Methods and systems for detecting outliers at a manufacturing system using machine learning are provided. Data collected by a sensors at a manufacturing system during a current process performed for a first set of substrates is provided as input to a trained machine learning model. One or more outputs are obtained from the trained machine learning model. A first amount of drift of a first set of parameter values for the first set of substrates from a target set of parameter values for the first set of substrates is extracted from the one or more outputs. A second amount of drift of each of the first set of parameter values for the first set of substrates from a corresponding parameter value of a second set of parameter values for a second set of substrates processed according to the current process at the manufacturing system prior to the performance of the current process for the first set of substrates is also extracted from the one or more outputs. A substrate health rating is assigned for each of the first set of substrates based on the first amount of drift. A sensor health rating is assigned for each of the sensors at the manufacturing system based on the second amount of drift. An indication of the substrate health rating for each of the first set of substrates and the sensor health rating for each of the sensors are transmitted to a client device connected to the manufacturing system.