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Data-driven algorithms require large and comprehensive training samples in order to provide reliable diagnostic solutions. However, in many gas turbine applications, it is hard to find fault data due to proprietary and liability issues. Operational data samples obtained from end-users through collaboration projects do not represent fault conditions sufficiently and are not labeled either. Conversely, model-based methods have some accuracy deficiencies due to measurement uncertainty and model smearing effects when the number of gas path components to be assessed is large. The present paper integrates physics-based and data-driven approaches aiming to overcome this limitation. In the proposed method, an adaptive gas path analysis (AGPA) is used to correct measurement data against the ambient condition variations and normalize. Fault signatures drawn from the AGPA are used to assess the health status of the case engine through a Bayesian network (BN) based fault diagnostic algorithm. The performance of the proposed technique is evaluated based on five different gas path component faults of a three-shaft turbofan engine, namely intermediate-pressure compressor fouling (IPCF), high-pressure compressor fouling (HPCF), high-pressure turbine erosion (HPTE), intermediate-pressure turbine erosion (IPTE), and low-pressure turbine erosion (LPTE). Robustness of the method under measurement uncertainty has also been tested using noise-contaminated data. Moreover, the fault diagnostic effectiveness of the BN algorithm on different number and type of measurements is also examined based on three different sensor groups. The test results verify the effectiveness of the proposed method to diagnose single gas path component faults correctly even under a significant noise level and different instrumentation suites. This enables to accommodate measurement suite inconsistencies between engines of the same type. The proposed method can further be used to support the gas turbine maintenance decision-making process when coupled with overall Engine Health Management (EHM) systems.