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FedGraphNN: A Federated Learning System and Benchmark for Graph Neural Networks

by   Chaoyang He, et al.
University of Southern California

Graph Neural Network (GNN) research is rapidly growing thanks to the capacity of GNNs to learn representations from graph-structured data. However, centralizing a massive amount of real-world graph data for GNN training is prohibitive due to user-side privacy concerns, regulation restrictions, and commercial competition. Federated learning (FL), a trending distributed learning paradigm, aims to solve this challenge while preserving privacy. Despite recent advances in vision and language domains, there is no suitable platform for the federated training of GNNs. To this end, we introduce FedGraphNN, an open research federated learning system and a benchmark to facilitate GNN-based FL research. FedGraphNN is built on a unified formulation of federated GNNs and supports commonly used datasets, GNN models, FL algorithms, and flexible APIs. We also contribute a new molecular dataset, hERG, to promote research exploration. Our experimental results present significant challenges in federated GNN training: federated GNNs perform worse in most datasets with a non-I.I.D split than centralized GNNs; the GNN model that attains the best result in the centralized setting may not hold its advantage in the federated setting. These results imply that more research efforts are needed to unravel the mystery behind federated GNN training. Moreover, our system performance analysis demonstrates that the FedGraphNN system is computationally affordable to most research labs with limited GPUs. We maintain the source code at


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