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Formulating the architecting process as an optimization problem may mitigate some of these challenges. This work investigates strategies for solving system architecture optimization (SAO) problems: expensive, black-box, hierarchical, mixed-discrete, constrained, multi-objective problems that may be subject to hidden constraints. Imputation ratio, correction ratio, correction fraction, and max rate diversity metrics are defined for characterizing hierarchical design spaces. This work considers two classes of optimization algorithms for SAO: multi-objective evolutionary algorithms such as NSGA-II, and Bayesian optimization (BO) algorithms. A new Gaussian process kernel is presented that enables modeling hierarchical categorical variables, extending previous work on modeling continuous and integer hierarchical variables. Next, a hierarchical sampling algorithm that uses design space hierarchy to group design vectors by active design variables is developed. Then, it is demonstrated that integrating more hierarchy information in the optimization algorithms yields better optimization results for BO algorithms. Several realistic single-objective and multi-objective test problems are used for investigations. Finally, the BO algorithm is applied to a jet engine architecture optimization problem. This work shows that the developed BO algorithm can effectively solve the problem with one order of magnitude less function evaluations than NSGA-II. 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