Daily Papers

Solving topological grid puzzles requires reasoning over global spatial invariants such as connectivity, loop closure, and region symmetry and remains challenging for even the most powerful large language models (LLMs). To study these abilities under controlled settings, we introduce TopoBench, a benchmark of six puzzle families across three difficulty levels. We evaluate strong reasoning LLMs on TopoBench and find that even frontier models solve fewer than one quarter of hard instances, with two families nearly unsolved. To investigate whether these failures stem from reasoning limitations or from difficulty extracting and maintaining spatial constraints, we annotate 750 chain of thought traces with an error taxonomy that surfaces four candidate causal failure modes, then test them with targeted interventions simulating each error type. These interventions show that certain error patterns like premature commitment and constraint forgetting have a direct impact on the ability to solve the puzzle, while repeated reasoning is a benign effect of search. Finally we study mitigation strategies including prompt guidance, cell-aligned grid representations and tool-based constraint checking, finding that the bottleneck lies in extracting constraints from spatial representations and not in reasoning over them. Code and data are available at github.com/mayug/topobench-benchmark.

All tables can be represented as grids. Based on this observation, we propose GridFormer, a novel approach for interpreting unconstrained table structures by predicting the vertex and edge of a grid. First, we propose a flexible table representation in the form of an MXN grid. In this representation, the vertexes and edges of the grid store the localization and adjacency information of the table. Then, we introduce a DETR-style table structure recognizer to efficiently predict this multi-objective information of the grid in a single shot. Specifically, given a set of learned row and column queries, the recognizer directly outputs the vertexes and edges information of the corresponding rows and columns. Extensive experiments on five challenging benchmarks which include wired, wireless, multi-merge-cell, oriented, and distorted tables demonstrate the competitive performance of our model over other methods.

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

This paper presents MetricGrids, a novel grid-based neural representation that combines elementary metric grids in various metric spaces to approximate complex nonlinear signals. While grid-based representations are widely adopted for their efficiency and scalability, the existing feature grids with linear indexing for continuous-space points can only provide degenerate linear latent space representations, and such representations cannot be adequately compensated to represent complex nonlinear signals by the following compact decoder. To address this problem while keeping the simplicity of a regular grid structure, our approach builds upon the standard grid-based paradigm by constructing multiple elementary metric grids as high-order terms to approximate complex nonlinearities, following the Taylor expansion principle. Furthermore, we enhance model compactness with hash encoding based on different sparsities of the grids to prevent detrimental hash collisions, and a high-order extrapolation decoder to reduce explicit grid storage requirements. experimental results on both 2D and 3D reconstructions demonstrate the superior fitting and rendering accuracy of the proposed method across diverse signal types, validating its robustness and generalizability. Code is available at https://github.com/wangshu31/MetricGrids}{https://github.com/wangshu31/MetricGrids.

Vision-Language Models (VLMs) excel on many multimodal reasoning benchmarks, but these evaluations often do not require an exhaustive readout of the image and can therefore obscure failures in faithfully capturing all visual details. We introduce Grid2Matrix (G2M), a controlled benchmark in which a model is shown a color grid and a color-to-number mapping, and must output the corresponding matrix. By varying grid size and the number of colors, G2M provides a simple way to increase visual complexity while minimizing semantic confounds. We find that VLMs exhibit a sharp early collapse in zero-shot end-to-end evaluation, failing on surprisingly small grids rather than degrading gradually as the task becomes denser. We probe the visual encoders of VLMs from two representative families and find that they preserve substantially more of the grid information than the corresponding end-to-end outputs. This suggests that the failure is not explained by visual encoding alone, but also reflects a gap between what remains recoverable from visual features and what is ultimately expressed in language. We term this gap Digital Agnosia. Further analyses show that these errors are highly structured and depend strongly on how grid cells overlap with visual patch boundaries. We also find that common strategies such as model scaling and multimodal alignment do not fully eliminate this failure mode. We expect G2M to serve as a useful testbed for understanding where and how VLMs lose fine visual details, and for evaluating tasks where missing even small visual details can matter, such as tables, charts, forms, and GUIs.

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

In this paper, we propose a new class of metric for table structure recognition (TSR) evaluation, called grid table similarity (GriTS). Unlike prior metrics, GriTS evaluates the correctness of a predicted table directly in its natural form as a matrix. To create a similarity measure between matrices, we generalize the two-dimensional largest common substructure (2D-LCS) problem, which is NP-hard, to the 2D most similar substructures (2D-MSS) problem and propose a polynomial-time heuristic for solving it. This algorithm produces both an upper and a lower bound on the true similarity between matrices. We show using evaluation on a large real-world dataset that in practice there is almost no difference between these bounds. We compare GriTS to other metrics and empirically validate that matrix similarity exhibits more desirable behavior than alternatives for TSR performance evaluation. Finally, GriTS unifies all three subtasks of cell topology recognition, cell location recognition, and cell content recognition within the same framework, which simplifies the evaluation and enables more meaningful comparisons across different types of TSR approaches. Code will be released at https://github.com/microsoft/table-transformer.

Implicit Neural Representations (INRs) have recently shown impressive results, but their fundamental capacity, implicit biases, and scaling behavior remain poorly understood. We investigate the performance of diverse INRs across a suite of 2D and 3D real and synthetic signals with varying effective bandwidth, as well as both overfitting and generalization tasks including tomography, super-resolution, and denoising. By stratifying performance according to model size as well as signal type and bandwidth, our results shed light on how different INR and grid representations allocate their capacity. We find that, for most tasks and signals, a simple regularized grid with interpolation trains faster and to higher quality than any INR with the same number of parameters. We also find limited settings where INRs outperform grids -- namely fitting signals with underlying lower-dimensional structure such as shape contours -- to guide future use of INRs towards the most advantageous applications. Code and synthetic signals used in our analysis are available at https://github.com/voilalab/INR-benchmark.

We propose a new representation for encoding 3D shapes as neural fields. The representation is designed to be compatible with the transformer architecture and to benefit both shape reconstruction and shape generation. Existing works on neural fields are grid-based representations with latents defined on a regular grid. In contrast, we define latents on irregular grids, enabling our representation to be sparse and adaptive. In the context of shape reconstruction from point clouds, our shape representation built on irregular grids improves upon grid-based methods in terms of reconstruction accuracy. For shape generation, our representation promotes high-quality shape generation using auto-regressive probabilistic models. We show different applications that improve over the current state of the art. First, we show results for probabilistic shape reconstruction from a single higher resolution image. Second, we train a probabilistic model conditioned on very low resolution images. Third, we apply our model to category-conditioned generation. All probabilistic experiments confirm that we are able to generate detailed and high quality shapes to yield the new state of the art in generative 3D shape modeling.

Neural graphics primitives are faster and achieve higher quality when their neural networks are augmented by spatial data structures that hold trainable features arranged in a grid. However, existing feature grids either come with a large memory footprint (dense or factorized grids, trees, and hash tables) or slow performance (index learning and vector quantization). In this paper, we show that a hash table with learned probes has neither disadvantage, resulting in a favorable combination of size and speed. Inference is faster than unprobed hash tables at equal quality while training is only 1.2-2.6x slower, significantly outperforming prior index learning approaches. We arrive at this formulation by casting all feature grids into a common framework: they each correspond to a lookup function that indexes into a table of feature vectors. In this framework, the lookup functions of existing data structures can be combined by simple arithmetic combinations of their indices, resulting in Pareto optimal compression and speed.

Spatial intelligence is a critical frontier for Multimodal Large Language Models (MLLMs), empowering them to comprehend the physical world. Drawing inspiration from human perception mechanisms, existing studies attempt to construct a coherent spatial understanding via grid-based cognitive maps from multi-frame visual inputs. However, current grid-based map methods rely on discretized raster representations, which limit the model's ability in fine-grained spatial reasoning. To overcome this limitation, we propose Video2Layout, a framework for reconstructing metric-grounded spatial layouts from video. The framework employs continuous object boundary coordinates to quantify inter-object physical distances and object size. This empowers the model with quantitative spatial computation capabilities, effectively alleviating the inherent ambiguity when describing spatial relationships in natural language. Specifically, our method comprises two core stages. First, in supervised fine-tuning stage, we construct a high-quality dataset from the AI2THOR simulator, which enables the model to learn the mapping from visual inputs to precise boundary coordinates. Subsequently, a reinforcement fine-tuning stage further enhances the model's real-world generalization capabilities. To systematically evaluate the correlation between cognitive map accuracy and image quantity, as well as how the quantity of image inputs affects spatial reasoning accuracy, we introduce QVS-Bench, a diagnostic benchmark designed to analyze the relevant mechanisms. Evaluated on QVS-Bench and mainstream spatial reasoning benchmarks, our model, V2LO-7B achieves an average improvement of 4.92% over the model trained on grid maps, validating the superiority of our method. Our code is available at https://github.com/ybrrraway/Video2Layout.

Convolutions (Convs) and multi-head self-attentions (MHSAs) are typically considered alternatives to each other for building vision backbones. Although some works try to integrate both, they apply the two operators simultaneously at the finest pixel granularity. With Convs responsible for per-pixel feature extraction already, the question is whether we still need to include the heavy MHSAs at such a fine-grained level. In fact, this is the root cause of the scalability issue w.r.t. the input resolution for vision transformers. To address this important problem, we propose in this work to use MSHAs and Convs in parallel at different granularity levels instead. Specifically, in each layer, we use two different ways to represent an image: a fine-grained regular grid and a coarse-grained set of semantic slots. We apply different operations to these two representations: Convs to the grid for local features, and MHSAs to the slots for global features. A pair of fully differentiable soft clustering and dispatching modules is introduced to bridge the grid and set representations, thus enabling local-global fusion. Through extensive experiments on various vision tasks, we empirically verify the potential of the proposed integration scheme, named GLMix: by offloading the burden of fine-grained features to light-weight Convs, it is sufficient to use MHSAs in a few (e.g., 64) semantic slots to match the performance of recent state-of-the-art backbones, while being more efficient. Our visualization results also demonstrate that the soft clustering module produces a meaningful semantic grouping effect with only IN1k classification supervision, which may induce better interpretability and inspire new weakly-supervised semantic segmentation approaches. Code will be available at https://github.com/rayleizhu/GLMix.

Masked image modelling (MIM) is a powerful self-supervised representation learning paradigm, whose potential has not been widely demonstrated in medical image analysis. In this work, we show the capacity of MIM to capture rich semantic representations of Haemotoxylin & Eosin (H&E)-stained images at the nuclear level. Inspired by Bidirectional Encoder representation from Image Transformers (BEiT), we split the images into smaller patches and generate corresponding discrete visual tokens. In addition to the regular grid-based patches, typically used in visual Transformers, we introduce patches of individual cell nuclei. We propose positional encoding of the irregular distribution of these structures within an image. We pre-train the model in a self-supervised manner on H&E-stained whole-slide images of diffuse large B-cell lymphoma, where cell nuclei have been segmented. The pre-training objective is to recover the original discrete visual tokens of the masked image on the one hand, and to reconstruct the visual tokens of the masked object instances on the other. Coupling these two pre-training tasks allows us to build powerful, context-aware representations of nuclei. Our model generalizes well and can be fine-tuned on downstream classification tasks, achieving improved cell classification accuracy on PanNuke dataset by more than 5% compared to current instance segmentation methods.

Current vision models typically maintain a fixed correspondence between their representation structure and image space. Each layer comprises a set of tokens arranged "on-the-grid," which biases patches or tokens to encode information at a specific spatio(-temporal) location. In this work we present Moving Off-the-Grid (MooG), a self-supervised video representation model that offers an alternative approach, allowing tokens to move "off-the-grid" to better enable them to represent scene elements consistently, even as they move across the image plane through time. By using a combination of cross-attention and positional embeddings we disentangle the representation structure and image structure. We find that a simple self-supervised objective--next frame prediction--trained on video data, results in a set of latent tokens which bind to specific scene structures and track them as they move. We demonstrate the usefulness of MooG's learned representation both qualitatively and quantitatively by training readouts on top of the learned representation on a variety of downstream tasks. We show that MooG can provide a strong foundation for different vision tasks when compared to "on-the-grid" baselines.

