The present invention relates to a method and system for detecting biologically relevant structures in a hierarchical fashion, beginning at a low-resolution and proceeding to higher levels of resolution. The present invention also provides probabilistic pairwise Markov models (PPMMs) to classify these relevant structures. The invention is directed to a novel classification approach which weighs the importance of these structures. The present invention also provides a fast, efficient computer-aided detection/diagnosis (CAD) system capable of rapidly processing medical images (i.e. high throughput). The computer-aided detection/diagnosis (CAD) system of the present invention allows for rapid analysis of medical images the improving the ability to effectively detect, diagnose, and treat certain diseases.