology. We will open-source our dataset docker container, Jupyter notebooks for ready-to-use out-of-the-box set of tools and command line options to advance ex vivo MRI clinical brain imaging research on the project webpage.

Although the recent rapid evolution of 3D generative neural networks greatly improves 3D shape generation, it is still not convenient for ordinary users to create 3D shapes and control the local geometry of generated shapes. To address these challenges, we propose a diffusion-based 3D generation framework -- locally attentional SDF diffusion, to model plausible 3D shapes, via 2D sketch image input. Our method is built on a two-stage diffusion model. The first stage, named occupancy-diffusion, aims to generate a low-resolution occupancy field to approximate the shape shell. The second stage, named SDF-diffusion, synthesizes a high-resolution signed distance field within the occupied voxels determined by the first stage to extract fine geometry. Our model is empowered by a novel view-aware local attention mechanism for image-conditioned shape generation, which takes advantage of 2D image patch features to guide 3D voxel feature learning, greatly improving local controllability and model generalizability. Through extensive experiments in sketch-conditioned and category-conditioned 3D shape generation tasks, we validate and demonstrate the ability of our method to provide plausible and diverse 3D shapes, as well as its superior controllability and generalizability over existing work. Our code and trained models are available at https://zhengxinyang.github.io/projects/LAS-Diffusion.html

We present a novel two-stage fully sparse convolutional 3D object detection framework, named CAGroup3D. Our proposed method first generates some high-quality 3D proposals by leveraging the class-aware local group strategy on the object surface voxels with the same semantic predictions, which considers semantic consistency and diverse locality abandoned in previous bottom-up approaches. Then, to recover the features of missed voxels due to incorrect voxel-wise segmentation, we build a fully sparse convolutional RoI pooling module to directly aggregate fine-grained spatial information from backbone for further proposal refinement. It is memory-and-computation efficient and can better encode the geometry-specific features of each 3D proposal. Our model achieves state-of-the-art 3D detection performance with remarkable gains of +3.6\% on ScanNet V2 and +2.6\% on SUN RGB-D in term of mAP@0.25. Code will be available at https://github.com/Haiyang-W/CAGroup3D.

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.

Conditional 3D generation is undergoing a significant advancement, enabling the free creation of 3D content from inputs such as text or 2D images. However, previous approaches have suffered from low inference efficiency, limited generation categories, and restricted downstream applications. In this work, we revisit the impact of different 3D representations on generation quality and efficiency. We propose a progressive generation method through Voxel-Point Progressive Representation (VPP). VPP leverages structured voxel representation in the proposed Voxel Semantic Generator and the sparsity of unstructured point representation in the Point Upsampler, enabling efficient generation of multi-category objects. VPP can generate high-quality 8K point clouds within 0.2 seconds. Additionally, the masked generation Transformer allows for various 3D downstream tasks, such as generation, editing, completion, and pre-training. Extensive experiments demonstrate that VPP efficiently generates high-fidelity and diverse 3D shapes across different categories, while also exhibiting excellent representation transfer performance. Codes will be released at https://github.com/qizekun/VPP.

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

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

Unsupervised learning of object-centric representations in dynamic visual scenes is challenging. Unlike most previous approaches that learn to decompose 2D images, we present DynaVol, a 3D scene generative model that unifies geometric structures and object-centric learning in a differentiable volume rendering framework. The key idea is to perform object-centric voxelization to capture the 3D nature of the scene, which infers the probability distribution over objects at individual spatial locations. These voxel features evolve over time through a canonical-space deformation function, forming the basis for global representation learning via slot attention. The voxel features and global features are complementary and are both leveraged by a compositional NeRF decoder for volume rendering. DynaVol remarkably outperforms existing approaches for unsupervised dynamic scene decomposition. Once trained, the explicitly meaningful voxel features enable additional capabilities that 2D scene decomposition methods cannot achieve: it is possible to freely edit the geometric shapes or manipulate the motion trajectories of the objects.

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.

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.

Window-based transformers excel in large-scale point cloud understanding by capturing context-aware representations with affordable attention computation in a more localized manner. However, the sparse nature of point clouds leads to a significant variance in the number of voxels per window. Existing methods group the voxels in each window into fixed-length sequences through extensive sorting and padding operations, resulting in a non-negligible computational and memory overhead. In this paper, we introduce ScatterFormer, which to the best of our knowledge, is the first to directly apply attention to voxels across different windows as a single sequence. The key of ScatterFormer is a Scattered Linear Attention (SLA) module, which leverages the pre-computation of key-value pairs in linear attention to enable parallel computation on the variable-length voxel sequences divided by windows. Leveraging the hierarchical structure of GPUs and shared memory, we propose a chunk-wise algorithm that reduces the SLA module's latency to less than 1 millisecond on moderate GPUs. Furthermore, we develop a cross-window interaction module that improves the locality and connectivity of voxel features across different windows, eliminating the need for extensive window shifting. Our proposed ScatterFormer demonstrates 73.8 mAP (L2) on the Waymo Open Dataset and 72.4 NDS on the NuScenes dataset, running at an outstanding detection rate of 23 FPS.The code is available at https://github.com/skyhehe123/ScatterFormer{https://github.com/skyhehe123/ScatterFormer}.

Foundation models are emerging as a powerful paradigm for fMRI analysis, but current approaches face a dual bottleneck of data- and training-efficiency. Atlas-based methods aggregate voxel signals into fixed regions of interest, reducing data dimensionality but discarding fine-grained spatial details, and requiring extremely large cohorts to train effectively as general-purpose foundation models. Atlas-free methods, on the other hand, operate directly on voxel-level information - preserving spatial fidelity but are prohibitively memory- and compute-intensive, making large-scale pre-training infeasible. We introduce SLIM-Brain (Sample-efficient, Low-memory fMRI Foundation Model for Human Brain), a new atlas-free foundation model that simultaneously improves both data- and training-efficiency. SLIM-Brain adopts a two-stage adaptive design: (i) a lightweight temporal extractor captures global context across full sequences and ranks data windows by saliency, and (ii) a 4D hierarchical encoder (Hiera-JEPA) learns fine-grained voxel-level representations only from the top-k selected windows, while deleting about 70% masked patches. Extensive experiments across seven public benchmarks show that SLIM-Brain establishes new state-of-the-art performance on diverse tasks, while requiring only 4 thousand pre-training sessions and approximately 30% of GPU memory comparing to traditional voxel-level methods.