Although polygon meshes have been a standard representation in geometry processing, their irregular and combinatorial nature hinders their suitability for learning-based applications. In this work, we introduce a novel learnable mesh representation through a set of local 3D sample Points and their associated Normals and Quadric error metrics (QEM) w.r.t. the underlying shape, which we denote PoNQ. A global mesh is directly derived from PoNQ by efficiently leveraging the knowledge of the local quadric errors. Besides marking the first use of QEM within a neural shape representation, our contribution guarantees both topological and geometrical properties by ensuring that a PoNQ mesh does not self-intersect and is always the boundary of a volume. Notably, our representation does not rely on a regular grid, is supervised directly by the target surface alone, and also handles open surfaces with boundaries and/or sharp features. We demonstrate the efficacy of PoNQ through a learning-based mesh prediction from SDF grids and show that our method surpasses recent state-of-the-art techniques in terms of both surface and edge-based metrics.

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

Implicit Neural Representations (INR) or neural fields have emerged as a popular framework to encode multimedia signals such as images and radiance fields while retaining high-quality. Recently, learnable feature grids proposed by Instant-NGP have allowed significant speed-up in the training as well as the sampling of INRs by replacing a large neural network with a multi-resolution look-up table of feature vectors and a much smaller neural network. However, these feature grids come at the expense of large memory consumption which can be a bottleneck for storage and streaming applications. In this work, we propose SHACIRA, a simple yet effective task-agnostic framework for compressing such feature grids with no additional post-hoc pruning/quantization stages. We reparameterize feature grids with quantized latent weights and apply entropy regularization in the latent space to achieve high levels of compression across various domains. Quantitative and qualitative results on diverse datasets consisting of images, videos, and radiance fields, show that our approach outperforms existing INR approaches without the need for any large datasets or domain-specific heuristics. Our project page is available at http://shacira.github.io .

Language models pretrained on large collections of tabular data have demonstrated their effectiveness in several downstream tasks. However, many of these models do not take into account the row/column permutation invariances, hierarchical structure, etc. that exist in tabular data. To alleviate these limitations, we propose HYTREL, a tabular language model, that captures the permutation invariances and three more structural properties of tabular data by using hypergraphs - where the table cells make up the nodes and the cells occurring jointly together in each row, column, and the entire table are used to form three different types of hyperedges. We show that HYTREL is maximally invariant under certain conditions for tabular data, i.e., two tables obtain the same representations via HYTREL iff the two tables are identical up to permutations. Our empirical results demonstrate that HYTREL consistently outperforms other competitive baselines on four downstream tasks with minimal pretraining, illustrating the advantages of incorporating the inductive biases associated with tabular data into the representations. Finally, our qualitative analyses showcase that HYTREL can assimilate the table structures to generate robust representations for the cells, rows, columns, and the entire table.

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.

This paper presents the Visual Place Cell Encoding (VPCE) model, a biologically inspired computational framework for simulating place cell-like activation using visual input. Drawing on evidence that visual landmarks play a central role in spatial encoding, the proposed VPCE model activates visual place cells by clustering high-dimensional appearance features extracted from images captured by a robot-mounted camera. Each cluster center defines a receptive field, and activation is computed based on visual similarity using a radial basis function. We evaluate whether the resulting activation patterns correlate with key properties of biological place cells, including spatial proximity, orientation alignment, and boundary differentiation. Experiments demonstrate that the VPCE can distinguish between visually similar yet spatially distinct locations and adapt to environment changes such as the insertion or removal of walls. These results suggest that structured visual input, even in the absence of motion cues or reward-driven learning, is sufficient to generate place-cell-like spatial representations and support biologically inspired cognitive mapping.

Neural fields such as DeepSDF and Neural Radiance Fields have recently revolutionized novel-view synthesis and 3D reconstruction from RGB images and videos. However, achieving high-quality representation, reconstruction, and rendering requires deep neural networks, which are slow to train and evaluate. Although several acceleration techniques have been proposed, they often trade off speed for memory. Gaussian splatting-based methods, on the other hand, accelerate the rendering time but remain costly in terms of training speed and memory needed to store the parameters of a large number of Gaussians. In this paper, we introduce a novel neural representation that is fast, both at training and inference times, and lightweight. Our key observation is that the neurons used in traditional MLPs perform simple computations (a dot product followed by ReLU activation) and thus one needs to use either wide and deep MLPs or high-resolution and high-dimensional feature grids to parameterize complex nonlinear functions. We show in this paper that by replacing traditional neurons with Radial Basis Function (RBF) kernels, one can achieve highly accurate representation of 2D (RGB images), 3D (geometry), and 5D (radiance fields) signals with just a single layer of such neurons. The representation is highly parallelizable, operates on low-resolution feature grids, and is compact and memory-efficient. We demonstrate that the proposed novel representation can be trained for 3D geometry representation in less than 15 seconds and for novel view synthesis in less than 15 mins. At runtime, it can synthesize novel views at more than 60 fps without sacrificing quality.

Temporal interpolation often plays a crucial role to learn meaningful representations in dynamic scenes. In this paper, we propose a novel method to train spatiotemporal neural radiance fields of dynamic scenes based on temporal interpolation of feature vectors. Two feature interpolation methods are suggested depending on underlying representations, neural networks or grids. In the neural representation, we extract features from space-time inputs via multiple neural network modules and interpolate them based on time frames. The proposed multi-level feature interpolation network effectively captures features of both short-term and long-term time ranges. In the grid representation, space-time features are learned via four-dimensional hash grids, which remarkably reduces training time. The grid representation shows more than 100 times faster training speed than the previous neural-net-based methods while maintaining the rendering quality. Concatenating static and dynamic features and adding a simple smoothness term further improve the performance of our proposed models. Despite the simplicity of the model architectures, our method achieved state-of-the-art performance both in rendering quality for the neural representation and in training speed for the grid representation.

Vision-and-language navigation (VLN) enables the agent to navigate to a remote location following the natural language instruction in 3D environments. To represent the previously visited environment, most approaches for VLN implement memory using recurrent states, topological maps, or top-down semantic maps. In contrast to these approaches, we build the top-down egocentric and dynamically growing Grid Memory Map (i.e., GridMM) to structure the visited environment. From a global perspective, historical observations are projected into a unified grid map in a top-down view, which can better represent the spatial relations of the environment. From a local perspective, we further propose an instruction relevance aggregation method to capture fine-grained visual clues in each grid region. Extensive experiments are conducted on both the REVERIE, R2R, SOON datasets in the discrete environments, and the R2R-CE dataset in the continuous environments, showing the superiority of our proposed method.

In a systematic way, we investigate a widely asked question: Do LLMs really understand what they say?, which relates to the more familiar term Stochastic Parrot. To this end, we propose a summative assessment over a carefully designed physical concept understanding task, PhysiCo. Our task alleviates the memorization issue via the usage of grid-format inputs that abstractly describe physical phenomena. The grids represents varying levels of understanding, from the core phenomenon, application examples to analogies to other abstract patterns in the grid world. A comprehensive study on our task demonstrates: (1) state-of-the-art LLMs, including GPT-4o, o1 and Gemini 2.0 flash thinking, lag behind humans by ~40%; (2) the stochastic parrot phenomenon is present in LLMs, as they fail on our grid task but can describe and recognize the same concepts well in natural language; (3) our task challenges the LLMs due to intrinsic difficulties rather than the unfamiliar grid format, as in-context learning and fine-tuning on same formatted data added little to their performance.

Implicit neural networks have emerged as a crucial technology in 3D surface reconstruction. To reconstruct continuous surfaces from discrete point clouds, encoding the input points into regular grid features (plane or volume) has been commonly employed in existing approaches. However, these methods typically use the grid as an index for uniformly scattering point features. Compared with the irregular point features, the regular grid features may sacrifice some reconstruction details but improve efficiency. To take full advantage of these two types of features, we introduce a novel and high-efficiency attention mechanism between the grid and point features named Point-Grid Transformer (GridFormer). This mechanism treats the grid as a transfer point connecting the space and point cloud. Our method maximizes the spatial expressiveness of grid features and maintains computational efficiency. Furthermore, optimizing predictions over the entire space could potentially result in blurred boundaries. To address this issue, we further propose a boundary optimization strategy incorporating margin binary cross-entropy loss and boundary sampling. This approach enables us to achieve a more precise representation of the object structure. Our experiments validate that our method is effective and outperforms the state-of-the-art approaches under widely used benchmarks by producing more precise geometry reconstructions. The code is available at https://github.com/list17/GridFormer.

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.

We investigate a challenging task of dynamic scene geometry estimation, which requires representing both spatial and temporal features. Typically, existing methods align the two features into a unified latent space to model scene geometry. However, this unified paradigm suffers from potential mismatched representation due to the heterogeneous nature between spatial and temporal features. In this work, we propose 4D-VGGT, a general foundation model with divide-and-conquer spatiotemporal representation for dynamic scene geometry. Our model is divided into three aspects: 1) Multi-setting input. We design an adaptive visual grid that supports input sequences with arbitrary numbers of views and time steps. 2) Multi-level representation. We propose a cross-view global fusion for spatial representation and a cross-time local fusion for temporal representation. 3) Multi-task prediction. We append multiple task-specific heads to spatiotemporal representations, enabling a comprehensive visual geometry estimation for dynamic scenes. Under this unified framework, these components enhance the feature discriminability and application universality of our model for dynamic scenes. In addition, we integrate multiple geometry datasets to train our model and conduct extensive experiments to verify the effectiveness of our method across various tasks on multiple dynamic scene geometry benchmarks.

Many methods have been proposed for removing batch effects and aligning single-cell RNA (scRNA) datasets. However, performance is typically evaluated based on multiple parameters and few datasets, creating challenges in assessing which method is best for aligning data at scale. Here, we introduce the K-Neighbors Intersection (KNI) score, a single score that both penalizes batch effects and measures accuracy at cross-dataset cell-type label prediction alongside carefully curated small (scMARK) and large (scREF) benchmarks comprising 11 and 46 human scRNA studies respectively, where we have standardized author labels. Using the KNI score, we evaluate and optimize approaches for cross-dataset single-cell RNA integration. We introduce Batch Adversarial single-cell Variational Inference (BA-scVI), as a new variant of scVI that uses adversarial training to penalize batch-effects in the encoder and decoder, and show this approach outperforms other methods. In the resulting aligned space, we find that the granularity of cell-type groupings is conserved, supporting the notion that whole-organism cell-type maps can be created by a single model without loss of information.

Scene flow estimation is a foundational task for many robotic applications, including robust dynamic object detection, automatic labeling, and sensor synchronization. Two types of approaches to the problem have evolved: 1) Supervised and 2) optimization-based methods. Supervised methods are fast during inference and achieve high-quality results, however, they are limited by the need for large amounts of labeled training data and are susceptible to domain gaps. In contrast, unsupervised test-time optimization methods do not face the problem of domain gaps but usually suffer from substantial runtime, exhibit artifacts, or fail to converge to the right solution. In this work, we mitigate several limitations of existing optimization-based methods. To this end, we 1) introduce a simple voxel grid-based model that improves over the standard MLP-based formulation in multiple dimensions and 2) introduce a new multiframe loss formulation. 3) We combine both contributions in our new method, termed Floxels. On the Argoverse 2 benchmark, Floxels is surpassed only by EulerFlow among unsupervised methods while achieving comparable performance at a fraction of the computational cost. Floxels achieves a massive speedup of more than ~60 - 140x over EulerFlow, reducing the runtime from a day to 10 minutes per sequence. Over the faster but low-quality baseline, NSFP, Floxels achieves a speedup of ~14x.

