A building management system includes a processing circuit configured to perform a system identification process to identify one or more parameters of a system model that predicts a behavior of a building system. The one or more parameters include one or more model parameters and one or more Kalman gain parameters. The system identification process includes identifying the one or more model parameters, generating an initial guess of the one or more Kalman gain parameters based on the training data and results of a simulation that uses the one or more model parameters, and identifying the one or more Kalman gain parameters by initializing a prediction error minimization problem with the initial guess. The building management system also includes a controller configured to control building equipment to affect the behavior of the building system based on predictions of the system model.
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