Papers › Fine-Tuning Graph Neural Networks via Graph Topology induced Optimal Transport

Fine-Tuning Graph Neural Networks via Graph Topology induced Optimal Transport

20 Mar 2022arXiv:2203.10453archive 2025-07-28

Jiying Zhang, Xi Xiao, Long-Kai Huang, Yu Rong, Yatao Bian

Recently, the pretrain-finetuning paradigm has attracted tons of attention in graph learning community due to its power of alleviating the lack of labels problem in many real-world applications. Current studies use existing techniques, such as weight constraint, representation constraint, which are derived from images or text data, to transfer the invariant knowledge from the pre-train stage to fine-tuning stage. However, these methods failed to preserve invariances from graph structure and Graph Neural Network (GNN) style models. In this paper, we present a novel optimal transport-based fine-tuning framework called GTOT-Tuning, namely, Graph Topology induced Optimal Transport fine-Tuning, for GNN style backbones. GTOT-Tuning is required to utilize the property of graph data to enhance the preservation of representation produced by fine-tuned networks. Toward this goal, we formulate graph local knowledge transfer as an Optimal Transport (OT) problem with a structural prior and construct the GTOT regularizer to constrain the fine-tuned model behaviors. By using the adjacency relationship amongst nodes, the GTOT regularizer achieves node-level optimal transport procedures and reduces redundant transport procedures, resulting in efficient knowledge transfer from the pre-trained models. We evaluate GTOT-Tuning on eight downstream tasks with various GNN backbones and demonstrate that it achieves state-of-the-art fine-tuning performance for GNNs.

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GTOT youjibiying/gtot-tuning/chem/ftlib/finetune/gtot_tuning.py official repository unverified MIT (permissive) · 4a82591e4f77c220 · report
GTOTRegularization youjibiying/gtot-tuning/chem/ftlib/finetune/gtot_tuning.py official repository unverified MIT (permissive) · dc6ca28379960dea · report

Tasks

Graph ClassificationGraph LearningGraph Neural NetworkMolecular Property PredictionTransfer Learning

Results from the paper archive 2025-07-28

TaskDatasetModelMetricValueRank at snapshotLeaderboardReport
Graph Classification BACE GTOT-Tuning ROC-AUC 83.4 #2 of 2 Archive leaderboard report
Graph Classification BBBP GTOT-Tuning ROC-AUC 70 #2 of 3 Archive leaderboard report
Graph Classification HIV GTOT-Tuning ROC-AUC 78.2 #1 of 3 Archive leaderboard report
Graph Classification MUV GTOT-Tuning ROC-AUC 80 #1 of 2 Archive leaderboard report
Graph Classification SIDER GTOT-Tuning ROC-AUC 63.5 #1 of 2 Archive leaderboard report
Graph Classification Tox21 GTOT-Tuning ROC-AUC 75.6 #3 of 3 Archive leaderboard report
Graph Classification ToxCast GTOT-Tuning ROC-AUC 64 #3 of 3 Archive leaderboard report
Graph Classification clintox GTOT-Tuning ROC-AUC 72 #2 of 2 Archive leaderboard report

Ranks are positions in the archive's leaderboards as they stood at the 2025-07-28 snapshot. Results published since then are not among these rows, so a rank here is not a current standing.

Methods

Graph Neural Network

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