Systems and methods are described herein for processing electronic medical images to predict a biomarker's presence, including receiving one or more digital medical images, the one or more digital medical images being of at least one pathology specimen associated with a patient. A machine learning system may determine a biomarker expression level prediction for the one or more digital medical images. The biomarker expression level prediction may be based on a determined transcriptomic score and protein expression score for the one or more digital medical images. A slide overlay indicating a region of tissue on the one or more digital medical images that is most likely to contribute to the slide level biomarker expression prediction may be generated.