Graph neural networks (GNNs) have attracted significant attention for their outstanding performance in graph learning and node classification tasks. However, their vulnerability to adversarial attacks, particularly through susceptible nodes, poses a challenge in decision-making. The need for robust graph summarization is evident in adversarial challenges resulting from the propagation of attacks throughout the entire graph. In this paper, we address both performance and adversarial robustness in graph input by introducing the novel technique SHERD (Subgraph Learning Hale through Early Training Representation Distances). SHERD leverages information from layers of a partially trained graph convolutional network (GCN) to detect susceptible nodes during adversarial attacks using standard distance metrics. The method identifies "vulnerable (bad)" nodes and removes such nodes to form a robust subgraph while maintaining node classification performance. Through our experiments, we demonstrate the increased performance of SHERD in enhancing robustness by comparing the network's performance on original and subgraph inputs against various baselines alongside existing adversarial attacks. Our experiments across multiple datasets, including citation datasets such as Cora, Citeseer, and Pubmed, as well as microanatomical tissue structures of cell graphs in the placenta, highlight that SHERD not only achieves substantial improvement in robust performance but also outperforms several baselines in terms of node classification accuracy and computational complexity.
The opioid crisis has been one of the most critical society concerns in the United States. Although the medication assisted treatment (MAT) is recognized as the most effective treatment for opioid misuse and addiction, the various side effects can trigger opioid relapse. In addition to MAT, the dietary nutrition intervention has been demonstrated its importance in opioid misuse prevention and recovery. However, research on the alarming connections between dietary patterns and opioid misuse remain under-explored. In response to this gap, in this paper, we first establish a large-scale multifaceted dietary benchmark dataset related to opioid users at the first attempt and then develop a novel framework - i.e., namely Opioid Misuse Detection with Interpretable Dietary Patterns (Diet-ODIN) - to bridge heterogeneous graph (HG) and large language model (LLM) for the identification of users with opioid misuse and the interpretation of their associated dietary patterns. Specifically, in Diet-ODIN, we first construct an HG to comprehensively incorporate both dietary and health-related information, and then we devise a holistic graph learning framework with noise reduction to fully capitalize both users' individual dietary habits and shared dietary patterns for the detection of users with opioid misuse. To further delve into the intricate correlations between dietary patterns and opioid misuse, we exploit an LLM by utilizing the knowledge obtained from the graph learning model for interpretation. The extensive experimental results based on our established benchmark with quantitative and qualitative measures demonstrate the outstanding performance of Diet-ODIN in exploring the complex interplay between opioid misuse and dietary patterns, by comparison with state-of-the-art baseline methods.
The generalization performance of deep neural networks in classification tasks is a major concern in machine learning research. Despite widespread techniques used to diminish the over-fitting issue such as data augmentation, pseudo-labeling, regularization, and ensemble learning, this performance still needs to be enhanced with other approaches. In recent years, it has been theoretically demonstrated that the loss function characteristics i.e. its Lipschitzness and maximum value affect the generalization performance of deep neural networks which can be utilized as a guidance to propose novel distance measures. In this paper, by analyzing the aforementioned characteristics, we introduce a distance called Reduced Jeffries-Matusita as a loss function for training deep classification models to reduce the over-fitting issue. In our experiments, we evaluate the new loss function in two different problems: image classification in computer vision and node classification in the context of graph learning. The results show that the new distance measure stabilizes the training process significantly, enhances the generalization ability, and improves the performance of the models in the Accuracy and F1-score metrics, even if the training set size is small.
Wildfire forecasting is notoriously hard due to the complex interplay of different factors such as weather conditions, vegetation types and human activities. Deep learning models show promise in dealing with this complexity by learning directly from data. However, to inform critical decision making, we argue that we need models that are right for the right reasons; that is, the implicit rules learned should be grounded by the underlying processes driving wildfires. In that direction, we propose integrating causality with Graph Neural Networks (GNNs) that explicitly model the causal mechanism among complex variables via graph learning. The causal adjacency matrix considers the synergistic effect among variables and removes the spurious links from highly correlated impacts. Our methodology's effectiveness is demonstrated through superior performance forecasting wildfire patterns in the European boreal and mediterranean biome. The gain is especially prominent in a highly imbalanced dataset, showcasing an enhanced robustness of the model to adapt to regime shifts in functional relationships. Furthermore, SHAP values from our trained model further enhance our understanding of the model's inner workings.
