GENIE: Watermarking Graph Neural Networks for Link Prediction

TMLR Paper6549 Authors

18 Nov 2025 (modified: 21 Nov 2025)Under review for TMLREveryoneRevisionsBibTeXCC BY 4.0
Abstract: The rapid adoption, usefulness, and resource-intensive training of Graph Neural Network~(GNN) models have made them an invaluable intellectual property in graph-based machine learning. However, their wide-spread adoption also makes them susceptible to stealing, necessitating robust Ownership Demonstration~(OD) techniques. Watermarking is a promising OD framework for deep neural networks, but existing methods fail to generalize to GNNs due to the non-Euclidean nature of graph data. Existing works on GNN watermarking primarily focus on node and graph classification, overlooking Link Prediction (LP). In this paper, we propose \genie~(watermarking \textbf{G}raph n\textbf{E}ural \textbf{N}etworks for l\textbf{I}nk pr\textbf{E}diction), the first scheme to watermark GNNs for LP. \genie creates a novel backdoor for both node-representation and subgraph-based LP methods, utilizing a unique trigger set and a secret watermark vector. Our OD scheme is equipped with Dynamic Watermark Thresholding~(DWT), ensuring high verification probability while addressing practical issues in existing OD schemes. We extensively evaluate \genie across 4~diverse model architectures~(\ie SEAL, GCN, GraphSAGE and NeoGNN), 7~real-world datasets and 21~watermark removal techniques and demonstrate its robustness to watermark removal and ownership piracy attacks. Finally, we discuss adaptive attacks against \genie and a defense strategy to counter it.
Submission Type: Regular submission (no more than 12 pages of main content)
Assigned Action Editor: ~Alessandro_De_Palma1
Submission Number: 6549
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