Data fields sampled on irregularly spaced points arise in many applications in the sciences and engineering. For regular grids, Convolutional Neural Networks (CNNs) have been successfully used to gaining benefits from weight sharing and invariances. We generalize CNNs by introducing methods for data on unstructured point clouds based on Generalized Moving Least Squares (GMLS). GMLS is a non-parametric technique for estimating linear bounded functionals from scattered data, and has recently been used in the literature for solving partial differential equations. By parameterizing the GMLS estimator, we obtain learning methods for operators with unstructured stencils. In GMLS-Nets the necessary calculations are local, readily parallelizable, and the estimator is supported by a rigorous approximation theory. We show how the framework may be used for unstructured physical data sets to perform functional regression to identify associated differential operators and to regress quantities of interest. The results suggest the architectures to be an attractive foundation for data-driven model development in scientific machine learning applications.

Neural Radiance Fields (NeRFs) can be dramatically accelerated by spatial grid representations. However, they do not explicitly reason about scale and so introduce aliasing artifacts when reconstructing scenes captured at different camera distances. Mip-NeRF and its extensions propose scale-aware renderers that project volumetric frustums rather than point samples but such approaches rely on positional encodings that are not readily compatible with grid methods. We propose a simple modification to grid-based models by training model heads at different spatial grid resolutions. At render time, we simply use coarser grids to render samples that cover larger volumes. Our method can be easily applied to existing accelerated NeRF methods and significantly improves rendering quality (reducing error rates by 20-90% across synthetic and unbounded real-world scenes) while incurring minimal performance overhead (as each model head is quick to evaluate). Compared to Mip-NeRF, we reduce error rates by 20% while training over 60x faster.

Zero-shot, training-free, image-based text-to-video generation is an emerging area that aims to generate videos using existing image-based diffusion models. Current methods in this space require specific architectural changes to image generation models, which limit their adaptability and scalability. In contrast to such methods, we provide a model-agnostic approach. We use intersections in diffusion trajectories, working only with the latent values. We could not obtain localized frame-wise coherence and diversity using only the intersection of trajectories. Thus, we instead use a grid-based approach. An in-context trained LLM is used to generate coherent frame-wise prompts; another is used to identify differences between frames. Based on these, we obtain a CLIP-based attention mask that controls the timing of switching the prompts for each grid cell. Earlier switching results in higher variance, while later switching results in more coherence. Therefore, our approach can ensure appropriate control between coherence and variance for the frames. Our approach results in state-of-the-art performance while being more flexible when working with diverse image-generation models. The empirical analysis using quantitative metrics and user studies confirms our model's superior temporal consistency, visual fidelity and user satisfaction, thus providing a novel way to obtain training-free, image-based text-to-video generation.

During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how every single cell decides to position itself relative to its neighboring cells. Despite its importance, it remains a major challenge to understand and predict the behavior of every cell within the living tissue over time during such intricate processes. To tackle this question, we propose a geometric deep learning model that can predict multicellular folding and embryogenesis, accurately capturing the highly convoluted spatial interactions among cells. We demonstrate that multicellular data can be represented with both granular and foam-like physical pictures through a unified graph data structure, considering both cellular interactions and cell junction networks. We successfully use our model to achieve two important tasks, interpretable 4-D morphological sequence alignment, and predicting local cell rearrangements before they occur at single-cell resolution. Furthermore, using an activation map and ablation studies, we demonstrate that cell geometries and cell junction networks together regulate local cell rearrangement which is critical for embryo morphogenesis. This approach provides a novel paradigm to study morphogenesis, highlighting a unified data structure and harnessing the power of geometric deep learning to accurately model the mechanisms and behaviors of cells during development. It offers a pathway toward creating a unified dynamic morphological atlas for a variety of developmental processes such as embryogenesis.

Cell painting is a popular technique for creating human-interpretable, high-contrast images of cell morphology. There are two major issues with cell paint: (1) it is labor-intensive and (2) it requires chemical fixation, making the study of cell dynamics impossible. We train a diffusion model (Morphological Observation Neural Enhancement Tool, or MONET) on a large dataset to predict cell paint channels from brightfield images. We show that model quality improves with scale. The model uses a consistency architecture to generate time-lapse videos, despite the impossibility of obtaining cell paint video training data. In addition, we show that this architecture enables a form of in-context learning, allowing the model to partially transfer to out-of-distribution cell lines and imaging protocols. Virtual cell painting is not intended to replace physical cell painting completely, but to act as a complementary tool enabling novel workflows in biological research.

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.

Neural representations of 3D data have been widely adopted across various applications, particularly in recent work leveraging coordinate-based networks to model scalar or vector fields. However, these approaches face inherent challenges, such as handling thin structures and non-watertight geometries, which limit their flexibility and accuracy. In contrast, we propose a novel geometric data representation that models geometry as distributions-a powerful representation that makes no assumptions about surface genus, connectivity, or boundary conditions. Our approach uses diffusion models with a novel network architecture to learn surface point distributions, capturing fine-grained geometric details. We evaluate our representation qualitatively and quantitatively across various object types, demonstrating its effectiveness in achieving high geometric fidelity. Additionally, we explore applications using our representation, such as textured mesh representation, neural surface compression, dynamic object modeling, and rendering, highlighting its potential to advance 3D geometric learning.

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.

Representational analysis explores how input data of a neural system are encoded in high dimensional spaces of its distributed neural activations, and how we can compare different systems, for instance, artificial neural networks and brains, on those grounds. While existing methods offer important insights, they typically do not account for local intrinsic geometrical properties within the high-dimensional representation spaces. To go beyond these limitations, we explore Ollivier-Ricci curvature and Ricci flow as tools to study the alignment of representations between humans and artificial neural systems on a geometric level. As a proof-of-principle study, we compared the representations of face stimuli between VGG-Face, a human-aligned version of VGG-Face, and corresponding human similarity judgments from a large online study. Using this discrete geometric framework, we were able to identify local structural similarities and differences by examining the distributions of node and edge curvature and higher-level properties by detecting and comparing community structure in the representational graphs.

Modern recurrent architectures, such as xLSTM and Mamba, have recently challenged the Transformer in language modeling. However, their structure constrains their applicability to sequences only or requires processing multi-dimensional data structures, such as images or molecular graphs, in a pre-defined sequential order. In contrast, Multi-Dimensional RNNs (MDRNNs) are well suited for data with a higher level structure, like 2D grids, trees, and directed acyclic graphs (DAGs). In this work, we extend the notion of multi-dimensionality to linear RNNs. We introduce parallelizable Linear Source Transition Mark networks (pLSTMs) using Source, Transition, and Mark gates that act on the line graph of a general DAG. This enables parallelization in analogy to parallel associative scans and the chunkwise-recurrent form of sequential linear RNNs, but for DAGs. For regular grids (1D and 2D), like images, this scheme can be efficiently implemented using einsum operations, concatenations, and padding in logarithmic time. pLSTMs tackle the vanishing/exploding activation/gradient problem for long distances in DAGs via two distinct modes: a directed propagation mode (P-mode) and a diffusive distribution mode (D-mode). To showcase the long-range capabilities of pLSTM, we introduce arrow-pointing extrapolation as a synthetic computer vision task that contains long-distance directional information. We demonstrate that pLSTMs generalize well to larger image sizes, whereas Transformers struggle to extrapolate. On established molecular graph and computer vision benchmarks, pLSTMs also show strong performance. Code and Datasets are available at: https://github.com/ml-jku/plstm_experiments.

Recent advancements in text-to-image diffusion models have demonstrated remarkable success, yet they often struggle to fully capture the user's intent. Existing approaches using textual inputs combined with bounding boxes or region masks fall short in providing precise spatial guidance, often leading to misaligned or unintended object orientation. To address these limitations, we propose Scribble-Guided Diffusion (ScribbleDiff), a training-free approach that utilizes simple user-provided scribbles as visual prompts to guide image generation. However, incorporating scribbles into diffusion models presents challenges due to their sparse and thin nature, making it difficult to ensure accurate orientation alignment. To overcome these challenges, we introduce moment alignment and scribble propagation, which allow for more effective and flexible alignment between generated images and scribble inputs. Experimental results on the PASCAL-Scribble dataset demonstrate significant improvements in spatial control and consistency, showcasing the effectiveness of scribble-based guidance in diffusion models. Our code is available at https://github.com/kaist-cvml-lab/scribble-diffusion.

Complex tables with multi-level headers, merged cells and heterogeneous layouts pose persistent challenges for LLMs in both understanding and reasoning. Existing approaches typically rely on table linearization or normalized grid modeling. However, these representations struggle to explicitly capture hierarchical structures and cross-dimensional dependencies, which can lead to misalignment between structural semantics and textual representations for non-standard tables. To address this issue, we propose an Orthogonal Hierarchical Decomposition (OHD) framework that constructs structure-preserving input representations of complex tables for LLMs. OHD introduces an Orthogonal Tree Induction (OTI) method based on spatial--semantic co-constraints, which decomposes irregular tables into a column tree and a row tree to capture vertical and horizontal hierarchical dependencies, respectively. Building on this representation, we design a dual-pathway association protocol to symmetrically reconstruct semantic lineage of each cell, and incorporate an LLM as a semantic arbitrator to align multi-level semantic information. We evaluate OHD framework on two complex table question answering benchmarks, AITQA and HiTab. Experimental results show that OHD consistently outperforms existing representation paradigms across multiple evaluation metrics.

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.

Grid-based structures are commonly used to encode explicit features for graphics primitives such as images, signed distance functions (SDF), and neural radiance fields (NeRF) due to their simple implementation. However, in n-dimensional space, calculating the value of a sampled point requires interpolating the values of its 2^n neighboring vertices. The exponential scaling with dimension leads to significant computational overheads. To address this issue, we propose a simplex-based approach for encoding graphics primitives. The number of vertices in a simplex-based structure increases linearly with dimension, making it a more efficient and generalizable alternative to grid-based representations. Using the non-axis-aligned simplicial structure property, we derive and prove a coordinate transformation, simplicial subdivision, and barycentric interpolation scheme for efficient sampling, which resembles transformation procedures in the simplex noise algorithm. Finally, we use hash tables to store multiresolution features of all interest points in the simplicial grid, which are passed into a tiny fully connected neural network to parameterize graphics primitives. We implemented a detailed simplex-based structure encoding algorithm in C++ and CUDA using the methods outlined in our approach. In the 2D image fitting task, the proposed method is capable of fitting a giga-pixel image with 9.4% less time compared to the baseline method proposed by instant-ngp, while maintaining the same quality and compression rate. In the volumetric rendering setup, we observe a maximum 41.2% speedup when the samples are dense enough.

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

Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce LangCell, the first Language-Cell pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.

Current diffusion or flow-based generative models for 3D shapes divide to two: distilling pre-trained 2D image diffusion models, and training directly on 3D shapes. When training a diffusion or flow models on 3D shapes a crucial design choice is the shape representation. An effective shape representation needs to adhere three design principles: it should allow an efficient conversion of large 3D datasets to the representation form; it should provide a good tradeoff of approximation power versus number of parameters; and it should have a simple tensorial form that is compatible with existing powerful neural architectures. While standard 3D shape representations such as volumetric grids and point clouds do not adhere to all these principles simultaneously, we advocate in this paper a new representation that does. We introduce Mosaic-SDF (M-SDF): a simple 3D shape representation that approximates the Signed Distance Function (SDF) of a given shape by using a set of local grids spread near the shape's boundary. The M-SDF representation is fast to compute for each shape individually making it readily parallelizable; it is parameter efficient as it only covers the space around the shape's boundary; and it has a simple matrix form, compatible with Transformer-based architectures. We demonstrate the efficacy of the M-SDF representation by using it to train a 3D generative flow model including class-conditioned generation with the 3D Warehouse dataset, and text-to-3D generation using a dataset of about 600k caption-shape pairs.

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

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream tasks: molecular property prediction against up to 19 baseline methods across four datasets, plus zero-shot molecule-morphology matching.