Functional MRI (fMRI) research, employing naturalistic stimuli like movies, explores brain network interactions in complex cognitive processes such as empathy. The empathy network encompasses multiple brain areas, including the Insula, PFC, ACC, and parietal regions. Our novel processing pipeline applies graph learning methods to whole-brain timeseries signals, incorporating high-pass filtering, voxel-level clustering, and windowed graph learning with a sparsity-based approach. The study involves two short movies shown to 14 healthy volunteers, considering 54 regions extracted from the AAL Atlas. The sparsity-based graph learning consistently outperforms, achieving over 88% accuracy in capturing emotion contagion variations. Temporal analysis reveals a gradual induction of empathy, supported by the method's effectiveness in capturing dynamic connectomes through graph clustering. Edge-weight dynamics analysis underscores sparsity-based learning's superiority, while connectome-network analysis highlights the pivotal role of the Insula, Amygdala, and Thalamus in empathy. Spectral filtering analysis emphasizes the band-pass filter's significance in isolating regions linked to emotional and empathetic processing during empathy HIGH states. Key regions like Amygdala, Insula, and Angular Gyrus consistently activate, supporting their critical role in immediate emotional responses. Strong similarities across movies in graph cluster labels, connectome-network analysis, and spectral filtering-based analyses reveal robust neural correlates of empathy. These findings advance our understanding of empathy-related neural dynamics and identify specific regions in empathetic responses, offering insights for targeted interventions and treatments associated with empathetic processing.
We formulate an XAI-based model improvement approach for Graph Neural Networks (GNNs) for node classification, called Explanation Enhanced Graph Learning (EEGL). The goal is to improve predictive performance of GNN using explanations. EEGL is an iterative self-improving algorithm, which starts with a learned "vanilla" GNN, and repeatedly uses frequent subgraph mining to find relevant patterns in explanation subgraphs. These patterns are then filtered further to obtain application-dependent features corresponding to the presence of certain subgraphs in the node neighborhoods. Giving an application-dependent algorithm for such a subgraph-based extension of the Weisfeiler-Leman (1-WL) algorithm has previously been posed as an open problem. We present experimental evidence, with synthetic and real-world data, which show that EEGL outperforms related approaches in predictive performance and that it has a node-distinguishing power beyond that of vanilla GNNs. We also analyze EEGL's training dynamics.
Graph Neural Networks (GNNs) have been extensively used in various real-world applications. However, the predictive uncertainty of GNNs stemming from diverse sources such as inherent randomness in data and model training errors can lead to unstable and erroneous predictions. Therefore, identifying, quantifying, and utilizing uncertainty are essential to enhance the performance of the model for the downstream tasks as well as the reliability of the GNN predictions. This survey aims to provide a comprehensive overview of the GNNs from the perspective of uncertainty with an emphasis on its integration in graph learning. We compare and summarize existing graph uncertainty theory and methods, alongside the corresponding downstream tasks. Thereby, we bridge the gap between theory and practice, meanwhile connecting different GNN communities. Moreover, our work provides valuable insights into promising directions in this field.
A key challenge in federated learning applications is the statistical heterogeneity of local datasets. Clustered federated learning addresses this challenge by identifying clusters of local datasets that are approximately homogeneous. One recent approach to clustered federated learning is generalized total variation minimization (GTVMin). This approach requires a similarity graph which can be obtained by domain expertise or in a data-driven fashion via graph learning techniques. Under a widely applicable clustering assumption, we derive an upper bound the deviation between GTVMin solutions and their cluster-wise averages. This bound provides valuable insights into the effectiveness and robustness of GTVMin in addressing statistical heterogeneity within federated learning environments.
