Daily Papers

Recently, research on Text-Attributed Graphs (TAGs) has gained significant attention due to the prevalence of free-text node features in real-world applications and the advancements in Large Language Models (LLMs) that bolster TAG methodologies. However, current TAG approaches face two primary challenges: (i) Heavy reliance on label information and (ii) Limited cross-domain zero/few-shot transferability. These issues constrain the scaling of both data and model size, owing to high labor costs and scaling laws, complicating the development of graph foundation models with strong transferability. In this work, we propose the GraphCLIP framework to address these challenges by learning graph foundation models with strong cross-domain zero/few-shot transferability through a self-supervised contrastive graph-summary pretraining method. Specifically, we generate and curate large-scale graph-summary pair data with the assistance of LLMs, and introduce a novel graph-summary pretraining method, combined with invariant learning, to enhance graph foundation models with strong cross-domain zero-shot transferability. For few-shot learning, we propose a novel graph prompt tuning technique aligned with our pretraining objective to mitigate catastrophic forgetting and minimize learning costs. Extensive experiments show the superiority of GraphCLIP in both zero-shot and few-shot settings, while evaluations across various downstream tasks confirm the versatility of GraphCLIP. Our code is available at: https://github.com/ZhuYun97/GraphCLIP

In recent years, graph pre-training has gained significant attention, focusing on acquiring transferable knowledge from unlabeled graph data to improve downstream performance. Despite these recent endeavors, the problem of negative transfer remains a major concern when utilizing graph pre-trained models to downstream tasks. Previous studies made great efforts on the issue of what to pre-train and how to pre-train by designing a variety of graph pre-training and fine-tuning strategies. However, there are cases where even the most advanced "pre-train and fine-tune" paradigms fail to yield distinct benefits. This paper introduces a generic framework W2PGNN to answer the crucial question of when to pre-train (i.e., in what situations could we take advantage of graph pre-training) before performing effortful pre-training or fine-tuning. We start from a new perspective to explore the complex generative mechanisms from the pre-training data to downstream data. In particular, W2PGNN first fits the pre-training data into graphon bases, each element of graphon basis (i.e., a graphon) identifies a fundamental transferable pattern shared by a collection of pre-training graphs. All convex combinations of graphon bases give rise to a generator space, from which graphs generated form the solution space for those downstream data that can benefit from pre-training. In this manner, the feasibility of pre-training can be quantified as the generation probability of the downstream data from any generator in the generator space. W2PGNN offers three broad applications: providing the application scope of graph pre-trained models, quantifying the feasibility of pre-training, and assistance in selecting pre-training data to enhance downstream performance. We provide a theoretically sound solution for the first application and extensive empirical justifications for the latter two applications.

Graph neural networks have shown significant success in the field of graph representation learning. Graph convolutions perform neighborhood aggregation and represent one of the most important graph operations. Nevertheless, one layer of these neighborhood aggregation methods only consider immediate neighbors, and the performance decreases when going deeper to enable larger receptive fields. Several recent studies attribute this performance deterioration to the over-smoothing issue, which states that repeated propagation makes node representations of different classes indistinguishable. In this work, we study this observation systematically and develop new insights towards deeper graph neural networks. First, we provide a systematical analysis on this issue and argue that the key factor compromising the performance significantly is the entanglement of representation transformation and propagation in current graph convolution operations. After decoupling these two operations, deeper graph neural networks can be used to learn graph node representations from larger receptive fields. We further provide a theoretical analysis of the above observation when building very deep models, which can serve as a rigorous and gentle description of the over-smoothing issue. Based on our theoretical and empirical analysis, we propose Deep Adaptive Graph Neural Network (DAGNN) to adaptively incorporate information from large receptive fields. A set of experiments on citation, co-authorship, and co-purchase datasets have confirmed our analysis and insights and demonstrated the superiority of our proposed methods.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

The success of deep learning notoriously requires larger amounts of costly annotated data. This has led to the development of self-supervised learning (SSL) that aims to alleviate this limitation by creating domain specific pretext tasks on unlabeled data. Simultaneously, there are increasing interests in generalizing deep learning to the graph domain in the form of graph neural networks (GNNs). GNNs can naturally utilize unlabeled nodes through the simple neighborhood aggregation that is unable to thoroughly make use of unlabeled nodes. Thus, we seek to harness SSL for GNNs to fully exploit the unlabeled data. Different from data instances in the image and text domains, nodes in graphs present unique structure information and they are inherently linked indicating not independent and identically distributed (or i.i.d.). Such complexity is a double-edged sword for SSL on graphs. On the one hand, it determines that it is challenging to adopt solutions from the image and text domains to graphs and dedicated efforts are desired. On the other hand, it provides rich information that enables us to build SSL from a variety of perspectives. Thus, in this paper, we first deepen our understandings on when, why, and which strategies of SSL work with GNNs by empirically studying numerous basic SSL pretext tasks on graphs. Inspired by deep insights from the empirical studies, we propose a new direction SelfTask to build advanced pretext tasks that are able to achieve state-of-the-art performance on various real-world datasets. The specific experimental settings to reproduce our results can be found in https://github.com/ChandlerBang/SelfTask-GNN.

Recent studies on Graph Convolutional Networks (GCNs) reveal that the initial node representations (i.e., the node representations before the first-time graph convolution) largely affect the final model performance. However, when learning the initial representation for a node, most existing work linearly combines the embeddings of node features, without considering the interactions among the features (or feature embeddings). We argue that when the node features are categorical, e.g., in many real-world applications like user profiling and recommender system, feature interactions usually carry important signals for predictive analytics. Ignoring them will result in suboptimal initial node representation and thus weaken the effectiveness of the follow-up graph convolution. In this paper, we propose a new GCN model named CatGCN, which is tailored for graph learning when the node features are categorical. Specifically, we integrate two ways of explicit interaction modeling into the learning of initial node representation, i.e., local interaction modeling on each pair of node features and global interaction modeling on an artificial feature graph. We then refine the enhanced initial node representations with the neighborhood aggregation-based graph convolution. We train CatGCN in an end-to-end fashion and demonstrate it on semi-supervised node classification. Extensive experiments on three tasks of user profiling (the prediction of user age, city, and purchase level) from Tencent and Alibaba datasets validate the effectiveness of CatGCN, especially the positive effect of performing feature interaction modeling before graph convolution.

We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We show that these data-driven features are more interpretable, and have better predictive performance on a variety of tasks.

