Hypergraphs are characterized by complex topological structure, representing higher-order interactions among multiple entities through hyperedges. Lately, hypergraph-based deep learning methods to learn informative data representations for the problem of node classification on text-attributed hypergraphs have garnered increasing research attention. However, existing methods struggle to simultaneously capture the full extent of hypergraph structural information and the rich linguistic attributes inherent in the nodes attributes, which largely hampers their effectiveness and generalizability. To overcome these challenges, we explore ways to further augment a pretrained BERT model with specialized hypergraph-aware layers for the task of node classification. Such layers introduce higher-order structural inductive bias into the language model, thus improving the model's capacity to harness both higher-order context information from the hypergraph structure and semantic information present in text. In this paper, we propose a new architecture, HyperBERT, a mixed text-hypergraph model which simultaneously models hypergraph relational structure while maintaining the high-quality text encoding capabilities of a pre-trained BERT. Notably, HyperBERT presents results that achieve a new state-of-the-art on five challenging text-attributed hypergraph node classification benchmarks.
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.
Large language models (LLMs) like ChatGPT, exhibit powerful zero-shot and instruction-following capabilities, have catalyzed a revolutionary transformation across diverse fields, especially for open-ended tasks. While the idea is less explored in the graph domain, despite the availability of numerous powerful graph models (GMs), they are restricted to tasks in a pre-defined form. Although several methods applying LLMs to graphs have been proposed, they fail to simultaneously handle the pre-defined and open-ended tasks, with LLM as a node feature enhancer or as a standalone predictor. To break this dilemma, we propose to bridge the pretrained GM and LLM by a Translator, named GraphTranslator, aiming to leverage GM to handle the pre-defined tasks effectively and utilize the extended interface of LLMs to offer various open-ended tasks for GM. To train such Translator, we propose a Producer capable of constructing the graph-text alignment data along node information, neighbor information and model information. By translating node representation into tokens, GraphTranslator empowers an LLM to make predictions based on language instructions, providing a unified perspective for both pre-defined and open-ended tasks. Extensive results demonstrate the effectiveness of our proposed GraphTranslator on zero-shot node classification. The graph question answering experiments reveal our GraphTranslator potential across a broad spectrum of open-ended tasks through language instructions. Our code is available at: https://github.com/alibaba/GraphTranslator.
A common theoretical approach to understanding neural networks is to take an infinite-width limit, at which point the outputs become Gaussian process (GP) distributed. This is known as a neural network Gaussian process (NNGP). However, the NNGP kernel is fixed, and tunable only through a small number of hyperparameters, eliminating any possibility of representation learning. This contrasts with finite-width NNs, which are often believed to perform well precisely because they are able to learn representations. Thus in simplifying NNs to make them theoretically tractable, NNGPs may eliminate precisely what makes them work well (representation learning). This motivated us to understand whether representation learning is necessary in a range of graph classification tasks. We develop a precise tool for this task, the graph convolutional deep kernel machine. This is very similar to an NNGP, in that it is an infinite width limit and uses kernels, but comes with a `knob' to control the amount of representation learning. We found that representation learning is necessary (in the sense that it gives dramatic performance improvements) in graph classification tasks and heterophilous node classification tasks, but not in homophilous node classification tasks.
Scalable graph neural networks (GNNs) have emerged as a promising technique, which exhibits superior predictive performance and high running efficiency across numerous large-scale graph-based web applications. However, (i) Most scalable GNNs tend to treat all nodes in graphs with the same propagation rules, neglecting their topological uniqueness; (ii) Existing node-wise propagation optimization strategies are insufficient on web-scale graphs with intricate topology, where a full portrayal of nodes' local properties is required. Intuitively, different nodes in web-scale graphs possess distinct topological roles, and therefore propagating them indiscriminately or neglect local contexts may compromise the quality of node representations. This intricate topology in web-scale graphs cannot be matched by small-scale scenarios. To address the above issues, we propose \textbf{A}daptive \textbf{T}opology-aware \textbf{P}ropagation (ATP), which reduces potential high-bias propagation and extracts structural patterns of each node in a scalable manner to improve running efficiency and predictive performance. Remarkably, ATP is crafted to be a plug-and-play node-wise propagation optimization strategy, allowing for offline execution independent of the graph learning process in a new perspective. Therefore, this approach can be seamlessly integrated into most scalable GNNs while remain orthogonal to existing node-wise propagation optimization strategies. Extensive experiments on 12 datasets, including the most representative large-scale ogbn-papers100M, have demonstrated the effectiveness of ATP. Specifically, ATP has proven to be efficient in improving the performance of prevalent scalable GNNs for semi-supervised node classification while addressing redundant computational costs.
