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The integration of spatial multi-omics data from single tissues is crucial for advancing biological research. However, a significant data imbalance impedes progress: while spatial transcriptomics data is relatively abundant, spatial proteomics data remains scarce due to technical limitations and high costs. To overcome this challenge we propose STProtein, a novel framework leveraging graph neural networks with multi-task learning strategy. STProtein is designed to accurately predict unknown spatial protein expression using more accessible spatial multi-omics data, such as spatial transcriptomics. We believe that STProtein can effectively addresses the scarcity of spatial proteomics, accelerating the integration of spatial multi-omics and potentially catalyzing transformative breakthroughs in life sciences. This tool enables scientists to accelerate discovery by identifying complex and previously hidden spatial patterns of proteins within tissues, uncovering novel relationships between different marker genes, and exploring the biological "Dark Matter".

In this paper, we explore spatial-aware humanoid whole-body manipulation task. Compared with tabletop settings, this task poses two key challenges: 1) Spatial understanding is challenging in complex 3D environments with diverse spatial relations. 2) Action generation is difficult to generalize, as limited and costly real-robot data restricts data-driven models generalization. To address these challenges, we propose a generalizable humanoid loco-manipulation framework that leverages the spatial perception and action generation capabilities of multi-agent large models. Specifically, our framework includes two components: Active Spatial Brain for active spatial perception and decision-making, and Generalizable Action Cerebellum for executable robot action generation. The first component actively perceives the spatial scene and makes decisions on task planning and subtask decomposition. The second component generate executable robot actions based on the decisions made by the first module without needs of task-specific real robot data. To benchmark our framework, we design a set of spatial manipulation tasks from two perspectives: evaluating spatial perception and understanding, and ass

Large vision-language models (VLMs) still struggle with reliable 3D spatial reasoning, a core capability for embodied and physical AI systems. This limitation arises from their inability to capture fine-grained 3D geometry and spatial relationships. While recent efforts have introduced multi-view geometry transformers into VLMs, they typically fuse only the deep-layer features from vision and geometry encoders, discarding rich hierarchical signals and creating a fundamental bottleneck for spatial understanding. To overcome this, we propose SpatialStack, a general hierarchical fusion framework that progressively aligns vision, geometry, and language representations across the model hierarchy. Moving beyond conventional late-stage vision-geometry fusion, SpatialStack stacks and synchronizes multi-level geometric features with the language backbone, enabling the model to capture both local geometric precision and global contextual semantics. Building upon this framework, we develop VLM-SpatialStack, a model that achieves state-of-the-art performance on multiple 3D spatial reasoning benchmarks. Extensive experiments and ablations demonstrate that our multi-level fusion strategy consist

The pursuit of spatial intelligence fundamentally relies on access to large-scale, fine-grained 3D data. However, existing approaches predominantly construct spatial understanding benchmarks by generating question-answer (QA) pairs from a limited number of manually annotated datasets, rather than systematically annotating new large-scale 3D scenes from raw web data. As a result, their scalability is severely constrained, and model performance is further hindered by domain gaps inherent in these narrowly curated datasets. In this work, we propose Holi-Spatial, the first fully automated, large-scale, spatially-aware multimodal dataset, constructed from raw video inputs without human intervention, using the proposed data curation pipeline. Holi-Spatial supports multi-level spatial supervision, ranging from geometrically accurate 3D Gaussian Splatting (3DGS) reconstructions with rendered depth maps to object-level and relational semantic annotations, together with corresponding spatial Question-Answer (QA) pairs. Following a principled and systematic pipeline, we further construct Holi-Spatial-4M, the first large-scale, high-quality 3D semantic dataset, containing 12K optimized 3DGS sc

Despite recent advances on multi-modal models, 3D spatial reasoning remains a challenging task for state-of-the-art open-source and proprietary models. Recent studies explore data-driven approaches and achieve enhanced spatial reasoning performance by fine-tuning models on 3D-related visual question-answering data. However, these methods typically perform spatial reasoning in an implicit manner and often fail on questions that are trivial to humans, even with long chain-of-thought reasoning. In this work, we introduce SpatialReasoner, a novel large vision-language model (LVLM) that addresses 3D spatial reasoning with explicit 3D representations shared between multiple stages--3D perception, computation, and reasoning. Explicit 3D representations provide a coherent interface that supports advanced 3D spatial reasoning and improves the generalization ability to novel question types. Furthermore, by analyzing the explicit 3D representations in multi-step reasoning traces of SpatialReasoner, we study the factual errors and identify key shortcomings of current LVLMs. Results show that our SpatialReasoner achieves improved performance on a variety of spatial reasoning benchmarks, outperf

