The exploration of Graph Neural Networks (GNNs) for processing graph-structured data has expanded, particularly their potential for causal analysis due to their universal approximation capabilities. Anticipated to significantly enhance common graph-based tasks such as classification and prediction, the development of a causally enhanced GNN framework is yet to be thoroughly investigated. Addressing this shortfall, our study delves into nine benchmark graph classification models, testing their strength and versatility across seven datasets spanning three varied domains to discern the impact of causality on the predictive prowess of GNNs. This research offers a detailed assessment of these models, shedding light on their efficiency, and flexibility in different data environments, and highlighting areas needing advancement. Our findings are instrumental in furthering the understanding and practical application of GNNs in diverse datacentric fields
Self-supervised graph representation learning has recently shown considerable promise in a range of fields, including bioinformatics and social networks. A large number of graph contrastive learning approaches have shown promising performance for representation learning on graphs, which train models by maximizing agreement between original graphs and their augmented views (i.e., positive views). Unfortunately, these methods usually involve pre-defined augmentation strategies based on the knowledge of human experts. Moreover, these strategies may fail to generate challenging positive views to provide sufficient supervision signals. In this paper, we present a novel approach named Graph Pooling ContraSt (GPS) to address these issues. Motivated by the fact that graph pooling can adaptively coarsen the graph with the removal of redundancy, we rethink graph pooling and leverage it to automatically generate multi-scale positive views with varying emphasis on providing challenging positives and preserving semantics, i.e., strongly-augmented view and weakly-augmented view. Then, we incorporate both views into a joint contrastive learning framework with similarity learning and consistency learning, where our pooling module is adversarially trained with respect to the encoder for adversarial robustness. Experiments on twelve datasets on both graph classification and transfer learning tasks verify the superiority of the proposed method over its counterparts.
Topological data analysis (TDA) is gaining prominence across a wide spectrum of machine learning tasks that spans from manifold learning to graph classification. A pivotal technique within TDA is persistent homology (PH), which furnishes an exclusive topological imprint of data by tracing the evolution of latent structures as a scale parameter changes. Present PH tools are confined to analyzing data through a single filter parameter. However, many scenarios necessitate the consideration of multiple relevant parameters to attain finer insights into the data. We address this issue by introducing the Effective Multidimensional Persistence (EMP) framework. This framework empowers the exploration of data by simultaneously varying multiple scale parameters. The framework integrates descriptor functions into the analysis process, yielding a highly expressive data summary. It seamlessly integrates established single PH summaries into multidimensional counterparts like EMP Landscapes, Silhouettes, Images, and Surfaces. These summaries represent data's multidimensional aspects as matrices and arrays, aligning effectively with diverse ML models. We provide theoretical guarantees and stability proofs for EMP summaries. We demonstrate EMP's utility in graph classification tasks, showing its effectiveness. Results reveal that EMP enhances various single PH descriptors, outperforming cutting-edge methods on multiple benchmark datasets.
Graph classification is an important learning task for graph-structured data. Graph neural networks (GNNs) have recently gained growing attention in graph learning and have shown significant improvements in many important graph problems. Despite their state-of-the-art performances, existing GNNs only use local information from a very limited neighborhood around each node, suffering from loss of multi-modal information and overheads of excessive computation. To address these issues, we propose a novel Tensor-view Topological Graph Neural Network (TTG-NN), a class of simple yet effective topological deep learning built upon persistent homology, graph convolution, and tensor operations. This new method incorporates tensor learning to simultaneously capture Tensor-view Topological (TT), as well as Tensor-view Graph (TG) structural information on both local and global levels. Computationally, to fully exploit graph topology and structure, we propose two flexible TT and TG representation learning modules that disentangle feature tensor aggregation and transformation and learn to preserve multi-modal structure with less computation. Theoretically, we derive high probability bounds on both the out-of-sample and in-sample mean squared approximation errors for our proposed Tensor Transformation Layer (TTL). Real data experiments show that the proposed TTG-NN outperforms 20 state-of-the-art methods on various graph benchmarks.