Graph Neural Networks (GNNs) have been a powerful tool for node classification tasks in complex networks. However, their decision-making processes remain a black-box to users, making it challenging to understand the reasoning behind their predictions. Counterfactual explanations (CFE) have shown promise in enhancing the interpretability of machine learning models. Prior approaches to compute CFE for GNNS often are learning-based approaches that require training additional graphs. In this paper, we propose a semivalue-based, non-learning approach to generate CFE for node classification tasks, eliminating the need for any additional training. Our results reveals that computing Banzhaf values requires lower sample complexity in identifying the counterfactual explanations compared to other popular methods such as computing Shapley values. Our empirical evidence indicates computing Banzhaf values can achieve up to a fourfold speed up compared to Shapley values. We also design a thresholding method for computing Banzhaf values and show theoretical and empirical results on its robustness in noisy environments, making it superior to Shapley values. Furthermore, the thresholded Banzhaf values are shown to enhance efficiency without compromising the quality (i.e., fidelity) in the explanations in three popular graph datasets.
Graph neural networks (GNNs) are the dominant paradigm for classifying nodes in a graph, but they have several undesirable attributes stemming from their message passing architecture. Recently, distillation methods succeeded in eliminating the use of GNNs at test time but they still require them during training. We perform a careful analysis of the role that GNNs play in distillation methods. This analysis leads us to propose a fully GNN-free approach for node classification, not requiring them at train or test time. Our method consists of three key components: smoothness constraints, pseudo-labeling iterations and neighborhood-label histograms. Our final approach can match the state-of-the-art accuracy on standard popular benchmarks such as citation and co-purchase networks, without training a GNN.
Hypergraphs are crucial for modelling higher-order interactions in real-world data. Hypergraph neural networks (HNNs) effectively utilise these structures by message passing to generate informative node features for various downstream tasks like node classification. However, the message passing module in existing HNNs typically requires a computationally intensive training process, which limits their practical use. To tackle this challenge, we propose an alternative approach by decoupling the usage of hypergraph structural information from the model learning stage. This leads to a novel training-free message passing module, named TF-MP-Module, which can be precomputed in the data preprocessing stage, thereby reducing the computational burden. We refer to the hypergraph neural network equipped with our TF-MP-Module as TF-HNN. We theoretically support the efficiency and effectiveness of TF-HNN by showing that: 1) It is more training-efficient compared to existing HNNs; 2) It utilises as much information as existing HNNs for node feature generation; and 3) It is robust against the oversmoothing issue while using long-range interactions. Experiments based on seven real-world hypergraph benchmarks in node classification and hyperlink prediction show that, compared to state-of-the-art HNNs, TF-HNN exhibits both competitive performance and superior training efficiency. Specifically, on the large-scale benchmark, Trivago, TF-HNN outperforms the node classification accuracy of the best baseline by 10% with just 1% of the training time of that baseline.
In service-oriented architectures, accurately predicting the Quality of Service (QoS) is crucial for maintaining reliability and enhancing user satisfaction. However, significant challenges remain due to existing methods always overlooking high-order latent collaborative relationships between users and services and failing to dynamically adjust feature learning for every specific user-service invocation, which are critical for learning accurate features. Additionally, reliance on RNNs for capturing QoS evolution hampers models' ability to detect long-term trends due to difficulties in managing long-range dependencies. To address these challenges, we propose the \underline{T}arget-Prompt \underline{O}nline \underline{G}raph \underline{C}ollaborative \underline{L}earning (TOGCL) framework for temporal-aware QoS prediction. TOGCL leverages a dynamic user-service invocation graph to model historical interactions, providing a comprehensive representation of user-service relationships. Building on this graph, it develops a target-prompt graph attention network to extract online deep latent features of users and services at each time slice, simultaneously considering implicit collaborative relationships between target users/services and their neighbors, as well as relevant historical QoS values. Additionally, a multi-layer Transformer encoder is employed to uncover temporal feature evolution patterns of users and services, leading to temporal-aware QoS prediction. Extensive experiments conducted on the WS-DREAM dataset demonstrate that our proposed TOGCL framework significantly outperforms state-of-the-art methods across multiple metrics, achieving improvements of up to 38.80\%. These results underscore the effectiveness of the TOGCL framework for precise temporal QoS prediction.
