Abstract: Methods and systems of using a trained machine-learning model to perform root cause analysis on a manufacturing process. A pre-trained machine learning model is provided that is trained to predict measurements of non-faulty parts. The pre-trained model is trained on training measurement data regarding physical characteristics of manufactured parts as measured by a plurality of sensors at a plurality of manufacturing stations. With the trained model, then measurement data from the sensors is received regarding the manufactured part and the stations. This new set of measurement data is back propagated through the pre-trained model to determine a magnitude of absolute gradients of the new measurement data. The root cause is then identified based on this magnitude of absolute gradients. In other embodiments the root cause is identified based on losses determined between a set of predicted measurement data of a part using the model, and actual measurement data.