DL models were trained on WSIs to predict mutations, treatment sensitivity, and recurrence-free survival (RFS).<h4>Results</h4>DL predicted mutational status in GIST from WSIs, with area under the curve (AUC) of 0.87 for <i>KIT</i>, 0.96 for <i>PDGFRA</i>. Here, KIT is linked to gastrointestinal stromal tumor.