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This research concerns the uncertainty analysis and quantification of the vibration system utilizing the frequency response function (FRF) representation with statistical metamodeling. Different from previous statistical metamodels that are built for individual frequency points, in this research we take advantage of the inherent correlation of FRF values at different frequency points and resort to the multiple response Gaussian process (MRGP) approach. To enable the analysis, vector fitting method is adopted to represent an FRF using a reduced set of parameters with high accuracy. Owing to the efficiency and accuracy of the statistical metamodel with a small set of parameters, Bayesian inference can then be incorporated to realize model updating and uncertainty identification as new measurement/evidence is acquired. The MRGP metamodel developed under this new framework can be used effectively for two-way uncertainty propagation analysis, i.e., FRF prediction and uncertainty identification. Case studies are conducted for illustration and verification.