Controlling product production in multi-stage manufacturing process automatically generates by machine learning causal relationships between the processing conditions and the product quality based on product genealogy data and product quality data. Real time sensor data from sensors coupled to processing units in a manufacturing facility implementing the multi-stage manufacturing process are received, and control rules are instantiated based on the real time sensor data. An instantiated control rule firing causes an actuator to automatically set a processing variable to a set point specified in the control rule.