Fair graph learning plays a pivotal role in numerous practical applications. Recently, many fair graph learning methods have been proposed; however, their evaluation often relies on poorly constructed semi-synthetic datasets or substandard real-world datasets. In such cases, even a basic Multilayer Perceptron (MLP) can outperform Graph Neural Networks (GNNs) in both utility and fairness. In this work, we illustrate that many datasets fail to provide meaningful information in the edges, which may challenge the necessity of using graph structures in these problems. To address these issues, we develop and introduce a collection of synthetic, semi-synthetic, and real-world datasets that fulfill a broad spectrum of requirements. These datasets are thoughtfully designed to include relevant graph structures and bias information crucial for the fair evaluation of models. The proposed synthetic and semi-synthetic datasets offer the flexibility to create data with controllable bias parameters, thereby enabling the generation of desired datasets with user-defined bias values with ease. Moreover, we conduct systematic evaluations of these proposed datasets and establish a unified evaluation approach for fair graph learning models. Our extensive experimental results with fair graph learning methods across our datasets demonstrate their effectiveness in benchmarking the performance of these methods. Our datasets and the code for reproducing our experiments are available at https://github.com/XweiQ/Benchmark-GraphFairness.
In recent times, a plethora of hardware accelerators have been put forth for graph learning applications such as vertex classification and graph classification. However, previous works have paid little attention to Knowledge Graph Completion (KGC), a task that is well-known for its significantly higher algorithm complexity. The state-of-the-art KGC solutions based on graph convolution neural network (GCN) involve extensive vertex/relation embedding updates and complicated score functions, which are inherently cumbersome for acceleration. As a result, existing accelerator designs are no longer optimal, and a novel algorithm-hardware co-design for KG reasoning is needed. Recently, brain-inspired HyperDimensional Computing (HDC) has been introduced as a promising solution for lightweight machine learning, particularly for graph learning applications. In this paper, we leverage HDC for an intrinsically more efficient and acceleration-friendly KGC algorithm. We also co-design an acceleration framework named HDReason targeting FPGA platforms. On the algorithm level, HDReason achieves a balance between high reasoning accuracy, strong model interpretability, and less computation complexity. In terms of architecture, HDReason offers reconfigurability, high training throughput, and low energy consumption. When compared with NVIDIA RTX 4090 GPU, the proposed accelerator achieves an average 10.6x speedup and 65x energy efficiency improvement. When conducting cross-models and cross-platforms comparison, HDReason yields an average 4.2x higher performance and 3.4x better energy efficiency with similar accuracy versus the state-of-the-art FPGA-based GCN training platform.
Bilevel optimization refers to scenarios whereby the optimal solution of a lower-level energy function serves as input features to an upper-level objective of interest. These optimal features typically depend on tunable parameters of the lower-level energy in such a way that the entire bilevel pipeline can be trained end-to-end. Although not generally presented as such, this paper demonstrates how a variety of graph learning techniques can be recast as special cases of bilevel optimization or simplifications thereof. In brief, building on prior work we first derive a more flexible class of energy functions that, when paired with various descent steps (e.g., gradient descent, proximal methods, momentum, etc.), form graph neural network (GNN) message-passing layers; critically, we also carefully unpack where any residual approximation error lies with respect to the underlying constituent message-passing functions. We then probe several simplifications of this framework to derive close connections with non-GNN-based graph learning approaches, including knowledge graph embeddings, various forms of label propagation, and efficient graph-regularized MLP models. And finally, we present supporting empirical results that demonstrate the versatility of the proposed bilevel lens, which we refer to as BloomGML, referencing that BiLevel Optimization Offers More Graph Machine Learning. Our code is available at https://github.com/amberyzheng/BloomGML. Let graph ML bloom.
In representation learning on graph-structured data, many popular graph neural networks (GNNs) fail to capture long-range dependencies, leading to performance degradation. Furthermore, this weakness is magnified when the concerned graph is characterized by heterophily (low homophily). To solve this issue, this paper proposes a novel graph learning framework called the graph convolutional network with self-attention (GCN-SA). The proposed scheme exhibits an exceptional generalization capability in node-level representation learning. The proposed GCN-SA contains two enhancements corresponding to edges and node features. For edges, we utilize a self-attention mechanism to design a stable and effective graph-structure-learning module that can capture the internal correlation between any pair of nodes. This graph-structure-learning module can identify reliable neighbors for each node from the entire graph. Regarding the node features, we modify the transformer block to make it more applicable to enable GCN to fuse valuable information from the entire graph. These two enhancements work in distinct ways to help our GCN-SA capture long-range dependencies, enabling it to perform representation learning on graphs with varying levels of homophily. The experimental results on benchmark datasets demonstrate the effectiveness of the proposed GCN-SA. Compared to other outstanding GNN counterparts, the proposed GCN-SA is competitive.