Transformers have recently emerged as powerful neural networks for graph learning, showcasing state-of-the-art performance on several graph property prediction tasks. However, these results have been limited to small-scale graphs, where the computational feasibility of the global attention mechanism is possible. The next goal is to scale up these architectures to handle very large graphs on the scale of millions or even billions of nodes. With large-scale graphs, global attention learning is proven impractical due to its quadratic complexity w.r.t. the number of nodes. On the other hand, neighborhood sampling techniques become essential to manage large graph sizes, yet finding the optimal trade-off between speed and accuracy with sampling techniques remains challenging. This work advances representation learning on single large-scale graphs with a focus on identifying model characteristics and critical design constraints for developing scalable graph transformer (GT) architectures. We argue such GT requires layers that can adeptly learn both local and global graph representations while swiftly sampling the graph topology. As such, a key innovation of this work lies in the creation of a fast neighborhood sampling technique coupled with a local attention mechanism that encompasses a 4-hop reception field, but achieved through just 2-hop operations. This local node embedding is then integrated with a global node embedding, acquired via another self-attention layer with an approximate global codebook, before finally sent through a downstream layer for node predictions. The proposed GT framework, named LargeGT, overcomes previous computational bottlenecks and is validated on three large-scale node classification benchmarks. We report a 3x speedup and 16.8% performance gain on ogbn-products and snap-patents, while we also scale LargeGT on ogbn-papers100M with a 5.9% performance improvement.

Graph Convolutional Network (GCN) is widely used in graph data learning tasks such as recommendation. However, when facing a large graph, the graph convolution is very computationally expensive thus is simplified in all existing GCNs, yet is seriously impaired due to the oversimplification. To address this gap, we leverage the original graph convolution in GCN and propose a Low-pass Collaborative Filter (LCF) to make it applicable to the large graph. LCF is designed to remove the noise caused by exposure and quantization in the observed data, and it also reduces the complexity of graph convolution in an unscathed way. Experiments show that LCF improves the effectiveness and efficiency of graph convolution and our GCN outperforms existing GCNs significantly. Codes are available on https://github.com/Wenhui-Yu/LCFN.

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into four categories, namely recurrent graph neural networks, convolutional graph neural networks, graph autoencoders, and spatial-temporal graph neural networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes, benchmark data sets, and model evaluation of graph neural networks. Finally, we propose potential research directions in this rapidly growing field.

Graph representation learning has emerged as a powerful technique for addressing real-world problems. Various downstream graph learning tasks have benefited from its recent developments, such as node classification, similarity search, and graph classification. However, prior arts on graph representation learning focus on domain specific problems and train a dedicated model for each graph dataset, which is usually non-transferable to out-of-domain data. Inspired by the recent advances in pre-training from natural language processing and computer vision, we design Graph Contrastive Coding (GCC) -- a self-supervised graph neural network pre-training framework -- to capture the universal network topological properties across multiple networks. We design GCC's pre-training task as subgraph instance discrimination in and across networks and leverage contrastive learning to empower graph neural networks to learn the intrinsic and transferable structural representations. We conduct extensive experiments on three graph learning tasks and ten graph datasets. The results show that GCC pre-trained on a collection of diverse datasets can achieve competitive or better performance to its task-specific and trained-from-scratch counterparts. This suggests that the pre-training and fine-tuning paradigm presents great potential for graph representation learning.

Graph Convolutional Networks (GCNs) have shown strong performance in learning text representations for various tasks such as text classification, due to its expressive power in modeling graph structure data (e.g., a literature citation network). Most existing GCNs are limited to deal with documents included in a pre-defined graph, i.e., it cannot be generalized to out-of-graph documents. To address this issue, we propose to transform the document graph into a word graph, to decouple data samples (i.e., documents in training and test sets) and a GCN model by using a document-independent graph. Such word-level GCN could therefore naturally inference out-of-graph documents in an inductive way. The proposed Word-level Graph (WGraph) can not only implicitly learning word presentation with commonly-used word co-occurrences in corpora, but also incorporate extra global semantic dependency derived from inter-document relationships (e.g., literature citations). An inductive Word-grounded Graph Convolutional Network (WGCN) is proposed to learn word and document representations based on WGraph in a supervised manner. Experiments on text classification with and without citation networks evidence that the proposed WGCN model outperforms existing methods in terms of effectiveness and efficiency.

Text-Attributed Graphs (TAGs) enhance graph structures with natural language descriptions, enabling detailed representation of data and their relationships across a broad spectrum of real-world scenarios. Despite the potential for deeper insights, existing TAG representation learning primarily relies on supervised methods, necessitating extensive labeled data and limiting applicability across diverse contexts. This paper introduces a new self-supervised learning framework, Text-And-Graph Multi-View Alignment (TAGA), which overcomes these constraints by integrating TAGs' structural and semantic dimensions. TAGA constructs two complementary views: Text-of-Graph view, which organizes node texts into structured documents based on graph topology, and the Graph-of-Text view, which converts textual nodes and connections into graph data. By aligning representations from both views, TAGA captures joint textual and structural information. In addition, a novel structure-preserving random walk algorithm is proposed for efficient training on large-sized TAGs. Our framework demonstrates strong performance in zero-shot and few-shot scenarios across eight real-world datasets.

Within the graph learning community, conventional wisdom dictates that spectral convolutional networks may only be deployed on undirected graphs: Only there could the existence of a well-defined graph Fourier transform be guaranteed, so that information may be translated between spatial- and spectral domains. Here we show this traditional reliance on the graph Fourier transform to be superfluous and -- making use of certain advanced tools from complex analysis and spectral theory -- extend spectral convolutions to directed graphs. We provide a frequency-response interpretation of newly developed filters, investigate the influence of the basis used to express filters and discuss the interplay with characteristic operators on which networks are based. In order to thoroughly test the developed theory, we conduct experiments in real world settings, showcasing that directed spectral convolutional networks provide new state of the art results for heterophilic node classification on many datasets and -- as opposed to baselines -- may be rendered stable to resolution-scale varying topological perturbations.

Graphs can model complex relationships between objects, enabling a myriad of Web applications such as online page/article classification and social recommendation. While graph neural networks(GNNs) have emerged as a powerful tool for graph representation learning, in an end-to-end supervised setting, their performance heavily rely on a large amount of task-specific supervision. To reduce labeling requirement, the "pre-train, fine-tune" and "pre-train, prompt" paradigms have become increasingly common. In particular, prompting is a popular alternative to fine-tuning in natural language processing, which is designed to narrow the gap between pre-training and downstream objectives in a task-specific manner. However, existing study of prompting on graphs is still limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template, but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-train model in a task-specific manner. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt.

Graph Convolutional Networks (GCNs) and their variants have experienced significant attention and have become the de facto methods for learning graph representations. GCNs derive inspiration primarily from recent deep learning approaches, and as a result, may inherit unnecessary complexity and redundant computation. In this paper, we reduce this excess complexity through successively removing nonlinearities and collapsing weight matrices between consecutive layers. We theoretically analyze the resulting linear model and show that it corresponds to a fixed low-pass filter followed by a linear classifier. Notably, our experimental evaluation demonstrates that these simplifications do not negatively impact accuracy in many downstream applications. Moreover, the resulting model scales to larger datasets, is naturally interpretable, and yields up to two orders of magnitude speedup over FastGCN.

