REST: Reliability-Guided Spatial Transcriptomics Supervision for Gene Expression Prediction from Histopathological HE-Stained Images

Overview & Synopsis

Histopathology is central to cancer diagnosis, but morphology in Hematoxylin and Eosin (HE)-stained images does not directly reveal the molecular states that characterize disease heterogeneity and inform tumor characterization, prognostic assessment, and biomarker discovery. Spatial Transcriptomics (ST) measures spatially resolved gene expression, providing molecular information within tissue architecture, yet differences in assay coverage and spot informativeness make paired HE--ST observations unequally reliable for representation learning. We propose Reliability-Guided Spatial Transcriptomics (REST) supervision with Biological Program Bank (BPB), a program-structured and reliability-guided ST-supervised training framework for predicting molecular information from H\&E images. REST constructs BPB from curated signature, pathway, and cell-type gene sets to provide a shared structure for ST encoding, reliability estimation, and molecular reconstruction. Guided by BPB, Spot-Reliability Contrastive Alignment (SRCA) measures the reliability of each spot from assay-level program coverage and spot-level activity dispersion, and reweights HE--ST alignment accordingly. Biology-Informed Program Reconstruction (BIPR) further uses learnable program queries to reconstruct member-gene expression from histological morphology. REST's training corpus comprised 209 samples (407,475 spots across 16 organs); evaluation used 70 disjoint samples (230,056 spots across eight organs) for gene-expression, pathway-activity, and cell-signature prediction. REST achieved the highest Macro correlation among state-of-the-art ST-supervised training methods and outperformed existing pathology foundation models. Code is available at https://github.com/lanfz2000/REST.