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In this paper, we target at recovering the exact routes taken by commuters inside a metro system that arenot captured by an Automated Fare Collection (AFC) system and hence remain unknown. We strategicallypropose two inference tasks to handle the recovering, one to infer the travel time of each travel link thatcontributes to the total duration of any trip inside a metro network and the other to infer the route preferencesbased on historical trip records and the travel time of each travel link inferred in the previous inferencetask. As these two inference tasks have interrelationship, most of existing works perform these two taskssimultaneously. However, our solutionTripDecoderadopts a totally different approach. To the best of ourknowledge,TripDecoderis the first model that points out and fully utilizes the fact that there are some tripsinside a metro system with only one practical route available. It strategically decouples these two inferencetasks by only taking those trip records with only one practical route as the input for the first inference taskof travel time and feeding the inferred travel time to the second inference task as an additional input whichnot only improves the accuracy but also effectively reduces the complexity of both inference tasks. Twocase studies have been performed based on the city-scale real trip records captured by the AFC systems inSingapore and Taipei to compare the accuracy and efficiency ofTripDecoderand its competitors. As expected,TripDecoderhas achieved the best accuracy in both datasets, and it also demonstrates its superior efficiencyand scalability.