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In order to escape from local optimum and get a higher accuracy, GEP based on gene diversity is proposed, which using initial population producing strategy based on gene diversity, introducing the population update strategy, improved genes diversity of population. The simulation results show that GD_GEP has a better global search ability and higher accuracy. Using the flight data recorded by FDR of a certain type of aircraft, the model of aircraft engine based on GD-GEP is set up and used to monitor the vibration of engine, real malfunction data proved the method to be effective.