Graph Neural Networks have become the preferred tool to process graph data, with their efficacy being boosted through graph data augmentation techniques. Despite the evolution of augmentation methods, issues like graph property distortions and restricted structural changes persist. This leads to the question: Is it possible to develop more property-conserving and structure-sensitive augmentation methods? Through a spectral lens, we investigate the interplay between graph properties, their augmentation, and their spectral behavior, and observe that keeping the low-frequency eigenvalues unchanged can preserve the critical properties at a large scale when generating augmented graphs. These observations inform our introduction of the Dual-Prism (DP) augmentation methods, including DP-Noise and DP-Mask, which retain essential graph properties while diversifying augmented graphs. Extensive experiments validate the efficiency of our approach, providing a new and promising direction for graph data augmentation.
As one of the most effective self-supervised representation learning methods, contrastive learning (CL) relies on multiple negative pairs to contrast against each positive pair. In the standard practice of contrastive learning, data augmentation methods are utilized to generate both positive and negative pairs. While existing works have been focusing on improving the positive sampling, the negative sampling process is often overlooked. In fact, the generated negative samples are often polluted by positive samples, which leads to a biased loss and performance degradation. To correct the negative sampling bias, we propose a novel contrastive learning method named Positive-Unlabeled Contrastive Learning (PUCL). PUCL treats the generated negative samples as unlabeled samples and uses information from positive samples to correct bias in contrastive loss. We prove that the corrected loss used in PUCL only incurs a negligible bias compared to the unbiased contrastive loss. PUCL can be applied to general contrastive learning problems and outperforms state-of-the-art methods on various image and graph classification tasks. The code of PUCL is in the supplementary file.
Graph neural networks are increasingly becoming the framework of choice for graph-based machine learning. In this paper, we propose a new graph neural network architecture that substitutes classical message passing with an analysis of the local distribution of node features. To this end, we extract the distribution of features in the egonet for each local neighbourhood and compare them against a set of learned label distributions by taking the histogram intersection kernel. The similarity information is then propagated to other nodes in the network, effectively creating a message passing-like mechanism where the message is determined by the ensemble of the features. We perform an ablation study to evaluate the network's performance under different choices of its hyper-parameters. Finally, we test our model on standard graph classification and regression benchmarks, and we find that it outperforms widely used alternative approaches, including both graph kernels and graph neural networks.
This paper studies four Graph Neural Network architectures (GNNs) for a graph classification task on a synthetic dataset created using classic generative models of Network Science. Since the synthetic networks do not contain (node or edge) features, five different augmentation strategies (artificial feature types) are applied to nodes. All combinations of the 4 GNNs (GCN with Hierarchical and Global aggregation, GIN and GATv2) and the 5 feature types (constant 1, noise, degree, normalized degree and ID -- a vector of the number of cycles of various lengths) are studied and their performances compared as a function of the hidden dimension of artificial neural networks used in the GNNs. The generalisation ability of these models is also analysed using a second synthetic network dataset (containing networks of different sizes).Our results point towards the balanced importance of the computational power of the GNN architecture and the the information level provided by the artificial features. GNN architectures with higher computational power, like GIN and GATv2, perform well for most augmentation strategies. On the other hand, artificial features with higher information content, like ID or degree, not only consistently outperform other augmentation strategies, but can also help GNN architectures with lower computational power to achieve good performance.
Spectral embedding is a powerful graph embedding technique that has received a lot of attention recently due to its effectiveness on Graph Transformers. However, from a theoretical perspective, the universal expressive power of spectral embedding comes at the price of losing two important invariance properties of graphs, sign and basis invariance, which also limits its effectiveness on graph data. To remedy this issue, many previous methods developed costly approaches to learn new invariants and suffer from high computation complexity. In this work, we explore a minimal approach that resolves the ambiguity issues by directly finding canonical directions for the eigenvectors, named Laplacian Canonization (LC). As a pure pre-processing method, LC is light-weighted and can be applied to any existing GNNs. We provide a thorough investigation, from theory to algorithm, on this approach, and discover an efficient algorithm named Maximal Axis Projection (MAP) that works for both sign and basis invariance and successfully canonizes more than 90% of all eigenvectors. Experiments on real-world benchmark datasets like ZINC, MOLTOX21, and MOLPCBA show that MAP consistently outperforms existing methods while bringing minimal computation overhead. Code is available at https://github.com/PKU-ML/LaplacianCanonization.
