Robust and interpretable prediction of gene markers and cell types from spatial transcriptomics data

Spatial transcriptomics (ST) links tissue morphology with gene expression values, opening new avenues for digital pathology. Deep learning models are used to predict gene expression or classify cell types directly from images, offering significant clinical potential but still requiring improvements in interpretability and robustness. We present STimage as a comprehensive suite of models to predict spatial gene expression and classify cell types directly from standard H&E images. STimage enhances robustness by estimating gene expression distributions and quantifying both data-driven (aleatoric) and model-based (epistemic) uncertainty using an ensemble approach with foundation models. Interpretability is…

• AR
  Australian Research Council

  Award: DE190100116
• NH
  National Health and Medical Research Council

  Award: GNT2008928