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Simultaneous Monitoring of Shape and Surface Color via 4D Point Clouds: A Registration-free Approach A Refined Generalization Analysis for Extreme Multi-class Supervised Contrastive Representation Learning Ensemble Distributionally Robust Bayesian Optimisation The Proxy Presumption: From Semantic Embeddings to Valid Social Measures Modulated learning for private and distributed regression with just a single sample per client device Query-efficient model evaluation using cached responses Functional-prior-based approaches to Bayesian PDE-constrained inversion using physics-informed neural networks Optimal Experiments for Partial Causal Effect Identification Order-Agnostic Autoregressive Modelling with Missing Data Grokking or Glitching? How Low-Precision Drives Slingshot Loss Spikes Tuning Derivatives for Causal Fairness in Machine Learning Spherical Flows for Sampling Categorical Data Bayesian Rain Field Reconstruction using Commercial Microwave Links and Diffusion Model Priors GRALIS: A Unified Canonical Framework for Linear Attribution Methods via Riesz Representation Sharp Capacity Thresholds in Linear Associative Memory: From Winner-Take-All to Listwise Retrieval Unified Framework of Distributional Regret in Multi-Armed Bandits and Reinforcement Learning Jacobian-Velocity Bounds for Deployment Risk Under Covariate Drift Self-Attention as Transport: Limits of Symmetric Spectral Diagnostics Perturbation is All You Need for Extrapolating Language Models Adapt or Forget: Provable Tradeoffs Between Adam and SGD in Nonstationary Optimization Realizable Bayes-Consistency for General Metric Losses Graph Convolutional Support Vector Regression for Robust Spatiotemporal Forecasting of Urban Air Pollution Segmenting Human-LLM Co-authored Text via Change Point Detection Stochastic Schrödinger Diffusion Models for Pure-State Ensemble Generation Understanding Self-Supervised Learning via Latent Distribution Matching The Geometric Mechanics of Contrastive Representation Learning: Alignment Potentials, Entropic Dispersion, and Cross-modal Divergence Imbalanced Classification under Capacity Constraints On the Spectral Structure and Objective Equivalence of Orthogonal Multilabel Fisher Discriminants Partially Observed Structural Causal Models First-Order Efficiency for Probabilistic Value Estimation via A Statistical Viewpoint
Large-scale spatial variable gene atlas for spatial trans...
[Submitted on 9 Oct 2025 (v1), last revised 31 Aug 2026 (this ve · 2025-10-09 · via stat updates on arXiv.org

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Abstract:Spatial variable genes (SVGs) reveal critical information about tissue architecture, cellular interactions, and disease microenvironments. As spatial transcriptomics (ST) technologies proliferate, accurately identifying SVGs across diverse platforms, tissue types, and disease contexts has become both a major opportunity and a significant computational challenge. Here, we present a comprehensive benchmarking study of 20 state-of-the-art SVG detection methods using human slides from STimage-1K4M, a large-scale resource of ST data comprising 662 slides from more than 18 tissue types. We evaluate each method across a range of biologically and technically meaningful criteria, including recovery of pathologist-annotated domain-specific markers, cross-slide reproducibility, scalability to high-resolution data, and robustness to technical variation. Our results reveal marked differences in performance depending on tissue type, spatial resolution, and study design. Beyond benchmarking, we construct the first cross-tissue atlas of SVGs, enabling comparative analysis of spatial gene programs across cancer and normal tissues. We observe similarities between pairs of tissues that reflect developmental and functional relationships, such as high overlap between thymus and lymph node, and uncover spatial gene programs associated with metastasis, immune infiltration, and tissue-of-origin identity in cancer. Together, our work defines a framework for evaluating and interpreting spatial gene expression and establishes a reference resource for the ST community.

Submission history

From: Jiawen Chen [view email]
[v1] Thu, 9 Oct 2025 01:03:58 UTC (12,716 KB)
[v2] Sun, 19 Oct 2025 00:10:16 UTC (15,366 KB)
[v3] Mon, 31 Aug 2026 03:28:12 UTC (15,366 KB)