While graph neural networks (GNNs) are widely used for node and graph representation learning tasks, the reliability of GNN uncertainty estimates under distribution shifts remains relatively under-explored. Indeed, while post-hoc calibration strategies can be used to improve in-distribution calibration, they need not also improve calibration under distribution shift. However, techniques which produce GNNs with better intrinsic uncertainty estimates are particularly valuable, as they can always be combined with post-hoc strategies later. Therefore, in this work, we propose G-$\Delta$UQ, a novel training framework designed to improve intrinsic GNN uncertainty estimates. Our framework adapts the principle of stochastic data centering to graph data through novel graph anchoring strategies, and is able to support partially stochastic GNNs. While, the prevalent wisdom is that fully stochastic networks are necessary to obtain reliable estimates, we find that the functional diversity induced by our anchoring strategies when sampling hypotheses renders this unnecessary and allows us to support G-$\Delta$UQ on pretrained models. Indeed, through extensive evaluation under covariate, concept and graph size shifts, we show that G-$\Delta$UQ leads to better calibrated GNNs for node and graph classification. Further, it also improves performance on the uncertainty-based tasks of out-of-distribution detection and generalization gap estimation. Overall, our work provides insights into uncertainty estimation for GNNs, and demonstrates the utility of G-$\Delta$UQ in obtaining reliable estimates.
Graph Neural Networks (GNNs) are a class of deep learning models capable of processing graph-structured data, and they have demonstrated significant performance in a variety of real-world applications. Recent studies have found that GNN models are vulnerable to backdoor attacks. When specific patterns (called backdoor triggers, e.g., subgraphs, nodes, etc.) appear in the input data, the backdoor embedded in the GNN models is activated, which misclassifies the input data into the target class label specified by the attacker, whereas when there are no backdoor triggers in the input, the backdoor embedded in the GNN models is not activated, and the models work normally. Backdoor attacks are highly stealthy and expose GNN models to serious security risks. Currently, research on backdoor attacks against GNNs mainly focus on tasks such as graph classification and node classification, and backdoor attacks against link prediction tasks are rarely studied. In this paper, we propose a backdoor attack against the link prediction tasks based on GNNs and reveal the existence of such security vulnerability in GNN models, which make the backdoored GNN models to incorrectly predict unlinked two nodes as having a link relationship when a trigger appear. The method uses a single node as the trigger and poison selected node pairs in the training graph, and then the backdoor will be embedded in the GNN models through the training process. In the inference stage, the backdoor in the GNN models can be activated by simply linking the trigger node to the two end nodes of the unlinked node pairs in the input data, causing the GNN models to produce incorrect link prediction results for the target node pairs.
Generating explanations for graph neural networks (GNNs) has been studied to understand their behavior in analytical tasks such as graph classification. Existing approaches aim to understand the overall results of GNNs rather than providing explanations for specific class labels of interest, and may return explanation structures that are hard to access, nor directly queryable.We propose GVEX, a novel paradigm that generates Graph Views for EXplanation. (1) We design a two-tier explanation structure called explanation views. An explanation view consists of a set of graph patterns and a set of induced explanation subgraphs. Given a database G of multiple graphs and a specific class label l assigned by a GNN-based classifier M, it concisely describes the fraction of G that best explains why l is assigned by M. (2) We propose quality measures and formulate an optimization problem to compute optimal explanation views for GNN explanation. We show that the problem is $\Sigma^2_P$-hard. (3) We present two algorithms. The first one follows an explain-and-summarize strategy that first generates high-quality explanation subgraphs which best explain GNNs in terms of feature influence maximization, and then performs a summarization step to generate patterns. We show that this strategy provides an approximation ratio of 1/2. Our second algorithm performs a single-pass to an input node stream in batches to incrementally maintain explanation views, having an anytime quality guarantee of 1/4 approximation. Using real-world benchmark data, we experimentally demonstrate the effectiveness, efficiency, and scalability of GVEX. Through case studies, we showcase the practical applications of GVEX.