How would randomly shuffling feature vectors among nodes from the same class affect graph neural networks (GNNs)? The feature shuffle, intuitively, perturbs the dependence between graph topology and features (A-X dependence) for GNNs to learn from. Surprisingly, we observe a consistent and significant improvement in GNN performance following the feature shuffle. Having overlooked the impact of A-X dependence on GNNs, the prior literature does not provide a satisfactory understanding of the phenomenon. Thus, we raise two research questions. First, how should A-X dependence be measured, while controlling for potential confounds? Second, how does A-X dependence affect GNNs? In response, we (i) propose a principled measure for A-X dependence, (ii) design a random graph model that controls A-X dependence, (iii) establish a theory on how A-X dependence relates to graph convolution, and (iv) present empirical analysis on real-world graphs that align with the theory. We conclude that A-X dependence mediates the effect of graph convolution, such that smaller dependence improves GNN-based node classification.
Masked graph autoencoders have emerged as a powerful graph self-supervised learning method that has yet to be fully explored. In this paper, we unveil that the existing discrete edge masking and binary link reconstruction strategies are insufficient to learn topologically informative representations, from the perspective of message propagation on graph neural networks. These limitations include blocking message flows, vulnerability to over-smoothness, and suboptimal neighborhood discriminability. Inspired by these understandings, we explore non-discrete edge masks, which are sampled from a continuous and dispersive probability distribution instead of the discrete Bernoulli distribution. These masks restrict the amount of output messages for each edge, referred to as "bandwidths". We propose a novel, informative, and effective topological masked graph autoencoder using bandwidth masking and a layer-wise bandwidth prediction objective. We demonstrate its powerful graph topological learning ability both theoretically and empirically. Our proposed framework outperforms representative baselines in both self-supervised link prediction (improving the discrete edge reconstructors by at most 20%) and node classification on numerous datasets, solely with a structure-learning pretext. Our implementation is available at https://github.com/Newiz430/Bandana.
Text-attributed graphs (TAGs) present unique challenges for direct processing by Language Learning Models (LLMs), yet their extensive commonsense knowledge and robust reasoning capabilities offer great promise for node classification in TAGs. Prior research in this field has grappled with issues such as over-squashing, heterophily, and ineffective graph information integration, further compounded by inconsistencies in dataset partitioning and underutilization of advanced LLMs. To address these challenges, we introduce Similarity-based Neighbor Selection (SNS). Using SimCSE and advanced neighbor selection techniques, SNS effectively improves the quality of selected neighbors, thereby improving graph representation and alleviating issues like over-squashing and heterophily. Besides, as an inductive and training-free approach, SNS demonstrates superior generalization and scalability over traditional GNN methods. Our comprehensive experiments, adhering to standard dataset partitioning practices, demonstrate that SNS, through simple prompt interactions with LLMs, consistently outperforms vanilla GNNs and achieves state-of-the-art results on datasets like PubMed in node classification, showcasing LLMs' potential in graph structure understanding. Our research further underscores the significance of graph structure integration in LLM applications and identifies key factors for their success in node classification. Code is available at https://github.com/ruili33/SNS.
