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Aug 29

Foveated Retinotopy Improves Classification and Localization in CNNs

From a falcon detecting prey to humans recognizing faces, many species exhibit extraordinary abilities in rapid visual localization and classification. These are made possible by a specialized retinal region called the fovea, which provides high acuity at the center of vision while maintaining lower resolution in the periphery. This distinctive spatial organization, preserved along the early visual pathway through retinotopic mapping, is fundamental to biological vision, yet remains largely unexplored in machine learning. Our study investigates how incorporating foveated retinotopy may benefit deep convolutional neural networks (CNNs) in image classification tasks. By implementing a foveated retinotopic transformation in the input layer of standard ResNet models and re-training them, we maintain comparable classification accuracy while enhancing the network's robustness to scale and rotational perturbations. Although this architectural modification introduces increased sensitivity to fixation point shifts, we demonstrate how this apparent limitation becomes advantageous: variations in classification probabilities across different gaze positions serve as effective indicators for object localization. Our findings suggest that foveated retinotopic mapping encodes implicit knowledge about visual object geometry, offering an efficient solution to the visual search problem - a capability crucial for many living species.

MIPHEI-ViT: Multiplex Immunofluorescence Prediction from H&E Images using ViT Foundation Models

Histopathological analysis is a cornerstone of cancer diagnosis, with Hematoxylin and Eosin (H&E) staining routinely acquired for every patient to visualize cell morphology and tissue architecture. On the other hand, multiplex immunofluorescence (mIF) enables more precise cell type identification via proteomic markers, but has yet to achieve widespread clinical adoption due to cost and logistical constraints. To bridge this gap, we introduce MIPHEI (Multiplex Immunofluorescence Prediction from H&E), a U-Net-inspired architecture that integrates state-of-the-art ViT foundation models as encoders to predict mIF signals from H&E images. MIPHEI targets a comprehensive panel of markers spanning nuclear content, immune lineages (T cells, B cells, myeloid), epithelium, stroma, vasculature, and proliferation. We train our model using the publicly available ORION dataset of restained H&E and mIF images from colorectal cancer tissue, and validate it on two independent datasets. MIPHEI achieves accurate cell-type classification from H&E alone, with F1 scores of 0.88 for Pan-CK, 0.57 for CD3e, 0.56 for SMA, 0.36 for CD68, and 0.30 for CD20, substantially outperforming both a state-of-the-art baseline and a random classifier for most markers. Our results indicate that our model effectively captures the complex relationships between nuclear morphologies in their tissue context, as visible in H&E images and molecular markers defining specific cell types. MIPHEI offers a promising step toward enabling cell-type-aware analysis of large-scale H&E datasets, in view of uncovering relationships between spatial cellular organization and patient outcomes.

From Local Cues to Global Percepts: Emergent Gestalt Organization in Self-Supervised Vision Models

Human vision organizes local cues into coherent global forms using Gestalt principles like closure, proximity, and figure-ground assignment -- functions reliant on global spatial structure. We investigate whether modern vision models show similar behaviors, and under what training conditions these emerge. We find that Vision Transformers (ViTs) trained with Masked Autoencoding (MAE) exhibit activation patterns consistent with Gestalt laws, including illusory contour completion, convexity preference, and dynamic figure-ground segregation. To probe the computational basis, we hypothesize that modeling global dependencies is necessary for Gestalt-like organization. We introduce the Distorted Spatial Relationship Testbench (DiSRT), which evaluates sensitivity to global spatial perturbations while preserving local textures. Using DiSRT, we show that self-supervised models (e.g., MAE, CLIP) outperform supervised baselines and sometimes even exceed human performance. ConvNeXt models trained with MAE also exhibit Gestalt-compatible representations, suggesting such sensitivity can arise without attention architectures. However, classification finetuning degrades this ability. Inspired by biological vision, we show that a Top-K activation sparsity mechanism can restore global sensitivity. Our findings identify training conditions that promote or suppress Gestalt-like perception and establish DiSRT as a diagnostic for global structure sensitivity across models.

A Large-Scale Benchmark of Cross-Modal Learning for Histology and Gene Expression in Spatial Transcriptomics

Spatial transcriptomics enables simultaneous measurement of gene expression and tissue morphology, offering unprecedented insights into cellular organization and disease mechanisms. However, the field lacks comprehensive benchmarks for evaluating multimodal learning methods that leverage both histology images and gene expression data. Here, we present HESCAPE, a large-scale benchmark for cross-modal contrastive pretraining in spatial transcriptomics, built on a curated pan-organ dataset spanning 6 different gene panels and 54 donors. We systematically evaluated state-of-the-art image and gene expression encoders across multiple pretraining strategies and assessed their effectiveness on two downstream tasks: gene mutation classification and gene expression prediction. Our benchmark demonstrates that gene expression encoders are the primary determinant of strong representational alignment, and that gene models pretrained on spatial transcriptomics data outperform both those trained without spatial data and simple baseline approaches. However, downstream task evaluation reveals a striking contradiction: while contrastive pretraining consistently improves gene mutation classification performance, it degrades direct gene expression prediction compared to baseline encoders trained without cross-modal objectives. We identify batch effects as a key factor that interferes with effective cross-modal alignment. Our findings highlight the critical need for batch-robust multimodal learning approaches in spatial transcriptomics. To accelerate progress in this direction, we release HESCAPE, providing standardized datasets, evaluation protocols, and benchmarking tools for the community

STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics

The advent of single-cell technology has significantly improved our understanding of cellular states and subpopulations in various tissues under normal and diseased conditions by employing data-driven approaches such as clustering and trajectory inference. However, these methods consider cells as independent data points of population distributions. With spatial transcriptomics, we can represent cellular organization, along with dynamic cell-cell interactions that lead to changes in cell state. Still, key computational advances are necessary to enable the data-driven learning of such complex interactive cellular dynamics. While agent-based modeling (ABM) provides a powerful framework, traditional approaches rely on handcrafted rules derived from domain knowledge rather than data-driven approaches. To address this, we introduce Spatio Temporal Agent-Based Graph Evolution Dynamics(STAGED) integrating ABM with deep learning to model intercellular communication, and its effect on the intracellular gene regulatory network. Using graph ODE networks (GDEs) with shared weights per cell type, our approach represents genes as vertices and interactions as directed edges, dynamically learning their strengths through a designed attention mechanism. Trained to match continuous trajectories of simulated as well as inferred trajectories from spatial transcriptomics data, the model captures both intercellular and intracellular interactions, enabling a more adaptive and accurate representation of cellular dynamics.

RoboSpatial: Teaching Spatial Understanding to 2D and 3D Vision-Language Models for Robotics

Spatial understanding is a crucial capability for robots to make grounded decisions based on their environment. This foundational skill enables robots not only to perceive their surroundings but also to reason about and interact meaningfully within the world. In modern robotics, these capabilities are taken on by visual language models, and they face significant challenges when applied to spatial reasoning context due to their training data sources. These sources utilize general-purpose image datasets, and they often lack sophisticated spatial scene understanding capabilities. For example, the datasets do not address reference frame comprehension - spatial relationships require clear contextual understanding, whether from an ego-centric, object-centric, or world-centric perspective, which allow for effective real-world interaction. To address this issue, we introduce RoboSpatial, a large-scale spatial understanding dataset consisting of real indoor and tabletop scenes captured as 3D scans and egocentric images, annotated with rich spatial information relevant to robotics. The dataset includes 1M images, 5K 3D scans, and 3M annotated spatial relationships, with paired 2D egocentric images and 3D scans to make it both 2D and 3D ready. Our experiments show that models trained with RoboSpatial outperform baselines on downstream tasks such as spatial affordance prediction, spatial relationship prediction, and robotics manipulation.

SoFar: Language-Grounded Orientation Bridges Spatial Reasoning and Object Manipulation

Spatial intelligence is a critical component of embodied AI, promoting robots to understand and interact with their environments. While recent advances have enhanced the ability of VLMs to perceive object locations and positional relationships, they still lack the capability to precisely understand object orientations-a key requirement for tasks involving fine-grained manipulations. Addressing this limitation not only requires geometric reasoning but also an expressive and intuitive way to represent orientation. In this context, we propose that natural language offers a more flexible representation space than canonical frames, making it particularly suitable for instruction-following robotic systems. In this paper, we introduce the concept of semantic orientation, which defines object orientations using natural language in a reference-frame-free manner (e.g., the ''plug-in'' direction of a USB or the ''handle'' direction of a knife). To support this, we construct OrienText300K, a large-scale dataset of 3D models annotated with semantic orientations that link geometric understanding to functional semantics. By integrating semantic orientation into a VLM system, we enable robots to generate manipulation actions with both positional and orientational constraints. Extensive experiments in simulation and real world demonstrate that our approach significantly enhances robotic manipulation capabilities, e.g., 48.7% accuracy on Open6DOR and 74.9% accuracy on SIMPLER.

Spatially-Aware Transformer for Embodied Agents

Episodic memory plays a crucial role in various cognitive processes, such as the ability to mentally recall past events. While cognitive science emphasizes the significance of spatial context in the formation and retrieval of episodic memory, the current primary approach to implementing episodic memory in AI systems is through transformers that store temporally ordered experiences, which overlooks the spatial dimension. As a result, it is unclear how the underlying structure could be extended to incorporate the spatial axis beyond temporal order alone and thereby what benefits can be obtained. To address this, this paper explores the use of Spatially-Aware Transformer models that incorporate spatial information. These models enable the creation of place-centric episodic memory that considers both temporal and spatial dimensions. Adopting this approach, we demonstrate that memory utilization efficiency can be improved, leading to enhanced accuracy in various place-centric downstream tasks. Additionally, we propose the Adaptive Memory Allocator, a memory management method based on reinforcement learning that aims to optimize efficiency of memory utilization. Our experiments demonstrate the advantages of our proposed model in various environments and across multiple downstream tasks, including prediction, generation, reasoning, and reinforcement learning. The source code for our models and experiments will be available at https://github.com/junmokane/spatially-aware-transformer.

