A system is provided for determining causes of faults in a manufacturing system. The system stores data associated with a processing system which includes machines and associated processes, wherein the data includes timestamp information, machine status information, and product-batch information. The system determines, based on the data, a topology of the processing system, wherein the topology indicates flows of outputs between the machines as part of the processes. The system determines information of machine faults in association with the topology. The system generates, based on the machine-fault information, one or more fault parameters which indicates frequency and severity of a respective fault. The system constructs, based on the topology and the machine-fault information, a system model which includes the one or more fault parameters, thereby facilitating diagnosis of the processing system.