The study of Graph Neural Networks has received considerable interest in the past few years. By extending deep learning to graph-structured data, GNNs can solve a diverse set of tasks in fields including social science, chemistry, and medicine. The development of GNN architectures has largely been focused on improving empirical performance on tasks like node or graph classification. However, a line of recent work has instead sought to find GNN architectures that have desirable theoretical properties - by studying their expressive power and designing architectures that maximize this expressiveness. While there is no consensus on the best way to define the expressiveness of a GNN, it can be viewed from several well-motivated perspectives. Perhaps the most natural approach is to study the universal approximation properties of GNNs, much in the way that this has been studied extensively for MLPs. Another direction focuses on the extent to which GNNs can distinguish between different graph structures, relating this to the graph isomorphism test. Besides, a GNN's ability to compute graph properties such as graph moments has been suggested as another form of expressiveness. All of these different definitions are complementary and have yielded different recommendations for GNN architecture choices. In this paper, we would like to give an overview of the notion of "expressive power" of GNNs and provide some valuable insights regarding the design choices of GNNs.
The crux of graph classification lies in the effective representation learning for the entire graph. Typical graph neural networks focus on modeling the local dependencies when aggregating features of neighboring nodes, and obtain the representation for the entire graph by aggregating node features. Such methods have two potential limitations: 1) the global node saliency w.r.t. graph classification is not explicitly modeled, which is crucial since different nodes may have different semantic relevance to graph classification; 2) the graph representation directly aggregated from node features may have limited effectiveness to reflect graph-level information. In this work, we propose the Saliency-Aware Regularized Graph Neural Network (SAR-GNN) for graph classification, which consists of two core modules: 1) a traditional graph neural network serving as the backbone for learning node features and 2) the Graph Neural Memory designed to distill a compact graph representation from node features of the backbone. We first estimate the global node saliency by measuring the semantic similarity between the compact graph representation and node features. Then the learned saliency distribution is leveraged to regularize the neighborhood aggregation of the backbone, which facilitates the message passing of features for salient nodes and suppresses the less relevant nodes. Thus, our model can learn more effective graph representation. We demonstrate the merits of SAR-GNN by extensive experiments on seven datasets across various types of graph data. Code will be released.
Neural networks are increasingly finding their way into the realm of graphs and modeling relationships between features. Concurrently graph neural network explanation approaches are being invented to uncover relationships between the nodes of the graphs. However, there is a disparity between the existing attribution methods, and it is unclear which attribution to trust. Therefore research has introduced evaluation experiments that assess them from different perspectives. In this work, we assess attribution methods from a perspective not previously explored in the graph domain: retraining. The core idea is to retrain the network on important (or not important) relationships as identified by the attributions and evaluate how networks can generalize based on these relationships. We reformulate the retraining framework to sidestep issues lurking in the previous formulation and propose guidelines for correct analysis. We run our analysis on four state-of-the-art GNN attribution methods and five synthetic and real-world graph classification datasets. The analysis reveals that attributions perform variably depending on the dataset and the network. Most importantly, we observe that the famous GNNExplainer performs similarly to an arbitrary designation of edge importance. The study concludes that the retraining evaluation cannot be used as a generalized benchmark and recommends it as a toolset to evaluate attributions on a specifically addressed network, dataset, and sparsity.
This paper analyses LightGCN in the context of graph recommendation algorithms. Despite the initial design of Graph Convolutional Networks for graph classification, the non-linear operations are not always essential. LightGCN enables linear propagation of embeddings, enhancing performance. We reproduce the original findings, assess LightGCN's robustness on diverse datasets and metrics, and explore Graph Diffusion as an augmentation of signal propagation in LightGCN.
Despite the remarkable accomplishments of graph neural networks (GNNs), they typically rely on task-specific labels, posing potential challenges in terms of their acquisition. Existing work have been made to address this issue through the lens of unsupervised domain adaptation, wherein labeled source graphs are utilized to enhance the learning process for target data. However, the simultaneous exploration of graph topology and reduction of domain disparities remains a substantial hurdle. In this paper, we introduce the Dual Adversarial Graph Representation Learning (DAGRL), which explore the graph topology from dual branches and mitigate domain discrepancies via dual adversarial learning. Our method encompasses a dual-pronged structure, consisting of a graph convolutional network branch and a graph kernel branch, which enables us to capture graph semantics from both implicit and explicit perspectives. Moreover, our approach incorporates adaptive perturbations into the dual branches, which align the source and target distribution to address domain discrepancies. Extensive experiments on a wild range graph classification datasets demonstrate the effectiveness of our proposed method.
