Methods and systems for vehicle fault detection include collecting operational data from sensors in a vehicle. The sensors are associated with vehicle sub-systems. The operational data is processed with a neural network to generate a fault score, which represents a similarity to fault state training scenarios, and an anomaly score, which represents a dissimilarity to normal state training scenarios. The fault score is determined to be above a fault score threshold and the anomaly score is determined to be above an anomaly score threshold to detect a fault. A corrective action is performed responsive the fault, based on a sub-system associated with the fault.