Random Spatial Networks: Small Worlds without Clustering, Traveling Waves, and Hop-and-Spread Disease Dynamics

Random network models play a prominent role in modeling, analyzing and understanding complex phenomena on real-life networks. However, a key property of networks is often neglected: many real-world networks exhibit spatial structure, the tendency of a node to select neighbors with a probability depending on physical distance. Here, we introduce a class of random spatial networks (RSNs) which generalizes many existing random network models but adds spatial structure. In these networks, nodes are placed randomly in space and joined in edges with a probability depending on their distance and their individual expected degrees, in a manner that crucially remains analytically tractable. We use this network class to propose a new generalization of small-world networks, where the average shortest path lengths in the graph are small, as in classical Watts-Strogatz small-world networks, but with close spatial proximity of nodes that are neighbors in the network playing the role of large clustering. Small-world effects are demonstrated on these spatial small-world networks without clustering. We are able to derive partial integro-differential equations governing susceptible-infectious-recovered disease spreading through an RSN, and we demonstrate the existence of traveling wave solutions. If the distance kernel governing edge placement decays slower than exponential, the population-scale dynamics are dominated by long-range hops followed by local spread of traveling waves. This provides a theoretical modeling framework for recent observations of how epidemics like Ebola evolve in modern connected societies, with long-range connections seeding new focal points from which the epidemic locally spreads in a wavelike manner.

Hierarchical Auto-Organizing System for Open-Ended Multi-Agent Navigation

Due to the dynamic and unpredictable open-world setting, navigating complex environments in Minecraft poses significant challenges for multi-agent systems. Agents must interact with the environment and coordinate their actions with other agents to achieve common objectives. However, traditional approaches often struggle to efficiently manage inter-agent communication and task distribution, crucial for effective multi-agent navigation. Furthermore, processing and integrating multi-modal information (such as visual, textual, and auditory data) is essential for agents to comprehend their goals and navigate the environment successfully and fully. To address this issue, we design the HAS framework to auto-organize groups of LLM-based agents to complete navigation tasks. In our approach, we devise a hierarchical auto-organizing navigation system, which is characterized by 1) a hierarchical system for multi-agent organization, ensuring centralized planning and decentralized execution; 2) an auto-organizing and intra-communication mechanism, enabling dynamic group adjustment under subtasks; 3) a multi-modal information platform, facilitating multi-modal perception to perform the three navigation tasks with one system. To assess organizational behavior, we design a series of navigation tasks in the Minecraft environment, which includes searching and exploring. We aim to develop embodied organizations that push the boundaries of embodied AI, moving it towards a more human-like organizational structure.

Sparkle: Mastering Basic Spatial Capabilities in Vision Language Models Elicits Generalization to Composite Spatial Reasoning

Vision language models (VLMs) have demonstrated impressive performance across a wide range of downstream tasks. However, their proficiency in spatial reasoning remains limited, despite its crucial role in tasks involving navigation and interaction with physical environments. Specifically, most of these tasks rely on the core spatial reasoning capabilities in two-dimensional (2D) environments, and our evaluation reveals that state-of-the-art VLMs frequently generate implausible and incorrect responses to composite spatial reasoning problems, including simple pathfinding tasks that humans can solve effortlessly at a glance. To address this, we explore an effective approach to enhance 2D spatial reasoning within VLMs by training the model solely on basic spatial capabilities. We begin by disentangling the key components of 2D spatial reasoning: direction comprehension, distance estimation, and localization. Our central hypothesis is that mastering these basic spatial capabilities can significantly enhance a model's performance on composite spatial tasks requiring advanced spatial understanding and combinatorial problem-solving, with generalized improvements in visual-spatial tasks. To investigate this hypothesis, we introduce Sparkle, a framework that fine-tunes VLMs on these three basic spatial capabilities by synthetic data generation and targeted supervision to form an instruction dataset for each capability. Our experiments demonstrate that VLMs fine-tuned with Sparkle achieve significant performance gains, not only in the basic tasks themselves but also in generalizing to composite and out-of-distribution spatial reasoning tasks. These findings underscore the effectiveness of mastering basic spatial capabilities in enhancing composite spatial problem-solving, offering insights into systematic strategies for improving VLMs' spatial reasoning capabilities.

From Occlusion to Insight: Object Search in Semantic Shelves using Large Language Models

How can a robot efficiently extract a desired object from a shelf when it is fully occluded by other objects? Prior works propose geometric approaches for this problem but do not consider object semantics. Shelves in pharmacies, restaurant kitchens, and grocery stores are often organized such that semantically similar objects are placed close to one another. Can large language models (LLMs) serve as semantic knowledge sources to accelerate robotic mechanical search in semantically arranged environments? With Semantic Spatial Search on Shelves (S^4), we use LLMs to generate affinity matrices, where entries correspond to semantic likelihood of physical proximity between objects. We derive semantic spatial distributions by synthesizing semantics with learned geometric constraints. S^4 incorporates Optical Character Recognition (OCR) and semantic refinement with predictions from ViLD, an open-vocabulary object detection model. Simulation experiments suggest that semantic spatial search reduces the search time relative to pure spatial search by an average of 24% across three domains: pharmacy, kitchen, and office shelves. A manually collected dataset of 100 semantic scenes suggests that OCR and semantic refinement improve object detection accuracy by 35%. Lastly, physical experiments in a pharmacy shelf suggest 47.1% improvement over pure spatial search. Supplementary material can be found at https://sites.google.com/view/s4-rss/home.

