Quantifying predictability of gene expression from histology image

Xia, C.-R.; Yao, J.-W.; Gao, G.

doi:10.1101/2025.11.04.686651

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bioRxiv · 10.1101/2025.11.04.686651

Quantifying predictability of gene expression from histology image

Xia, C.-R.·Yao, J.-W.·Gao, G.

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Abstract

Histopathological images are indispensable in clinical diagnosis, yet provide limited insight into underlying molecular states. Numerous computational models attempt to predict gene expression from histopathological images. However, a fundamental question remains unresolved: which genes can be accurately predicted and which cannot. Here, we introduce Expression Predictability Score (EPS), a metric that quantifies the predictability of each gene from images through expression-image mutual information. Empirical analyses across more than 500 slices further reveal consistent sets of highly predictable and unpredictable genes, as well as their underlying association with the physicochemical nature of H&E staining.

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Xia, C.-R., Yao, J.-W., Gao, G.. 2025-11-05. Quantifying predictability of gene expression from histology image. https://doi.org/10.1101/2025.11.04.686651

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