Multimodal large language models (MLLMs) have achieved remarkable performance on complex tasks with multimodal context. However, it is still understudied whether they exhibit modality preference when processing multimodal contexts. To study this question, we first build a MC\textsuperscript{2} benchmark under controlled evidence conflict scenarios to systematically evaluate modality preference, which is the tendency to favor one modality over another when making decisions based on multimodal conflicting evidence. Our extensive evaluation reveals that all 18 tested MLLMs generally demonstrate clear modality bias, and modality preference can be influenced by external interventions. An in-depth analysis reveals that the preference direction can be captured within the latent representations of MLLMs. Built on this, we propose a probing and steering method based on representation engineering to explicitly control modality preference without additional fine-tuning or carefully crafted prompts. Our method effectively amplifies modality preference toward a desired direction and applies to downstream tasks such as hallucination mitigation and multimodal machine translation, yielding promising improvements.

We propose a formal mathematical model for sparse representations and active dendrites in neocortex. Our model is inspired by recent experimental findings on active dendritic processing and NMDA spikes in pyramidal neurons. These experimental and modeling studies suggest that the basic unit of pattern memory in the neocortex is instantiated by small clusters of synapses operated on by localized non-linear dendritic processes. We derive a number of scaling laws that characterize the accuracy of such dendrites in detecting activation patterns in a neuronal population under adverse conditions. We introduce the union property which shows that synapses for multiple patterns can be randomly mixed together within a segment and still lead to highly accurate recognition. We describe simulation results that provide further insight into sparse representations as well as two primary results. First we show that pattern recognition by a neuron with active dendrites can be extremely accurate and robust with high dimensional sparse inputs even when using a tiny number of synapses to recognize large patterns. Second, equations representing recognition accuracy of a dendrite predict optimal NMDA spiking thresholds under a generous set of assumptions. The prediction tightly matches NMDA spiking thresholds measured in the literature. Our model matches many of the known properties of pyramidal neurons. As such the theory provides a mathematical framework for understanding the benefits and limits of sparse representations in cortical networks.

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.

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.

Activation steering presupposes that task-relevant behaviors correspond to linear directions in activation space -- directions that should both steer the model and be readable along the unembedding. Function vectors (FVs), extracted as mean differences across ICL demonstrations, are the canonical test case; the prediction: steering and decoding succeed or fail together. Across 12 tasks, 6 models from 3 families, and 4,032 directed cross-template pairs, we find the opposite. FV steering routinely succeeds where the logit lens cannot decode the correct answer at any intermediate layer, while the converse -- decodable without steerable -- is nearly empty (3 of 72). The gap is not representational dialect. A diagonal tuned lens closes 1 of 14 steerable-not-decodable cases; a 2-layer MLP probe with a Hewitt \& Liang control closes 5 of 10 via nonlinearly encoded structure but leaves 5 invisible to every decoder tested. Even at > 0.90 steering accuracy, projecting the FV through the unembedding yields incoherent token distributions: FVs encode computational instructions, not answer directions. A model-family asymmetry sharpens the picture. Mistral FVs rewrite intermediate representations, while Llama and Gemma FVs steer the final output without leaving a logit-lens-visible trace, corroborated by three signals (post-steering deltas, activation-patching recovery, FV norm-transfer correlations). A previously reported negative cosine-transfer correlation dissolves at scale, adding at most ΔR^2 = 0.011 beyond task identity. These results decompose the linear representation hypothesis into linear decodability and linear steerability and show they come apart opposite to intuition, with implications for safety monitoring: vocabulary-projection tools are blind to FV-style interventions on widely deployed model families.

Current medical vision-language models (VLMs) process volumetric brain MRI using 2D slice-based approximations, fragmenting the spatial context required for accurate neuroradiological interpretation. We developed Brain3D, a staged vision-language framework for automated radiology report generation from 3D brain tumor MRI. Our approach inflates a pretrained 2D medical encoder into a native 3D architecture and progressively aligns it with a causal language model through three stages: contrastive grounding, supervised projector warmup, and LoRA-based linguistic specialization. Unlike generalist 3D medical VLMs, Brain3D is tailored to neuroradiology, where hemispheric laterality, tumor infiltration patterns, and anatomical localization are critical. Evaluated on 468 subjects (BraTS pathological cases plus healthy controls), our model achieves a Clinical Pathology F1 of 0.951 versus 0.413 for a strong 2D baseline while maintaining perfect specificity on healthy scans. The staged alignment proves essential: contrastive grounding establishes visual-textual correspondence, projector warmup stabilizes conditioning, and LoRA adaptation shifts output from verbose captions to structured clinical reports\footnote{Our code is publicly available for transparency and reproducibility

Cortical visual prostheses aim to restore sight by electrically stimulating neurons in early visual cortex (V1). With the emergence of high-density and flexible neural interfaces, electrode placement within three-dimensional cortex has become a critical surgical planning problem. Existing strategies emphasize visual field coverage and anatomical heuristics but do not directly optimize predicted perceptual outcomes under safety constraints. We present a percept-aware framework for surgical planning of cortical visual prostheses that formulates electrode placement as a constrained optimization problem in anatomical space. Electrode coordinates are treated as learnable parameters and optimized end-to-end using a differentiable forward model of prosthetic vision. The objective minimizes task-level perceptual error while incorporating vascular avoidance and gray matter feasibility constraints. Evaluated on simulated reading and natural image tasks using realistic folded cortical geometry (FreeSurfer fsaverage), percept-aware optimization consistently improves reconstruction fidelity relative to coverage-based placement strategies. Importantly, vascular safety constraints eliminate margin violations while preserving perceptual performance. The framework further enables co-optimization of multi-electrode thread configurations under fixed insertion budgets. These results demonstrate how differentiable percept models can inform anatomically grounded, safety-aware computer-assisted planning for cortical neural interfaces and provide a foundation for optimizing next-generation visual prostheses.

