Histopathological whole slide images (WSIs) classification has become a foundation task in medical microscopic imaging processing. Prevailing approaches involve learning WSIs as instance-bag representations, emphasizing significant instances but struggling to capture the interactions between instances. Additionally, conventional graph representation methods utilize explicit spatial positions to construct topological structures but restrict the flexible interaction capabilities between instances at arbitrary locations, particularly when spatially distant. In response, we propose a novel dynamic graph representation algorithm that conceptualizes WSIs as a form of the knowledge graph structure. Specifically, we dynamically construct neighbors and directed edge embeddings based on the head and tail relationships between instances. Then, we devise a knowledge-aware attention mechanism that can update the head node features by learning the joint attention score of each neighbor and edge. Finally, we obtain a graph-level embedding through the global pooling process of the updated head, serving as an implicit representation for the WSI classification. Our end-to-end graph representation learning approach has outperformed the state-of-the-art WSI analysis methods on three TCGA benchmark datasets and in-house test sets. Our code is available at https://github.com/WonderLandxD/WiKG.
Knowledge graphs have garnered significant research attention and are widely used to enhance downstream applications. However, most current studies mainly focus on static knowledge graphs, whose facts do not change with time, and disregard their dynamic evolution over time. As a result, temporal knowledge graphs have attracted more attention because a large amount of structured knowledge exists only within a specific period. Knowledge graph representation learning aims to learn low-dimensional vector embeddings for entities and relations in a knowledge graph. The representation learning of temporal knowledge graphs incorporates time information into the standard knowledge graph framework and can model the dynamics of entities and relations over time. In this paper, we conduct a comprehensive survey of temporal knowledge graph representation learning and its applications. We begin with an introduction to the definitions, datasets, and evaluation metrics for temporal knowledge graph representation learning. Next, we propose a taxonomy based on the core technologies of temporal knowledge graph representation learning methods, and provide an in-depth analysis of different methods in each category. Finally, we present various downstream applications related to the temporal knowledge graphs. In the end, we conclude the paper and have an outlook on the future research directions in this area.
In this paper, we study the problem of unsupervised graph representation learning by harnessing the control properties of dynamical networks defined on graphs. Our approach introduces a novel framework for contrastive learning, a widely prevalent technique for unsupervised representation learning. A crucial step in contrastive learning is the creation of 'augmented' graphs from the input graphs. Though different from the original graphs, these augmented graphs retain the original graph's structural characteristics. Here, we propose a unique method for generating these augmented graphs by leveraging the control properties of networks. The core concept revolves around perturbing the original graph to create a new one while preserving the controllability properties specific to networks and graphs. Compared to the existing methods, we demonstrate that this innovative approach enhances the effectiveness of contrastive learning frameworks, leading to superior results regarding the accuracy of the classification tasks. The key innovation lies in our ability to decode the network structure using these control properties, opening new avenues for unsupervised graph representation learning.
Graph Contrastive Learning (GCL) has emerged as a popular unsupervised graph representation learning method. However, it has been shown that GCL is vulnerable to adversarial attacks on both the graph structure and node attributes. Although empirical approaches have been proposed to enhance the robustness of GCL, the certifiable robustness of GCL is still remain unexplored. In this paper, we develop the first certifiably robust framework in GCL. Specifically, we first propose a unified criteria to evaluate and certify the robustness of GCL. We then introduce a novel technique, RES (Randomized Edgedrop Smoothing), to ensure certifiable robustness for any GCL model, and this certified robustness can be provably preserved in downstream tasks. Furthermore, an effective training method is proposed for robust GCL. Extensive experiments on real-world datasets demonstrate the effectiveness of our proposed method in providing effective certifiable robustness and enhancing the robustness of any GCL model. The source code of RES is available at https://github.com/ventr1c/RES-GCL.
Graph is a fundamental mathematical structure in characterizing relations between different objects and has been widely used on various learning tasks. Most methods implicitly assume a given graph to be accurate and complete. However, real data is inevitably noisy and sparse, which will lead to inferior results. Despite the remarkable success of recent graph representation learning methods, they inherently presume that the graph is homophilic, and largely overlook heterophily, where most connected nodes are from different classes. In this regard, we propose a novel robust graph structure learning method to achieve a high-quality graph from heterophilic data for downstream tasks. We first apply a high-pass filter to make each node more distinctive from its neighbors by encoding structure information into the node features. Then, we learn a robust graph with an adaptive norm characterizing different levels of noise. Afterwards, we propose a novel regularizer to further refine the graph structure. Clustering and semi-supervised classification experiments on heterophilic graphs verify the effectiveness of our method.