Generating bitmap graphics from text has gained considerable attention, yet for scientific figures, vector graphics are often preferred. Given that vector graphics are typically encoded using low-level graphics primitives, generating them directly is difficult. To address this, we propose the use of TikZ, a well-known abstract graphics language that can be compiled to vector graphics, as an intermediate representation of scientific figures. TikZ offers human-oriented, high-level commands, thereby facilitating conditional language modeling with any large language model. To this end, we introduce DaTikZ the first large-scale TikZ dataset, consisting of 120k TikZ drawings aligned with captions. We fine-tune LLaMA on DaTikZ, as well as our new model CLiMA, which augments LLaMA with multimodal CLIP embeddings. In both human and automatic evaluation, CLiMA and LLaMA outperform commercial GPT-4 and Claude 2 in terms of similarity to human-created figures, with CLiMA additionally improving text-image alignment. Our detailed analysis shows that all models generalize well and are not susceptible to memorization. GPT-4 and Claude 2, however, tend to generate more simplistic figures compared to both humans and our models. We make our framework, AutomaTikZ, along with model weights and datasets, publicly available.

Recent extensions of Cellular Automata (CA) have incorporated key ideas from modern deep learning, dramatically extending their capabilities and catalyzing a new family of Neural Cellular Automata (NCA) techniques. Inspired by Transformer-based architectures, our work presents a new class of attention-based NCAs formed using a spatially localizedx2014yet globally organizedx2014self-attention scheme. We introduce an instance of this class named Vision Transformer Cellular Automata (ViTCA). We present quantitative and qualitative results on denoising autoencoding across six benchmark datasets, comparing ViTCA to a U-Net, a U-Net-based CA baseline (UNetCA), and a Vision Transformer (ViT). When comparing across architectures configured to similar parameter complexity, ViTCA architectures yield superior performance across all benchmarks and for nearly every evaluation metric. We present an ablation study on various architectural configurations of ViTCA, an analysis of its effect on cell states, and an investigation on its inductive biases. Finally, we examine its learned representations via linear probes on its converged cell state hidden representations, yielding, on average, superior results when compared to our U-Net, ViT, and UNetCA baselines.

Recently, text-to-image generation has exhibited remarkable advancements, with the ability to produce visually impressive results. In contrast, text-to-3D generation has not yet reached a comparable level of quality. Existing methods primarily rely on text-guided score distillation sampling (SDS), and they encounter difficulties in transferring 2D attributes of the generated images to 3D content. In this work, we aim to develop an effective 3D generative model capable of synthesizing high-resolution textured meshes by leveraging both textual and image information. To this end, we introduce Guide3D, a zero-shot text-and-image-guided generative model for 3D avatar generation based on diffusion models. Our model involves (1) generating sparse-view images of a text-consistent character using diffusion models, and (2) jointly optimizing multi-resolution differentiable marching tetrahedral grids with pixel-aligned image features. We further propose a similarity-aware feature fusion strategy for efficiently integrating features from different views. Moreover, we introduce two novel training objectives as an alternative to calculating SDS, significantly enhancing the optimization process. We thoroughly evaluate the performance and components of our framework, which outperforms the current state-of-the-art in producing topologically and structurally correct geometry and high-resolution textures. Guide3D enables the direct transfer of 2D-generated images to the 3D space. Our code will be made publicly available.

This paper presents an end-to-end neural architecture based on Diffusion Models for spatial puzzle solving, particularly jigsaw puzzle and room arrangement tasks. In the latter task, for instance, the proposed system "PuzzleFusion" takes a set of room layouts as polygonal curves in the top-down view and aligns the room layout pieces by estimating their 2D translations and rotations, akin to solving the jigsaw puzzle of room layouts. A surprising discovery of the paper is that the simple use of a Diffusion Model effectively solves these challenging spatial puzzle tasks as a conditional generation process. To enable learning of an end-to-end neural system, the paper introduces new datasets with ground-truth arrangements: 1) 2D Voronoi jigsaw dataset, a synthetic one where pieces are generated by Voronoi diagram of 2D pointset; and 2) MagicPlan dataset, a real one offered by MagicPlan from its production pipeline, where pieces are room layouts constructed by augmented reality App by real-estate consumers. The qualitative and quantitative evaluations demonstrate that our approach outperforms the competing methods by significant margins in all the tasks.

Multimodal large language models (MLLMs) have achieved remarkable performance across a wide range of vision language tasks. However, their ability in low-level visual perception, particularly in detecting fine-grained visual discrepancies, remains underexplored and lacks systematic analysis. In this work, we introduce OddGridBench, a controllable benchmark for evaluating the visual discrepancy sensitivity of MLLMs. OddGridBench comprises over 1,400 grid-based images, where a single element differs from all others by one or multiple visual attributes such as color, size, rotation, or position. Experiments reveal that all evaluated MLLMs, including open-source families such as Qwen3-VL and InternVL3.5, and proprietary systems like Gemini-2.5-Pro and GPT-5, perform far below human levels in visual discrepancy detection. We further propose OddGrid-GRPO, a reinforcement learning framework that integrates curriculum learning and distance-aware reward. By progressively controlling the difficulty of training samples and incorporating spatial proximity constraints into the reward design, OddGrid-GRPO significantly enhances the model's fine-grained visual discrimination ability. We hope OddGridBench and OddGrid-GRPO will lay the groundwork for advancing perceptual grounding and visual discrepancy sensitivity in multimodal intelligence. Code and dataset are available at https://wwwtttjjj.github.io/OddGridBench/.

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.

Neural Radiance Field training can be accelerated through the use of grid-based representations in NeRF's learned mapping from spatial coordinates to colors and volumetric density. However, these grid-based approaches lack an explicit understanding of scale and therefore often introduce aliasing, usually in the form of jaggies or missing scene content. Anti-aliasing has previously been addressed by mip-NeRF 360, which reasons about sub-volumes along a cone rather than points along a ray, but this approach is not natively compatible with current grid-based techniques. We show how ideas from rendering and signal processing can be used to construct a technique that combines mip-NeRF 360 and grid-based models such as Instant NGP to yield error rates that are 8% - 77% lower than either prior technique, and that trains 24x faster than mip-NeRF 360.

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/.

This paper aims to tackle the challenge of dynamic view synthesis from multi-view videos. The key observation is that while previous grid-based methods offer consistent rendering, they fall short in capturing appearance details of a complex dynamic scene, a domain where multi-view image-based rendering methods demonstrate the opposite properties. To combine the best of two worlds, we introduce Im4D, a hybrid scene representation that consists of a grid-based geometry representation and a multi-view image-based appearance representation. Specifically, the dynamic geometry is encoded as a 4D density function composed of spatiotemporal feature planes and a small MLP network, which globally models the scene structure and facilitates the rendering consistency. We represent the scene appearance by the original multi-view videos and a network that learns to predict the color of a 3D point from image features, instead of memorizing detailed appearance totally with networks, thereby naturally making the learning of networks easier. Our method is evaluated on five dynamic view synthesis datasets including DyNeRF, ZJU-MoCap, NHR, DNA-Rendering and ENeRF-Outdoor datasets. The results show that Im4D exhibits state-of-the-art performance in rendering quality and can be trained efficiently, while realizing real-time rendering with a speed of 79.8 FPS for 512x512 images, on a single RTX 3090 GPU.

This paper introduces a novel hierarchical autoencoder that maps 3D models into a highly compressed latent space. The hierarchical autoencoder is specifically designed to tackle the challenges arising from large-scale datasets and generative modeling using diffusion. Different from previous approaches that only work on a regular image or volume grid, our hierarchical autoencoder operates on unordered sets of vectors. Each level of the autoencoder controls different geometric levels of detail. We show that the model can be used to represent a wide range of 3D models while faithfully representing high-resolution geometry details. The training of the new architecture takes 0.70x time and 0.58x memory compared to the baseline. We also explore how the new representation can be used for generative modeling. Specifically, we propose a cascaded diffusion framework where each stage is conditioned on the previous stage. Our design extends existing cascaded designs for image and volume grids to vector sets.

Stimulated by the sophisticated reasoning capabilities of recent Large Language Models (LLMs), a variety of strategies for bridging video modality have been devised. A prominent strategy involves Video Language Models (VideoLMs), which train a learnable interface with video data to connect advanced vision encoders with LLMs. Recently, an alternative strategy has surfaced, employing readily available foundation models, such as VideoLMs and LLMs, across multiple stages for modality bridging. In this study, we introduce a simple yet novel strategy where only a single Vision Language Model (VLM) is utilized. Our starting point is the plain insight that a video comprises a series of images, or frames, interwoven with temporal information. The essence of video comprehension lies in adeptly managing the temporal aspects along with the spatial details of each frame. Initially, we transform a video into a single composite image by arranging multiple frames in a grid layout. The resulting single image is termed as an image grid. This format, while maintaining the appearance of a solitary image, effectively retains temporal information within the grid structure. Therefore, the image grid approach enables direct application of a single high-performance VLM without necessitating any video-data training. Our extensive experimental analysis across ten zero-shot video question answering benchmarks, including five open-ended and five multiple-choice benchmarks, reveals that the proposed Image Grid Vision Language Model (IG-VLM) surpasses the existing methods in nine out of ten benchmarks.

When faced with complex spatial problems, humans naturally sketch layouts to organize their thinking, and the act of drawing further sharpens their understanding. In this work, we ask whether a similar principle holds for Large Language Models (LLMs): can learning to construct explicit visual layouts from spatial descriptions instill genuine spatial understanding? We introduce Text2Space, a dataset that pairs natural language descriptions with ground-truth ASCII grid layouts and spatial QA pairs, enabling us to separate failures in constructing spatial representations from failures in reasoning over them. We adopt ASCII because it is human-readable, operates entirely within the token space of language models, and encodes spatial relations in a structurally verifiable form. Our evaluation reveals a pronounced "Read-Write Asymmetry": LLMs interpret ASCII representations effectively but struggle to produce them from text, and these construction errors propagate to incorrect answers downstream. To address this limitation, we train models on layout construction (TextrightarrowASCII) and find that it significantly improves spatial reasoning from text alone, even without producing any ASCII at inference time. Combining construction with comprehension training further amplifies these gains. Crucially, these improvements transfer to three external spatial reasoning benchmarks, demonstrating that, much as sketching sharpens human spatial thinking, learning to construct explicit layouts instills spatial understanding that generalizes beyond the training format.

We test the Platonic Representation Hypothesis (PRH) in astronomy by measuring representational convergence across a range of foundation models trained on different data types. Using spectroscopic and imaging observations from JWST, HSC, Legacy Survey, and DESI, we compare representations from vision transformers, self-supervised models, and astronomy-specific architectures via mutual k-nearest neighbour analysis. We observe consistent scaling: representational alignment generally increases with model capacity across our tested architectures, supporting convergence toward a shared representation of galaxy astrophysics. Our results suggest that astronomical foundation models can use pre-trained general-purpose architectures, allowing us to capitalise on the broader machine learning community's already-spent computational investment.

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.

Self-supervised vision models have achieved notable success in digital pathology. However, their domain-agnostic transformer architectures are not originally designed to account for fundamental biological elements of histopathology images, namely cells and their complex interactions. In this work, we hypothesize that a biologically-informed modeling of tissues as cell graphs offers a more efficient representation learning. Thus, we introduce GrapHist, a novel graph-based self-supervised learning framework for histopathology, which learns generalizable and structurally-informed embeddings that enable diverse downstream tasks. GrapHist integrates masked autoencoders and heterophilic graph neural networks that are explicitly designed to capture the heterogeneity of tumor microenvironments. We pre-train GrapHist on a large collection of 11 million cell graphs derived from breast tissues and evaluate its transferability across in- and out-of-domain benchmarks. Our results show that GrapHist achieves competitive performance compared to its vision-based counterparts in slide-, region-, and cell-level tasks, while requiring four times fewer parameters. It also drastically outperforms fully-supervised graph models on cancer subtyping tasks. Finally, we also release five graph-based digital pathology datasets used in our study at https://huggingface.co/ogutsevda/datasets , establishing the first large-scale graph benchmark in this field. Our code is available at https://github.com/ogutsevda/graphist .