Traditional fluorescence staining is phototoxic to live cells, slow, and expensive; thus, the subcellular structure prediction (SSP) from transmitted light (TL) images is emerging as a label-free, faster, low-cost alternative. However, existing approaches utilize 3D networks for one-to-one voxel level dense prediction, which necessitates a frequent and time-consuming Z-axis imaging process. Moreover, 3D convolutions inevitably lead to significant computation and GPU memory overhead. Therefore, we propose an efficient framework, SparseSSP, predicting fluorescent intensities within the target voxel grid in an efficient paradigm instead of relying entirely on 3D topologies. In particular, SparseSSP makes two pivotal improvements to prior works. First, SparseSSP introduces a one-to-many voxel mapping paradigm, which permits the sparse TL slices to reconstruct the subcellular structure. Secondly, we propose a hybrid dimensions topology, which folds the Z-axis information into channel features, enabling the 2D network layers to tackle SSP under low computational cost. We conduct extensive experiments to validate the effectiveness and advantages of SparseSSP on diverse sparse imaging ratios, and our approach achieves a leading performance compared to pure 3D topologies. SparseSSP reduces imaging frequencies compared to previous dense-view SSP (i.e., the number of imaging is reduced up to 87.5% at most), which is significant in visualizing rapid biological dynamics on low-cost devices and samples.

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

We develop a learning framework for building deformable templates, which play a fundamental role in many image analysis and computational anatomy tasks. Conventional methods for template creation and image alignment to the template have undergone decades of rich technical development. In these frameworks, templates are constructed using an iterative process of template estimation and alignment, which is often computationally very expensive. Due in part to this shortcoming, most methods compute a single template for the entire population of images, or a few templates for specific sub-groups of the data. In this work, we present a probabilistic model and efficient learning strategy that yields either universal or conditional templates, jointly with a neural network that provides efficient alignment of the images to these templates. We demonstrate the usefulness of this method on a variety of domains, with a special focus on neuroimaging. This is particularly useful for clinical applications where a pre-existing template does not exist, or creating a new one with traditional methods can be prohibitively expensive. Our code and atlases are available online as part of the VoxelMorph library at http://voxelmorph.csail.mit.edu.

Current volumetric biomedical foundation models struggle to generalize as public 3D datasets are small and do not cover the broad diversity of medical procedures, conditions, anatomical regions, and imaging protocols. We address this by creating a representation learning method that instead anticipates strong domain shifts at training time itself. We first propose a data engine that synthesizes highly variable training samples that would enable generalization to new biomedical contexts. To then train a single 3D network for any voxel-level task, we develop a contrastive learning method that pretrains the network to be stable against nuisance imaging variation simulated by the data engine, a key inductive bias for generalization. This network's features can be used as robust representations of input images for downstream tasks and its weights provide a strong, dataset-agnostic initialization for finetuning on new datasets. As a result, we set new standards across both multimodality registration and few-shot segmentation, a first for any 3D biomedical vision model, all without (pre-)training on any existing dataset of real images.

Recent advancements in 3D generative modeling have significantly improved the generation realism, yet the field is still hampered by existing representations, which struggle to capture assets with complex topologies and detailed appearance. This paper present an approach for learning a structured latent representation from native 3D data to address this challenge. At its core is a new sparse voxel structure called O-Voxel, an omni-voxel representation that encodes both geometry and appearance. O-Voxel can robustly model arbitrary topology, including open, non-manifold, and fully-enclosed surfaces, while capturing comprehensive surface attributes beyond texture color, such as physically-based rendering parameters. Based on O-Voxel, we design a Sparse Compression VAE which provides a high spatial compression rate and a compact latent space. We train large-scale flow-matching models comprising 4B parameters for 3D generation using diverse public 3D asset datasets. Despite their scale, inference remains highly efficient. Meanwhile, the geometry and material quality of our generated assets far exceed those of existing models. We believe our approach offers a significant advancement in 3D generative modeling.

Diffusion Magnetic Resonance Imaging (dMRI) plays a crucial role in the noninvasive investigation of tissue microstructural properties and structural connectivity in the in vivo human brain. However, to effectively capture the intricate characteristics of water diffusion at various directions and scales, it is important to employ comprehensive q-space sampling. Unfortunately, this requirement leads to long scan times, limiting the clinical applicability of dMRI. To address this challenge, we propose SSOR, a Simultaneous q-Space sampling Optimization and Reconstruction framework. We jointly optimize a subset of q-space samples using a continuous representation of spherical harmonic functions and a reconstruction network. Additionally, we integrate the unique properties of diffusion magnetic resonance imaging (dMRI) in both the q-space and image domains by applying l1-norm and total-variation regularization. The experiments conducted on HCP data demonstrate that SSOR has promising strengths both quantitatively and qualitatively and exhibits robustness to noise.

We present a super-fast convergence approach to reconstructing the per-scene radiance field from a set of images that capture the scene with known poses. This task, which is often applied to novel view synthesis, is recently revolutionized by Neural Radiance Field (NeRF) for its state-of-the-art quality and flexibility. However, NeRF and its variants require a lengthy training time ranging from hours to days for a single scene. In contrast, our approach achieves NeRF-comparable quality and converges rapidly from scratch in less than 15 minutes with a single GPU. We adopt a representation consisting of a density voxel grid for scene geometry and a feature voxel grid with a shallow network for complex view-dependent appearance. Modeling with explicit and discretized volume representations is not new, but we propose two simple yet non-trivial techniques that contribute to fast convergence speed and high-quality output. First, we introduce the post-activation interpolation on voxel density, which is capable of producing sharp surfaces in lower grid resolution. Second, direct voxel density optimization is prone to suboptimal geometry solutions, so we robustify the optimization process by imposing several priors. Finally, evaluation on five inward-facing benchmarks shows that our method matches, if not surpasses, NeRF's quality, yet it only takes about 15 minutes to train from scratch for a new scene.

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

Our goal is to create a convenient natural language interface for performing well-specified but complex actions such as analyzing data, manipulating text, and querying databases. However, existing natural language interfaces for such tasks are quite primitive compared to the power one wields with a programming language. To bridge this gap, we start with a core programming language and allow users to "naturalize" the core language incrementally by defining alternative, more natural syntax and increasingly complex concepts in terms of compositions of simpler ones. In a voxel world, we show that a community of users can simultaneously teach a common system a diverse language and use it to build hundreds of complex voxel structures. Over the course of three days, these users went from using only the core language to using the naturalized language in 85.9\% of the last 10K utterances.

