The present disclosure provides methods and systems using machine learning to assess one or more of a patient's biomarkers to analyze various conditions, including cancers, such as breast cancer. The present systems and methods can be trained to analyze patient's biomarker data to form prognoses, diagnoses, and treatment suggestions. Further, the present systems and methods can use biomarker feature data and clinical feature data to create novel correlations in order to provide more accurate, patient-specific diagnoses, prognoses, and treatment suggestions.