Transformers have revolutionized performance in Natural Language Processing and Vision, paving the way for their integration with Graph Neural Networks (GNNs). One key challenge in enhancing graph transformers is strengthening the discriminative power of distinguishing isomorphisms of graphs, which plays a crucial role in boosting their predictive performances. To address this challenge, we introduce 'Topology-Informed Graph Transformer (TIGT)', a novel transformer enhancing both discriminative power in detecting graph isomorphisms and the overall performance of Graph Transformers. TIGT consists of four components: A topological positional embedding layer using non-isomorphic universal covers based on cyclic subgraphs of graphs to ensure unique graph representation: A dual-path message-passing layer to explicitly encode topological characteristics throughout the encoder layers: A global attention mechanism: And a graph information layer to recalibrate channel-wise graph features for better feature representation. TIGT outperforms previous Graph Transformers in classifying synthetic dataset aimed at distinguishing isomorphism classes of graphs. Additionally, mathematical analysis and empirical evaluations highlight our model's competitive edge over state-of-the-art Graph Transformers across various benchmark datasets.
Temporal graph representation learning (TGRL) is essential for modeling dynamic systems in real-world networks. However, traditional TGRL methods, despite their effectiveness, often face significant computational challenges and inference delays due to the inefficient sampling of temporal neighbors. Conventional sampling methods typically involve backtracking through the interaction history of each node. In this paper, we propose a novel TGRL framework, No-Looking-Back (NLB), which overcomes these challenges by introducing a forward recent sampling strategy. This strategy eliminates the need to backtrack through historical interactions by utilizing a GPU-executable, size-constrained hash table for each node. The hash table records a down-sampled set of recent interactions, enabling rapid query responses with minimal inference latency. The maintenance of this hash table is highly efficient, operating with $O(1)$ complexity. Fully compatible with GPU processing, NLB maximizes programmability, parallelism, and power efficiency. Empirical evaluations demonstrate that NLB not only matches or surpasses state-of-the-art methods in accuracy for tasks like link prediction and node classification across six real-world datasets but also achieves 1.32-4.40x faster training, 1.2-7.94x greater energy efficiency, and 1.63-12.95x lower inference latency compared to competitive baselines. The link to the code: https://github.com/Graph-COM/NLB.
Graph Neural Networks (GNNs) have seen significant success in tasks such as node classification, largely contingent upon the availability of sufficient labeled nodes. Yet, the excessive cost of labeling large-scale graphs led to a focus on active learning on graphs, which aims for effective data selection to maximize downstream model performance. Notably, most existing methods assume reliable graph topology, while real-world scenarios often present noisy graphs. Given this, designing a successful active learning framework for noisy graphs is highly needed but challenging, as selecting data for labeling and obtaining a clean graph are two tasks naturally interdependent: selecting high-quality data requires clean graph structure while cleaning noisy graph structure requires sufficient labeled data. Considering the complexity mentioned above, we propose an active learning framework, GALClean, which has been specifically designed to adopt an iterative approach for conducting both data selection and graph purification simultaneously with best information learned from the prior iteration. Importantly, we summarize GALClean as an instance of the Expectation-Maximization algorithm, which provides a theoretical understanding of its design and mechanisms. This theory naturally leads to an enhanced version, GALClean+. Extensive experiments have demonstrated the effectiveness and robustness of our proposed method across various types and levels of noisy graphs.
Large Language Models (LLMs) are increasingly used for various tasks with graph structures. Though LLMs can process graph information in a textual format, they overlook the rich vision modality, which is an intuitive way for humans to comprehend structural information and conduct general graph reasoning. The potential benefits and capabilities of representing graph structures as visual images (i.e., $\textit{visual graph}$) are still unexplored. To fill the gap, we innovatively propose an end-to-end framework, called $\textbf{G}$raph to v$\textbf{I}$sual and $\textbf{T}$extual Integr$\textbf{A}$tion (GITA), which firstly incorporates visual graphs into general graph reasoning. Besides, we establish $\textbf{G}$raph-based $\textbf{V}$ision-$\textbf{L}$anguage $\textbf{Q}$uestion $\textbf{A}$nswering (GVLQA) dataset from existing graph data, which is the first vision-language dataset for general graph reasoning purposes. Extensive experiments on the GVLQA dataset and five real-world datasets show that GITA outperforms mainstream LLMs in terms of general graph reasoning capabilities. Moreover, We highlight the effectiveness of the layout augmentation on visual graphs and pretraining on the GVLQA dataset.