Previous work has shown correlations between the hidden states of large language models and fMRI brain responses, on language tasks. These correlations have been taken as evidence of the representational similarity of these models and brain states. This study tests whether these previous results are robust to several possible concerns. Specifically this study shows: (i) that the previous results are still found after dimensionality reduction, and thus are not attributable to the curse of dimensionality; (ii) that previous results are confirmed when using new measures of similarity; (iii) that correlations between brain representations and those from models are specific to models trained on human language; and (iv) that the results are dependent on the presence of positional encoding in the models. These results confirm and strengthen the results of previous research and contribute to the debate on the biological plausibility and interpretability of state-of-the-art large language models.

Brain MRI scans are often found in four modalities, consisting of T1-weighted with and without contrast enhancement (T1ce and T1w), T2-weighted imaging (T2w), and Flair. Leveraging complementary information from these different modalities enables models to learn richer, more discriminative features for understanding brain anatomy, which could be used in downstream tasks such as anomaly detection. However, in clinical practice, not all MRI modalities are always available due to various reasons. This makes missing modality generation a critical challenge in medical image analysis. In this paper, we propose SLaM-DiMM, a novel missing modality generation framework that harnesses the power of diffusion models to synthesize any of the four target MRI modalities from other available modalities. Our approach not only generates high-fidelity images but also ensures structural coherence across the depth of the volume through a dedicated coherence enhancement mechanism. Qualitative and quantitative evaluations on the BraTS-Lighthouse-2025 Challenge dataset demonstrate the effectiveness of the proposed approach in synthesizing anatomically plausible and structurally consistent results. Code is available at https://github.com/BheeshmSharma/SLaM-DiMM-MICCAI-BraTS-Challenge-2025.

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.

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

Historically, neuroscience has progressed by fragmenting into specialized domains, each focusing on isolated modalities, tasks, or brain regions. While fruitful, this approach hinders the development of a unified model of cognition. Here, we introduce TRIBE, the first deep neural network trained to predict brain responses to stimuli across multiple modalities, cortical areas and individuals. By combining the pretrained representations of text, audio and video foundational models and handling their time-evolving nature with a transformer, our model can precisely model the spatial and temporal fMRI responses to videos, achieving the first place in the Algonauts 2025 brain encoding competition with a significant margin over competitors. Ablations show that while unimodal models can reliably predict their corresponding cortical networks (e.g. visual or auditory networks), they are systematically outperformed by our multimodal model in high-level associative cortices. Currently applied to perception and comprehension, our approach paves the way towards building an integrative model of representations in the human brain. Our code is available at https://github.com/facebookresearch/algonauts-2025.

Accurate detection of objects in 3D point clouds is a central problem in many applications, such as autonomous navigation, housekeeping robots, and augmented/virtual reality. To interface a highly sparse LiDAR point cloud with a region proposal network (RPN), most existing efforts have focused on hand-crafted feature representations, for example, a bird's eye view projection. In this work, we remove the need of manual feature engineering for 3D point clouds and propose VoxelNet, a generic 3D detection network that unifies feature extraction and bounding box prediction into a single stage, end-to-end trainable deep network. Specifically, VoxelNet divides a point cloud into equally spaced 3D voxels and transforms a group of points within each voxel into a unified feature representation through the newly introduced voxel feature encoding (VFE) layer. In this way, the point cloud is encoded as a descriptive volumetric representation, which is then connected to a RPN to generate detections. Experiments on the KITTI car detection benchmark show that VoxelNet outperforms the state-of-the-art LiDAR based 3D detection methods by a large margin. Furthermore, our network learns an effective discriminative representation of objects with various geometries, leading to encouraging results in 3D detection of pedestrians and cyclists, based on only LiDAR.

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

We propose OpenVoxel, a training-free algorithm for grouping and captioning sparse voxels for the open-vocabulary 3D scene understanding tasks. Given the sparse voxel rasterization (SVR) model obtained from multi-view images of a 3D scene, our OpenVoxel is able to produce meaningful groups that describe different objects in the scene. Also, by leveraging powerful Vision Language Models (VLMs) and Multi-modal Large Language Models (MLLMs), our OpenVoxel successfully build an informative scene map by captioning each group, enabling further 3D scene understanding tasks such as open-vocabulary segmentation (OVS) or referring expression segmentation (RES). Unlike previous methods, our method is training-free and does not introduce embeddings from a CLIP/BERT text encoder. Instead, we directly proceed with text-to-text search using MLLMs. Through extensive experiments, our method demonstrates superior performance compared to recent studies, particularly in complex referring expression segmentation (RES) tasks. The code will be open.

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.

Recent advances in multimodal large language models enable new possibilities for image-based decision support. However, their reliability and operational trade-offs in neuroimaging remain insufficiently understood. We present a comprehensive benchmarking study of vision-enabled large language models for 2D neuroimaging using curated MRI and CT datasets covering multiple sclerosis, stroke, brain tumors, other abnormalities, and normal controls. Models are required to generate multiple outputs simultaneously, including diagnosis, diagnosis subtype, imaging modality, specialized sequence, and anatomical plane. Performance is evaluated across four directions: discriminative classification with abstention, calibration, structured-output validity, and computational efficiency. A multi-phase framework ensures fair comparison while controlling for selection bias. Across twenty frontier multimodal models, the results show that technical imaging attributes such as modality and plane are nearly solved, whereas diagnostic reasoning, especially subtype prediction, remains challenging. Tumor classification emerges as the most reliable task, stroke is moderately solvable, while multiple sclerosis and rare abnormalities remain difficult. Few-shot prompting improves performance for several models but increases token usage, latency, and cost. Gemini-2.5-Pro and GPT-5-Chat achieve the strongest overall diagnostic performance, while Gemini-2.5-Flash offers the best efficiency-performance trade-off. Among open-weight architectures, MedGemma-1.5-4B demonstrates the most promising results, as under few-shot prompting, it approaches the zero-shot performance of several proprietary models, while maintaining perfect structured output. These findings provide practical insights into performance, reliability, and efficiency trade-offs, supporting standardized evaluation of multimodal LLMs in neuroimaging.