Large language models (LLMs) and vision language models (VLMs), such as DeepSeek R1,OpenAI o3, and Gemini 2.5 Pro, have demonstrated remarkable reasoning capabilities across logical inference, problem solving, and decision making. However, spatial reasoning:a fundamental component of human cognition that includes mental rotation, navigation, and spatial relationship comprehension remains a significant challenge for current advanced VLMs. We hypothesize that imagination, the internal simulation of spatial states, is the dominant reasoning mechanism within a spatial world model. To test this hypothesis and systematically probe current VLM spatial reasoning mechanisms, we introduce SpatiaLite, a fully synthetic benchmark that jointly measures spatial reasoning accuracy and reasoning efficiency. Comprehensive experiments reveal three key findings. First, advanced VLMs predominantly rely on linguistic representations for reasoning and imagination, resulting in significant deficiencies on visual centric tasks that demand perceptual spatial relations and 3D geometry transformations such as mental rotation or projection prediction. Second, advanced VLMs exhibit severe inefficiency in their

We introduce compute-grounded reasoning (CGR), a design paradigm for spatial-aware research agents in which every answerable sub-problem is resolved by deterministic computation before a language model is asked to generate. Spatial Atlas instantiates CGR as a single Agent-to-Agent (A2A) server that handles two challenging benchmarks: FieldWorkArena, a multimodal spatial question-answering benchmark spanning factory, warehouse, and retail environments, and MLE-Bench, a suite of 75 Kaggle machine learning competitions requiring end-to-end ML engineering. A structured spatial scene graph engine extracts entities and relations from vision descriptions, computes distances and safety violations deterministically, then feeds computed facts to large language models, thereby avoiding hallucinated spatial reasoning. Entropy-guided action selection maximizes information gain per step and routes queries across a three-tier frontier model stack (OpenAI + Anthropic). A self-healing ML pipeline with strategy-aware code generation, a score-driven iterative refinement loop, and a prompt-based leak audit registry round out the system. We evaluate across both benchmarks and show that CGR yields compe

Video world models that maintain 3D spatial consistency across generated frames typically rely on explicit point cloud memory constructed in RGB space. This design is both computationally expensive, requiring repeated rendering and VAE encoding, and inherently lossy, as the round trip through pixel space discards rich features of the learned latent representation. In this paper, we introduce \emph{latent spatial memory} for video world models, a persistent 3D cache that stores scene information directly in the diffusion latent space, avoiding pixel-space reconstruction. Building on this, we propose Mirage, a latent-space spatial memory framework that constructs the memory by lifting latent tokens into 3D via depth-guided back-projection and queries it by synthesizing novel views through direct latent-space warping. This unified formulation eliminates both the information loss of pixel-space reconstruction and the computational burden of repeated encoding and rendering. Experiments show that latent spatial memory achieves up to \textbf{10.57}$\times$ faster end-to-end video generation and \textbf{55}$\times$ reduction in memory footprint relative to explicit 3D baselines. Leveraging

Visual Spatial Reasoning (VSR) is a core human cognitive ability and a critical requirement for advancing embodied intelligence and autonomous systems. Despite recent progress in Vision-Language Models (VLMs), achieving human-level VSR remains highly challenging due to the complexity of representing and reasoning over three-dimensional space. In this paper, we present a systematic investigation of VSR in VLMs, encompassing a review of existing methodologies across input modalities, model architectures, training strategies, and reasoning mechanisms. Furthermore, we categorize spatial intelligence into three levels of capability, ie, basic perception, spatial understanding, spatial planning, and curate SIBench, a spatial intelligence benchmark encompassing nearly 20 open-source datasets across 23 task settings. Experiments with state-of-the-art VLMs reveal a pronounced gap between perception and reasoning, as models show competence in basic perceptual tasks but consistently underperform in understanding and planning tasks, particularly in numerical estimation, multi-view reasoning, temporal dynamics, and spatial imagination. These findings underscore the substantial challenges that r

