Phenotype-associated spatial biomarker discovery in spatial transcriptomics with spHOT

Spatial transcriptomics now profiles patient cohorts at single-cell resolution, enabling analysis of disease-associated cell organization in situ. However, discovering such spatial biomarkers remains challenging because relevant structures occur at unknown scales and cell- or niche-level annotations are rarely available. We present spHOT, a deep learning framework that localizes phenotype-associated spatial biomarkers from sample-level labels. spHOT combines spatial foundation model embeddings, a hierarchical domain tree for multi-resolution tissue representation, and a teacher-student multiple instance learning architecture that converts sample labels into cell-level biomarker scores. In controlled simulations and real-tissue benchmarks, spHOT outperformed existing spatial and single-cell methods in localizing ground-truth biomarkers. Across fibrotic, metabolic, and autoimmune disease datasets, spHOT recovered disease-relevant niches and tissue states reported by supervised analyses in the original studies. Cross-disease application of spHOT transferred biomarkers across chronic lung diseases without retraining. spHOT enables scalable, annotation-efficient spatial biomarker discovery in cohort-scale spatial transcriptomics.