An engine system includes an air handling and fuel system whose states are managed by a reference managing unit. The engine system has a plurality of sensors whose sensor signals at least partially define a current state of the engine system. The reference managing unit includes a controller which controls the air handling and fuel system of the engine system as well as a processing unit coupled to the sensors and the controller. The processing unit includes an agent which learns a policy function that is trained to process the current state, determines air handling references and fuel system references by using the policy function after receiving the current state as an input, and outputs the air handling references and fuel system references to the controller. Then, the agent receives a next state and a reward value from the processing unit and updates the policy function using a policy evaluation algorithm and a policy improvement algorithm based on the received reward value. Subsequently, the controller controls the air handling and fuel system of the engine in response to receiving the air handling references and the fuel system references.