Many data mining tasks rely on graphs to model relational structures among individuals (nodes). Since relational data are often sensitive, there is an urgent need to evaluate the privacy risks in graph data. One famous privacy attack against data analysis models is the model inversion attack, which aims to infer sensitive data in the training dataset and leads to great privacy concerns. Despite its success in grid-like domains, directly applying model inversion attacks on non-grid domains such as graph leads to poor attack performance. This is mainly due to the failure to consider the unique properties of graphs. To bridge this gap, we conduct a systematic study on model inversion attacks against Graph Neural Networks (GNNs), one of the state-of-the-art graph analysis tools in this paper. First, in the white-box setting where the attacker has full access to the target GNN model, we present GraphMI to infer the private training graph data. Specifically in GraphMI, a projected gradient module is proposed to tackle the discreteness of graph edges and preserve the sparsity and smoothness of graph features; a graph auto-encoder module is used to efficiently exploit graph topology, node attributes, and target model parameters for edge inference; a random sampling module can finally sample discrete edges. Furthermore, in the hard-label black-box setting where the attacker can only query the GNN API and receive the classification results, we propose two methods based on gradient estimation and reinforcement learning (RL-GraphMI). With the proposed methods, we study the connection between model inversion risk and edge influence and show that edges with greater influence are more likely to be recovered. Extensive experiments over several public datasets demonstrate the effectiveness of our methods. We also evaluate our attacks under two defenses: one is the well-designed differential private training, and the other is graph preprocessing. Our experimental results show that such defenses are not sufficiently effective and call for more advanced defenses against privacy attacks.

Despite the recent progress in Graph Neural Networks (GNNs), it remains challenging to explain the predictions made by GNNs. Existing explanation methods mainly focus on post-hoc explanations where another explanatory model is employed to provide explanations for a trained GNN. The fact that post-hoc methods fail to reveal the original reasoning process of GNNs raises the need of building GNNs with built-in interpretability. In this work, we propose Prototype Graph Neural Network (ProtGNN), which combines prototype learning with GNNs and provides a new perspective on the explanations of GNNs. In ProtGNN, the explanations are naturally derived from the case-based reasoning process and are actually used during classification. The prediction of ProtGNN is obtained by comparing the inputs to a few learned prototypes in the latent space. Furthermore, for better interpretability and higher efficiency, a novel conditional subgraph sampling module is incorporated to indicate which part of the input graph is most similar to each prototype in ProtGNN+. Finally, we evaluate our method on a wide range of datasets and perform concrete case studies. Extensive results show that ProtGNN and ProtGNN+ can provide inherent interpretability while achieving accuracy on par with the non-interpretable counterparts.

The Transformer architecture has achieved remarkable success in a number of domains including natural language processing and computer vision. However, when it comes to graph-structured data, transformers have not achieved competitive performance, especially on large graphs. In this paper, we identify the main deficiencies of current graph transformers: (1) Existing node sampling strategies in Graph Transformers are agnostic to the graph characteristics and the training process. (2) Most sampling strategies only focus on local neighbors and neglect the long-range dependencies in the graph. We conduct experimental investigations on synthetic datasets to show that existing sampling strategies are sub-optimal. To tackle the aforementioned problems, we formulate the optimization strategies of node sampling in Graph Transformer as an adversary bandit problem, where the rewards are related to the attention weights and can vary in the training procedure. Meanwhile, we propose a hierarchical attention scheme with graph coarsening to capture the long-range interactions while reducing computational complexity. Finally, we conduct extensive experiments on real-world datasets to demonstrate the superiority of our method over existing graph transformers and popular GNNs.

Predicting molecular properties with data-driven methods has drawn much attention in recent years. Particularly, Graph Neural Networks (GNNs) have demonstrated remarkable success in various molecular generation and prediction tasks. In cases where labeled data is scarce, GNNs can be pre-trained on unlabeled molecular data to first learn the general semantic and structural information before being finetuned for specific tasks. However, most existing self-supervised pretraining frameworks for GNNs only focus on node-level or graph-level tasks. These approaches cannot capture the rich information in subgraphs or graph motifs. For example, functional groups (frequently-occurred subgraphs in molecular graphs) often carry indicative information about the molecular properties. To bridge this gap, we propose Motif-based Graph Self-supervised Learning (MGSSL) by introducing a novel self-supervised motif generation framework for GNNs. First, for motif extraction from molecular graphs, we design a molecule fragmentation method that leverages a retrosynthesis-based algorithm BRICS and additional rules for controlling the size of motif vocabulary. Second, we design a general motif-based generative pretraining framework in which GNNs are asked to make topological and label predictions. This generative framework can be implemented in two different ways, i.e., breadth-first or depth-first. Finally, to take the multi-scale information in molecular graphs into consideration, we introduce a multi-level self-supervised pre-training. Extensive experiments on various downstream benchmark tasks show that our methods outperform all state-of-the-art baselines.

Molecular property prediction (e.g., energy) is an essential problem in chemistry and biology. Unfortunately, many supervised learning methods usually suffer from the problem of scarce labeled molecules in the chemical space, where such property labels are generally obtained by Density Functional Theory (DFT) calculation which is extremely computational costly. An effective solution is to incorporate the unlabeled molecules in a semi-supervised fashion. However, learning semi-supervised representation for large amounts of molecules is challenging, including the joint representation issue of both molecular essence and structure, the conflict between representation and property leaning. Here we propose a novel framework called Active Semi-supervised Graph Neural Network (ASGN) by incorporating both labeled and unlabeled molecules. Specifically, ASGN adopts a teacher-student framework. In the teacher model, we propose a novel semi-supervised learning method to learn general representation that jointly exploits information from molecular structure and molecular distribution. Then in the student model, we target at property prediction task to deal with the learning loss conflict. At last, we proposed a novel active learning strategy in terms of molecular diversities to select informative data during the whole framework learning. We conduct extensive experiments on several public datasets. Experimental results show the remarkable performance of our ASGN framework.