Recently, the paradigm of pre-training and fine-tuning graph neural networks has been intensively studied and applied in a wide range of graph mining tasks. Its success is generally attributed to the structural consistency between pre-training and downstream datasets, which, however, does not hold in many real-world scenarios. Existing works have shown that the structural divergence between pre-training and downstream graphs significantly limits the transferability when using the vanilla fine-tuning strategy. This divergence leads to model overfitting on pre-training graphs and causes difficulties in capturing the structural properties of the downstream graphs. In this paper, we identify the fundamental cause of structural divergence as the discrepancy of generative patterns between the pre-training and downstream graphs. Furthermore, we propose G-Tuning to preserve the generative patterns of downstream graphs. Given a downstream graph G, the core idea is to tune the pre-trained GNN so that it can reconstruct the generative patterns of G, the graphon W. However, the exact reconstruction of a graphon is known to be computationally expensive. To overcome this challenge, we provide a theoretical analysis that establishes the existence of a set of alternative graphons called graphon bases for any given graphon. By utilizing a linear combination of these graphon bases, we can efficiently approximate W. This theoretical finding forms the basis of our proposed model, as it enables effective learning of the graphon bases and their associated coefficients. Compared with existing algorithms, G-Tuning demonstrates an average improvement of 0.5% and 2.6% on in-domain and out-of-domain transfer learning experiments, respectively.
Recent research demonstrates that GNNs are vulnerable to the model stealing attack, a nefarious endeavor geared towards duplicating the target model via query permissions. However, they mainly focus on node classification tasks, neglecting the potential threats entailed within the domain of graph classification tasks. Furthermore, their practicality is questionable due to unreasonable assumptions, specifically concerning the large data requirements and extensive model knowledge. To this end, we advocate following strict settings with limited real data and hard-label awareness to generate synthetic data, thereby facilitating the stealing of the target model. Specifically, following important data generation principles, we introduce three model stealing attacks to adapt to different actual scenarios: MSA-AU is inspired by active learning and emphasizes the uncertainty to enhance query value of generated samples; MSA-AD introduces diversity based on Mixup augmentation strategy to alleviate the query inefficiency issue caused by over-similar samples generated by MSA-AU; MSA-AUD combines the above two strategies to seamlessly integrate the authenticity, uncertainty, and diversity of the generated samples. Finally, extensive experiments consistently demonstrate the superiority of the proposed methods in terms of concealment, query efficiency, and stealing performance.
Graph representation learning is a fundamental research theme and can be generalized to benefit multiple downstream tasks from the node and link levels to the higher graph level. In practice, it is desirable to develop task-agnostic general graph representation learning methods that are typically trained in an unsupervised manner. Related research reveals that the power of graph representation learning methods depends on whether they can differentiate distinct graph structures as different embeddings and map isomorphic graphs to consistent embeddings (i.e., the isomorphic consistency of graph models). However, for task-agnostic general graph representation learning, existing unsupervised graph models, represented by the variational graph auto-encoders (VGAEs), can only keep the isomorphic consistency within the subgraphs of 1-hop neighborhoods and thus usually manifest inferior performance on the more difficult higher-level tasks. To overcome the limitations of existing unsupervised methods, in this paper, we propose the Isomorphic-Consistent VGAE (IsoC-VGAE) for multi-level task-agnostic graph representation learning. We first devise a decoding scheme to provide a theoretical guarantee of keeping the isomorphic consistency under the settings of unsupervised learning. We then propose the Inverse Graph Neural Network (Inv-GNN) decoder as its intuitive realization, which trains the model via reconstructing the GNN node embeddings with multi-hop neighborhood information, so as to maintain the high-order isomorphic consistency within the VGAE framework. We conduct extensive experiments on the representative graph learning tasks at different levels, including node classification, link prediction and graph classification, and the results verify that our proposed model generally outperforms both the state-of-the-art unsupervised methods and representative supervised methods.