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Freeze, Prompt, and Adapt: A Framework for Source-free Unsupervised GNN Prompting

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Prompt tuning has become a key mechanism for adapting pre-trained Graph Neural Networks (GNNs) to new downstream tasks. However, existing approaches are predominantly supervised, relying on labeled data to optimize the prompting parameters and typically fine-tuning a task-specific prediction head -- practices that undermine the promise of parameter-efficient adaptation. We propose Unsupervised Graph Prompting Problem (UGPP), a challenging new setting where the pre-trained GNN is kept entirely frozen, labels on the target domain are unavailable, the source data is inaccessible, and the target distribution exhibits covariate shift. To address this, we propose UGPrompt, the first fully unsupervised GNN prompting framework. UGPrompt leverages consistency regularization and pseudo-labeling to train a prompting function, complemented with diversity and domain regularization to mitigate class imbalance and distribution mismatch. Our extensive experiments demonstrate that UGPrompt consistently outperforms state-of-the-art supervised prompting methods with access to labeled data, demonstrating the viability of unsupervised prompting as a practical adaptation paradigm for GNNs.

Peyman Baghershahi, Sourav Medya• 2025

Related benchmarks

TaskDatasetResultRank
Graph ClassificationPROTEINS--
1383
Node ClassificationTexas--
859
Graph ClassificationENZYMES--
419
Node ClassificationCiteseer
F1 Score45.7
20
Node ClassificationPubmed
F1 Score61.2
20
Node ClassificationFlickr
F1 Score17.6
19
Node ClassificationCora
F1 Score57.3
16
Node ClassificationCornell
F1 Score23.2
16
Node ClassificationWisconsin
F1 Score28
16
Node ClassificationCora
F1 Score0.573
16
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