LOBSTUR: A Local Bootstrap Framework for Tuning Unsupervised Representations in Graph Neural Networks

Abstract: Graph Neural Networks (GNNs) are increasingly used in conjunction with unsupervised learning techniques to learn powerful node representations, but their deployment is hindered by their high sensitivity to hyperparameter tuning and the absence of established methodologies for selecting the optimal models. To address these challenges, we propose LOBSTUR-GNN ({\bf Lo}cal {\bf B}oot{\bf s}trap for {\bf T}uning {\bf U}nsupervised {\bf R}epresentations in GNNs) i), a novel framework designed to adapt bootstrapping techniques for unsupervised graph representation learning. LOBSTUR-GNN tackles two main challenges: (a) adapting the bootstrap edge and feature resampling process to account for local graph dependencies in creating alternative versions of the same graph, and (b) establishing robust metrics for evaluating learned representations without ground-truth labels. Using locally bootstrapped resampling and leveraging Canonical Correlation Analysis (CCA) to assess embedding consistency, LOBSTUR provides a principled approach for hyperparameter tuning in unsupervised GNNs. We validate the effectiveness and efficiency of our proposed method through extensive experiments on established academic datasets, showing an 65.9\% improvement in the classification accuracy compared to an uninformed selection of hyperparameters. Finally, we deploy our framework on a real-world application, thereby demonstrating its validity and practical utility in various settings. \footnote{The code is available at \href{https://github.com/sowonjeong/lobstur-graph-bootstrap}{github.com/sowonjeong/lobstur-graph-bootstrap}.}