SINC: Spatial Composition of 3D Human Motions for Simultaneous Action Generation

Our goal is to synthesize 3D human motions given textual inputs describing simultaneous actions, for example 'waving hand' while 'walking' at the same time. We refer to generating such simultaneous movements as performing 'spatial compositions'. In contrast to temporal compositions that seek to transition from one action to another, spatial compositing requires understanding which body parts are involved in which action, to be able to move them simultaneously. Motivated by the observation that the correspondence between actions and body parts is encoded in powerful language models, we extract this knowledge by prompting GPT-3 with text such as "what are the body parts involved in the action <action name>?", while also providing the parts list and few-shot examples. Given this action-part mapping, we combine body parts from two motions together and establish the first automated method to spatially compose two actions. However, training data with compositional actions is always limited by the combinatorics. Hence, we further create synthetic data with this approach, and use it to train a new state-of-the-art text-to-motion generation model, called SINC ("SImultaneous actioN Compositions for 3D human motions"). In our experiments, that training with such GPT-guided synthetic data improves spatial composition generation over baselines. Our code is publicly available at https://sinc.is.tue.mpg.de/.

Continual Vision-Language Representation Learning with Off-Diagonal Information

Large-scale multi-modal contrastive learning frameworks like CLIP typically require a large amount of image-text samples for training. However, these samples are always collected continuously in real scenarios. This paper discusses the feasibility of continual CLIP training using streaming data. Unlike continual learning based on self-supervised learning methods for pure images, which is empirically robust against catastrophic forgetting, CLIP's performance degeneration in the continual setting is significant and non-neglectable. By analyzing the changes in the model's representation space during continual CLIP training from a spatial geometry perspective, we explore and summarize these spatial variations as Spatial Disorder (SD), which can be divided into Intra-modal Rotation and Inter-modal Deviation. Moreover, we empirically and theoretically demonstrate how SD leads to a performance decline for CLIP on cross-modal retrieval tasks. To alleviate SD, we propose a new continual vision-language representation learning framework Mod-X: Maintain off-diagonal information-matriX. By selectively aligning the off-diagonal information distribution of contrastive matrices, the Mod-X improves the capability of the multi-modal model by maintaining the multi-modal representation space alignment on the old data domain during continuously fitting the new training data domain. Experiments on commonly used datasets with different scales and scopes have demonstrated the effectiveness of our method.

Spatial-MLLM: Boosting MLLM Capabilities in Visual-based Spatial Intelligence

Recent advancements in Multimodal Large Language Models (MLLMs) have significantly enhanced performance on 2D visual tasks. However, improving their spatial intelligence remains a challenge. Existing 3D MLLMs always rely on additional 3D or 2.5D data to incorporate spatial awareness, restricting their utility in scenarios with only 2D inputs, such as images or videos. In this paper, we present Spatial-MLLM, a novel framework for visual-based spatial reasoning from purely 2D observations. Unlike conventional video MLLMs which rely on CLIP-based visual encoders optimized for semantic understanding, our key insight is to unleash the strong structure prior from the feed-forward visual geometry foundation model. Specifically, we propose a dual-encoder architecture: a pretrained 2D visual encoder to extract semantic features, and a spatial encoder-initialized from the backbone of the visual geometry model-to extract 3D structure features. A connector then integrates both features into unified visual tokens for enhanced spatial understanding. Furthermore, we propose a space-aware frame sampling strategy at inference time, which selects the spatially informative frames of a video sequence, ensuring that even under limited token length, the model focuses on frames critical for spatial reasoning. Beyond architecture improvements, we construct the Spatial-MLLM-120k dataset and train the model on it using supervised fine-tuning and GRPO. Extensive experiments on various real-world datasets demonstrate that our spatial-MLLM achieves state-of-the-art performance in a wide range of visual-based spatial understanding and reasoning tasks. Project page: https://diankun-wu.github.io/Spatial-MLLM/.

3DSRBench: A Comprehensive 3D Spatial Reasoning Benchmark

3D spatial reasoning is the ability to analyze and interpret the positions, orientations, and spatial relationships of objects within the 3D space. This allows models to develop a comprehensive understanding of the 3D scene, enabling their applicability to a broader range of areas, such as autonomous navigation, robotics, and AR/VR. While large multi-modal models (LMMs) have achieved remarkable progress in a wide range of image and video understanding tasks, their capabilities to perform 3D spatial reasoning on diverse natural images are less studied. In this work we present the first comprehensive 3D spatial reasoning benchmark, 3DSRBench, with 2,772 manually annotated visual question-answer pairs across 12 question types. We conduct robust and thorough evaluation of 3D spatial reasoning capabilities by balancing the data distribution and adopting a novel FlipEval strategy. To further study the robustness of 3D spatial reasoning w.r.t. camera 3D viewpoints, our 3DSRBench includes two subsets with 3D spatial reasoning questions on paired images with common and uncommon viewpoints. We benchmark a wide range of open-sourced and proprietary LMMs, uncovering their limitations in various aspects of 3D awareness, such as height, orientation, location, and multi-object reasoning, as well as their degraded performance on images with uncommon camera viewpoints. Our 3DSRBench provide valuable findings and insights about the future development of LMMs with strong 3D reasoning capabilities. Our project page and dataset is available https://3dsrbench.github.io.

