A method and apparatus for analyzing an input electron microscope image of a first area on a first wafer are disclosed. The method comprises obtaining a plurality of mode images from the input electron microscope image corresponding to a plurality of interpretable modes. The method further comprises evaluating the plurality of mode images, and determining, based on evaluation results, contributions from the plurality of interpretable modes to the input electron microscope image. The method also comprises predicting one or more characteristics in the first area on the first wafer based on the determined contributions. In some embodiments, a method and apparatus for performing an automatic root cause analysis based on an input electron microscope image of a wafer are also disclosed.