H&E slides skip spatial transcriptomics: ALHENA distills cell and neighborhood similarity, reaching 0.341 patient-level signature correlation
ALHENA distills spatial transcriptomic information into a routine H&E encoder that reads only images at inference. Rather than regressing individual genes, it trains the H&E representation to match the sample-to-sample similarity structure of two frozen transcriptomic models at cell and neighborhood scales. Across 110 cancer-type and signature combinations in TCGA, mean Spearman correlation was 0.341 versus 0.161 for unadapted UNI2-h; on the Thunder pathology benchmark the median change was −0.004.