Recent years have witnessed the great success of graph pre-training for graph representation learning. With hundreds of graph pre-training tasks proposed, integrating knowledge acquired from multiple pre-training tasks has become a popular research topic. In this paper, we identify two important collaborative processes for this topic: (1) select: how to select an optimal task combination from a given task pool based on their compatibility, and (2) weigh: how to weigh the selected tasks based on their importance. While there currently has been a lot of work focused on weighing, comparatively little effort has been devoted to selecting. This paper proposes a novel instance-level framework for integrating multiple graph pre-training tasks, Weigh And Select (WAS), where the two collaborative processes, weighing and selecting, are combined by decoupled siamese networks. Specifically, it first adaptively learns an optimal combination of tasks for each instance from a given task pool, based on which a customized instance-level task weighing strategy is learned. Extensive experiments on 16 graph datasets across node-level and graph-level downstream tasks have demonstrated that by combining a few simple but classical tasks, WAS can achieve comparable performance to other leading counterparts. The code is available at https://github.com/TianyuFan0504/WAS.
Addressing the challenge of limited labeled data in clinical settings, particularly in the prediction of fatty liver disease, this study explores the potential of graph representation learning within a semi-supervised learning framework. Leveraging graph neural networks (GNNs), our approach constructs a subject similarity graph to identify risk patterns from health checkup data. The effectiveness of various GNN approaches in this context is demonstrated, even with minimal labeled samples. Central to our methodology is the inclusion of human-centric explanations through explainable GNNs, providing personalized feature importance scores for enhanced interpretability and clinical relevance, thereby underscoring the potential of our approach in advancing healthcare practices with a keen focus on graph representation learning and human-centric explanation.
Knowledge Graph Representation Learning (KGRL), or Knowledge Graph Embedding (KGE), is essential for AI applications such as knowledge construction and information retrieval. These models encode entities and relations into lower-dimensional vectors, supporting tasks like link prediction and recommendation systems. Training KGE models relies on both positive and negative samples for effective learning, but generating high-quality negative samples from existing knowledge graphs is challenging. The quality of these samples significantly impacts the model's accuracy. This comprehensive survey paper systematically reviews various negative sampling (NS) methods and their contributions to the success of KGRL. Their respective advantages and disadvantages are outlined by categorizing existing NS methods into six distinct categories. Moreover, this survey identifies open research questions that serve as potential directions for future investigations. By offering a generalization and alignment of fundamental NS concepts, this survey provides valuable insights for designing effective NS methods in the context of KGRL and serves as a motivating force for further advancements in the field.
In recent years, unsupervised and self-supervised graph representation learning has gained popularity in the research community. However, most proposed methods are focused on homogeneous networks, whereas real-world graphs often contain multiple node and edge types. Multiplex graphs, a special type of heterogeneous graphs, possess richer information, provide better modeling capabilities and integrate more detailed data from potentially different sources. The diverse edge types in multiplex graphs provide more context and insights into the underlying processes of representation learning. In this paper, we tackle the problem of learning representations for nodes in multiplex networks in an unsupervised or self-supervised manner. To that end, we explore diverse information fusion schemes performed at different levels of the graph processing pipeline. The detailed analysis and experimental evaluation of various scenarios inspired us to propose improvements in how to construct GNN architectures that deal with multiplex graphs.
Most existing methods for predicting drug-drug interactions (DDI) predominantly concentrate on capturing the explicit relationships among drugs, overlooking the valuable implicit correlations present between drug pairs (DPs), which leads to weak predictions. To address this issue, this paper introduces a hierarchical multi-relational graph representation learning (HMGRL) approach. Within the framework of HMGRL, we leverage a wealth of drug-related heterogeneous data sources to construct heterogeneous graphs, where nodes represent drugs and edges denote clear and various associations. The relational graph convolutional network (RGCN) is employed to capture diverse explicit relationships between drugs from these heterogeneous graphs. Additionally, a multi-view differentiable spectral clustering (MVDSC) module is developed to capture multiple valuable implicit correlations between DPs. Within the MVDSC, we utilize multiple DP features to construct graphs, where nodes represent DPs and edges denote different implicit correlations. Subsequently, multiple DP representations are generated through graph cutting, each emphasizing distinct implicit correlations. The graph-cutting strategy enables our HMGRL to identify strongly connected communities of graphs, thereby reducing the fusion of irrelevant features. By combining every representation view of a DP, we create high-level DP representations for predicting DDIs. Two genuine datasets spanning three distinct tasks are adopted to gauge the efficacy of our HMGRL. Experimental outcomes unequivocally indicate that HMGRL surpasses several leading-edge methods in performance.