In recent years, quantum computing has emerged as a transformative force in the field of combinatorial optimization, offering novel approaches to tackling complex problems that have long challenged classical computational methods. Among these, the Quantum Approximate Optimization Algorithm (QAOA) stands out for its potential to efficiently solve the Max-Cut problem, a quintessential example of combinatorial optimization. However, practical application faces challenges due to current limitations on quantum computational resource. Our work optimizes QAOA initialization, using Graph Neural Networks (GNN) as a warm-start technique. This sacrifices affordable computational resource on classical computer to reduce quantum computational resource overhead, enhancing QAOA's effectiveness. Experiments with various GNN architectures demonstrate the adaptability and stability of our framework, highlighting the synergy between quantum algorithms and machine learning. Our findings show GNN's potential in improving QAOA performance, opening new avenues for hybrid quantum-classical approaches in quantum computing and contributing to practical applications.
In recent years, Cross-Domain Recommendation (CDR) has drawn significant attention, which utilizes user data from multiple domains to enhance the recommendation performance. However, current CDR methods require sharing user data across domains, thereby violating the General Data Protection Regulation (GDPR). Consequently, numerous approaches have been proposed for Federated Cross-Domain Recommendation (FedCDR). Nevertheless, the data heterogeneity across different domains inevitably influences the overall performance of federated learning. In this study, we propose FedHCDR, a novel Federated Cross-Domain Recommendation framework with Hypergraph signal decoupling. Specifically, to address the data heterogeneity across domains, we introduce an approach called hypergraph signal decoupling (HSD) to decouple the user features into domain-exclusive and domain-shared features. The approach employs high-pass and low-pass hypergraph filters to decouple domain-exclusive and domain-shared user representations, which are trained by the local-global bi-directional transfer algorithm. In addition, a hypergraph contrastive learning (HCL) module is devised to enhance the learning of domain-shared user relationship information by perturbing the user hypergraph. Extensive experiments conducted on three real-world scenarios demonstrate that FedHCDR outperforms existing baselines significantly.
We consider the problem of jointly learning row-wise and column-wise dependencies of matrix-variate observations, which are modelled separately by two precision matrices. Due to the complicated structure of Kronecker-product precision matrices in the commonly used matrix-variate Gaussian graphical models, a sparser Kronecker-sum structure was proposed recently based on the Cartesian product of graphs. However, existing methods for estimating Kronecker-sum structured precision matrices do not scale well to large scale datasets. In this paper, we introduce DNNLasso, a diagonally non-negative graphical lasso model for estimating the Kronecker-sum structured precision matrix, which outperforms the state-of-the-art methods by a large margin in both accuracy and computational time. Our code is available at https://github.com/YangjingZhang/DNNLasso.
Graph learning has become essential in various domains, including recommendation systems and social network analysis. Graph Neural Networks (GNNs) have emerged as promising techniques for encoding structural information and improving performance in tasks like link prediction and node classification. However, a key challenge remains: the difficulty of generalizing to unseen graph data with different properties. In this work, we propose a novel graph foundation model, called OpenGraph, to address this challenge. Our approach tackles several technical obstacles. Firstly, we enhance data augmentation using a large language model (LLM) to overcome data scarcity in real-world scenarios. Secondly, we introduce a unified graph tokenizer that enables the model to generalize effectively to diverse graph data, even when encountering unseen properties during training. Thirdly, our developed scalable graph transformer captures node-wise dependencies within the global topological context. Extensive experiments validate the effectiveness of our framework. By adapting OpenGraph to new graph characteristics and comprehending diverse graphs, our approach achieves remarkable zero-shot graph learning performance across various settings. We release the model implementation at https://github.com/HKUDS/OpenGraph.
