← 研踪 PaperTrailarXiv:2611.13649 · v1
Predicting Single-Cell Spatial Gene Expression from H&E using Pathology Foundation Models
首次提交 2026-11-10 14:44
版本更新 2026-11-10 14:44
雷达观测 2026-11-11 11:04
摘要
Predicting gene expression directly from hematoxylin and eosin (H&E) images offers a scalable and cost-effective approach to deriving spatial molecular insights from routine histology. Pathology foundation models, typically pretrained using tile-level objectives, may not adequately capture the fine-grained cellular features required for single-cell molecular prediction. In this work, we systematically evaluate and establish domain-informed and task-specific strategies for adapting pathology foundation models to single-cell spatial gene expression prediction. Using paired H&E and Xenium 5K data, our approach improves mean gene-wise Pearson correlation by 2.67x over the standard zero-shot baseline and achieves state-of-the-art performance on this task. We demonstrate strong gene-detection performance across the full gene panel (AUROC = 0.800) and importantly identify that predictive performance varies substantially across biological contexts, with our model achieving its highest Pearson correlation for spatially variable genes (r = 0.643). Our findings demonstrate that, despite the challenges of sparse single-cell measurements, H&E-derived representations can recover biologically meaningful spatial expression patterns, highlighting both the opportunities and limitations of morphology-based molecular inference at cellular resolution.
作者备注：NeurIPS 2026 Workshop on AI at Scale for Clinical Impact. Project page: https://he2sc-st.github.io/
观测到的版本
相邻记录可能跳过中间版本；首次发现 v2 及以上也会标为版本更新。
v1 · 2026-11-10 14:44 · 最新观测版本
Predicting Single-Cell Spatial Gene Expression from H&E using Pathology Foundation Models
Predicting gene expression directly from hematoxylin and eosin (H&E) images offers a scalable and cost-effective approach to deriving spatial molecular insights from routine histology. Pathology foundation models, typically pretrained using tile-level objectives, may not adequately capture the fine-grained cellular features required for single-cell molecular prediction. In this work, we systematically evaluate and establish domain-informed and task-specific strategies for adapting pathology foundation models to single-cell spatial gene expression prediction. Using paired H&E and Xenium 5K data, our approach improves mean gene-wise Pearson correlation by 2.67x over the standard zero-shot baseline and achieves state-of-the-art performance on this task. We demonstrate strong gene-detection performance across the full gene panel (AUROC = 0.800) and importantly identify that predictive performance varies substantially across biological contexts, with our model achieving its highest Pearson correlation for spatially variable genes (r = 0.643). Our findings demonstrate that, despite the challenges of sparse single-cell measurements, H&E-derived representations can recover biologically meaningful spatial expression patterns, highlighting both the opportunities and limitations of morphology-based molecular inference at cellular resolution.
查看此版本解读 →查看此版本原文 ↗