In this work we develop a theory of hierarchical clustering for graphs. Our modelling assumption is that graphs are sampled from a graphon, which is a powerful and general model for generating graphs and analyzing large networks. Graphons are a far richer class of graph models than stochastic blockmodels, the primary setting for recent progress in the statistical theory of graph clustering. We define what it means for an algorithm to produce the ``correct clustering, give sufficient conditions in which a method is statistically consistent, and provide an explicit algorithm satisfying these properties.

Recovering the random graph model from an observed collection of networks is known to present significant challenges in the setting, where the networks do not share a common node set and have different sizes. More specifically, the goal is the estimation of the graphon function that parametrizes the nonparametric exchangeable random graph model. Existing methods typically suffer from either limited accuracy or high computational complexity. We introduce a new histogram-based estimator with low algorithmic complexity that achieves high accuracy by jointly aligning the nodes of all graphs, in contrast to most conventional methods that order nodes graph by graph. Consistency results of the proposed graphon estimator are established. A numerical study shows that the proposed estimator outperforms existing methods in terms of accuracy, especially when the dataset comprises only small and variable-size networks. Moreover, the computing time of the new method is considerably shorter than that of other consistent methodologies. Additionally, when applied to a graph neural network classification task, the proposed estimator enables more effective data augmentation, yielding improved performance across diverse real-world datasets.

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