# Robust and Generalizable GNN Fine-Tuning via Uncertainty-aware Adapter Learning

arXiv: https://arxiv.org/abs/2511.18859 · HTML: https://mlsanity.com/paper/2511.18859/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 29 of its 35 references that are in the map.
- First posted on arXiv 24 Nov 2025.

## Builds on (most cited first, 29 of 29)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Parameter-Efficient Transfer Learning for NLP](https://mlsanity.com/paper/1902.00751/) (2019)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [What Uncertainties Do We Need in Bayesian Deep Learning for Computer Vision?](https://mlsanity.com/paper/1703.04977/) (2017)
- [Conditional Prompt Learning for Vision-Language Models](https://mlsanity.com/paper/2203.05557/) (2022)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [GCC: Graph Contrastive Coding for Graph Neural Network Pre-Training](https://mlsanity.com/paper/2006.09963/) (2020)
- [GPT-GNN: Generative Pre-Training of Graph Neural Networks](https://mlsanity.com/paper/2006.15437/) (2020)
- [Graph Self-Supervised Learning: A Survey](https://mlsanity.com/paper/2103.00111/) (2021)
- [Graph Random Neural Network for Semi-Supervised Learning on Graphs](https://mlsanity.com/paper/2005.11079/) (2020)
- [Self-Supervised Learning of Graph Neural Networks: A Unified Review](https://mlsanity.com/paper/2102.10757/) (2021)
- [SimGRACE: A Simple Framework for Graph Contrastive Learning without Data Augmentation](https://mlsanity.com/paper/2202.03104/) (2022)
- [GraphPrompt: Unifying Pre-Training and Downstream Tasks for Graph Neural Networks](https://mlsanity.com/paper/2302.08043/) (2023)
- [Universal Prompt Tuning for Graph Neural Networks](https://mlsanity.com/paper/2209.15240/) (2022)
- [A Survey of Knowledge Enhanced Pre-trained Language Models](https://mlsanity.com/paper/2211.05994/) (2022)
- [MAP: Multimodal Uncertainty-Aware Vision-Language Pre-training Model](https://mlsanity.com/paper/2210.05335/) (2022)
- [AdapterGNN: Parameter-Efficient Fine-Tuning Improves Generalization in GNNs](https://mlsanity.com/paper/2304.09595/) (2023)
- [G-Adapter: Towards Structure-Aware Parameter-Efficient Transfer Learning for Graph Transformer Networks](https://mlsanity.com/paper/2305.10329/) (2023)
- [GraphLoRA: Structure-Aware Contrastive Low-Rank Adaptation for Cross-Graph Transfer Learning](https://mlsanity.com/paper/2409.16670/) (2024)
- [Edge Prompt Tuning for Graph Neural Networks](https://mlsanity.com/paper/2503.00750/) (2025)
- [Uncertainty Aware Learning for Language Model Alignment](https://mlsanity.com/paper/2406.04854/) (2024)
- [MolCPT: Molecule Continuous Prompt Tuning to Generalize Molecular Representation Learning](https://mlsanity.com/paper/2212.10614/) (2022)
- [Beyond Graph Model: Reliable VLM Fine-Tuning via Random Graph Adapter](https://mlsanity.com/paper/2507.10355/) (2025)

## Abstract (arXiv)

Recently, fine-tuning large-scale pre-trained GNNs has yielded remarkable attention in adapting pre-trained GNN models for downstream graph learning tasks. One representative fine-tuning method is to exploit adapter (termed AdapterGNN) which aims to 'augment' the pre-trained model by inserting a lightweight module to make the 'augmented' model better adapt to the downstream tasks. However, graph data may contain various types of noise in downstream tasks, such as noisy edges and ambiguous node attributes. Existing AdapterGNNs are often prone to graph noise and exhibit limited generalizability. How to enhance the robustness and generalization ability of GNNs' fine tuning remains an open problem. In this paper, we show that the above problem can be well addressed by integrating uncertainty learning into the GNN adapter. We propose the Uncertainty-aware Adapter (UAdapterGNN) that fortifies pre-trained GNN models against noisy graph data in the fine-tuning process. Specifically, in contrast to regular AdapterGNN, our UAdapterGNN exploits Gaussian probabilistic adapter to augment the pre-trained GNN model. In this way, when the graph contains various noises,our method can automatically absorb the effects of changes in the variances of the Gaussian distribution, thereby significantly enhancing the model's robustness. Also, UAdapterGNN can further improve the generalization ability of the model on the downstream tasks. Extensive experiments on several benchmarks demonstrate the effectiveness, robustness and high generalization ability of the proposed UAdapterGNN method.