Systems and methods are disclosed for predicting coronary plaque vulnerability, using a computer system. One method includes acquiring anatomical image data of at least part of the patient's vascular system； performing, using a processor, one or more image characteristics analysis, geometrical analysis, computational fluid dynamics analysis, and structural mechanics analysis on the anatomical image data； calculating an adverse plaque characteristic from said one or more； determining locations of the patient's vascular system for which plaque vulnerability may be identified； determining, for each determined location, a feature vector comprising a numerical description of at least one of: the geometry, biophysical hemodynamics, and wall or plaque biomechanical characteristics at that location, and physiological or phenotypic parameters of the patient； and determining, using the processor, a plaque vulnerability present in the patient's vascular system based on the feature vectors.