Generalizable, transferrable, and robust representation learning on graph-structured data remains a challenge for current graph neural networks (GNNs). Unlike what has been developed for convolutional neural networks (CNNs) for image data, self-supervised learning and pre-training are less explored for GNNs. In this paper, we propose a graph contrastive learning (GraphCL) framework for learning unsupervised representations of graph data. We first design four types of graph augmentations to incorporate various priors. We then systematically study the impact of various combinations of graph augmentations on multiple datasets, in four different settings: semi-supervised, unsupervised, and transfer learning as well as adversarial attacks. The results show that, even without tuning augmentation extents nor using sophisticated GNN architectures, our GraphCL framework can produce graph representations of similar or better generalizability, transferrability, and robustness compared to state-of-the-art methods. We also investigate the impact of parameterized graph augmentation extents and patterns, and observe further performance gains in preliminary experiments. Our codes are available at https://github.com/Shen-Lab/GraphCL.

State-of-the-art visual perception models for a wide range of tasks rely on supervised pretraining. ImageNet classification is the de facto pretraining task for these models. Yet, ImageNet is now nearly ten years old and is by modern standards "small". Even so, relatively little is known about the behavior of pretraining with datasets that are multiple orders of magnitude larger. The reasons are obvious: such datasets are difficult to collect and annotate. In this paper, we present a unique study of transfer learning with large convolutional networks trained to predict hashtags on billions of social media images. Our experiments demonstrate that training for large-scale hashtag prediction leads to excellent results. We show improvements on several image classification and object detection tasks, and report the highest ImageNet-1k single-crop, top-1 accuracy to date: 85.4% (97.6% top-5). We also perform extensive experiments that provide novel empirical data on the relationship between large-scale pretraining and transfer learning performance.

Graph embedding methods produce unsupervised node features from graphs that can then be used for a variety of machine learning tasks. Modern graphs, particularly in industrial applications, contain billions of nodes and trillions of edges, which exceeds the capability of existing embedding systems. We present PyTorch-BigGraph (PBG), an embedding system that incorporates several modifications to traditional multi-relation embedding systems that allow it to scale to graphs with billions of nodes and trillions of edges. PBG uses graph partitioning to train arbitrarily large embeddings on either a single machine or in a distributed environment. We demonstrate comparable performance with existing embedding systems on common benchmarks, while allowing for scaling to arbitrarily large graphs and parallelization on multiple machines. We train and evaluate embeddings on several large social network graphs as well as the full Freebase dataset, which contains over 100 million nodes and 2 billion edges.

Graph convolutional networks (GCNs) enable end-to-end learning on graph structured data. However, many works assume a given graph structure. When the input graph is noisy or unavailable, one approach is to construct or learn a latent graph structure. These methods typically fix the choice of node degree for the entire graph, which is suboptimal. Instead, we propose a novel end-to-end differentiable graph generator which builds graph topologies where each node selects both its neighborhood and its size. Our module can be readily integrated into existing pipelines involving graph convolution operations, replacing the predetermined or existing adjacency matrix with one that is learned, and optimized, as part of the general objective. As such it is applicable to any GCN. We integrate our module into trajectory prediction, point cloud classification and node classification pipelines resulting in improved accuracy over other structure-learning methods across a wide range of datasets and GCN backbones.

This work studies self-supervised graph learning for text-attributed graphs (TAGs) where nodes are represented by textual attributes. Unlike traditional graph contrastive methods that perturb the numerical feature space and alter the graph's topological structure, we aim to improve view generation through language supervision. This is driven by the prevalence of textual attributes in real applications, which complement graph structures with rich semantic information. However, this presents challenges because of two major reasons. First, text attributes often vary in length and quality, making it difficulty to perturb raw text descriptions without altering their original semantic meanings. Second, although text attributes complement graph structures, they are not inherently well-aligned. To bridge the gap, we introduce GAugLLM, a novel framework for augmenting TAGs. It leverages advanced large language models like Mistral to enhance self-supervised graph learning. Specifically, we introduce a mixture-of-prompt-expert technique to generate augmented node features. This approach adaptively maps multiple prompt experts, each of which modifies raw text attributes using prompt engineering, into numerical feature space. Additionally, we devise a collaborative edge modifier to leverage structural and textual commonalities, enhancing edge augmentation by examining or building connections between nodes. Empirical results across five benchmark datasets spanning various domains underscore our framework's ability to enhance the performance of leading contrastive methods as a plug-in tool. Notably, we observe that the augmented features and graph structure can also enhance the performance of standard generative methods, as well as popular graph neural networks. The open-sourced implementation of our GAugLLM is available at Github.

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.

Learning on text-attributed graphs (TAGs), in which nodes are associated with one or more texts, has been the subject of much recent work. However, most approaches tend to make strong assumptions about the downstream task of interest, are reliant on hand-labeled data, or fail to equally balance the importance of both text and graph representations. In this work, we propose Contrastive Graph-Text pretraining (ConGraT), a general, self-supervised approach for jointly learning separate representations of texts and nodes in a TAG. Our method trains a language model (LM) and a graph neural network (GNN) to align their representations in a common latent space using a batch-wise contrastive learning objective inspired by CLIP. We further propose an extension to the CLIP objective that leverages graph structure to incorporate information about inter-node similarity. Extensive experiments demonstrate that ConGraT outperforms baselines on various downstream tasks, including node and text category classification, link prediction, and language modeling. Finally, we present an application of our method to community detection in social graphs, which enables finding more textually grounded communities, rather than purely graph-based ones. Code and certain datasets are available at https://github.com/wwbrannon/congrat.

Despite that going deep has proven successful in many neural architectures, the existing graph transformers are relatively shallow. In this work, we explore whether more layers are beneficial to graph transformers, and find that current graph transformers suffer from the bottleneck of improving performance by increasing depth. Our further analysis reveals the reason is that deep graph transformers are limited by the vanishing capacity of global attention, restricting the graph transformer from focusing on the critical substructure and obtaining expressive features. To this end, we propose a novel graph transformer model named DeepGraph that explicitly employs substructure tokens in the encoded representation, and applies local attention on related nodes to obtain substructure based attention encoding. Our model enhances the ability of the global attention to focus on substructures and promotes the expressiveness of the representations, addressing the limitation of self-attention as the graph transformer deepens. Experiments show that our method unblocks the depth limitation of graph transformers and results in state-of-the-art performance across various graph benchmarks with deeper models.

