Hierarchical Bayesian models are increasingly used in large, inhomogeneous complex network dynamical systems by modeling parameters as draws from a hyperparameter-governed distribution. However, theoretical guarantees for these estimates as the network population size grows have been lacking. A critical concern is that hyperparameter estimation may diverge for larger networks, undermining the model's reliability. Formulating the system's evolution in a measure transport perspective, we propose a theoretical framework for estimating hyperparameters with mean-type observations, which are prevalent in many scientific applications. Our primary contribution is a nonasymptotic bound for the deviation of estimate of hyperparameters in inhomogeneous complex network dynamical systems with respect to network population size, which is established for a general family of optimization algorithms within a fixed observation duration. For systems with independent nodes, we first establish a fixed-accuracy probabilistic hyperparameter bound and then use it to derive an explicit nonasymptotic hyperparameter bound. We subsequently extend both bounds to the more challenging and practically relevant setting of systems with weakly-dependent nodes. We validate our theoretical findings with numerical experiments on two representative models: a Susceptible-Infected-Susceptible model and a Spiking Neuronal Network model. In both cases, the results confirm that the estimation error decreases as the network population size increases, aligning with our theoretical guarantees. This research proposes the foundational theory to ensure that hierarchical Bayesian methods are statistically consistent for large-scale inhomogeneous systems, filling a gap in this area of theoretical research and justifying their application in practice.

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