Deep graph models (e.g., graph neural networks and graph transformers) have become important techniques for leveraging knowledge across various types of graphs. Yet, the neural scaling laws on graphs, i.e., how the performance of deep graph models changes with model and dataset sizes, have not been systematically investigated, casting doubts on the feasibility of achieving large graph models. To fill this gap, we benchmark many graph datasets from different tasks and make an attempt to establish the neural scaling laws on graphs from both model and data perspectives. The model size we investigated is up to 100 million parameters, and the dataset size investigated is up to 50 million samples. We first verify the validity of such laws on graphs, establishing proper formulations to describe the scaling behaviors. For model scaling, we identify that despite the parameter numbers, the model depth also plays an important role in affecting the model scaling behaviors, which differs from observations in other domains such as CV and NLP. For data scaling, we suggest that the number of graphs can not effectively measure the graph data volume in scaling law since the sizes of different graphs are highly irregular. Instead, we reform the data scaling law with the number of nodes or edges as the metric to address the irregular graph sizes. We further demonstrate that the reformed law offers a unified view of the data scaling behaviors for various fundamental graph tasks including node classification, link prediction, and graph classification. This work provides valuable insights into neural scaling laws on graphs, which can serve as an important tool for collecting new graph data and developing large graph models.
For analysing real-world networks, graph representation learning is a popular tool. These methods, such as a graph autoencoder (GAE), typically rely on low-dimensional representations, also called embeddings, which are obtained through minimising a loss function; these embeddings are used with a decoder for downstream tasks such as node classification and edge prediction. While GAEs tend to be fairly accurate, they suffer from scalability issues. For improved speed, a Local2Global approach, which combines graph patch embeddings based on eigenvector synchronisation, was shown to be fast and achieve good accuracy. Here we propose L2G2G, a Local2Global method which improves GAE accuracy without sacrificing scalability. This improvement is achieved by dynamically synchronising the latent node representations, while training the GAEs. It also benefits from the decoder computing an only local patch loss. Hence, aligning the local embeddings in each epoch utilises more information from the graph than a single post-training alignment does, while maintaining scalability. We illustrate on synthetic benchmarks, as well as real-world examples, that L2G2G achieves higher accuracy than the standard Local2Global approach and scales efficiently on the larger data sets. We find that for large and dense networks, it even outperforms the slow, but assumed more accurate, GAEs.
Graph Neural Networks (GNNs) have made significant advancements in node classification, but their success relies on sufficient labeled nodes per class in the training data. Real-world graph data often exhibits a long-tail distribution with sparse labels, emphasizing the importance of GNNs' ability in few-shot node classification, which entails categorizing nodes with limited data. Traditional episodic meta-learning approaches have shown promise in this domain, but they face an inherent limitation: it might lead the model to converge to suboptimal solutions because of random and uniform task assignment, ignoring task difficulty levels. This could lead the meta-learner to face complex tasks too soon, hindering proper learning. Ideally, the meta-learner should start with simple concepts and advance to more complex ones, like human learning. So, we introduce CPT, a novel two-stage curriculum learning method that aligns task difficulty with the meta-learner's progressive competence, enhancing overall performance. Specifically, in CPT's initial stage, the focus is on simpler tasks, fostering foundational skills for engaging with complex tasks later. Importantly, the second stage dynamically adjusts task difficulty based on the meta-learner's growing competence, aiming for optimal knowledge acquisition. Extensive experiments on popular node classification datasets demonstrate significant improvements of our strategy over existing methods.
Developing computational tools for integrative analysis across multiple types of omics data has been of immense importance in cancer molecular biology and precision medicine research. While recent advancements have yielded integrative prediction solutions for multi-omics data, these methods lack a comprehensive and cohesive understanding of the rationale behind their specific predictions. To shed light on personalized medicine and unravel previously unknown characteristics within integrative analysis of multi-omics data, we introduce a novel integrative neural network approach for cancer molecular subtype and biomedical classification applications, named Integrative Graph Convolutional Networks (IGCN). IGCN can identify which types of omics receive more emphasis for each patient to predict a certain class. Additionally, IGCN has the capability to pinpoint significant biomarkers from a range of omics data types. To demonstrate the superiority of IGCN, we compare its performance with other state-of-the-art approaches across different cancer subtype and biomedical classification tasks.