1. A computer-implemented method of evaluating a patient with vascular disease, the method comprising: receiving patient-specific data regarding a geometry of the patient's vasculature; determining an anatomic model representing at least a portion of a location of disease in the patient's vasculature based on the received patient-specific data; determining a plaque remodeling characteristic characterizing a propensity of the disease in the patient's vasculature to progress or regress; modeling, using the determined plaque remodeling characteristic, one or more changes in the geometry of the anatomic model at the location of disease due to the progression or regression of the disease; calculating one or more values of a blood flow characteristic within the patient's vasculature using a computational model of blood flow through the anatomical model, taking into account the one or more modeled changes in geometry of the anatomic model; and generating a display including a plot of the one or more values of the calculated blood flow characteristic versus the one or more modeled changes in geometry of the anatomic model due to the progression or regression of disease according to the determined plaque remodeling characteristic.