Illuminating search spaces by mapping elites

Many fields use search algorithms, which automatically explore a search space to find high-performing solutions: chemists search through the space of molecules to discover new drugs; engineers search for stronger, cheaper, safer designs, scientists search for models that best explain data, etc. The goal of search algorithms has traditionally been to return the single highest-performing solution in a search space. Here we describe a new, fundamentally different type of algorithm that is more useful because it provides a holistic view of how high-performing solutions are distributed throughout a search space. It creates a map of high-performing solutions at each point in a space defined by dimensions of variation that a user gets to choose. This Multi-dimensional Archive of Phenotypic Elites (MAP-Elites) algorithm illuminates search spaces, allowing researchers to understand how interesting attributes of solutions combine to affect performance, either positively or, equally of interest, negatively. For example, a drug company may wish to understand how performance changes as the size of molecules and their cost-to-produce vary. MAP-Elites produces a large diversity of high-performing, yet qualitatively different solutions, which can be more helpful than a single, high-performing solution. Interestingly, because MAP-Elites explores more of the search space, it also tends to find a better overall solution than state-of-the-art search algorithms. We demonstrate the benefits of this new algorithm in three different problem domains ranging from producing modular neural networks to designing simulated and real soft robots. Because MAP- Elites (1) illuminates the relationship between performance and dimensions of interest in solutions, (2) returns a set of high-performing, yet diverse solutions, and (3) improves finding a single, best solution, it will advance science and engineering.

SURPRISE3D: A Dataset for Spatial Understanding and Reasoning in Complex 3D Scenes

The integration of language and 3D perception is critical for embodied AI and robotic systems to perceive, understand, and interact with the physical world. Spatial reasoning, a key capability for understanding spatial relationships between objects, remains underexplored in current 3D vision-language research. Existing datasets often mix semantic cues (e.g., object name) with spatial context, leading models to rely on superficial shortcuts rather than genuinely interpreting spatial relationships. To address this gap, we introduce Surprise3D, a novel dataset designed to evaluate language-guided spatial reasoning segmentation in complex 3D scenes. Surprise3D consists of more than 200k vision language pairs across 900+ detailed indoor scenes from ScanNet++ v2, including more than 2.8k unique object classes. The dataset contains 89k+ human-annotated spatial queries deliberately crafted without object name, thereby mitigating shortcut biases in spatial understanding. These queries comprehensively cover various spatial reasoning skills, such as relative position, narrative perspective, parametric perspective, and absolute distance reasoning. Initial benchmarks demonstrate significant challenges for current state-of-the-art expert 3D visual grounding methods and 3D-LLMs, underscoring the necessity of our dataset and the accompanying 3D Spatial Reasoning Segmentation (3D-SRS) benchmark suite. Surprise3D and 3D-SRS aim to facilitate advancements in spatially aware AI, paving the way for effective embodied interaction and robotic planning. The code and datasets can be found in https://github.com/liziwennba/SUPRISE.

Persistent homology of the cosmic web. I: Hierarchical topology in ΛCDM cosmologies

Using a set of LambdaCDM simulations of cosmic structure formation, we study the evolving connectivity and changing topological structure of the cosmic web using state-of-the-art tools of multiscale topological data analysis (TDA). We follow the development of the cosmic web topology in terms of the evolution of Betti number curves and feature persistence diagrams of the three (topological) classes of structural features: matter concentrations, filaments and tunnels, and voids. The Betti curves specify the prominence of features as a function of density level, and their evolution with cosmic epoch reflects the changing network connections between these structural features. The persistence diagrams quantify the longevity and stability of topological features. In this study we establish, for the first time, the link between persistence diagrams, the features they show, and the gravitationally driven cosmic structure formation process. By following the diagrams' development over cosmic time, the link between the multiscale topology of the cosmic web and the hierarchical buildup of cosmic structure is established. The sharp apexes in the diagrams are intimately related to key transitions in the structure formation process. The apex in the matter concentration diagrams coincides with the density level at which, typically, they detach from the Hubble expansion and begin to collapse. At that level many individual islands merge to form the network of the cosmic web and a large number of filaments and tunnels emerge to establish its connecting bridges. The location trends of the apex possess a self-similar character that can be related to the cosmic web's hierarchical buildup. We find that persistence diagrams provide a significantly higher and more profound level of information on the structure formation process than more global summary statistics like Euler characteristic or Betti numbers.

Segmentation of 3D pore space from CT images using curvilinear skeleton: application to numerical simulation of microbial decomposition

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

LEGO-Puzzles: How Good Are MLLMs at Multi-Step Spatial Reasoning?

Multi-step spatial reasoning entails understanding and reasoning about spatial relationships across multiple sequential steps, which is crucial for tackling complex real-world applications, such as robotic manipulation, autonomous navigation, and automated assembly. To assess how well current Multimodal Large Language Models (MLLMs) have acquired this fundamental capability, we introduce LEGO-Puzzles, a scalable benchmark designed to evaluate both spatial understanding and sequential reasoning in MLLMs through LEGO-based tasks. LEGO-Puzzles consists of 1,100 carefully curated visual question-answering (VQA) samples spanning 11 distinct tasks, ranging from basic spatial understanding to complex multi-step reasoning. Based on LEGO-Puzzles, we conduct a comprehensive evaluation of state-of-the-art MLLMs and uncover significant limitations in their spatial reasoning capabilities: even the most powerful MLLMs can answer only about half of the test cases, whereas human participants achieve over 90\% accuracy. In addition to VQA tasks, we evaluate MLLMs' abilities to generate LEGO images following assembly illustrations. Our experiments show that only Gemini-2.0-Flash and GPT-4o exhibit a limited ability to follow these instructions, while other MLLMs either replicate the input image or generate completely irrelevant outputs. Overall, LEGO-Puzzles exposes critical deficiencies in existing MLLMs' spatial understanding and sequential reasoning capabilities, and underscores the need for further advancements in multimodal spatial reasoning.