Implicit Neural Spatial Representation (INSR) has emerged as an effective representation of spatially-dependent vector fields. This work explores solving time-dependent PDEs with INSR. Classical PDE solvers introduce both temporal and spatial discretizations. Common spatial discretizations include meshes and meshless point clouds, where each degree-of-freedom corresponds to a location in space. While these explicit spatial correspondences are intuitive to model and understand, these representations are not necessarily optimal for accuracy, memory usage, or adaptivity. Keeping the classical temporal discretization unchanged (e.g., explicit/implicit Euler), we explore INSR as an alternative spatial discretization, where spatial information is implicitly stored in the neural network weights. The network weights then evolve over time via time integration. Our approach does not require any training data generated by existing solvers because our approach is the solver itself. We validate our approach on various PDEs with examples involving large elastic deformations, turbulent fluids, and multi-scale phenomena. While slower to compute than traditional representations, our approach exhibits higher accuracy and lower memory consumption. Whereas classical solvers can dynamically adapt their spatial representation only by resorting to complex remeshing algorithms, our INSR approach is intrinsically adaptive. By tapping into the rich literature of classic time integrators, e.g., operator-splitting schemes, our method enables challenging simulations in contact mechanics and turbulent flows where previous neural-physics approaches struggle. Videos and codes are available on the project page: http://www.cs.columbia.edu/cg/INSR-PDE/

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.

We introduce a novel 3D generation method for versatile and high-quality 3D asset creation. The cornerstone is a unified Structured LATent (SLAT) representation which allows decoding to different output formats, such as Radiance Fields, 3D Gaussians, and meshes. This is achieved by integrating a sparsely-populated 3D grid with dense multiview visual features extracted from a powerful vision foundation model, comprehensively capturing both structural (geometry) and textural (appearance) information while maintaining flexibility during decoding. We employ rectified flow transformers tailored for SLAT as our 3D generation models and train models with up to 2 billion parameters on a large 3D asset dataset of 500K diverse objects. Our model generates high-quality results with text or image conditions, significantly surpassing existing methods, including recent ones at similar scales. We showcase flexible output format selection and local 3D editing capabilities which were not offered by previous models. Code, model, and data will be released.

Recently, polar-based representation has shown promising properties in perceptual tasks. In addition to Cartesian-based approaches, which separate point clouds unevenly, representing point clouds as polar grids has been recognized as an alternative due to (1) its advantage in robust performance under different resolutions and (2) its superiority in streaming-based approaches. However, state-of-the-art polar-based detection methods inevitably suffer from the feature distortion problem because of the non-uniform division of polar representation, resulting in a non-negligible performance gap compared to Cartesian-based approaches. To tackle this issue, we present PARTNER, a novel 3D object detector in the polar coordinate. PARTNER alleviates the dilemma of feature distortion with global representation re-alignment and facilitates the regression by introducing instance-level geometric information into the detection head. Extensive experiments show overwhelming advantages in streaming-based detection and different resolutions. Furthermore, our method outperforms the previous polar-based works with remarkable margins of 3.68% and 9.15% on Waymo and ONCE validation set, thus achieving competitive results over the state-of-the-art methods.

Prevailing 3D texture generation methods, which often rely on multi-view fusion, are frequently hindered by inter-view inconsistencies and incomplete coverage of complex surfaces, limiting the fidelity and completeness of the generated content. To overcome these challenges, we introduce TEXTRIX, a native 3D attribute generation framework for high-fidelity texture synthesis and downstream applications such as precise 3D part segmentation. Our approach constructs a latent 3D attribute grid and leverages a Diffusion Transformer equipped with sparse attention, enabling direct coloring of 3D models in volumetric space and fundamentally avoiding the limitations of multi-view fusion. Built upon this native representation, the framework naturally extends to high-precision 3D segmentation by training the same architecture to predict semantic attributes on the grid. Extensive experiments demonstrate state-of-the-art performance on both tasks, producing seamless, high-fidelity textures and accurate 3D part segmentation with precise boundaries.

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences and 2D graphs, recent advancements have incorporated 3D conformational information to capture rich atomic interactions. However, these prior models treat molecules merely as discrete atom sets, overlooking the space surrounding them. We argue from a physical perspective that only modeling these discrete points is insufficient. We first present a simple yet insightful observation: naively adding randomly sampled virtual points beyond atoms can surprisingly enhance MPR performance. In light of this, we propose a principled framework that incorporates the entire 3D space spanned by molecules. We implement the framework via a novel Transformer-based architecture, dubbed SpaceFormer, with three key components: (1) grid-based space discretization; (2) grid sampling/merging; and (3) efficient 3D positional encoding. Extensive experiments show that SpaceFormer significantly outperforms previous 3D MPR models across various downstream tasks with limited data, validating the benefit of leveraging the additional 3D space beyond atoms in MPR models.

Although data diffusion embeddings are ubiquitous in unsupervised learning and have proven to be a viable technique for uncovering the underlying intrinsic geometry of data, diffusion embeddings are inherently limited due to their discrete nature. To this end, we propose neural FIM, a method for computing the Fisher information metric (FIM) from point cloud data - allowing for a continuous manifold model for the data. Neural FIM creates an extensible metric space from discrete point cloud data such that information from the metric can inform us of manifold characteristics such as volume and geodesics. We demonstrate Neural FIM's utility in selecting parameters for the PHATE visualization method as well as its ability to obtain information pertaining to local volume illuminating branching points and cluster centers embeddings of a toy dataset and two single-cell datasets of IPSC reprogramming and PBMCs (immune cells).

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.

We introduce 3DShape2VecSet, a novel shape representation for neural fields designed for generative diffusion models. Our shape representation can encode 3D shapes given as surface models or point clouds, and represents them as neural fields. The concept of neural fields has previously been combined with a global latent vector, a regular grid of latent vectors, or an irregular grid of latent vectors. Our new representation encodes neural fields on top of a set of vectors. We draw from multiple concepts, such as the radial basis function representation and the cross attention and self-attention function, to design a learnable representation that is especially suitable for processing with transformers. Our results show improved performance in 3D shape encoding and 3D shape generative modeling tasks. We demonstrate a wide variety of generative applications: unconditioned generation, category-conditioned generation, text-conditioned generation, point-cloud completion, and image-conditioned generation.

Self-supervised learning (SSL) approaches have recently shown substantial success in learning visual representations from unannotated images. Compared with photographic images, medical images acquired with the same imaging protocol exhibit high consistency in anatomy. To exploit this anatomical consistency, this paper introduces a novel SSL approach, called PEAC (patch embedding of anatomical consistency), for medical image analysis. Specifically, in this paper, we propose to learn global and local consistencies via stable grid-based matching, transfer pre-trained PEAC models to diverse downstream tasks, and extensively demonstrate that (1) PEAC achieves significantly better performance than the existing state-of-the-art fully/self-supervised methods, and (2) PEAC captures the anatomical structure consistency across views of the same patient and across patients of different genders, weights, and healthy statuses, which enhances the interpretability of our method for medical image analysis.

Large-scale cell microscopy screens are used in drug discovery and molecular biology research to study the effects of millions of chemical and genetic perturbations on cells. To use these images in downstream analysis, we need models that can map each image into a feature space that represents diverse biological phenotypes consistently, in the sense that perturbations with similar biological effects have similar representations. In this work, we present the largest foundation model for cell microscopy data to date, a new 1.9 billion-parameter ViT-G/8 MAE trained on over 8 billion microscopy image crops. Compared to a previous published ViT-L/8 MAE, our new model achieves a 60% improvement in linear separability of genetic perturbations and obtains the best overall performance on whole-genome biological relationship recall and replicate consistency benchmarks. Beyond scaling, we developed two key methods that improve performance: (1) training on a curated and diverse dataset; and, (2) using biologically motivated linear probing tasks to search across each transformer block for the best candidate representation of whole-genome screens. We find that many self-supervised vision transformers, pretrained on either natural or microscopy images, yield significantly more biologically meaningful representations of microscopy images in their intermediate blocks than in their typically used final blocks. More broadly, our approach and results provide insights toward a general strategy for successfully building foundation models for large-scale biological data.

Accurate detection and segmentation of cell nuclei in volumetric (3D) fluorescence microscopy datasets is an important step in many biomedical research projects. Although many automated methods for these tasks exist, they often struggle for images with low signal-to-noise ratios and/or dense packing of nuclei. It was recently shown for 2D microscopy images that these issues can be alleviated by training a neural network to directly predict a suitable shape representation (star-convex polygon) for cell nuclei. In this paper, we adopt and extend this approach to 3D volumes by using star-convex polyhedra to represent cell nuclei and similar shapes. To that end, we overcome the challenges of 1) finding parameter-efficient star-convex polyhedra representations that can faithfully describe cell nuclei shapes, 2) adapting to anisotropic voxel sizes often found in fluorescence microscopy datasets, and 3) efficiently computing intersections between pairs of star-convex polyhedra (required for non-maximum suppression). Although our approach is quite general, since star-convex polyhedra include common shapes like bounding boxes and spheres as special cases, our focus is on accurate detection and segmentation of cell nuclei. Finally, we demonstrate on two challenging datasets that our approach (StarDist-3D) leads to superior results when compared to classical and deep learning based methods.

We present LATTICE, a new framework for high-fidelity 3D asset generation that bridges the quality and scalability gap between 3D and 2D generative models. While 2D image synthesis benefits from fixed spatial grids and well-established transformer architectures, 3D generation remains fundamentally more challenging due to the need to predict both spatial structure and detailed geometric surfaces from scratch. These challenges are exacerbated by the computational complexity of existing 3D representations and the lack of structured and scalable 3D asset encoding schemes. To address this, we propose VoxSet, a semi-structured representation that compresses 3D assets into a compact set of latent vectors anchored to a coarse voxel grid, enabling efficient and position-aware generation. VoxSet retains the simplicity and compression advantages of prior VecSet methods while introducing explicit structure into the latent space, allowing positional embeddings to guide generation and enabling strong token-level test-time scaling. Built upon this representation, LATTICE adopts a two-stage pipeline: first generating a sparse voxelized geometry anchor, then producing detailed geometry using a rectified flow transformer. Our method is simple at its core, but supports arbitrary resolution decoding, low-cost training, and flexible inference schemes, achieving state-of-the-art performance on various aspects, and offering a significant step toward scalable, high-quality 3D asset creation.

Recent visual autoregressive (AR) models have shown promising capabilities in text-to-image generation, operating in a manner similar to large language models. While test-time computation scaling has brought remarkable success in enabling reasoning-enhanced outputs for challenging natural language tasks, its adaptation to visual AR models remains unexplored and poses unique challenges. Naively applying test-time scaling strategies such as Best-of-N can be suboptimal: they consume full-length computation on erroneous generation trajectories, while the raster-scan decoding scheme lacks a blueprint of the entire canvas, limiting scaling benefits as only a few prompt-aligned candidates are generated. To address these, we introduce GridAR, a test-time scaling framework designed to elicit the best possible results from visual AR models. GridAR employs a grid-partitioned progressive generation scheme in which multiple partial candidates for the same position are generated within a canvas, infeasible ones are pruned early, and viable ones are fixed as anchors to guide subsequent decoding. Coupled with this, we present a layout-specified prompt reformulation strategy that inspects partial views to infer a feasible layout for satisfying the prompt. The reformulated prompt then guides subsequent image generation to mitigate the blueprint deficiency. Together, GridAR achieves higher-quality results under limited test-time scaling: with N=4, it even outperforms Best-of-N (N=8) by 14.4% on T2I-CompBench++ while reducing cost by 25.6%. It also generalizes to autoregressive image editing, showing comparable edit quality and a 13.9% gain in semantic preservation on PIE-Bench over larger-N baselines.