Graph neural networks (GNNs) have been demonstrated to be powerful in modeling graph-structured data. However, training GNNs usually requires abundant task-specific labeled data, which is often arduously expensive to obtain. One effective way to reduce the labeling effort is to pre-train an expressive GNN model on unlabeled data with self-supervision and then transfer the learned model to downstream tasks with only a few labels. In this paper, we present the GPT-GNN framework to initialize GNNs by generative pre-training. GPT-GNN introduces a self-supervised attributed graph generation task to pre-train a GNN so that it can capture the structural and semantic properties of the graph. We factorize the likelihood of the graph generation into two components: 1) Attribute Generation and 2) Edge Generation. By modeling both components, GPT-GNN captures the inherent dependency between node attributes and graph structure during the generative process. Comprehensive experiments on the billion-scale Open Academic Graph and Amazon recommendation data demonstrate that GPT-GNN significantly outperforms state-of-the-art GNN models without pre-training by up to 9.1% across various downstream tasks.

Self-supervision as an emerging technique has been employed to train convolutional neural networks (CNNs) for more transferrable, generalizable, and robust representation learning of images. Its introduction to graph convolutional networks (GCNs) operating on graph data is however rarely explored. In this study, we report the first systematic exploration and assessment of incorporating self-supervision into GCNs. We first elaborate three mechanisms to incorporate self-supervision into GCNs, analyze the limitations of pretraining & finetuning and self-training, and proceed to focus on multi-task learning. Moreover, we propose to investigate three novel self-supervised learning tasks for GCNs with theoretical rationales and numerical comparisons. Lastly, we further integrate multi-task self-supervision into graph adversarial training. Our results show that, with properly designed task forms and incorporation mechanisms, self-supervision benefits GCNs in gaining more generalizability and robustness. Our codes are available at https://github.com/Shen-Lab/SS-GCNs.

Machine learning frameworks such as graph neural networks typically rely on a given, fixed graph to exploit relational inductive biases and thus effectively learn from network data. However, when said graphs are (partially) unobserved, noisy, or dynamic, the problem of inferring graph structure from data becomes relevant. In this paper, we postulate a graph convolutional relationship between the observed and latent graphs, and formulate the graph learning task as a network inverse (deconvolution) problem. In lieu of eigendecomposition-based spectral methods or iterative optimization solutions, we unroll and truncate proximal gradient iterations to arrive at a parameterized neural network architecture that we call a Graph Deconvolution Network (GDN). GDNs can learn a distribution of graphs in a supervised fashion, perform link prediction or edge-weight regression tasks by adapting the loss function, and they are inherently inductive. We corroborate GDN's superior graph recovery performance and its generalization to larger graphs using synthetic data in supervised settings. Furthermore, we demonstrate the robustness and representation power of GDNs on real world neuroimaging and social network datasets.

Recent studies often exploit Graph Convolutional Network (GCN) to model label dependencies to improve recognition accuracy for multi-label image recognition. However, constructing a graph by counting the label co-occurrence possibilities of the training data may degrade model generalizability, especially when there exist occasional co-occurrence objects in test images. Our goal is to eliminate such bias and enhance the robustness of the learnt features. To this end, we propose an Attention-Driven Dynamic Graph Convolutional Network (ADD-GCN) to dynamically generate a specific graph for each image. ADD-GCN adopts a Dynamic Graph Convolutional Network (D-GCN) to model the relation of content-aware category representations that are generated by a Semantic Attention Module (SAM). Extensive experiments on public multi-label benchmarks demonstrate the effectiveness of our method, which achieves mAPs of 85.2%, 96.0%, and 95.5% on MS-COCO, VOC2007, and VOC2012, respectively, and outperforms current state-of-the-art methods with a clear margin. All codes can be found at https://github.com/Yejin0111/ADD-GCN.

Contrastive pretraining techniques for text classification has been largely studied in an unsupervised setting. However, oftentimes labeled data from related tasks which share label semantics with current task is available. We hypothesize that using this labeled data effectively can lead to better generalization on current task. In this paper, we propose a novel way to effectively utilize labeled data from related tasks with a graph based supervised contrastive learning approach. We formulate a token-graph by extrapolating the supervised information from examples to tokens. Our formulation results in an embedding space where tokens with high/low probability of belonging to same class are near/further-away from one another. We also develop detailed theoretical insights which serve as a motivation for our method. In our experiments with 13 datasets, we show our method outperforms pretraining schemes by 2.5% and also example-level contrastive learning based formulation by 1.8% on average. In addition, we show cross-domain effectiveness of our method in a zero-shot setting by 3.91% on average. Lastly, we also demonstrate our method can be used as a noisy teacher in a knowledge distillation setting to significantly improve performance of transformer based models in low labeled data regime by 4.57% on average.

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.

Can we model non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The non-Euclidean property have posed a long term challenge in graph modeling. Despite recent GNN and Graphformer efforts encoding graphs as Euclidean vectors, recovering original graph from the vectors remains a challenge. We introduce GraphsGPT, featuring a Graph2Seq encoder that transforms non-Euclidean graphs into learnable graph words in a Euclidean space, along with a GraphGPT decoder that reconstructs the original graph from graph words to ensure information equivalence. We pretrain GraphsGPT on 100M molecules and yield some interesting findings: (1) Pretrained Graph2Seq excels in graph representation learning, achieving state-of-the-art results on 8/9 graph classification and regression tasks. (2) Pretrained GraphGPT serves as a strong graph generator, demonstrated by its ability to perform both unconditional and conditional graph generation. (3) Graph2Seq+GraphGPT enables effective graph mixup in the Euclidean space, overcoming previously known non-Euclidean challenge. (4) Our proposed novel edge-centric GPT pretraining task is effective in graph fields, underscoring its success in both representation and generation.

Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very interesting applications, ranging from drug discovery to recommender systems. To achieve such tasks, tremendous work has been accomplished to learn embedding of nodes and edges into finite-dimension vector spaces. This task is called Graph Representation Learning. However, Graph Representation Learning techniques often display prohibitive time and memory complexities, preventing their use in real-time with business size graphs. In this paper, we address this issue by leveraging a degeneracy property of Graphs - the K-Core Decomposition. We present two techniques taking advantage of this decomposition to reduce the time and memory consumption of walk-based Graph Representation Learning algorithms. We evaluate the performances, expressed in terms of quality of embedding and computational resources, of the proposed techniques on several academic datasets. Our code is available at https://github.com/SBrandeis/kcore-embedding

We consider the problem of zero-shot recognition: learning a visual classifier for a category with zero training examples, just using the word embedding of the category and its relationship to other categories, which visual data are provided. The key to dealing with the unfamiliar or novel category is to transfer knowledge obtained from familiar classes to describe the unfamiliar class. In this paper, we build upon the recently introduced Graph Convolutional Network (GCN) and propose an approach that uses both semantic embeddings and the categorical relationships to predict the classifiers. Given a learned knowledge graph (KG), our approach takes as input semantic embeddings for each node (representing visual category). After a series of graph convolutions, we predict the visual classifier for each category. During training, the visual classifiers for a few categories are given to learn the GCN parameters. At test time, these filters are used to predict the visual classifiers of unseen categories. We show that our approach is robust to noise in the KG. More importantly, our approach provides significant improvement in performance compared to the current state-of-the-art results (from 2 ~ 3% on some metrics to whopping 20% on a few).