Open-set graph learning is a practical task that aims to classify the known class nodes and to identify unknown class samples as unknowns. Conventional node classification methods usually perform unsatisfactorily in open-set scenarios due to the complex data they encounter, such as out-of-distribution (OOD) data and in-distribution (IND) noise. OOD data are samples that do not belong to any known classes. They are outliers if they occur in training (OOD noise), and open-set samples if they occur in testing. IND noise are training samples which are assigned incorrect labels. The existence of IND noise and OOD noise is prevalent, which usually cause the ambiguity problem, including the intra-class variety problem and the inter-class confusion problem. Thus, to explore robust open-set learning methods is necessary and difficult, and it becomes even more difficult for non-IID graph data.To this end, we propose a unified framework named ROG$_{PL}$ to achieve robust open-set learning on complex noisy graph data, by introducing prototype learning. In specific, ROG$_{PL}$ consists of two modules, i.e., denoising via label propagation and open-set prototype learning via regions. The first module corrects noisy labels through similarity-based label propagation and removes low-confidence samples, to solve the intra-class variety problem caused by noise. The second module learns open-set prototypes for each known class via non-overlapped regions and remains both interior and border prototypes to remedy the inter-class confusion problem.The two modules are iteratively updated under the constraints of classification loss and prototype diversity loss. To the best of our knowledge, the proposed ROG$_{PL}$ is the first robust open-set node classification method for graph data with complex noise.
We introduce Hyperdimensional Graph Learner (HDGL), a novel method for node classification and link prediction in graphs. HDGL maps node features into a very high-dimensional space (\textit{hyperdimensional} or HD space for short) using the \emph{injectivity} property of node representations in a family of Graph Neural Networks (GNNs) and then uses HD operators such as \textit{bundling} and \textit{binding} to aggregate information from the local neighborhood of each node yielding latent node representations that can support both node classification and link prediction tasks. HDGL, unlike GNNs that rely on computationally expensive iterative optimization and hyperparameter tuning, requires only a single pass through the data set. We report results of experiments using widely used benchmark datasets which demonstrate that, on the node classification task, HDGL achieves accuracy that is competitive with that of the state-of-the-art GNN methods at substantially reduced computational cost; and on the link prediction task, HDGL matches the performance of DeepWalk and related methods, although it falls short of computationally demanding state-of-the-art GNNs.
The rise of self-supervised learning, which operates without the need for labeled data, has garnered significant interest within the graph learning community. This enthusiasm has led to the development of numerous Graph Contrastive Learning (GCL) techniques, all aiming to create a versatile graph encoder that leverages the wealth of unlabeled data for various downstream tasks. However, the current evaluation standards for GCL approaches are flawed due to the need for extensive hyper-parameter tuning during pre-training and the reliance on a single downstream task for assessment. These flaws can skew the evaluation away from the intended goals, potentially leading to misleading conclusions. In our paper, we thoroughly examine these shortcomings and offer fresh perspectives on how GCL methods are affected by hyper-parameter choices and the choice of downstream tasks for their evaluation. Additionally, we introduce an enhanced evaluation framework designed to more accurately gauge the effectiveness, consistency, and overall capability of GCL methods.
Graph learning plays a pivotal role and has gained significant attention in various application scenarios, from social network analysis to recommendation systems, for its effectiveness in modeling complex data relations represented by graph structural data. In reality, the real-world graph data typically show dynamics over time, with changing node attributes and edge structure, leading to the severe graph data distribution shift issue. This issue is compounded by the diverse and complex nature of distribution shifts, which can significantly impact the performance of graph learning methods in degraded generalization and adaptation capabilities, posing a substantial challenge to their effectiveness. In this survey, we provide a comprehensive review and summary of the latest approaches, strategies, and insights that address distribution shifts within the context of graph learning. Concretely, according to the observability of distributions in the inference stage and the availability of sufficient supervision information in the training stage, we categorize existing graph learning methods into several essential scenarios, including graph domain adaptation learning, graph out-of-distribution learning, and graph continual learning. For each scenario, a detailed taxonomy is proposed, with specific descriptions and discussions of existing progress made in distribution-shifted graph learning. Additionally, we discuss the potential applications and future directions for graph learning under distribution shifts with a systematic analysis of the current state in this field. The survey is positioned to provide general guidance for the development of effective graph learning algorithms in handling graph distribution shifts, and to stimulate future research and advancements in this area.