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

Table structure recognition is a key task in document analysis. However, the geometric deformation in deformed tables causes a weak correlation between content information and structure, resulting in downstream tasks not being able to obtain accurate content information. To obtain fine-grained spatial coordinates of cells, we propose the OG-HFYOLO model, which enhances the edge response by Gradient Orientation-aware Extractor, combines a Heterogeneous Kernel Cross Fusion module and a scale-aware loss function to adapt to multi-scale objective features, and introduces mask-driven non-maximal suppression in the post-processing, which replaces the traditional bounding box suppression mechanism. Furthermore, we also propose a data generator, filling the gap in the dataset for fine-grained deformation table cell spatial coordinate localization, and derive a large-scale dataset named Deformation Wired Table (DWTAL). Experiments show that our proposed model demonstrates excellent segmentation accuracy on all mainstream instance segmentation models. The dataset and the source code are open source: https://github.com/justliulong/OGHFYOLO.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

This paper studies implicit surface reconstruction leveraging differentiable ray casting. Previous works such as IDR and NeuS overlook the spatial context in 3D space when predicting and rendering the surface, thereby may fail to capture sharp local topologies such as small holes and structures. To mitigate the limitation, we propose a flexible neural implicit representation leveraging hierarchical voxel grids, namely Neural Deformable Anchor (NeuDA), for high-fidelity surface reconstruction. NeuDA maintains the hierarchical anchor grids where each vertex stores a 3D position (or anchor) instead of the direct embedding (or feature). We optimize the anchor grids such that different local geometry structures can be adaptively encoded. Besides, we dig into the frequency encoding strategies and introduce a simple hierarchical positional encoding method for the hierarchical anchor structure to flexibly exploit the properties of high-frequency and low-frequency geometry and appearance. Experiments on both the DTU and BlendedMVS datasets demonstrate that NeuDA can produce promising mesh surfaces.

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

Large language models (LLMs) are increasingly applied in scientific research, offering new capabilities for knowledge discovery and reasoning. In single-cell biology, however, evaluation practices for both general and specialized LLMs remain inadequate: existing benchmarks are fragmented across tasks, adopt formats such as multiple-choice classification that diverge from real-world usage, and rely on metrics lacking interpretability and biological grounding. We present SC-ARENA, a natural language evaluation framework tailored to single-cell foundation models. SC-ARENA formalizes a virtual cell abstraction that unifies evaluation targets by representing both intrinsic attributes and gene-level interactions. Within this paradigm, we define five natural language tasks (cell type annotation, captioning, generation, perturbation prediction, and scientific QA) that probe core reasoning capabilities in cellular biology. To overcome the limitations of brittle string-matching metrics, we introduce knowledge-augmented evaluation, which incorporates external ontologies, marker databases, and scientific literature to support biologically faithful and interpretable judgments. Experiments and analysis across both general-purpose and domain-specialized LLMs demonstrate that (i) under the Virtual Cell unified evaluation paradigm, current models achieve uneven performance on biologically complex tasks, particularly those demanding mechanistic or causal understanding; and (ii) our knowledge-augmented evaluation framework ensures biological correctness, provides interpretable, evidence-grounded rationales, and achieves high discriminative capacity, overcoming the brittleness and opacity of conventional metrics. SC-Arena thus provides a unified and interpretable framework for assessing LLMs in single-cell biology, pointing toward the development of biology-aligned, generalizable foundation models.

We present PVSeRF, a learning framework that reconstructs neural radiance fields from single-view RGB images, for novel view synthesis. Previous solutions, such as pixelNeRF, rely only on pixel-aligned features and suffer from feature ambiguity issues. As a result, they struggle with the disentanglement of geometry and appearance, leading to implausible geometries and blurry results. To address this challenge, we propose to incorporate explicit geometry reasoning and combine it with pixel-aligned features for radiance field prediction. Specifically, in addition to pixel-aligned features, we further constrain the radiance field learning to be conditioned on i) voxel-aligned features learned from a coarse volumetric grid and ii) fine surface-aligned features extracted from a regressed point cloud. We show that the introduction of such geometry-aware features helps to achieve a better disentanglement between appearance and geometry, i.e. recovering more accurate geometries and synthesizing higher quality images of novel views. Extensive experiments against state-of-the-art methods on ShapeNet benchmarks demonstrate the superiority of our approach for single-image novel view synthesis.

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.

Recent research in medical image analysis with deep learning almost exclusively focuses on grid- or voxel-based data representations. We challenge this common choice by introducing MedFuncta, a modality-agnostic continuous data representation based on neural fields. We demonstrate how to scale neural fields from single instances to large datasets by exploiting redundancy in medical signals and by applying an efficient meta-learning approach with a context reduction scheme. We further address the spectral bias in commonly used SIREN activations, by introducing an omega_0-schedule, improving reconstruction quality and convergence speed. We validate our proposed approach on a large variety of medical signals of different dimensions and modalities (1D: ECG; 2D: Chest X-ray, Retinal OCT, Fundus Camera, Dermatoscope, Colon Histopathology, Cell Microscopy; 3D: Brain MRI, Lung CT) and successfully demonstrate that we can solve relevant downstream tasks on these representations. We additionally release a large-scale dataset of > 550k annotated neural fields to promote research in this direction.

The segmentation of cell nuclei in tissue images stained with the blood dye hematoxylin and eosin (H&E) is essential for various clinical applications and analyses. Due to the complex characteristics of cellular morphology, a large receptive field is considered crucial for generating high-quality segmentation. However, previous methods face challenges in achieving a balance between the receptive field and computational burden. To address this issue, we propose LKCell, a high-accuracy and efficient cell segmentation method. Its core insight lies in unleashing the potential of large convolution kernels to achieve computationally efficient large receptive fields. Specifically, (1) We transfer pre-trained large convolution kernel models to the medical domain for the first time, demonstrating their effectiveness in cell segmentation. (2) We analyze the redundancy of previous methods and design a new segmentation decoder based on large convolution kernels. It achieves higher performance while significantly reducing the number of parameters. We evaluate our method on the most challenging benchmark and achieve state-of-the-art results (0.5080 mPQ) in cell nuclei instance segmentation with only 21.6% FLOPs compared with the previous leading method. Our source code and models are available at https://github.com/hustvl/LKCell.

Cortical circuits exhibit intricate recurrent architectures that are remarkably similar across different brain areas. Such stereotyped structure suggests the existence of common computational principles. However, such principles have remained largely elusive. Inspired by gated-memory networks, namely long short-term memory networks (LSTMs), we introduce a recurrent neural network in which information is gated through inhibitory cells that are subtractive (subLSTM). We propose a natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical microcircuits. Our empirical evaluation across sequential image classification and language modelling tasks shows that subLSTM units can achieve similar performance to LSTM units. These results suggest that cortical circuits can be optimised to solve complex contextual problems and proposes a novel view on their computational function. Overall our work provides a step towards unifying recurrent networks as used in machine learning with their biological counterparts.

Recent advances in text-to-video generation have enabled high-quality synthesis from text and image prompts. While the personalization of dynamic concepts, which capture subject-specific appearance and motion from a single video, is now feasible, most existing methods require per-instance fine-tuning, limiting scalability. We introduce a fully zero-shot framework for dynamic concept personalization in text-to-video models. Our method leverages structured 2x2 video grids that spatially organize input and output pairs, enabling the training of lightweight Grid-LoRA adapters for editing and composition within these grids. At inference, a dedicated Grid Fill module completes partially observed layouts, producing temporally coherent and identity preserving outputs. Once trained, the entire system operates in a single forward pass, generalizing to previously unseen dynamic concepts without any test-time optimization. Extensive experiments demonstrate high-quality and consistent results across a wide range of subjects beyond trained concepts and editing scenarios.

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.

The success of deep learning is frequently described as the ability to train all parameters of a network on a specific application in an end-to-end fashion. Yet, several design choices on the camera level, including the pixel layout of the sensor, are considered as pre-defined and fixed, and high resolution, regular pixel layouts are considered to be the most generic ones in computer vision and graphics, treating all regions of an image as equally important. While several works have considered non-uniform, \eg, hexagonal or foveated, pixel layouts in hardware and image processing, the layout has not been integrated into the end-to-end learning paradigm so far. In this work, we present the first truly end-to-end trained imaging pipeline that optimizes the size and distribution of pixels on the imaging sensor jointly with the parameters of a given neural network on a specific task. We derive an analytic, differentiable approach for the sensor layout parameterization that allows for task-specific, local varying pixel resolutions. We present two pixel layout parameterization functions: rectangular and curvilinear grid shapes that retain a regular topology. We provide a drop-in module that approximates sensor simulation given existing high-resolution images to directly connect our method with existing deep learning models. We show that network predictions benefit from learnable pixel layouts for two different downstream tasks, classification and semantic segmentation.

Two-Tower Vision--Language Models (VLMs) have demonstrated strong performance across various downstream VL tasks. While BridgeTower further enhances performance by building bridges between encoders, it (i) suffers from ineffective layer-by-layer utilization of unimodal representations, (ii) restricts the flexible exploitation of different levels of unimodal semantic knowledge, and (iii) is limited to the evaluation on traditional low-resolution datasets only with the Two-Tower VLM architecture. In this work, we propose Manager, a lightweight, efficient and effective plugin that adaptively aggregates insights from different levels of pre-trained unimodal experts to facilitate more comprehensive VL alignment and fusion. First, under the Two-Tower VLM architecture, we introduce ManagerTower, a novel VLM that introduces the manager in each cross-modal layer. Whether with or without VL pre-training, ManagerTower outperforms previous strong baselines and achieves superior performance on 4 downstream VL tasks. Moreover, we extend our exploration to the latest Multimodal Large Language Model (MLLM) architecture. We demonstrate that LLaVA-OV-Manager significantly boosts the zero-shot performance of LLaVA-OV across different categories of capabilities, images, and resolutions on 20 downstream datasets, whether the multi-grid algorithm is enabled or not. In-depth analysis reveals that both our manager and the multi-grid algorithm can be viewed as a plugin that improves the visual representation by capturing more diverse visual details from two orthogonal perspectives (depth and width). Their synergy can mitigate the semantic ambiguity caused by the multi-grid algorithm and further improve performance. Code and models are available at https://github.com/LooperXX/ManagerTower.

Convolutional Neural Networks (CNN) have been successful in processing data signals that are uniformly sampled in the spatial domain (e.g., images). However, most data signals do not natively exist on a grid, and in the process of being sampled onto a uniform physical grid suffer significant aliasing error and information loss. Moreover, signals can exist in different topological structures as, for example, points, lines, surfaces and volumes. It has been challenging to analyze signals with mixed topologies (for example, point cloud with surface mesh). To this end, we develop mathematical formulations for Non-Uniform Fourier Transforms (NUFT) to directly, and optimally, sample nonuniform data signals of different topologies defined on a simplex mesh into the spectral domain with no spatial sampling error. The spectral transform is performed in the Euclidean space, which removes the translation ambiguity from works on the graph spectrum. Our representation has four distinct advantages: (1) the process causes no spatial sampling error during the initial sampling, (2) the generality of this approach provides a unified framework for using CNNs to analyze signals of mixed topologies, (3) it allows us to leverage state-of-the-art backbone CNN architectures for effective learning without having to design a particular architecture for a particular data structure in an ad-hoc fashion, and (4) the representation allows weighted meshes where each element has a different weight (i.e., texture) indicating local properties. We achieve results on par with the state-of-the-art for the 3D shape retrieval task, and a new state-of-the-art for the point cloud to surface reconstruction task.

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.