Graph Convolutional Networks (GCNs) have been drawing significant attention with the power of representation learning on graphs. Unlike Convolutional Neural Networks (CNNs), which are able to take advantage of stacking very deep layers, GCNs suffer from vanishing gradient, over-smoothing and over-fitting issues when going deeper. These challenges limit the representation power of GCNs on large-scale graphs. This paper proposes DeeperGCN that is capable of successfully and reliably training very deep GCNs. We define differentiable generalized aggregation functions to unify different message aggregation operations (e.g. mean, max). We also propose a novel normalization layer namely MsgNorm and a pre-activation version of residual connections for GCNs. Extensive experiments on Open Graph Benchmark (OGB) show DeeperGCN significantly boosts performance over the state-of-the-art on the large scale graph learning tasks of node property prediction and graph property prediction. Please visit https://www.deepgcns.org for more information.

Graph Convolutional Networks (GCNs) are powerful models for learning representations of attributed graphs. To scale GCNs to large graphs, state-of-the-art methods use various layer sampling techniques to alleviate the "neighbor explosion" problem during minibatch training. We propose GraphSAINT, a graph sampling based inductive learning method that improves training efficiency and accuracy in a fundamentally different way. By changing perspective, GraphSAINT constructs minibatches by sampling the training graph, rather than the nodes or edges across GCN layers. Each iteration, a complete GCN is built from the properly sampled subgraph. Thus, we ensure fixed number of well-connected nodes in all layers. We further propose normalization technique to eliminate bias, and sampling algorithms for variance reduction. Importantly, we can decouple the sampling from the forward and backward propagation, and extend GraphSAINT with many architecture variants (e.g., graph attention, jumping connection). GraphSAINT demonstrates superior performance in both accuracy and training time on five large graphs, and achieves new state-of-the-art F1 scores for PPI (0.995) and Reddit (0.970).

Representation learning on text-attributed graphs (TAGs) has become a critical research problem in recent years. A typical example of a TAG is a paper citation graph, where the text of each paper serves as node attributes. Initial graph neural network (GNN) pipelines handled these text attributes by transforming them into shallow or hand-crafted features, such as skip-gram or bag-of-words features. Recent efforts have focused on enhancing these pipelines with language models (LMs), which typically demand intricate designs and substantial computational resources. With the advent of powerful large language models (LLMs) such as GPT or Llama2, which demonstrate an ability to reason and to utilize general knowledge, there is a growing need for techniques which combine the textual modelling abilities of LLMs with the structural learning capabilities of GNNs. Hence, in this work, we focus on leveraging LLMs to capture textual information as features, which can be used to boost GNN performance on downstream tasks. A key innovation is our use of explanations as features: we prompt an LLM to perform zero-shot classification, request textual explanations for its decision-making process, and design an LLM-to-LM interpreter to translate these explanations into informative features for downstream GNNs. Our experiments demonstrate that our method achieves state-of-the-art results on well-established TAG datasets, including Cora, PubMed, ogbn-arxiv, as well as our newly introduced dataset, tape-arxiv23. Furthermore, our method significantly speeds up training, achieving a 2.88 times improvement over the closest baseline on ogbn-arxiv. Lastly, we believe the versatility of the proposed method extends beyond TAGs and holds the potential to enhance other tasks involving graph-text data. Our codes and datasets are available at: https://github.com/XiaoxinHe/TAPE.

Attention-based graph neural networks (GNNs), such as graph attention networks (GATs), have become popular neural architectures for processing graph-structured data and learning node embeddings. Despite their empirical success, these models rely on labeled data and the theoretical properties of these models have yet to be fully understood. In this work, we propose a novel attention-based node embedding framework for graphs. Our framework builds upon a hierarchical kernel for multisets of subgraphs around nodes (e.g. neighborhoods) and each kernel leverages the geometry of a smooth statistical manifold to compare pairs of multisets, by "projecting" the multisets onto the manifold. By explicitly computing node embeddings with a manifold of Gaussian mixtures, our method leads to a new attention mechanism for neighborhood aggregation. We provide theoretical insights into generalizability and expressivity of our embeddings, contributing to a deeper understanding of attention-based GNNs. We propose both efficient unsupervised and supervised methods for learning the embeddings. Through experiments on several node classification benchmarks, we demonstrate that our proposed method outperforms existing attention-based graph models like GATs. Our code is available at https://github.com/BorgwardtLab/fisher_information_embedding.

We present graph attention networks (GATs), novel neural network architectures that operate on graph-structured data, leveraging masked self-attentional layers to address the shortcomings of prior methods based on graph convolutions or their approximations. By stacking layers in which nodes are able to attend over their neighborhoods' features, we enable (implicitly) specifying different weights to different nodes in a neighborhood, without requiring any kind of costly matrix operation (such as inversion) or depending on knowing the graph structure upfront. In this way, we address several key challenges of spectral-based graph neural networks simultaneously, and make our model readily applicable to inductive as well as transductive problems. Our GAT models have achieved or matched state-of-the-art results across four established transductive and inductive graph benchmarks: the Cora, Citeseer and Pubmed citation network datasets, as well as a protein-protein interaction dataset (wherein test graphs remain unseen during training).

With the increasing number of new neural architecture designs and substantial existing neural architectures, it becomes difficult for the researchers to situate their contributions compared with existing neural architectures or establish the connections between their designs and other relevant ones. To discover similar neural architectures in an efficient and automatic manner, we define a new problem Neural Architecture Retrieval which retrieves a set of existing neural architectures which have similar designs to the query neural architecture. Existing graph pre-training strategies cannot address the computational graph in neural architectures due to the graph size and motifs. To fulfill this potential, we propose to divide the graph into motifs which are used to rebuild the macro graph to tackle these issues, and introduce multi-level contrastive learning to achieve accurate graph representation learning. Extensive evaluations on both human-designed and synthesized neural architectures demonstrate the superiority of our algorithm. Such a dataset which contains 12k real-world network architectures, as well as their embedding, is built for neural architecture retrieval.

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.

The use of graph neural networks has produced significant advances in point cloud problems, such as those found in high energy physics. The question of how to produce a graph structure in these problems is usually treated as a matter of heuristics, employing fully connected graphs or K-nearest neighbors. In this work, we elevate this question to utmost importance as the Topology Problem. We propose an attention mechanism that allows a graph to be constructed in a learned space that handles geometrically the flow of relevance, providing one solution to the Topology Problem. We test this architecture, called GravNetNorm, on the task of top jet tagging, and show that it is competitive in tagging accuracy, and uses far fewer computational resources than all other comparable models.