We extend the recently proposed sparse voxel rasterization paradigm to the task of high-fidelity surface reconstruction by integrating Signed Distance Function (SDF), named SVRecon. Unlike 3D Gaussians, sparse voxels are spatially disentangled from their neighbors and have sharp boundaries, which makes them prone to local minima during optimization. Although SDF values provide a naturally smooth and continuous geometric field, preserving this smoothness across independently parameterized sparse voxels is nontrivial. To address this challenge, we promote coherent and smooth voxel-wise structure through (1) robust geometric initialization using a visual geometry model and (2) a spatial smoothness loss that enforces coherent relationships across parent-child and sibling voxel groups. Extensive experiments across various benchmarks show that our method achieves strong reconstruction accuracy while having consistently speedy convergence. The code will be made public.

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.

Native Omni-modal Large Language Models (OLLMs) have shifted from pipeline architectures to unified representation spaces. However, this native integration gives rise to a critical yet underexplored phenomenon: modality preference. To bridge this gap, we first systematically quantify modality preference of OLLMs using a newly-curated conflict-based benchmark and the modality selection rate metric. Our evaluation of ten representative OLLMs reveals a notable paradigm shift: unlike the ``text-dominance'' of traditional VLMs, most OLLMs exhibit a pronounced visual preference. To further understand the underlying mechanism, we conduct layer-wise probing and demonstrate that such modality preference is not static but emerges progressively in the mid-to-late layers. Building upon these insights, we leverage these internal signals to diagnose cross-modal hallucinations, achieving competitive performance across three downstream multi-modal benchmarks without task-specific data. Our work provides both a mechanistic understanding and a practical tool for building more trustworthy OLLMs. Our code and related resources are publicly available at: https://github.com/icip-cas/OmniPreference

Large scale text-guided diffusion models have garnered significant attention due to their ability to synthesize diverse images that convey complex visual concepts. This generative power has more recently been leveraged to perform text-to-3D synthesis. In this work, we present a technique that harnesses the power of latent diffusion models for editing existing 3D objects. Our method takes oriented 2D images of a 3D object as input and learns a grid-based volumetric representation of it. To guide the volumetric representation to conform to a target text prompt, we follow unconditional text-to-3D methods and optimize a Score Distillation Sampling (SDS) loss. However, we observe that combining this diffusion-guided loss with an image-based regularization loss that encourages the representation not to deviate too strongly from the input object is challenging, as it requires achieving two conflicting goals while viewing only structure-and-appearance coupled 2D projections. Thus, we introduce a novel volumetric regularization loss that operates directly in 3D space, utilizing the explicit nature of our 3D representation to enforce correlation between the global structure of the original and edited object. Furthermore, we present a technique that optimizes cross-attention volumetric grids to refine the spatial extent of the edits. Extensive experiments and comparisons demonstrate the effectiveness of our approach in creating a myriad of edits which cannot be achieved by prior works.

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.

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

Multi-site neuroimaging analysis is fundamentally confounded by scanner-induced covariate shifts, where the marginal distribution of voxel intensities P(x) varies non-linearly across acquisition protocols while the conditional anatomy P(y|x) remains constant. This is particularly detrimental to radiomic reproducibility, where acquisition variance often exceeds biological pathology variance. Existing statistical harmonization methods (e.g., ComBat) operate in feature space, precluding spatial downstream tasks, while standard deep learning approaches are theoretically bounded by local effective receptive fields (ERF), failing to model the global intensity correlations characteristic of field-strength bias. We propose SA-CycleGAN-2.5D, a domain adaptation framework motivated by the HΔH-divergence bound of Ben-David et al., integrating three architectural innovations: (1) A 2.5D tri-planar manifold injection preserving through-plane gradients nabla_z at O(HW) complexity; (2) A U-ResNet generator with dense voxel-to-voxel self-attention, surpassing the O(L) receptive field limit of CNNs to model global scanner field biases; and (3) A spectrally-normalized discriminator constraining the Lipschitz constant (K_D le 1) for stable adversarial optimization. Evaluated on 654 glioma patients across two institutional domains (BraTS and UPenn-GBM), our method reduces Maximum Mean Discrepancy (MMD) by 99.1% (1.729 to 0.015) and degrades domain classifier accuracy to near-chance (59.7%). Ablation confirms that global attention is statistically essential (Cohen's d = 1.32, p < 0.001) for the harder heterogeneous-to-homogeneous translation direction. By bridging 2D efficiency and 3D consistency, our framework yields voxel-level harmonized images that preserve tumor pathophysiology, enabling reproducible multi-center radiomic analysis.

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

3D object detectors usually rely on hand-crafted proxies, e.g., anchors or centers, and translate well-studied 2D frameworks to 3D. Thus, sparse voxel features need to be densified and processed by dense prediction heads, which inevitably costs extra computation. In this paper, we instead propose VoxelNext for fully sparse 3D object detection. Our core insight is to predict objects directly based on sparse voxel features, without relying on hand-crafted proxies. Our strong sparse convolutional network VoxelNeXt detects and tracks 3D objects through voxel features entirely. It is an elegant and efficient framework, with no need for sparse-to-dense conversion or NMS post-processing. Our method achieves a better speed-accuracy trade-off than other mainframe detectors on the nuScenes dataset. For the first time, we show that a fully sparse voxel-based representation works decently for LIDAR 3D object detection and tracking. Extensive experiments on nuScenes, Waymo, and Argoverse2 benchmarks validate the effectiveness of our approach. Without bells and whistles, our model outperforms all existing LIDAR methods on the nuScenes tracking test benchmark.

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

This work presents SGCDet, a novel multi-view indoor 3D object detection framework based on adaptive 3D volume construction. Unlike previous approaches that restrict the receptive field of voxels to fixed locations on images, we introduce a geometry and context aware aggregation module to integrate geometric and contextual information within adaptive regions in each image and dynamically adjust the contributions from different views, enhancing the representation capability of voxel features. Furthermore, we propose a sparse volume construction strategy that adaptively identifies and selects voxels with high occupancy probabilities for feature refinement, minimizing redundant computation in free space. Benefiting from the above designs, our framework achieves effective and efficient volume construction in an adaptive way. Better still, our network can be supervised using only 3D bounding boxes, eliminating the dependence on ground-truth scene geometry. Experimental results demonstrate that SGCDet achieves state-of-the-art performance on the ScanNet, ScanNet200 and ARKitScenes datasets. The source code is available at https://github.com/RM-Zhang/SGCDet.