Whole Slide Images (WSIs) exhibit hierarchical structure, where diagnostic information emerges from cellular morphology, regional tissue organization, and global context. Existing Computational Pathology (CPath) Multimodal Large Language Models (MLLMs) typically compress an entire WSI into a single embedding, which hinders fine-grained grounding and ignores how pathologists synthesize evidence across different scales. We introduce MLLM-HWSI, a Hierarchical WSI-level MLLM that aligns visual features with pathology language at four distinct scales, cell as word, patch as phrase, region as sentence, and WSI as paragraph to support interpretable evidence-grounded reasoning. MLLM-HWSI decomposes each WSI into multi-scale embeddings with scale-specific projectors and jointly enforces (i) a hierarchical contrastive objective and (ii) a cross-scale consistency loss, preserving semantic coherence from cells to the WSI. We compute diagnostically relevant patches and aggregate segmented cell embeddings into a compact cellular token per-patch using a lightweight Cell-Cell Attention Fusion (CCAF) transformer. The projected multi-scale tokens are fused with text tokens and fed to an instruction-tuned LLM for open-ended reasoning, VQA, report, and caption generation tasks. Trained in three stages, MLLM-HWSI achieves new SOTA results on 13 WSI-level benchmarks across six CPath tasks. By aligning language with multi-scale visual evidence, MLLM-HWSI provides accurate, interpretable outputs that mirror diagnostic workflows and advance holistic WSI understanding. Code is available at: https://github.com/BasitAlawode/HWSI-MLLM{GitHub}.

Scientific archives now contain hundreds of petabytes of data across genomics, ecology, climate, and molecular biology that could reveal undiscovered patterns if systematically analyzed at scale. Large-scale, weakly-supervised datasets in language and vision have driven the development of foundation models whose internal representations encode structure (patterns, co-occurrences and statistical regularities) beyond their training objectives. Most existing methods extract structure only for pre-specified targets; they excel at confirmation but do not support open-ended discovery of unknown patterns. We ask whether sparse autoencoders (SAEs) can enable open-ended feature discovery from foundation model representations. We evaluate this question in controlled rediscovery studies, where the learned SAE features are tested for alignment with semantic concepts on a standard segmentation benchmark and compared against strong label-free alternatives on concept-alignment metrics. Applied to ecological imagery, the same procedure surfaces fine-grained anatomical structure without access to segmentation or part labels, providing a scientific case study with ground-truth validation. While our experiments focus on vision with an ecology case study, the method is domain-agnostic and applicable to models in other sciences (e.g., proteins, genomics, weather). Our results indicate that sparse decomposition provides a practical instrument for exploring what scientific foundation models have learned, an important prerequisite for moving from confirmation to genuine discovery.

While representation alignment with self-supervised models has been shown to improve diffusion model training, its potential for enhancing inference-time conditioning remains largely unexplored. We introduce Representation-Aligned Guidance (REPA-G), a framework that leverages these aligned representations, with rich semantic properties, to enable test-time conditioning from features in generation. By optimizing a similarity objective (the potential) at inference, we steer the denoising process toward a conditioned representation extracted from a pre-trained feature extractor. Our method provides versatile control at multiple scales, ranging from fine-grained texture matching via single patches to broad semantic guidance using global image feature tokens. We further extend this to multi-concept composition, allowing for the faithful combination of distinct concepts. REPA-G operates entirely at inference time, offering a flexible and precise alternative to often ambiguous text prompts or coarse class labels. We theoretically justify how this guidance enables sampling from the potential-induced tilted distribution. Quantitative results on ImageNet and COCO demonstrate that our approach achieves high-quality, diverse generations. Code is available at https://github.com/valeoai/REPA-G.

We introduce the Nexus Adapters, novel text-guided efficient adapters to the diffusion-based framework for the Structure Preserving Conditional Generation (SPCG). Recently, structure-preserving methods have achieved promising results in conditional image generation by using a base model for prompt conditioning and an adapter for structure input, such as sketches or depth maps. These approaches are highly inefficient and sometimes require equal parameters in the adapter compared to the base architecture. It is not always possible to train the model since the diffusion model is itself costly, and doubling the parameter is highly inefficient. In these approaches, the adapter is not aware of the input prompt; therefore, it is optimal only for the structural input but not for the input prompt. To overcome the above challenges, we proposed two efficient adapters, Nexus Prime and Slim, which are guided by prompts and structural inputs. Each Nexus Block incorporates cross-attention mechanisms to enable rich multimodal conditioning. Therefore, the proposed adapter has a better understanding of the input prompt while preserving the structure. We conducted extensive experiments on the proposed models and demonstrated that the Nexus Prime adapter significantly enhances performance, requiring only 8M additional parameters compared to the baseline, T2I-Adapter. Furthermore, we also introduced a lightweight Nexus Slim adapter with 18M fewer parameters than the T2I-Adapter, which still achieved state-of-the-art results. Code: https://github.com/arya-domain/Nexus-Adapters

Recent success in training deep neural networks have prompted active investigation into the features learned on their intermediate layers. Such research is difficult because it requires making sense of non-linear computations performed by millions of parameters, but valuable because it increases our ability to understand current models and create improved versions of them. In this paper we investigate the extent to which neural networks exhibit what we call convergent learning, which is when the representations learned by multiple nets converge to a set of features which are either individually similar between networks or where subsets of features span similar low-dimensional spaces. We propose a specific method of probing representations: training multiple networks and then comparing and contrasting their individual, learned representations at the level of neurons or groups of neurons. We begin research into this question using three techniques to approximately align different neural networks on a feature level: a bipartite matching approach that makes one-to-one assignments between neurons, a sparse prediction approach that finds one-to-many mappings, and a spectral clustering approach that finds many-to-many mappings. This initial investigation reveals a few previously unknown properties of neural networks, and we argue that future research into the question of convergent learning will yield many more. The insights described here include (1) that some features are learned reliably in multiple networks, yet other features are not consistently learned; (2) that units learn to span low-dimensional subspaces and, while these subspaces are common to multiple networks, the specific basis vectors learned are not; (3) that the representation codes show evidence of being a mix between a local code and slightly, but not fully, distributed codes across multiple units.

The Platonic Representation Hypothesis suggests that independently trained neural networks converge to increasingly similar latent spaces. However, current strategies for mapping these representations are inherently pairwise, scaling quadratically with the number of models and failing to yield a consistent global reference. In this paper, we study the alignment of M ge 3 models. We first adapt Generalized Procrustes Analysis (GPA) to construct a shared orthogonal universe that preserves the internal geometry essential for tasks like model stitching. We then show that strict isometric alignment is suboptimal for retrieval, where agreement-maximizing methods like Canonical Correlation Analysis (CCA) typically prevail. To bridge this gap, we finally propose Geometry-Corrected Procrustes Alignment (GCPA), which establishes a robust GPA-based universe followed by a post-hoc correction for directional mismatch. Extensive experiments demonstrate that GCPA consistently improves any-to-any retrieval while retaining a practical shared reference space.

Coordinate-based neural representations have shown significant promise as an alternative to discrete, array-based representations for complex low dimensional signals. However, optimizing a coordinate-based network from randomly initialized weights for each new signal is inefficient. We propose applying standard meta-learning algorithms to learn the initial weight parameters for these fully-connected networks based on the underlying class of signals being represented (e.g., images of faces or 3D models of chairs). Despite requiring only a minor change in implementation, using these learned initial weights enables faster convergence during optimization and can serve as a strong prior over the signal class being modeled, resulting in better generalization when only partial observations of a given signal are available. We explore these benefits across a variety of tasks, including representing 2D images, reconstructing CT scans, and recovering 3D shapes and scenes from 2D image observations.

Representing visual signals by coordinate-based deep fully-connected networks has been shown advantageous in fitting complex details and solving inverse problems than discrete grid-based representation. However, acquiring such a continuous Implicit Neural Representation (INR) requires tedious per-scene training on tons of signal measurements, which limits its practicality. In this paper, we present a generic INR framework that achieves both data and training efficiency by learning a Neural Implicit Dictionary (NID) from a data collection and representing INR as a functional combination of basis sampled from the dictionary. Our NID assembles a group of coordinate-based subnetworks which are tuned to span the desired function space. After training, one can instantly and robustly acquire an unseen scene representation by solving the coding coefficients. To parallelly optimize a large group of networks, we borrow the idea from Mixture-of-Expert (MoE) to design and train our network with a sparse gating mechanism. Our experiments show that, NID can improve reconstruction of 2D images or 3D scenes by 2 orders of magnitude faster with up to 98% less input data. We further demonstrate various applications of NID in image inpainting and occlusion removal, which are considered to be challenging with vanilla INR. Our codes are available in https://github.com/VITA-Group/Neural-Implicit-Dict.

Learning 3D representations that generalize well to arbitrarily oriented inputs is a challenge of practical importance in applications varying from computer vision to physics and chemistry. We propose a novel multi-resolution convolutional architecture for learning over concentric spherical feature maps, of which the single sphere representation is a special case. Our hierarchical architecture is based on alternatively learning to incorporate both intra-sphere and inter-sphere information. We show the applicability of our method for two different types of 3D inputs, mesh objects, which can be regularly sampled, and point clouds, which are irregularly distributed. We also propose an efficient mapping of point clouds to concentric spherical images, thereby bridging spherical convolutions on grids with general point clouds. We demonstrate the effectiveness of our approach in improving state-of-the-art performance on 3D classification tasks with rotated data.

We present GeoGrid-Bench, a benchmark designed to evaluate the ability of foundation models to understand geo-spatial data in the grid structure. Geo-spatial datasets pose distinct challenges due to their dense numerical values, strong spatial and temporal dependencies, and unique multimodal representations including tabular data, heatmaps, and geographic visualizations. To assess how foundation models can support scientific research in this domain, GeoGrid-Bench features large-scale, real-world data covering 16 climate variables across 150 locations and extended time frames. The benchmark includes approximately 3,200 question-answer pairs, systematically generated from 8 domain expert-curated templates to reflect practical tasks encountered by human scientists. These range from basic queries at a single location and time to complex spatiotemporal comparisons across regions and periods. Our evaluation reveals that vision-language models perform best overall, and we provide a fine-grained analysis of the strengths and limitations of different foundation models in different geo-spatial tasks. This benchmark offers clearer insights into how foundation models can be effectively applied to geo-spatial data analysis and used to support scientific research.

We present a novel alignment-before-generation approach to tackle the challenging task of generating general 3D shapes based on 2D images or texts. Directly learning a conditional generative model from images or texts to 3D shapes is prone to producing inconsistent results with the conditions because 3D shapes have an additional dimension whose distribution significantly differs from that of 2D images and texts. To bridge the domain gap among the three modalities and facilitate multi-modal-conditioned 3D shape generation, we explore representing 3D shapes in a shape-image-text-aligned space. Our framework comprises two models: a Shape-Image-Text-Aligned Variational Auto-Encoder (SITA-VAE) and a conditional Aligned Shape Latent Diffusion Model (ASLDM). The former model encodes the 3D shapes into the shape latent space aligned to the image and text and reconstructs the fine-grained 3D neural fields corresponding to given shape embeddings via the transformer-based decoder. The latter model learns a probabilistic mapping function from the image or text space to the latent shape space. Our extensive experiments demonstrate that our proposed approach can generate higher-quality and more diverse 3D shapes that better semantically conform to the visual or textural conditional inputs, validating the effectiveness of the shape-image-text-aligned space for cross-modality 3D shape generation.

While recent advancements in generative modeling have significantly improved text-image alignment, some residual misalignment between text and image representations still remains. Although many approaches have attempted to address this issue by fine-tuning models using various reward models, etc., we revisit the challenge from the perspective of representation alignment-an approach that has gained popularity with the success of REPresentation Alignment (REPA). We first argue that conventional text-to-image (T2I) diffusion models, typically trained on paired image and text data (i.e., positive pairs) by minimizing score matching or flow matching losses, is suboptimal from the standpoint of representation alignment. Instead, a better alignment can be achieved through contrastive learning that leverages both positive and negative pairs. To achieve this efficiently even with pretrained models, we introduce a lightweight contrastive fine tuning strategy called SoftREPA that uses soft text tokens. This approach improves alignment with minimal computational overhead by adding fewer than 1M trainable parameters to the pretrained model. Our theoretical analysis demonstrates that our method explicitly increases the mutual information between text and image representations, leading to enhanced semantic consistency. Experimental results across text-to-image generation and text-guided image editing tasks validate the effectiveness of our approach in improving the semantic consistency of T2I generative models.