We introduce a self-supervised approach for learning node and graph level representations by contrasting structural views of graphs. We show that unlike visual representation learning, increasing the number of views to more than two or contrasting multi-scale encodings do not improve performance, and the best performance is achieved by contrasting encodings from first-order neighbors and a graph diffusion. We achieve new state-of-the-art results in self-supervised learning on 8 out of 8 node and graph classification benchmarks under the linear evaluation protocol. For example, on Cora (node) and Reddit-Binary (graph) classification benchmarks, we achieve 86.8% and 84.5% accuracy, which are 5.5% and 2.4% relative improvements over previous state-of-the-art. When compared to supervised baselines, our approach outperforms them in 4 out of 8 benchmarks. Source code is released at: https://github.com/kavehhassani/mvgrl

Model pre-training is a cornerstone of modern visual recognition systems. Although fully supervised pre-training on datasets like ImageNet is still the de-facto standard, recent studies suggest that large-scale weakly supervised pre-training can outperform fully supervised approaches. This paper revisits weakly-supervised pre-training of models using hashtag supervision with modern versions of residual networks and the largest-ever dataset of images and corresponding hashtags. We study the performance of the resulting models in various transfer-learning settings including zero-shot transfer. We also compare our models with those obtained via large-scale self-supervised learning. We find our weakly-supervised models to be very competitive across all settings, and find they substantially outperform their self-supervised counterparts. We also include an investigation into whether our models learned potentially troubling associations or stereotypes. Overall, our results provide a compelling argument for the use of weakly supervised learning in the development of visual recognition systems. Our models, Supervised Weakly through hashtAGs (SWAG), are available publicly.

The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared to mainstream GNN variants. Therefore, it remains a mystery how Transformers could perform well for graph representation learning. In this paper, we solve this mystery by presenting Graphormer, which is built upon the standard Transformer architecture, and could attain excellent results on a broad range of graph representation learning tasks, especially on the recent OGB Large-Scale Challenge. Our key insight to utilizing Transformer in the graph is the necessity of effectively encoding the structural information of a graph into the model. To this end, we propose several simple yet effective structural encoding methods to help Graphormer better model graph-structured data. Besides, we mathematically characterize the expressive power of Graphormer and exhibit that with our ways of encoding the structural information of graphs, many popular GNN variants could be covered as the special cases of Graphormer.

Subgraph matching is a fundamental building block for graph-based applications and is challenging due to its high-order combinatorial nature. Existing studies usually tackle it by combinatorial optimization or learning-based methods. However, they suffer from exponential computational costs or searching the matching without theoretical guarantees. In this paper, we develop D2Match by leveraging the efficiency of Deep learning and Degeneracy for subgraph matching. More specifically, we first prove that subgraph matching can degenerate to subtree matching, and subsequently is equivalent to finding a perfect matching on a bipartite graph. We can then yield an implementation of linear time complexity by the built-in tree-structured aggregation mechanism on graph neural networks. Moreover, circle structures and node attributes can be easily incorporated in D2Match to boost the matching performance. Finally, we conduct extensive experiments to show the superior performance of our D2Match and confirm that our D2Match indeed exploits the subtrees and differs from existing GNNs-based subgraph matching methods that depend on memorizing the data distribution divergence

Representation learning on heterogeneous graphs aims to obtain meaningful node representations to facilitate various downstream tasks, such as node classification and link prediction. Existing heterogeneous graph learning methods are primarily developed by following the propagation mechanism of node representations. There are few efforts on studying the role of relations for improving the learning of more fine-grained node representations. Indeed, it is important to collaboratively learn the semantic representations of relations and discern node representations with respect to different relation types. To this end, in this paper, we propose a novel Relation-aware Heterogeneous Graph Neural Network, namely R-HGNN, to learn node representations on heterogeneous graphs at a fine-grained level by considering relation-aware characteristics. Specifically, a dedicated graph convolution component is first designed to learn unique node representations from each relation-specific graph separately. Then, a cross-relation message passing module is developed to improve the interactions of node representations across different relations. Also, the relation representations are learned in a layer-wise manner to capture relation semantics, which are used to guide the node representation learning process. Moreover, a semantic fusing module is presented to aggregate relation-aware node representations into a compact representation with the learned relation representations. Finally, we conduct extensive experiments on a variety of graph learning tasks, and experimental results demonstrate that our approach consistently outperforms existing methods among all the tasks.

We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of graph representation learning with a variety of recent publications but they lack a common foundation about what constitutes a good positional or structural encoding, and what differentiates them. In this paper, we summarize the different types of encodings with a clearer definition and categorize them as being local, global or relative. The prior GTs are constrained to small graphs with a few hundred nodes, here we propose the first architecture with a complexity linear in the number of nodes and edges O(N+E) by decoupling the local real-edge aggregation from the fully-connected Transformer. We argue that this decoupling does not negatively affect the expressivity, with our architecture being a universal function approximator on graphs. Our GPS recipe consists of choosing 3 main ingredients: (i) positional/structural encoding, (ii) local message-passing mechanism, and (iii) global attention mechanism. We provide a modular framework GraphGPS that supports multiple types of encodings and that provides efficiency and scalability both in small and large graphs. We test our architecture on 16 benchmarks and show highly competitive results in all of them, show-casing the empirical benefits gained by the modularity and the combination of different strategies.

Graph transformers (GTs) have emerged as a promising architecture that is theoretically more expressive than message-passing graph neural networks (GNNs). However, typical GT models have at least quadratic complexity and thus cannot scale to large graphs. While there are several linear GTs recently proposed, they still lag behind GNN counterparts on several popular graph datasets, which poses a critical concern on their practical expressivity. To balance the trade-off between expressivity and scalability of GTs, we propose Polynormer, a polynomial-expressive GT model with linear complexity. Polynormer is built upon a novel base model that learns a high-degree polynomial on input features. To enable the base model permutation equivariant, we integrate it with graph topology and node features separately, resulting in local and global equivariant attention models. Consequently, Polynormer adopts a linear local-to-global attention scheme to learn high-degree equivariant polynomials whose coefficients are controlled by attention scores. Polynormer has been evaluated on 13 homophilic and heterophilic datasets, including large graphs with millions of nodes. Our extensive experiment results show that Polynormer outperforms state-of-the-art GNN and GT baselines on most datasets, even without the use of nonlinear activation functions.