Latent Compass: Creation by Navigation

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

SAT: Dynamic Spatial Aptitude Training for Multimodal Language Models

Reasoning about motion and space is a fundamental cognitive capability that is required by multiple real-world applications. While many studies highlight that large multimodal language models (MLMs) struggle to reason about space, they only focus on static spatial relationships, and not dynamic awareness of motion and space, i.e., reasoning about the effect of egocentric and object motions on spatial relationships. Manually annotating such object and camera movements is expensive. Hence, we introduce SAT, a simulated spatial aptitude training dataset comprising both static and dynamic spatial reasoning across 175K question-answer (QA) pairs and 20K scenes. Complementing this, we also construct a small (150 image-QAs) yet challenging dynamic spatial test set using real-world images. Leveraging our SAT datasets and 6 existing static spatial benchmarks, we systematically investigate what improves both static and dynamic spatial awareness. Our results reveal that simulations are surprisingly effective at imparting spatial aptitude to MLMs that translate to real images. We show that perfect annotations in simulation are more effective than existing approaches of pseudo-annotating real images. For instance, SAT training improves a LLaVA-13B model by an average 11% and a LLaVA-Video-7B model by an average 8% on multiple spatial benchmarks, including our real-image dynamic test set and spatial reasoning on long videos -- even outperforming some large proprietary models. While reasoning over static relationships improves with synthetic training data, there is still considerable room for improvement for dynamic reasoning questions.

CRASAR-U-DROIDs: A Large Scale Benchmark Dataset for Building Alignment and Damage Assessment in Georectified sUAS Imagery

This document presents the Center for Robot Assisted Search And Rescue - Uncrewed Aerial Systems - Disaster Response Overhead Inspection Dataset (CRASAR-U-DROIDs) for building damage assessment and spatial alignment collected from small uncrewed aerial systems (sUAS) geospatial imagery. This dataset is motivated by the increasing use of sUAS in disaster response and the lack of previous work in utilizing high-resolution geospatial sUAS imagery for machine learning and computer vision models, the lack of alignment with operational use cases, and with hopes of enabling further investigations between sUAS and satellite imagery. The CRASAR-U-DRIODs dataset consists of fifty-two (52) orthomosaics from ten (10) federally declared disasters (Hurricane Ian, Hurricane Ida, Hurricane Harvey, Hurricane Idalia, Hurricane Laura, Hurricane Michael, Musset Bayou Fire, Mayfield Tornado, Kilauea Eruption, and Champlain Towers Collapse) spanning 67.98 square kilometers (26.245 square miles), containing 21,716 building polygons and damage labels, and 7,880 adjustment annotations. The imagery was tiled and presented in conjunction with overlaid building polygons to a pool of 130 annotators who provided human judgments of damage according to the Joint Damage Scale. These annotations were then reviewed via a two-stage review process in which building polygon damage labels were first reviewed individually and then again by committee. Additionally, the building polygons have been aligned spatially to precisely overlap with the imagery to enable more performant machine learning models to be trained. It appears that CRASAR-U-DRIODs is the largest labeled dataset of sUAS orthomosaic imagery.

Compact 3D Scene Representation via Self-Organizing Gaussian Grids

3D Gaussian Splatting has recently emerged as a highly promising technique for modeling of static 3D scenes. In contrast to Neural Radiance Fields, it utilizes efficient rasterization allowing for very fast rendering at high-quality. However, the storage size is significantly higher, which hinders practical deployment, e.g.~on resource constrained devices. In this paper, we introduce a compact scene representation organizing the parameters of 3D Gaussian Splatting (3DGS) into a 2D grid with local homogeneity, ensuring a drastic reduction in storage requirements without compromising visual quality during rendering. Central to our idea is the explicit exploitation of perceptual redundancies present in natural scenes. In essence, the inherent nature of a scene allows for numerous permutations of Gaussian parameters to equivalently represent it. To this end, we propose a novel highly parallel algorithm that regularly arranges the high-dimensional Gaussian parameters into a 2D grid while preserving their neighborhood structure. During training, we further enforce local smoothness between the sorted parameters in the grid. The uncompressed Gaussians use the same structure as 3DGS, ensuring a seamless integration with established renderers. Our method achieves a reduction factor of 8x to 26x in size for complex scenes with no increase in training time, marking a substantial leap forward in the domain of 3D scene distribution and consumption. Additional information can be found on our project page: https://fraunhoferhhi.github.io/Self-Organizing-Gaussians/