In stark contrast to the case of images, finding a concise, learnable discrete representation of 3D surfaces remains a challenge. In particular, while polygon meshes are arguably the most common surface representation used in geometry processing, their irregular and combinatorial structure often make them unsuitable for learning-based applications. In this work, we present VoroMesh, a novel and differentiable Voronoi-based representation of watertight 3D shape surfaces. From a set of 3D points (called generators) and their associated occupancy, we define our boundary representation through the Voronoi diagram of the generators as the subset of Voronoi faces whose two associated (equidistant) generators are of opposite occupancy: the resulting polygon mesh forms a watertight approximation of the target shape's boundary. To learn the position of the generators, we propose a novel loss function, dubbed VoroLoss, that minimizes the distance from ground truth surface samples to the closest faces of the Voronoi diagram which does not require an explicit construction of the entire Voronoi diagram. A direct optimization of the Voroloss to obtain generators on the Thingi32 dataset demonstrates the geometric efficiency of our representation compared to axiomatic meshing algorithms and recent learning-based mesh representations. We further use VoroMesh in a learning-based mesh prediction task from input SDF grids on the ABC dataset, and show comparable performance to state-of-the-art methods while guaranteeing closed output surfaces free of self-intersections.

Positional embeddings (PE) play a crucial role in Vision Transformers (ViTs) by providing spatial information otherwise lost due to the permutation invariant nature of self attention. While absolute positional embeddings (APE) have shown theoretical advantages over relative positional embeddings (RPE), particularly due to the ability of sinusoidal functions to preserve spatial inductive biases like monotonicity and shift invariance, a fundamental challenge arises when mapping a 2D grid to a 1D sequence. Existing methods have mostly overlooked or never explored the impact of patch ordering in positional embeddings. To address this, we propose LOOPE, a learnable patch-ordering method that optimizes spatial representation for a given set of frequencies, providing a principled approach to patch order optimization. Empirical results show that our PE significantly improves classification accuracy across various ViT architectures. To rigorously evaluate the effectiveness of positional embeddings, we introduce the "Three Cell Experiment", a novel benchmarking framework that assesses the ability of PEs to retain relative and absolute positional information across different ViT architectures. Unlike standard evaluations, which typically report a performance gap of 4 to 6% between models with and without PE, our method reveals a striking 30 to 35% difference, offering a more sensitive diagnostic tool to measure the efficacy of PEs. Our experimental analysis confirms that the proposed LOOPE demonstrates enhanced effectiveness in retaining both relative and absolute positional information.

Recent advances have discussed cell complexes as ideal learning representations. However, there is a lack of available machine learning methods suitable for learning on CW complexes. In this paper, we derive an explicit expression for the Wasserstein distance between cell complex signal distributions in terms of a Hodge-Laplacian matrix. This leads to a structurally meaningful measure to compare CW complexes and define the optimal transportation map. In order to simultaneously include both feature and structure information, we extend the Fused Gromov-Wasserstein distance to CW complexes. Finally, we introduce novel kernels over the space of probability measures on CW complexes based on the dual formulation of optimal transport.

We introduce a novel FSVOS model that employs a local matching strategy to restrict the search space to the most relevant neighboring pixels. Rather than relying on inefficient standard im2col-like implementations (e.g., spatial convolutions, depthwise convolutions and feature-shifting mechanisms) or hardware-specific CUDA kernels (e.g., deformable and neighborhood attention), which often suffer from limited portability across non-CUDA devices, we reorganize the local sampling process through a direction-based sampling perspective. Specifically, we implement a non-parametric sampling mechanism that enables dynamically varying sampling regions. This approach provides the flexibility to adapt to diverse spatial structures without the computational costs of parametric layers and the need for model retraining. To further enhance feature coherence across frames, we design a supervised spatio-temporal contrastive learning scheme that enforces consistency in feature representations. In addition, we introduce a publicly available benchmark dataset for multi-object segmentation in X-ray angiography videos (MOSXAV), featuring detailed, manually labeled segmentation ground truth. Extensive experiments on the CADICA, XACV, and MOSXAV datasets show that our proposed FSVOS method outperforms current state-of-the-art video segmentation methods in terms of segmentation accuracy and generalization capability (i.e., seen and unseen categories). This work offers enhanced flexibility and potential for a wide range of clinical applications.

We introduce a parameter-efficient adaptation method for panel-aware in-context image generation with pre-trained diffusion transformers. The key idea is to compose learnable, panel-specific orthogonal operators onto the backbone's frozen positional encodings. This design provides two desirable properties: (1) isometry, which preserves the geometry of internal features, and (2) same-panel invariance, which maintains the model's pre-trained intra-panel synthesis behavior. Through controlled experiments, we demonstrate that the effectiveness of our adaptation method is not tied to a specific positional encoding design but generalizes across diverse positional encoding regimes. By enabling effective panel-relative conditioning, the proposed method consistently improves in-context image-based instructional editing pipelines, including state-of-the-art approaches.

The digitization of histology slides has revolutionized pathology, providing massive datasets for cancer diagnosis and research. Contrastive self-supervised and vision-language models have been shown to effectively mine large pathology datasets to learn discriminative representations. On the other hand, generative models, capable of synthesizing realistic and diverse images, present a compelling solution to address unique problems in pathology that involve synthesizing images; overcoming annotated data scarcity, enabling privacy-preserving data sharing, and performing inherently generative tasks, such as virtual staining. We introduce PixCell, the first diffusion-based generative foundation model for histopathology. We train PixCell on PanCan-30M, a vast, diverse dataset derived from 69,184 H\&E-stained whole slide images covering various cancer types. We employ a progressive training strategy and a self-supervision-based conditioning that allows us to scale up training without any annotated data. PixCell generates diverse and high-quality images across multiple cancer types, which we find can be used in place of real data to train a self-supervised discriminative model. Synthetic images shared between institutions are subject to fewer regulatory barriers than would be the case with real clinical images. Furthermore, we showcase the ability to precisely control image generation using a small set of annotated images, which can be used for both data augmentation and educational purposes. Testing on a cell segmentation task, a mask-guided PixCell enables targeted data augmentation, improving downstream performance. Finally, we demonstrate PixCell's ability to use H\&E structural staining to infer results from molecular marker studies; we use this capability to infer IHC staining from H\&E images. Our trained models are publicly released to accelerate research in computational pathology.

Creative thinking is a fundamental aspect of human cognition, and divergent thinking-the capacity to generate novel and varied ideas-is widely regarded as its core generative engine. Large language models (LLMs) have recently demonstrated impressive performance on divergent thinking tests and prior work has shown that models with higher task performance tend to be more aligned to human brain activity. However, existing brain-LLM alignment studies have focused on passive, non-creative tasks. Here, we explore brain alignment during creative thinking using fMRI data from 170 participants performing the Alternate Uses Task (AUT). We extract representations from LLMs varying in size (270M-72B) and measure alignment to brain responses via Representational Similarity Analysis (RSA), targeting the creativity-related default mode and frontoparietal networks. We find that brain-LLM alignment scales with model size (default mode network only) and idea originality (both networks), with effects strongest early in the creative process. We further show that post-training objectives shape alignment in functionally selective ways: a creativity-optimized Llama-3.1-8B-Instruct preserves alignment with high-creativity neural responses while reducing alignment with low-creativity ones; a human behavior fine-tuned model elevates alignment with both; and a reasoning-trained variant shows the opposite pattern, suggesting chain-of-thought training steers representations away from creative neural geometry toward analytical processing. These results demonstrate that post-training objectives selectively reshape LLM representations relative to the neural geometry of human creative thought.

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.

Emerging from low-level vision theory, steerable filters found their counterpart in prior work on steerable convolutional neural networks equivariant to rigid transformations. In our work, we propose a steerable feed-forward learning-based approach that consists of neurons with spherical decision surfaces and operates on point clouds. Such spherical neurons are obtained by conformal embedding of Euclidean space and have recently been revisited in the context of learning representations of point sets. Focusing on 3D geometry, we exploit the isometry property of spherical neurons and derive a 3D steerability constraint. After training spherical neurons to classify point clouds in a canonical orientation, we use a tetrahedron basis to quadruplicate the neurons and construct rotation-equivariant spherical filter banks. We then apply the derived constraint to interpolate the filter bank outputs and, thus, obtain a rotation-invariant network. Finally, we use a synthetic point set and real-world 3D skeleton data to verify our theoretical findings. The code is available at https://github.com/pavlo-melnyk/steerable-3d-neurons.

Developing 3D-VL generalists capable of understanding 3D scenes and following natural language instructions to perform a wide range of tasks has been a long-standing goal in the 3D-VL community. Despite recent progress, 3D-VL models still lag behind their 2D counterparts in capability and robustness, falling short of the generalist standard. A key obstacle to developing 3D-VL generalists lies in data scalability, hindered by the lack of an efficient scene representation. We propose LEO-VL, a 3D-VL model built upon condensed feature grid (CFG), an efficient scene representation that bridges 2D perception and 3D spatial structure while significantly reducing token overhead. This efficiency unlocks large-scale training towards 3D-VL generalist, for which we curate over 700k high-quality 3D-VL data spanning four domains of real-world indoor scenes and five tasks such as captioning and dialogue. LEO-VL achieves state-of-the-art performance on a variety of 3D QA benchmarks, including SQA3D, MSQA, and Beacon3D. Ablation studies confirm the efficiency of our representation, the importance of task and scene diversity, and the validity of our data curation principle. Furthermore, we introduce SceneDPO, a novel post-training objective that enhances the robustness of 3D-VL models. We hope our findings contribute to the advancement of scalable and robust 3D-VL generalists.

Implicit Neural Representations (INRs) have emerged as a powerful paradigm for representing signals such as images, 3D shapes, signed distance fields, and radiance fields. While significant progress has been made in architecture design (e.g., SIREN, FFC, KAN-based INRs) and optimization strategies (meta-learning, amortization, distillation), existing approaches still suffer from two core limitations: (1) a representation bottleneck that forces a single MLP to uniformly model heterogeneous local structures, and (2) limited scalability due to the absence of a hierarchical mechanism that dynamically adapts to signal complexity. This work introduces Hyper-Coordinate Implicit Neural Representations (HC-INR), a new class of INRs that break the representational bottleneck by learning signal-adaptive coordinate transformations using a hypernetwork. HC-INR decomposes the representation task into two components: (i) a learned multiscale coordinate transformation module that warps the input domain into a disentangled latent space, and (ii) a compact implicit field network that models the transformed signal with significantly reduced complexity. The proposed model introduces a hierarchical hypernetwork architecture that conditions coordinate transformations on local signal features, enabling dynamic allocation of representation capacity. We theoretically show that HC-INR strictly increases the upper bound of representable frequency bands while maintaining Lipschitz stability. Extensive experiments across image fitting, shape reconstruction, and neural radiance field approximation demonstrate that HC-INR achieves up to 4 times higher reconstruction fidelity than strong INR baselines while using 30--60\% fewer parameters.

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.

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.

Text-to-image synthesis has progressed to the point where models can generate visually compelling images from natural language prompts. Yet, existing methods often fail to reconcile high-level semantic fidelity with explicit spatial control, particularly in scenes involving multiple objects, nuanced relations, or complex layouts. To bridge this gap, we propose a Hierarchical Cross-Modal Alignment (HCMA) framework for grounded text-to-image generation. HCMA integrates two alignment modules into each diffusion sampling step: a global module that continuously aligns latent representations with textual descriptions to ensure scene-level coherence, and a local module that employs bounding-box layouts to anchor objects at specified locations, enabling fine-grained spatial control. Extensive experiments on the MS-COCO 2014 validation set show that HCMA surpasses state-of-the-art baselines, achieving a 0.69 improvement in Frechet Inception Distance (FID) and a 0.0295 gain in CLIP Score. These results demonstrate HCMA's effectiveness in faithfully capturing intricate textual semantics while adhering to user-defined spatial constraints, offering a robust solution for semantically grounded image generation. Our code is available at https://github.com/hwang-cs-ime/HCMA.