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

We introduce VoxTell, a vision-language model for text-prompted volumetric medical image segmentation. It maps free-form descriptions, from single words to full clinical sentences, to 3D masks. Trained on 62K+ CT, MRI, and PET volumes spanning over 1K anatomical and pathological classes, VoxTell uses multi-stage vision-language fusion across decoder layers to align textual and visual features at multiple scales. It achieves state-of-the-art zero-shot performance across modalities on unseen datasets, excelling on familiar concepts while generalizing to related unseen classes. Extensive experiments further demonstrate strong cross-modality transfer, robustness to linguistic variations and clinical language, as well as accurate instance-specific segmentation from real-world text. Code is available at: https://www.github.com/MIC-DKFZ/VoxTell

Place recognition based on point clouds (LiDAR) is an important component for autonomous robots or self-driving vehicles. Current SOTA performance is achieved on accumulated LiDAR submaps using either point-based or voxel-based structures. While voxel-based approaches nicely integrate spatial context across multiple scales, they do not exhibit the local precision of point-based methods. As a result, existing methods struggle with fine-grained matching of subtle geometric features in sparse single-shot Li- DAR scans. To overcome these limitations, we propose CASSPR as a method to fuse point-based and voxel-based approaches using cross attention transformers. CASSPR leverages a sparse voxel branch for extracting and aggregating information at lower resolution and a point-wise branch for obtaining fine-grained local information. CASSPR uses queries from one branch to try to match structures in the other branch, ensuring that both extract self-contained descriptors of the point cloud (rather than one branch dominating), but using both to inform the output global descriptor of the point cloud. Extensive experiments show that CASSPR surpasses the state-of-the-art by a large margin on several datasets (Oxford RobotCar, TUM, USyd). For instance, it achieves AR@1 of 85.6% on the TUM dataset, surpassing the strongest prior model by ~15%. Our code is publicly available.

Latent diffusion models (LDMs) exhibit an impressive ability to produce realistic images, yet the inner workings of these models remain mysterious. Even when trained purely on images without explicit depth information, they typically output coherent pictures of 3D scenes. In this work, we investigate a basic interpretability question: does an LDM create and use an internal representation of simple scene geometry? Using linear probes, we find evidence that the internal activations of the LDM encode linear representations of both 3D depth data and a salient-object / background distinction. These representations appear surprisingly early in the denoising process-well before a human can easily make sense of the noisy images. Intervention experiments further indicate these representations play a causal role in image synthesis, and may be used for simple high-level editing of an LDM's output. Project page: https://yc015.github.io/scene-representation-diffusion-model/

Typical inverse rendering methods focus on learning implicit neural scene representations by modeling the geometry, materials and illumination separately, which entails significant computations for optimization. In this work we design a Unified Voxelization framework for explicit learning of scene representations, dubbed UniVoxel, which allows for efficient modeling of the geometry, materials and illumination jointly, thereby accelerating the inverse rendering significantly. To be specific, we propose to encode a scene into a latent volumetric representation, based on which the geometry, materials and illumination can be readily learned via lightweight neural networks in a unified manner. Particularly, an essential design of UniVoxel is that we leverage local Spherical Gaussians to represent the incident light radiance, which enables the seamless integration of modeling illumination into the unified voxelization framework. Such novel design enables our UniVoxel to model the joint effects of direct lighting, indirect lighting and light visibility efficiently without expensive multi-bounce ray tracing. Extensive experiments on multiple benchmarks covering diverse scenes demonstrate that UniVoxel boosts the optimization efficiency significantly compared to other methods, reducing the per-scene training time from hours to 18 minutes, while achieving favorable reconstruction quality. Code is available at https://github.com/freemantom/UniVoxel.

Visual grounding aims to identify objects or regions in a scene based on natural language descriptions, essential for spatially aware perception in autonomous driving. However, existing visual grounding tasks typically depend on bounding boxes that often fail to capture fine-grained details. Not all voxels within a bounding box are occupied, resulting in inaccurate object representations. To address this, we introduce a benchmark for 3D occupancy grounding in challenging outdoor scenes. Built on the nuScenes dataset, it integrates natural language with voxel-level occupancy annotations, offering more precise object perception compared to the traditional grounding task. Moreover, we propose GroundingOcc, an end-to-end model designed for 3D occupancy grounding through multi-modal learning. It combines visual, textual, and point cloud features to predict object location and occupancy information from coarse to fine. Specifically, GroundingOcc comprises a multimodal encoder for feature extraction, an occupancy head for voxel-wise predictions, and a grounding head to refine localization. Additionally, a 2D grounding module and a depth estimation module enhance geometric understanding, thereby boosting model performance. Extensive experiments on the benchmark demonstrate that our method outperforms existing baselines on 3D occupancy grounding. The dataset is available at https://github.com/RONINGOD/GroundingOcc.

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

LLMs are multilingual by training, yet their lingua franca is often English, reflecting English language dominance in pretraining. Other languages remain in parametric memory but are systematically suppressed. We argue that language defaultness is governed by a sparse, low-rank control circuit, language neurons, that can be mechanistically isolated and safely steered. We introduce Neural FOXP2, that makes a chosen language (Hindi or Spanish) primary in a model by steering language-specific neurons. Neural FOXP2 proceeds in three stages: (i) Localize: We train per-layer SAEs so each activation decomposes into a small set of active feature components. For every feature, we quantify English vs. Hindi/Spanish selectivity overall logit-mass lift toward the target-language token set. Tracing the top-ranked features back to their strongest contributing units yields a compact language-neuron set. (ii) Steering directions: We localize controllable language-shift geometry via a spectral low-rank analysis. For each layer, we build English to target activation-difference matrices and perform layerwise SVD to extract the dominant singular directions governing language change. The eigengap and effective-rank spectra identify a compact steering subspace and an empirically chosen intervention window (where these directions are strongest and most stable). (iii) Steer: We apply a signed, sparse activation shift targeted to the language neurons. Concretely, within low to mid layers we add a positive steering along the target-language dominant directions and a compensating negative shift toward the null space for the English neurons, yielding controllable target-language defaultness.

