The paradigm of pre-training and fine-tuning graph neural networks has attracted wide research attention. In previous studies, the pre-trained models are viewed as universally versatile, and applied for a diverse range of downstream tasks. In many situations, however, this practice results in limited or even negative transfer. This paper, for the first time, emphasizes the specific application scope of graph pre-trained models: not all downstream tasks can effectively benefit from a graph pre-trained model. In light of this, we introduce the measure task consistency to quantify the similarity between graph pre-training and downstream tasks. This measure assesses the extent to which downstream tasks can benefit from specific pre-training tasks. Moreover, a novel fine-tuning strategy, Bridge-Tune, is proposed to further diminish the impact of the difference between pre-training and downstream tasks. The key innovation in Bridge-Tune is an intermediate step that bridges pre-training and downstream tasks. This step takes into account the task differences and further refines the pre-trained model. The superiority of the presented fine-tuning strategy is validated via numerous experiments with different pre-trained models and downstream tasks.

Graph neural networks (GNNs) have demonstrated remarkable success in numerous graph analytical tasks. Yet, their effectiveness is often compromised in real-world scenarios due to distribution shifts, limiting their capacity for knowledge transfer across changing environments or domains. Recently, Unsupervised Graph Domain Adaptation (UGDA) has been introduced to resolve this issue. UGDA aims to facilitate knowledge transfer from a labeled source graph to an unlabeled target graph. Current UGDA efforts primarily focus on model-centric methods, such as employing domain invariant learning strategies and designing model architectures. However, our critical examination reveals the limitations inherent to these model-centric methods, while a data-centric method allowed to modify the source graph provably demonstrates considerable potential. This insight motivates us to explore UGDA from a data-centric perspective. By revisiting the theoretical generalization bound for UGDA, we identify two data-centric principles for UGDA: alignment principle and rescaling principle. Guided by these principles, we propose GraphAlign, a novel UGDA method that generates a small yet transferable graph. By exclusively training a GNN on this new graph with classic Empirical Risk Minimization (ERM), GraphAlign attains exceptional performance on the target graph. Extensive experiments under various transfer scenarios demonstrate the GraphAlign outperforms the best baselines by an average of 2.16%, training on the generated graph as small as 0.25~1% of the original training graph.

Graph Neural Networks (GNNs) have significantly advanced the field of drug discovery, enhancing the speed and efficiency of molecular identification. However, training these GNNs demands vast amounts of molecular data, which has spurred the emergence of collaborative model-sharing initiatives. These initiatives facilitate the sharing of molecular pre-trained models among organizations without exposing proprietary training data. Despite the benefits, these molecular pre-trained models may still pose privacy risks. For example, malicious adversaries could perform data extraction attack to recover private training data, thereby threatening commercial secrets and collaborative trust. This work, for the first time, explores the risks of extracting private training molecular data from molecular pre-trained models. This task is nontrivial as the molecular pre-trained models are non-generative and exhibit a diversity of model architectures, which differs significantly from language and image models. To address these issues, we introduce a molecule generation approach and propose a novel, model-independent scoring function for selecting promising molecules. To efficiently reduce the search space of potential molecules, we further introduce a Molecule Extraction Policy Network for molecule extraction. Our experiments demonstrate that even with only query access to molecular pre-trained models, there is a considerable risk of extracting training data, challenging the assumption that model sharing alone provides adequate protection against data extraction attacks. Our codes are publicly available at: \url{https://github.com/renH2/Molextract}.

Pre-training on graph neural networks (GNNs) aims to learn transferable knowledge for downstream tasks with unlabeled data, and it has recently become an active research area. The success of graph pre-training models is often attributed to the massive amount of input data. In this paper, however, we identify the curse of big data phenomenon in graph pre-training: more training data do not necessarily lead to better downstream performance. Motivated by this observation, we propose a better-with-less framework for graph pre-training: fewer, but carefully chosen data are fed into a GNN model to enhance pre-training. The proposed pre-training pipeline is called the data-active graph pre-training (APT) framework, and is composed of a graph selector and a pre-training model. The graph selector chooses the most representative and instructive data points based on the inherent properties of graphs as well as predictive uncertainty. The proposed predictive uncertainty, as feedback from the pre-training model, measures the confidence level of the model in the data. When fed with the chosen data, on the other hand, the pre-training model grasps an initial understanding of the new, unseen data, and at the same time attempts to remember the knowledge learned from previous data. Therefore, the integration and interaction between these two components form a unified framework (APT), in which graph pre-training is performed in a progressive and iterative way. Experiment results show that the proposed APT is able to obtain an efficient pre-training model with fewer training data and better downstream performance.

Adversarial attacks on graphs have attracted considerable research interests. Existing works assume the attacker is either (partly) aware of the victim model, or able to send queries to it. These assumptions are, however, unrealistic. To bridge the gap between theoretical graph attacks and real-world scenarios, in this work, we propose a novel and more realistic setting: strict black-box graph attack, in which the attacker has no knowledge about the victim model at all and is not allowed to send any queries. To design such an attack strategy, we first propose a generic graph filter to unify different families of graph-based models. The strength of attacks can then be quantified by the change in the graph filter before and after attack. By maximizing this change, we are able to find an effective attack strategy, regardless of the underlying model. To solve this optimization problem, we also propose a relaxation technique and approximation theories to reduce the difficulty as well as the computational expense. Experiments demonstrate that, even with no exposure to the model, the Macro-F1 drops 6.4% in node classification and 29.5% in graph classification, which is a significant result compared with existent works.

Unsupervised/self-supervised pre-training methods for graph representation learning have recently attracted increasing research interests, and they are shown to be able to generalize to various downstream applications. Yet, the adversarial robustness of such pre-trained graph learning models remains largely unexplored. More importantly, most existing defense techniques designed for end-to-end graph representation learning methods require pre-specified label definitions, and thus cannot be directly applied to the pre-training methods. In this paper, we propose an unsupervised defense technique to robustify pre-trained deep graph models, so that the perturbations on the input graph can be successfully identified and blocked before the model is applied to different downstream tasks. Specifically, we introduce a mutual information-based measure, graph representation vulnerability (GRV), to quantify the robustness of graph encoders on the representation space. We then formulate an optimization problem to learn the graph representation by carefully balancing the trade-off between the expressive power and the robustness (i.e., GRV) of the graph encoder. The discrete nature of graph topology and the joint space of graph data make the optimization problem intractable to solve. To handle the above difficulty and to reduce computational expense, we further relax the problem and thus provide an approximate solution. Additionally, we explore a provable connection between the robustness of the unsupervised graph encoder and that of models on downstream tasks. Extensive experiments demonstrate that even without access to labels and tasks, our model is still able to enhance robustness against adversarial attacks on three downstream tasks (node classification, link prediction, and community detection) by an average of +16.5% compared with existing methods.