Graph learning has become indispensable for interpreting and harnessing relational data in diverse fields, ranging from recommendation systems to social network analysis. In this context, a variety of GNNs have emerged as promising methodologies for encoding the structural information of graphs. By effectively capturing the graph's underlying structure, these GNNs have shown great potential in enhancing performance in graph learning tasks, such as link prediction and node classification. However, despite their successes, a significant challenge persists: these advanced methods often face difficulties in generalizing to unseen graph data that significantly differs from the training instances. In this work, our aim is to advance the graph learning paradigm by developing a general graph foundation model. This model is designed to understand the complex topological patterns present in diverse graph data, enabling it to excel in zero-shot graph learning tasks across different downstream datasets. To achieve this goal, we address several key technical challenges in our OpenGraph model. Firstly, we propose a unified graph tokenizer to adapt our graph model to generalize well on unseen graph data, even when the underlying graph properties differ significantly from those encountered during training. Secondly, we develop a scalable graph transformer as the foundational encoder, which effectively captures node-wise dependencies within the global topological context. Thirdly, we introduce a data augmentation mechanism enhanced by a LLM to alleviate the limitations of data scarcity in real-world scenarios. Extensive experiments validate the effectiveness of our framework. By adapting our OpenGraph to new graph characteristics and comprehending the nuances of diverse graphs, our approach achieves remarkable zero-shot graph learning performance across various settings and domains.

This paper introduces Graph Convolutional Recurrent Network (GCRN), a deep learning model able to predict structured sequences of data. Precisely, GCRN is a generalization of classical recurrent neural networks (RNN) to data structured by an arbitrary graph. Such structured sequences can represent series of frames in videos, spatio-temporal measurements on a network of sensors, or random walks on a vocabulary graph for natural language modeling. The proposed model combines convolutional neural networks (CNN) on graphs to identify spatial structures and RNN to find dynamic patterns. We study two possible architectures of GCRN, and apply the models to two practical problems: predicting moving MNIST data, and modeling natural language with the Penn Treebank dataset. Experiments show that exploiting simultaneously graph spatial and dynamic information about data can improve both precision and learning speed.

We present a novel learning-based approach to graph representations of road networks employing state-of-the-art graph convolutional neural networks. Our approach is applied to realistic road networks of 17 cities from Open Street Map. While edge features are crucial to generate descriptive graph representations of road networks, graph convolutional networks usually rely on node features only. We show that the highly representative edge features can still be integrated into such networks by applying a line graph transformation. We also propose a method for neighborhood sampling based on a topological neighborhood composed of both local and global neighbors. We compare the performance of learning representations using different types of neighborhood aggregation functions in transductive and inductive tasks and in supervised and unsupervised learning. Furthermore, we propose a novel aggregation approach, Graph Attention Isomorphism Network, GAIN. Our results show that GAIN outperforms state-of-the-art methods on the road type classification problem.

Large Generative Models (LGMs) such as GPT, Stable Diffusion, Sora, and Suno are trained on a huge amount of language corpus, images, videos, and audio that are extremely diverse from numerous domains. This training paradigm over diverse well-curated data lies at the heart of generating creative and sensible content. However, all previous graph generative models (e.g., GraphRNN, MDVAE, MoFlow, GDSS, and DiGress) have been trained only on one dataset each time, which cannot replicate the revolutionary success achieved by LGMs in other fields. To remedy this crucial gap, we propose a new class of graph generative model called Large Graph Generative Model (LGGM) that is trained on a large corpus of graphs (over 5000 graphs) from 13 different domains. We empirically demonstrate that the pre-trained LGGM has superior zero-shot generative capability to existing graph generative models. Furthermore, our pre-trained LGGM can be easily fine-tuned with graphs from target domains and demonstrate even better performance than those directly trained from scratch, behaving as a solid starting point for real-world customization. Inspired by Stable Diffusion, we further equip LGGM with the capability to generate graphs given text prompts (Text-to-Graph), such as the description of the network name and domain (i.e., "The power-1138-bus graph represents a network of buses in a power distribution system."), and network statistics (i.e., "The graph has a low average degree, suitable for modeling social media interactions."). This Text-to-Graph capability integrates the extensive world knowledge in the underlying language model, offering users fine-grained control of the generated graphs. We release the code, the model checkpoint, and the datasets at https://lggm-lg.github.io/.

Following the success of Word2Vec embeddings, graph embeddings (GEs) have gained substantial traction. GEs are commonly generated and evaluated extrinsically on downstream applications, but intrinsic evaluations of the original graph properties in terms of topological structure and semantic information have been lacking. Understanding these will help identify the deficiency of the various families of GE methods when vectorizing graphs in terms of preserving the relevant knowledge or learning incorrect knowledge. To address this, we propose RESTORE, a framework for intrinsic GEs assessment through graph reconstruction. We show that reconstructing the original graph from the underlying GEs yields insights into the relative amount of information preserved in a given vector form. We first introduce the graph reconstruction task. We generate GEs from three GE families based on factorization methods, random walks, and deep learning (with representative algorithms from each family) on the CommonSense Knowledge Graph (CSKG). We analyze their effectiveness in preserving the (a) topological structure of node-level graph reconstruction with an increasing number of hops and (b) semantic information on various word semantic and analogy tests. Our evaluations show deep learning-based GE algorithm (SDNE) is overall better at preserving (a) with a mean average precision (mAP) of 0.54 and 0.35 for 2 and 3-hop reconstruction respectively, while the factorization-based algorithm (HOPE) is better at encapsulating (b) with an average Euclidean distance of 0.14, 0.17, and 0.11 for 1, 2, and 3-hop reconstruction respectively. The modest performance of these GEs leaves room for further research avenues on better graph representation learning.

Relation Extraction is a way of obtaining the semantic relationship between entities in text. The state-of-the-art methods use linguistic tools to build a graph for the text in which the entities appear and then a Graph Convolutional Network (GCN) is employed to encode the pre-built graphs. Although their performance is promising, the reliance on linguistic tools results in a non end-to-end process. In this work, we propose a novel model, the Self-determined Graph Convolutional Network (SGCN), which determines a weighted graph using a self-attention mechanism, rather using any linguistic tool. Then, the self-determined graph is encoded using a GCN. We test our model on the TACRED dataset and achieve the state-of-the-art result. Our experiments show that SGCN outperforms the traditional GCN, which uses dependency parsing tools to build the graph.

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular "graph convolutions", a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph---atoms, bonds, distances, etc.---which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.