Graph representation learning (GRL) makes considerable progress recently, which encodes graphs with topological structures into low-dimensional embeddings. Meanwhile, the time-consuming and costly process of annotating graph labels manually prompts the growth of self-supervised learning (SSL) techniques. As a dominant approach of SSL, Contrastive learning (CL) learns discriminative representations by differentiating between positive and negative samples. However, when applied to graph data, it overemphasizes global patterns while neglecting local structures. To tackle the above issue, we propose \underline{Local}-aware \underline{G}raph \underline{C}ontrastive \underline{L}earning (\textbf{\methnametrim}), a self-supervised learning framework that supplementarily captures local graph information with masking-based modeling compared with vanilla contrastive learning. Extensive experiments validate the superiority of \methname against state-of-the-art methods, demonstrating its promise as a comprehensive graph representation learner.
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.
Graph contrastive learning (GCL) has emerged as a pivotal technique in the domain of graph representation learning. A crucial aspect of effective GCL is the caliber of generated positive and negative samples, which is intrinsically dictated by their resemblance to the original data. Nevertheless, precise control over similarity during sample generation presents a formidable challenge, often impeding the effective discovery of representative graph patterns. To address this challenge, we propose an innovative framework: Adversarial Curriculum Graph Contrastive Learning (ACGCL), which capitalizes on the merits of pair-wise augmentation to engender graph-level positive and negative samples with controllable similarity, alongside subgraph contrastive learning to discern effective graph patterns therein. Within the ACGCL framework, we have devised a novel adversarial curriculum training methodology that facilitates progressive learning by sequentially increasing the difficulty of distinguishing the generated samples. Notably, this approach transcends the prevalent sparsity issue inherent in conventional curriculum learning strategies by adaptively concentrating on more challenging training data. Finally, a comprehensive assessment of ACGCL is conducted through extensive experiments on six well-known benchmark datasets, wherein ACGCL conspicuously surpasses a set of state-of-the-art baselines.
As new research on Large Language Models (LLMs) continues, it is difficult to keep up with new research and models. To help researchers synthesize the new research many have written survey papers, but even those have become numerous. In this paper, we develop a method to automatically assign survey papers to a taxonomy. We collect the metadata of 144 LLM survey papers and explore three paradigms to classify papers within the taxonomy. Our work indicates that leveraging graph structure information on co-category graphs can significantly outperform the language models in two paradigms; pre-trained language models' fine-tuning and zero-shot/few-shot classifications using LLMs. We find that our model surpasses an average human recognition level and that fine-tuning LLMs using weak labels generated by a smaller model, such as the GCN in this study, can be more effective than using ground-truth labels, revealing the potential of weak-to-strong generalization in the taxonomy classification task.
Topological deep learning (TDL) is a rapidly evolving field that uses topological features to understand and design deep learning models. This paper posits that TDL is the new frontier for relational learning. TDL may complement graph representation learning and geometric deep learning by incorporating topological concepts, and can thus provide a natural choice for various machine learning settings. To this end, this paper discusses open problems in TDL, ranging from practical benefits to theoretical foundations. For each problem, it outlines potential solutions and future research opportunities. At the same time, this paper serves as an invitation to the scientific community to actively participate in TDL research to unlock the potential of this emerging field.
Graph Neural Networks (GNNs) have shown promising potential in graph representation learning. The majority of GNNs define a local message-passing mechanism, propagating information over the graph by stacking multiple layers. These methods, however, are known to suffer from two major limitations: over-squashing and poor capturing of long-range dependencies. Recently, Graph Transformers (GTs) emerged as a powerful alternative to Message-Passing Neural Networks (MPNNs). GTs, however, have quadratic computational cost, lack inductive biases on graph structures, and rely on complex Positional/Structural Encodings (SE/PE). In this paper, we show that while Transformers, complex message-passing, and SE/PE are sufficient for good performance in practice, neither is necessary. Motivated by the recent success of State Space Models (SSMs), such as Mamba, we present Graph Mamba Networks (GMNs), a general framework for a new class of GNNs based on selective SSMs. We discuss and categorize the new challenges when adapting SSMs to graph-structured data, and present four required and one optional steps to design GMNs, where we choose (1) Neighborhood Tokenization, (2) Token Ordering, (3) Architecture of Bidirectional Selective SSM Encoder, (4) Local Encoding, and dispensable (5) PE and SE. We further provide theoretical justification for the power of GMNs. Experiments demonstrate that despite much less computational cost, GMNs attain an outstanding performance in long-range, small-scale, large-scale, and heterophilic benchmark datasets.