Image registration is the process of bringing different images into a common coordinate system - a technique widely used in various applications of computer vision, such as remote sensing, image retrieval, and, most commonly, medical imaging. Deep learning based techniques have been applied successfully to tackle various complex medical image processing problems, including medical image registration. Over the years, several image registration techniques have been proposed using deep learning. Deformable image registration techniques such as Voxelmorph have been successful in capturing finer changes and providing smoother deformations. However, Voxelmorph, as well as ICNet and FIRE, do not explicitly encode global dependencies (i.e. the overall anatomical view of the supplied image) and, therefore, cannot track large deformations. In order to tackle the aforementioned problems, this paper extends the Voxelmorph approach in three different ways. To improve the performance in case of small as well as large deformations, supervision of the model at different resolutions has been integrated using a multi-scale UNet. To support the network to learn and encode the minute structural co-relations of the given image-pairs, a self-constructing graph network (SCGNet) has been used as the latent of the multi-scale UNet - which can improve the learning process of the model and help the model to generalise better. And finally, to make the deformations inverse-consistent, cycle consistency loss has been employed. On the task of registration of brain MRIs, the proposed method achieved significant improvements over ANTs and VoxelMorph, obtaining a Dice score of 0.8013 \pm 0.0243 for intramodal and 0.6211 \pm 0.0309 for intermodal, while VoxelMorph achieved 0.7747 \pm 0.0260 and 0.6071 \pm 0.0510, respectively

Reconstructing 3D visuals from functional Magnetic Resonance Imaging (fMRI) data, introduced as Recon3DMind in our conference work, is of significant interest to both cognitive neuroscience and computer vision. To advance this task, we present the fMRI-3D dataset, which includes data from 15 participants and showcases a total of 4768 3D objects. The dataset comprises two components: fMRI-Shape, previously introduced and accessible at https://huggingface.co/datasets/Fudan-fMRI/fMRI-Shape, and fMRI-Objaverse, proposed in this paper and available at https://huggingface.co/datasets/Fudan-fMRI/fMRI-Objaverse. fMRI-Objaverse includes data from 5 subjects, 4 of whom are also part of the Core set in fMRI-Shape, with each subject viewing 3142 3D objects across 117 categories, all accompanied by text captions. This significantly enhances the diversity and potential applications of the dataset. Additionally, we propose MinD-3D, a novel framework designed to decode 3D visual information from fMRI signals. The framework first extracts and aggregates features from fMRI data using a neuro-fusion encoder, then employs a feature-bridge diffusion model to generate visual features, and finally reconstructs the 3D object using a generative transformer decoder. We establish new benchmarks by designing metrics at both semantic and structural levels to evaluate model performance. Furthermore, we assess our model's effectiveness in an Out-of-Distribution setting and analyze the attribution of the extracted features and the visual ROIs in fMRI signals. Our experiments demonstrate that MinD-3D not only reconstructs 3D objects with high semantic and spatial accuracy but also deepens our understanding of how human brain processes 3D visual information. Project page at: https://jianxgao.github.io/MinD-3D.

We characterise the dynamics of neuronal activity, in terms of field theory, using neural units placed on a 2D-lattice modelling the cortical surface. The electrical activity of neuronal units was analysed with the aim of deriving a neural field model with a simple functional form that still able to predict or reproduce empirical findings. Each neural unit was modelled using a neural mass and the accompanying field theory was derived in the continuum limit. The field theory comprised coupled (real) Klein-Gordon fields, where predictions of the model fall within the range of experimental findings. These predictions included the frequency spectrum of electric activity measured from the cortex, which was derived using an equipartition of energy over eigenfunctions of the neural fields. Moreover, the neural field model was invariant, within a set of parameters, to the dynamical system used to model each neuronal mass. Specifically, topologically equivalent dynamical systems resulted in the same neural field model when connected in a lattice; indicating that the fields derived could be read as a canonical cortical field theory. We specifically investigated non-dispersive fields that provide a structure for the coding (or representation) of afferent information. Further elaboration of the ensuing neural field theory, including the effect of dispersive forces, could be of importance in the understanding of the cortical processing of information.

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

Large vision-language models (VLMs) are highly capable, yet often hallucinate by favoring textual prompts over visual evidence. We study this failure mode in a controlled object-counting setting, where the prompt overstates the number of objects in the image (e.g., asking a model to describe four waterlilies when only three are present). At low object counts, models often correct the overestimation, but as the number of objects increases, they increasingly conform to the prompt regardless of the discrepancy. Through mechanistic analysis of three VLMs, we identify a small set of attention heads whose ablation substantially reduces prompt-induced hallucinations (PIH) by at least 40% without additional training. Across models, PIH-heads mediate prompt copying in model-specific ways. We characterize these differences and show that PIH ablation increases correction toward visual evidence. Our findings offer insights into the internal mechanisms driving prompt-induced hallucinations, revealing model-specific differences in how these behaviors are implemented.

Humans can easily imagine the complete 3D geometry of occluded objects and scenes. This appealing ability is vital for recognition and understanding. To enable such capability in AI systems, we propose VoxFormer, a Transformer-based semantic scene completion framework that can output complete 3D volumetric semantics from only 2D images. Our framework adopts a two-stage design where we start from a sparse set of visible and occupied voxel queries from depth estimation, followed by a densification stage that generates dense 3D voxels from the sparse ones. A key idea of this design is that the visual features on 2D images correspond only to the visible scene structures rather than the occluded or empty spaces. Therefore, starting with the featurization and prediction of the visible structures is more reliable. Once we obtain the set of sparse queries, we apply a masked autoencoder design to propagate the information to all the voxels by self-attention. Experiments on SemanticKITTI show that VoxFormer outperforms the state of the art with a relative improvement of 20.0% in geometry and 18.1% in semantics and reduces GPU memory during training to less than 16GB. Our code is available on https://github.com/NVlabs/VoxFormer.

