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Quantification and propagation of aleatoric uncertainties distributed in complex topological structures remain a challenge. Existing uncertainty quantification and propagation approaches can only handle parametric uncertainties or high dimensional random quantities distributed in a simply connected spatial domain. There lacks a systematic method that captures the topological characteristics of the structural domain in uncertainty analysis. Therefore, this paper presents a new methodology that quantifies and propagates aleatoric uncertainties, such as the spatially varying local material properties and defects, distributed in a topological spatial domain. We propose a new random field-based uncertainty representation approach that captures the topological characteristics using the shortest interior path distance. Parameterization methods like PPCA and β-Variational Autoencoder (βVAE) are employed to convert the random field representation of uncertainty to a small set of independent random variables. Then non-intrusive uncertainties propagation methods such as polynomial chaos expansion and univariate dimension reduction are employed to propagate the parametric uncertainties to the output of the problem. The effectiveness of the proposed methodology is demonstrated by engineering case studies. The accuracy and computational efficiency of the proposed method is confirmed by comparing with the reference values of Monte Carlo simulations with a sufficiently large number of samples.