Spatial competence is the quality of maintaining a consistent internal representation of an environment and using it to infer discrete structure and plan actions under constraints. Prevailing spatial evaluations for large models are limited to probing isolated primitives through 3D transformations or visual question answering. We introduce the Spatial Competence Benchmark (SCBench), spanning three hierarchical capability buckets whose tasks require executable outputs verified by deterministic checkers or simulator-based evaluators. On SCBench, three frontier models exhibit monotonically decreasing accuracy up the capability ladder. Sweeping output-token caps shows that accuracy gains concentrate at low budgets and saturate quickly, and failures are dominated by locally plausible geometry that breaks global constraints. We release the task generators, verifiers, and visualisation tooling.

Understanding user instructions and object spatial relations in surrounding environments is crucial for intelligent robot systems to assist humans in various tasks. The natural language and spatial reasoning capabilities of Vision-Language Models (VLMs) have the potential to enhance the generalization of robot planners on new tasks, objects, and motion specifications. While foundation models have been applied to task planning, it is still unclear the degree to which they have the capability of spatial reasoning required to enforce user preferences or constraints on motion, such as desired distances from objects, topological properties, or motion style preferences. In this paper, we evaluate the capability of four state-of-the-art VLMs at spatial reasoning over robot motion, using four different querying methods. Our results show that, with the highest-performing querying method, Qwen2.5-VL achieves 71.4% accuracy zero-shot and 75% on a smaller model after fine-tuning, and GPT-4o leads to lower performance. We evaluate two types of motion preferences (object-proximity and path-style), and we also analyze the trade-off between accuracy and computation cost in number of tokens. This w

Text-to-image (T2I) generation has advanced rapidly, yet faithfully capturing spatial relationships described in natural language prompts remains a major challenge. Prior efforts have addressed this issue through prompt optimization, spatially grounded generation, and semantic refinement. This work introduces a lightweight approach that augments prompts with tuple-based structured information, using a fine-tuned language model for automatic conversion and seamless integration into T2I pipelines. Experimental results demonstrate substantial improvements in spatial accuracy, without compromising overall image quality as measured by Inception Score. Furthermore, the automatically generated tuples exhibit quality comparable to human-crafted tuples. This structured information provides a practical and portable solution to enhance spatial relationships in T2I generation, addressing a key limitation of current large-scale generative systems.

We present a novel Bayesian spatial disaggregation model for count data, providing fast and flexible inference at high resolution. First, it incorporates non-linear covariate effects using penalized splines, a flexible approach that is not typically included in existing spatial disaggregation methods. Additionally, it employs a spline-based low-rank kriging approximation for modeling spatial dependencies. The use of Laplace approximation provides computational advantages over traditional Markov Chain Monte Carlo (MCMC) approaches, facilitating scalability to large datasets. We explore two estimation strategies: one using the exact likelihood and another leveraging a spatially discrete approximation for enhanced computational efficiency. Simulation studies demonstrate that both methods perform well, with the approximate method offering significant computational gains. We illustrate the applicability of our model by disaggregating disease rates in the United Kingdom and Belgium, showcasing its potential for generating high-resolution risk maps. By combining flexibility in covariate modeling, computational efficiency and ease of implementation, our approach offers a practical and effe

Spatial association measures for univariate static spatial data are widely used. When the data is in the form of a collection of spatial vectors with the same temporal domain of interest, we construct a measure of similarity between the regions' series, using Bergsma's correlation coefficient $ρ$. Due to the special properties of $ρ$, unlike other spatial association measures which test for spatial randomness, our statistic can account for spatial pairwise independence. We have derived the asymptotic behavior of our statistic under null (independence of the regions) and alternate cases (the regions are dependent). We explore the alternate scenario of spatial dependence further, using simulations for the SAR and SMA dependence models. Finally, we provide application to modelling and testing for the presence of spatial association in COVID-19 incidence data, by using our statistic on the residuals obtained after model fitting.