Self-supervised Learning (SSL) has emerged as a powerful technique in pre-training deep learning models without relying on expensive annotated labels, instead leveraging embedded signals in unlabeled data. While SSL has shown remarkable success in computer vision tasks through intuitive data augmentation, its application to graph-structured data poses challenges due to the semantic-altering and counter-intuitive nature of graph augmentations. Addressing this limitation, this paper introduces a novel non-contrastive SSL approach to Explicitly Generate a compositional Relation Graph (ExGRG) instead of relying solely on the conventional augmentation-based implicit relation graph. ExGRG offers a framework for incorporating prior domain knowledge and online extracted information into the SSL invariance objective, drawing inspiration from the Laplacian Eigenmap and Expectation-Maximization (EM). Employing an EM perspective on SSL, our E-step involves relation graph generation to identify candidates to guide the SSL invariance objective, and M-step updates the model parameters by integrating the derived relational information. Extensive experimentation on diverse node classification datasets demonstrates the superiority of our method over state-of-the-art techniques, affirming ExGRG as an effective adoption of SSL for graph representation learning.
Graph representation learning on vast datasets, like web data, has made significant strides. However, the associated computational and storage overheads raise concerns. In sight of this, Graph condensation (GCond) has been introduced to distill these large real datasets into a more concise yet information-rich synthetic graph. Despite acceleration efforts, existing GCond methods mainly grapple with efficiency, especially on expansive web data graphs. Hence, in this work, we pinpoint two major inefficiencies of current paradigms: (1) the concurrent updating of a vast parameter set, and (2) pronounced parameter redundancy. To counteract these two limitations correspondingly, we first (1) employ the Mean-Field variational approximation for convergence acceleration, and then (2) propose the objective of Gradient Information Bottleneck (GDIB) to prune redundancy. By incorporating the leading explanation techniques (e.g., GNNExplainer and GSAT) to instantiate the GDIB, our EXGC, the Efficient and eXplainable Graph Condensation method is proposed, which can markedly boost efficiency and inject explainability. Our extensive evaluations across eight datasets underscore EXGC's superiority and relevance. Code is available at https://github.com/MangoKiller/EXGC.
The integration of Large Language Models (LLMs) with Graph Representation Learning (GRL) marks a significant evolution in analyzing complex data structures. This collaboration harnesses the sophisticated linguistic capabilities of LLMs to improve the contextual understanding and adaptability of graph models, thereby broadening the scope and potential of GRL. Despite a growing body of research dedicated to integrating LLMs into the graph domain, a comprehensive review that deeply analyzes the core components and operations within these models is notably lacking. Our survey fills this gap by proposing a novel taxonomy that breaks down these models into primary components and operation techniques from a novel technical perspective. We further dissect recent literature into two primary components including knowledge extractors and organizers, and two operation techniques including integration and training stratigies, shedding light on effective model design and training strategies. Additionally, we identify and explore potential future research avenues in this nascent yet underexplored field, proposing paths for continued progress.
Recently, Temporal Graph Neural Networks (TGNNs) have demonstrated state-of-the-art performance in various high-impact applications, including fraud detection and content recommendation. Despite the success of TGNNs, they are prone to the prevalent noise found in real-world dynamic graphs like time-deprecated links and skewed interaction distribution. The noise causes two critical issues that significantly compromise the accuracy of TGNNs: (1) models are supervised by inferior interactions, and (2) noisy input induces high variance in the aggregated messages. However, current TGNN denoising techniques do not consider the diverse and dynamic noise pattern of each node. In addition, they also suffer from the excessive mini-batch generation overheads caused by traversing more neighbors. We believe the remedy for fast and accurate TGNNs lies in temporal adaptive sampling. In this work, we propose TASER, the first adaptive sampling method for TGNNs optimized for accuracy, efficiency, and scalability. TASER adapts its mini-batch selection based on training dynamics and temporal neighbor selection based on the contextual, structural, and temporal properties of past interactions. To alleviate the bottleneck in mini-batch generation, TASER implements a pure GPU-based temporal neighbor finder and a dedicated GPU feature cache. We evaluate the performance of TASER using two state-of-the-art backbone TGNNs. On five popular datasets, TASER outperforms the corresponding baselines by an average of 2.3% in Mean Reciprocal Rank (MRR) while achieving an average of 5.1x speedup in training time.