ResPlan: A Large-Scale Vector-Graph Dataset of 17,000 Residential Floor Plans

We introduce ResPlan, a large-scale dataset of 17,000 detailed, structurally rich, and realistic residential floor plans, created to advance spatial AI research. Each plan includes precise annotations of architectural elements (walls, doors, windows, balconies) and functional spaces (such as kitchens, bedrooms, and bathrooms). ResPlan addresses key limitations of existing datasets such as RPLAN (Wu et al., 2019) and MSD (van Engelenburg et al., 2024) by offering enhanced visual fidelity and greater structural diversity, reflecting realistic and non-idealized residential layouts. Designed as a versatile, general-purpose resource, ResPlan supports a wide range of applications including robotics, reinforcement learning, generative AI, virtual and augmented reality, simulations, and game development. Plans are provided in both geometric and graph-based formats, enabling direct integration into simulation engines and fast 3D conversion. A key contribution is an open-source pipeline for geometry cleaning, alignment, and annotation refinement. Additionally, ResPlan includes structured representations of room connectivity, supporting graph-based spatial reasoning tasks. Finally, we present comparative analyses with existing benchmarks and outline several open benchmark tasks enabled by ResPlan. Ultimately, ResPlan offers a significant advance in scale, realism, and usability, providing a robust foundation for developing and benchmarking next-generation spatial intelligence systems.

Agentic 3D Scene Generation with Spatially Contextualized VLMs

Despite recent advances in multimodal content generation enabled by vision-language models (VLMs), their ability to reason about and generate structured 3D scenes remains largely underexplored. This limitation constrains their utility in spatially grounded tasks such as embodied AI, immersive simulations, and interactive 3D applications. We introduce a new paradigm that enables VLMs to generate, understand, and edit complex 3D environments by injecting a continually evolving spatial context. Constructed from multimodal input, this context consists of three components: a scene portrait that provides a high-level semantic blueprint, a semantically labeled point cloud capturing object-level geometry, and a scene hypergraph that encodes rich spatial relationships, including unary, binary, and higher-order constraints. Together, these components provide the VLM with a structured, geometry-aware working memory that integrates its inherent multimodal reasoning capabilities with structured 3D understanding for effective spatial reasoning. Building on this foundation, we develop an agentic 3D scene generation pipeline in which the VLM iteratively reads from and updates the spatial context. The pipeline features high-quality asset generation with geometric restoration, environment setup with automatic verification, and ergonomic adjustment guided by the scene hypergraph. Experiments show that our framework can handle diverse and challenging inputs, achieving a level of generalization not observed in prior work. Further results demonstrate that injecting spatial context enables VLMs to perform downstream tasks such as interactive scene editing and path planning, suggesting strong potential for spatially intelligent systems in computer graphics, 3D vision, and embodied applications.

Modular versus Hierarchical: A Structural Signature of Topic Popularity in Mathematical Research

Mathematical researchers, especially those in early-career positions, face critical decisions about topic specialization with limited information about the collaborative environments of different research areas. The aim of this paper is to study how the popularity of a research topic is associated with the structure of that topic's collaboration network, as observed by a suite of measures capturing organizational structure at several scales. We apply these measures to 1,938 algorithmically discovered topics across 121,391 papers sourced from arXiv metadata during the period 2020--2025. Our analysis, which controls for the confounding effects of network size, reveals a structural dichotomy--we find that popular topics organize into modular "schools of thought," while niche topics maintain hierarchical core-periphery structures centered around established experts. This divide is not an artifact of scale, but represents a size-independent structural pattern correlated with popularity. We also document a "constraint reversal": after controlling for size, researchers in popular fields face greater structural constraints on collaboration opportunities, contrary to conventional expectations. Our findings suggest that topic selection is an implicit choice between two fundamentally different collaborative environments, each with distinct implications for a researcher's career. To make these structural patterns transparent to the research community, we developed the Math Research Compass (https://mathresearchcompass.com), an interactive platform providing data on topic popularity and collaboration patterns across mathematical topics.

Non-Uniform Spatial Alignment Errors in sUAS Imagery From Wide-Area Disasters

This work presents the first quantitative study of alignment errors between small uncrewed aerial systems (sUAS) geospatial imagery and a priori building polygons and finds that alignment errors are non-uniform and irregular. The work also introduces a publicly available dataset of imagery, building polygons, and human-generated and curated adjustments that can be used to evaluate existing strategies for aligning building polygons with sUAS imagery. There are no efforts that have aligned pre-existing spatial data with sUAS imagery, and thus, there is no clear state of practice. However, this effort and analysis show that the translational alignment errors present in this type of data, averaging 82px and an intersection over the union of 0.65, which would induce further errors and biases in downstream machine learning systems unless addressed. This study identifies and analyzes the translational alignment errors of 21,619 building polygons in fifty-one orthomosaic images, covering 16787.2 Acres (26.23 square miles), constructed from sUAS raw imagery from nine wide-area disasters (Hurricane Ian, Hurricane Harvey, Hurricane Michael, Hurricane Ida, Hurricane Idalia, Hurricane Laura, the Mayfield Tornado, the Musset Bayou Fire, and the Kilauea Eruption). The analysis finds no uniformity among the angle and distance metrics of the building polygon alignments as they present an average degree variance of 0.4 and an average pixel distance variance of 0.45. This work alerts the sUAS community to the problem of spatial alignment and that a simple linear transform, often used to align satellite imagery, will not be sufficient to align spatial data in sUAS orthomosaic imagery.