Large Chunk Test-Time Training (LaCT) has shown strong performance on long-context 3D reconstruction, but its fully plastic inference-time updates remain vulnerable to catastrophic forgetting and overfitting. As a result, LaCT is typically instantiated with a single large chunk spanning the full input sequence, falling short of the broader goal of handling arbitrarily long sequences in a single pass. We propose Elastic Test-Time Training inspired by elastic weight consolidation, that stabilizes LaCT fast-weight updates with a Fisher-weighted elastic prior around a maintained anchor state. The anchor evolves as an exponential moving average of past fast weights to balance stability and plasticity. Based on this updated architecture, we introduce Fast Spatial Memory (FSM), an efficient and scalable model for 4D reconstruction that learns spatiotemporal representations from long observation sequences and renders novel view-time combinations. We pre-trained FSM on large-scale curated 3D/4D data to capture the dynamics and semantics of complex spatial environments. Extensive experiments show that FSM supports fast adaptation over long sequences and delivers high-quality 3D/4D reconstruc

Spatial areal models encounter the well-known and challenging problem of spatial confounding. This issue makes it arduous to distinguish between the impacts of observed covariates and spatial random effects. Despite previous research and various proposed methods to tackle this problem, finding a definitive solution remains elusive. In this paper, we propose a simplified version of the spatial+ approach that involves dividing the covariate into two components. One component captures large-scale spatial dependence, while the other accounts for short-scale dependence. This approach eliminates the need to separately fit spatial models for the covariates. We apply this method to analyse two forms of crimes against women, namely rapes and dowry deaths, in Uttar Pradesh, India, exploring their relationship with socio-demographic covariates. To evaluate the performance of the new approach, we conduct extensive simulation studies under different spatial confounding scenarios. The results demonstrate that the proposed method provides reliable estimates of fixed effects and posterior correlations between different responses.

This article studies the use of asymmetric loss functions for the optimal prediction of positive-valued spatial processes. We focus on the family of power-divergence loss functions due to its many convenient properties, such as its continuity, convexity, relationship to well known divergence measures, and the ability to control the asymmetry and behaviour of the loss function via a power parameter. The properties of power-divergence loss functions, optimal power-divergence (OPD) spatial predictors, and related measures of uncertainty quantification are examined. In addition, we examine the notion of asymmetry in loss functions defined for positive-valued spatial processes and define an asymmetry measure that is applied to the power-divergence loss function and other common loss functions. The paper concludes with a spatial statistical analysis of zinc measurements in the soil of a floodplain of the Meuse River, Netherlands, using OPD spatial prediction.

While video generation models excel at producing high-quality monocular videos, generating 3D stereoscopic and spatial videos for immersive applications remains an underexplored challenge. We present a pose-free and training-free method that leverages an off-the-shelf monocular video generation model to produce immersive 3D videos. Our approach first warps the generated monocular video into pre-defined camera viewpoints using estimated depth information, then applies a novel \textit{frame matrix} inpainting framework. This framework utilizes the original video generation model to synthesize missing content across different viewpoints and timestamps, ensuring spatial and temporal consistency without requiring additional model fine-tuning. Moreover, we develop a \dualupdate~scheme that further improves the quality of video inpainting by alleviating the negative effects propagated from disoccluded areas in the latent space. The resulting multi-view videos are then adapted into stereoscopic pairs or optimized into 4D Gaussians for spatial video synthesis. We validate the efficacy of our proposed method by conducting experiments on videos from various generative models, such as Sora, Lu

Implementation of spatial generalized linear models with a functional covariate can be accomplished through the use of a truncated basis expansion of the covariate process. In practice, one must select a truncation level for use. We compare five criteria for the selection of an appropriate truncation level, including AIC and BIC based on a log composite likelihood, a fraction of variance explained criterion, a fitted mean squared error, and a prediction error with one standard error rule. Based on the use of extensive simulation studies, we propose that BIC constitutes a reasonable default criterion for the selection of the truncation level for use in a spatial functional generalized linear model. In addition, we demonstrate that the spatial model with a functional covariate outperforms other models when the data contain spatial structure and response variables are in fact influenced by a functional covariate process. We apply the spatial functional generalized linear model to a problem in which the objective is to relate COVID-19 vaccination rates in counties of states in the Midwestern United States to the number of new cases from previous weeks in those same geographic regions.