A human assisted method of debugging training data used to train a machine learning classifier is provided. The method includes obtaining a classifier training data set. The training data set is then debugged using an integrated debugging tool configured to implement a debugging loop to obtain a debugged data set. The debugging tool can be configured to perform an estimation and simplification step to reduce data noise in the training data set prior to further analysis. The debugging tool also runs a panel of prediction-centric diagnostic metrics on the training data set, and provides the user prediction based listings of the results of the panel of prediction-centric diagnostic metrics.