CAD-GPT: Synthesising CAD Construction Sequence with Spatial Reasoning-Enhanced Multimodal LLMs

Computer-aided design (CAD) significantly enhances the efficiency, accuracy, and innovation of design processes by enabling precise 2D and 3D modeling, extensive analysis, and optimization. Existing methods for creating CAD models rely on latent vectors or point clouds, which are difficult to obtain and costly to store. Recent advances in Multimodal Large Language Models (MLLMs) have inspired researchers to use natural language instructions and images for CAD model construction. However, these models still struggle with inferring accurate 3D spatial location and orientation, leading to inaccuracies in determining the spatial 3D starting points and extrusion directions for constructing geometries. This work introduces CAD-GPT, a CAD synthesis method with spatial reasoning-enhanced MLLM that takes either a single image or a textual description as input. To achieve precise spatial inference, our approach introduces a 3D Modeling Spatial Mechanism. This method maps 3D spatial positions and 3D sketch plane rotation angles into a 1D linguistic feature space using a specialized spatial unfolding mechanism, while discretizing 2D sketch coordinates into an appropriate planar space to enable precise determination of spatial starting position, sketch orientation, and 2D sketch coordinate translations. Extensive experiments demonstrate that CAD-GPT consistently outperforms existing state-of-the-art methods in CAD model synthesis, both quantitatively and qualitatively.

StarCraftImage: A Dataset For Prototyping Spatial Reasoning Methods For Multi-Agent Environments

Spatial reasoning tasks in multi-agent environments such as event prediction, agent type identification, or missing data imputation are important for multiple applications (e.g., autonomous surveillance over sensor networks and subtasks for reinforcement learning (RL)). StarCraft II game replays encode intelligent (and adversarial) multi-agent behavior and could provide a testbed for these tasks; however, extracting simple and standardized representations for prototyping these tasks is laborious and hinders reproducibility. In contrast, MNIST and CIFAR10, despite their extreme simplicity, have enabled rapid prototyping and reproducibility of ML methods. Following the simplicity of these datasets, we construct a benchmark spatial reasoning dataset based on StarCraft II replays that exhibit complex multi-agent behaviors, while still being as easy to use as MNIST and CIFAR10. Specifically, we carefully summarize a window of 255 consecutive game states to create 3.6 million summary images from 60,000 replays, including all relevant metadata such as game outcome and player races. We develop three formats of decreasing complexity: Hyperspectral images that include one channel for every unit type (similar to multispectral geospatial images), RGB images that mimic CIFAR10, and grayscale images that mimic MNIST. We show how this dataset can be used for prototyping spatial reasoning methods. All datasets, code for extraction, and code for dataset loading can be found at https://starcraftdata.davidinouye.com

Reconstructing 4D Spatial Intelligence: A Survey

Reconstructing 4D spatial intelligence from visual observations has long been a central yet challenging task in computer vision, with broad real-world applications. These range from entertainment domains like movies, where the focus is often on reconstructing fundamental visual elements, to embodied AI, which emphasizes interaction modeling and physical realism. Fueled by rapid advances in 3D representations and deep learning architectures, the field has evolved quickly, outpacing the scope of previous surveys. Additionally, existing surveys rarely offer a comprehensive analysis of the hierarchical structure of 4D scene reconstruction. To address this gap, we present a new perspective that organizes existing methods into five progressive levels of 4D spatial intelligence: (1) Level 1 -- reconstruction of low-level 3D attributes (e.g., depth, pose, and point maps); (2) Level 2 -- reconstruction of 3D scene components (e.g., objects, humans, structures); (3) Level 3 -- reconstruction of 4D dynamic scenes; (4) Level 4 -- modeling of interactions among scene components; and (5) Level 5 -- incorporation of physical laws and constraints. We conclude the survey by discussing the key challenges at each level and highlighting promising directions for advancing toward even richer levels of 4D spatial intelligence. To track ongoing developments, we maintain an up-to-date project page: https://github.com/yukangcao/Awesome-4D-Spatial-Intelligence.

4D-VLA: Spatiotemporal Vision-Language-Action Pretraining with Cross-Scene Calibration

Leveraging diverse robotic data for pretraining remains a critical challenge. Existing methods typically model the dataset's action distribution using simple observations as inputs. However, these inputs are often incomplete, resulting in a dispersed conditional action distribution-an issue we refer to as coordinate system chaos and state chaos. This inconsistency significantly hampers pretraining efficiency. To address this, we propose 4D-VLA, a novel approach that effectively integrates 4D information into the input to mitigate these sources of chaos. Our model introduces depth and temporal information into visual features with sequential RGB-D inputs, aligning the coordinate systems of the robot and the scene. This alignment endows the model with strong spatiotemporal reasoning capabilities while minimizing training overhead. Additionally, we introduce memory bank sampling, a frame sampling strategy designed to extract informative frames from historical images, further improving effectiveness and efficiency. Experimental results demonstrate that our pretraining method and architectural components substantially enhance model performance. In both simulated and real-world experiments, our model achieves a significant increase in success rate over OpenVLA. To further assess spatial perception and generalization to novel views, we introduce MV-Bench, a multi-view simulation benchmark. Our model consistently outperforms existing methods, demonstrating stronger spatial understanding and adaptability.