Benchmarking the hundreds of functional connectivity (FC) modeling methods on large-scale fMRI datasets is critical for reproducible neuroscience. However, the combinatorial explosion of model-data pairings makes exhaustive evaluation computationally prohibitive, preventing such assessments from becoming a routine pre-analysis step. To break this bottleneck, we reframe the challenge of FC benchmarking by selecting a small, representative core-set whose sole purpose is to preserve the relative performance ranking of FC operators. We formalize this as a ranking-preserving subset selection problem and propose Structure-aware Contrastive Learning for Core-set Selection (SCLCS), a self-supervised framework to select these core-sets. SCLCS first uses an adaptive Transformer to learn each sample's unique FC structure. It then introduces a novel Structural Perturbation Score (SPS) to quantify the stability of these learned structures during training, identifying samples that represent foundational connectivity archetypes. Finally, while SCLCS identifies stable samples via a top-k ranking, we further introduce a density-balanced sampling strategy as a necessary correction to promote diversity, ensuring the final core-set is both structurally robust and distributionally representative. On the large-scale REST-meta-MDD dataset, SCLCS preserves the ground-truth model ranking with just 10% of the data, outperforming state-of-the-art (SOTA) core-set selection methods by up to 23.2% in ranking consistency (nDCG@k). To our knowledge, this is the first work to formalize core-set selection for FC operator benchmarking, thereby making large-scale operators comparisons a feasible and integral part of computational neuroscience. Code is publicly available on https://github.com/lzhan94swu/SCLCS

In Marius von Senden's Space and Sight, a newly sighted blind patient describes the experience of a corner as lemon-like, because corners "prick" sight like lemons prick the tongue. Prickliness, here, is a dimension in the feature space of sensory experience, an effect of the perceived on the perceiver that arises where the two interact. In the account of the newly sighted, an effect familiar from one interaction translates to a novel context. Perception serves as the vehicle for generalization, in that an effect shared across different experiences produces a concrete abstraction grounded in those experiences. Cezanne and the post-impressionists, fluent in the language of experience translation, realized that the way to paint a concrete form that best reflected reality was to paint not what they saw, but what it was like to see. We envision a future of creation using AI where what it is like to see is replicable, transferrable, manipulable - part of the artist's palette that is both grounded in a particular context, and generalizable beyond it. An active line of research maps human-interpretable features onto directions in GAN latent space. Supervised and self-supervised approaches that search for anticipated directions or use off-the-shelf classifiers to drive image manipulation in embedding space are limited in the variety of features they can uncover. Unsupervised approaches that discover useful new directions show that the space of perceptually meaningful directions is nowhere close to being fully mapped. As this space is broad and full of creative potential, we want tools for direction discovery that capture the richness and generalizability of human perception. Our approach puts creators in the discovery loop during real-time tool use, in order to identify directions that are perceptually meaningful to them, and generate interpretable image translations along those directions.

Neurons in the brain are spatially organized such that neighbors on tissue often exhibit similar response profiles. In the human language system, experimental studies have observed clusters for syntactic and semantic categories, but the mechanisms underlying this functional organization remain unclear. Here, building on work from the vision literature, we develop TopoLM, a transformer language model with an explicit two-dimensional spatial representation of model units. By combining a next-token prediction objective with a spatial smoothness loss, representations in this model assemble into clusters that correspond to semantically interpretable groupings of text and closely match the functional organization in the brain's language system. TopoLM successfully predicts the emergence of the spatio-functional organization of a cortical language system as well as the organization of functional clusters selective for fine-grained linguistic features empirically observed in human cortex. Our results suggest that the functional organization of the human language system is driven by a unified spatial objective, and provide a functionally and spatially aligned model of language processing in the brain.

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

The field of psychology has long recognized a basic level of categorization that humans use when labeling visual stimuli, a term coined by Rosch in 1976. This level of categorization has been found to be used most frequently, to have higher information density, and to aid in visual language tasks with priming in humans. Here, we investigate basic level categorization in two recently released, open-source vision-language models (VLMs). This paper demonstrates that Llama 3.2 Vision Instruct (11B) and Molmo 7B-D both prefer basic level categorization consistent with human behavior. Moreover, the models' preferences are consistent with nuanced human behaviors like the biological versus non-biological basic level effects and the well established expert basic level shift, further suggesting that VLMs acquire cognitive categorization behaviors from the human data on which they are trained.

Mechanistic interpretability aims to understand model behaviors in terms of specific, interpretable features, often hypothesized to manifest as low-dimensional subspaces of activations. Specifically, recent studies have explored subspace interventions (such as activation patching) as a way to simultaneously manipulate model behavior and attribute the features behind it to given subspaces. In this work, we demonstrate that these two aims diverge, potentially leading to an illusory sense of interpretability. Counterintuitively, even if a subspace intervention makes the model's output behave as if the value of a feature was changed, this effect may be achieved by activating a dormant parallel pathway leveraging another subspace that is causally disconnected from model outputs. We demonstrate this phenomenon in a distilled mathematical example, in two real-world domains (the indirect object identification task and factual recall), and present evidence for its prevalence in practice. In the context of factual recall, we further show a link to rank-1 fact editing, providing a mechanistic explanation for previous work observing an inconsistency between fact editing performance and fact localization. However, this does not imply that activation patching of subspaces is intrinsically unfit for interpretability. To contextualize our findings, we also show what a success case looks like in a task (indirect object identification) where prior manual circuit analysis informs an understanding of the location of a feature. We explore the additional evidence needed to argue that a patched subspace is faithful.

Training tool-use agents typically relies on outcome-based filtering: Supervised Fine-Tuning (SFT) on successful trajectories and Reinforcement Learning (RL) on pass-rate-selected tasks. However, this paradigm ignores interaction dynamics: successful trajectories may lack error recovery or exhibit redundancy, while pass rates fail to distinguish structurally informative tasks from trivial ones. We propose TopoCurate, an interaction-aware framework that projects multi-trial rollouts from the same task into a unified semantic quotient topology. By merging equivalent action-observation states, this projection transforms scattered linear trajectories into a structured manifold that explicitly captures how tool invocations and environmental responses drive the divergence between effective strategies and failure modes. Leveraging this representation, we introduce a dual-selection mechanism: for SFT, we prioritize trajectories demonstrating reflective recovery, semantic efficiency, and strategic diversity to mitigate covariate shift and mode collapse; for RL, we select tasks with high error branch ratios and strategic heterogeneity, maximizing gradient Signal-to-Noise Ratio to address vanishing signals in sparse-reward settings. Evaluations on BFCLv3 and Tau2 Bench show that TopoCurate achieves consistent gains of 4.2\% (SFT) and 6.9\% (RL) over state-of-the-art baselines. We will release the code and data soon for further investigations.