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 a plaque remodeling characteristic characterizing a propensity of the disease in the patient's vasculature to progress or regress; determining, using the received patient-specific data and the determined plaque remodeling characteristic, a geometric model of a progression or regression of disease at a location in the patient's vasculature; calculating a value of a blood flow characteristic within the patient's vasculature using a blood flow model determined based on the received patient-specific data and the determined plaque remodeling characteristic; and generating a treatment recommendation or risk assessment based on the value of the blood flow characteristic calculated using the blood flow model based on the received patient-specific data and the determined plaque remodeling characteristic.