Graph Transformers (GTs) have achieved impressive results on various graph-related tasks. However, the huge computational cost of GTs hinders their deployment and application, especially in resource-constrained environments. Therefore, in this paper, we explore the feasibility of sparsifying GTs, a significant yet under-explored topic. We first discuss the redundancy of GTs based on the characteristics of existing GT models, and then propose a comprehensive Graph Transformer SParsification (GTSP) framework that helps to reduce the computational complexity of GTs from four dimensions: the input graph data, attention heads, model layers, and model weights. Specifically, GTSP designs differentiable masks for each individual compressible component, enabling effective end-to-end pruning. We examine our GTSP through extensive experiments on prominent GTs, including GraphTrans, Graphormer, and GraphGPS. The experimental results substantiate that GTSP effectively cuts computational costs, accompanied by only marginal decreases in accuracy or, in some cases, even improvements. For instance, GTSP yields a reduction of 30\% in Floating Point Operations while contributing to a 1.8\% increase in Area Under the Curve accuracy on OGBG-HIV dataset. Furthermore, we provide several insights on the characteristics of attention heads and the behavior of attention mechanisms, all of which have immense potential to inspire future research endeavors in this domain.

We present an end-to-end deep learning segmentation method by combining a 3D UNet architecture with a graph neural network (GNN) model. In this approach, the convolutional layers at the deepest level of the UNet are replaced by a GNN-based module with a series of graph convolutions. The dense feature maps at this level are transformed into a graph input to the GNN module. The incorporation of graph convolutions in the UNet provides nodes in the graph with information that is based on node connectivity, in addition to the local features learnt through the downsampled paths. This information can help improve segmentation decisions. By stacking several graph convolution layers, the nodes can access higher order neighbourhood information without substantial increase in computational expense. We propose two types of node connectivity in the graph adjacency: i) one predefined and based on a regular node neighbourhood, and ii) one dynamically computed during training and using the nearest neighbour nodes in the feature space. We have applied this method to the task of segmenting the airway tree from chest CT scans. Experiments have been performed on 32 CTs from the Danish Lung Cancer Screening Trial dataset. We evaluate the performance of the UNet-GNN models with two types of graph adjacency and compare it with the baseline UNet.

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}

Graph Transformer (GT) recently has emerged as a new paradigm of graph learning algorithms, outperforming the previously popular Message Passing Neural Network (MPNN) on multiple benchmarks. Previous work (Kim et al., 2022) shows that with proper position embedding, GT can approximate MPNN arbitrarily well, implying that GT is at least as powerful as MPNN. In this paper, we study the inverse connection and show that MPNN with virtual node (VN), a commonly used heuristic with little theoretical understanding, is powerful enough to arbitrarily approximate the self-attention layer of GT. In particular, we first show that if we consider one type of linear transformer, the so-called Performer/Linear Transformer (Choromanski et al., 2020; Katharopoulos et al., 2020), then MPNN + VN with only O(1) depth and O(1) width can approximate a self-attention layer in Performer/Linear Transformer. Next, via a connection between MPNN + VN and DeepSets, we prove the MPNN + VN with O(n^d) width and O(1) depth can approximate the self-attention layer arbitrarily well, where d is the input feature dimension. Lastly, under some assumptions, we provide an explicit construction of MPNN + VN with O(1) width and O(n) depth approximating the self-attention layer in GT arbitrarily well. On the empirical side, we demonstrate that 1) MPNN + VN is a surprisingly strong baseline, outperforming GT on the recently proposed Long Range Graph Benchmark (LRGB) dataset, 2) our MPNN + VN improves over early implementation on a wide range of OGB datasets and 3) MPNN + VN outperforms Linear Transformer and MPNN on the climate modeling task.

In this study, we focus on the graph representation learning (a.k.a. network embedding) in attributed graphs. Different from existing embedding methods that treat the incorporation of graph structure and semantic as the simple combination of two optimization objectives, we propose a novel semantic graph representation (SGR) method to formulate the joint optimization of the two heterogeneous sources into a common high-order proximity based framework. Concretely, we first construct an auxiliary weighted graph, where the complex homogeneous and heterogeneous relations among nodes and attributes in the original graph are comprehensively encoded. Conventional embedding methods that consider high-order topology proximities can then be easily applied to the newly constructed graph to learn the representations of both node and attribute while capturing the nonlinear high-order intrinsic correlation inside or among graph structure and semantic. The learned attribute embeddings can also effectively support some semantic-oriented inference tasks (e.g., semantic community detection), helping to reveal the graph's deep semantic. The effectiveness of SGR is further verified on a series of real graphs, where it achieves impressive performance over other baselines.

Graph transformers have emerged as a promising architecture for a variety of graph learning and representation tasks. Despite their successes, though, it remains challenging to scale graph transformers to large graphs while maintaining accuracy competitive with message-passing networks. In this paper, we introduce Exphormer, a framework for building powerful and scalable graph transformers. Exphormer consists of a sparse attention mechanism based on two mechanisms: virtual global nodes and expander graphs, whose mathematical characteristics, such as spectral expansion, pseduorandomness, and sparsity, yield graph transformers with complexity only linear in the size of the graph, while allowing us to prove desirable theoretical properties of the resulting transformer models. We show that incorporating Exphormer into the recently-proposed GraphGPS framework produces models with competitive empirical results on a wide variety of graph datasets, including state-of-the-art results on three datasets. We also show that Exphormer can scale to datasets on larger graphs than shown in previous graph transformer architectures. Code can be found at https://github.com/hamed1375/Exphormer.

We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections between the words in a sequence. Such architecture does not leverage the graph connectivity inductive bias, and can perform poorly when the graph topology is important and has not been encoded into the node features. We introduce a graph transformer with four new properties compared to the standard model. First, the attention mechanism is a function of the neighborhood connectivity for each node in the graph. Second, the positional encoding is represented by the Laplacian eigenvectors, which naturally generalize the sinusoidal positional encodings often used in NLP. Third, the layer normalization is replaced by a batch normalization layer, which provides faster training and better generalization performance. Finally, the architecture is extended to edge feature representation, which can be critical to tasks s.a. chemistry (bond type) or link prediction (entity relationship in knowledge graphs). Numerical experiments on a graph benchmark demonstrate the performance of the proposed graph transformer architecture. This work closes the gap between the original transformer, which was designed for the limited case of line graphs, and graph neural networks, that can work with arbitrary graphs. As our architecture is simple and generic, we believe it can be used as a black box for future applications that wish to consider transformer and graphs.

The robustness of a model for real-world deployment is decided by how well it performs on unseen data and distinguishes between in-domain and out-of-domain samples. Visual document classifiers have shown impressive performance on in-distribution test sets. However, they tend to have a hard time correctly classifying and differentiating out-of-distribution examples. Image-based classifiers lack the text component, whereas multi-modality transformer-based models face the token serialization problem in visual documents due to their diverse layouts. They also require a lot of computing power during inference, making them impractical for many real-world applications. We propose, GVdoc, a graph-based document classification model that addresses both of these challenges. Our approach generates a document graph based on its layout, and then trains a graph neural network to learn node and graph embeddings. Through experiments, we show that our model, even with fewer parameters, outperforms state-of-the-art models on out-of-distribution data while retaining comparable performance on the in-distribution test set.

Transformers serve as the backbone architectures of Foundational Models, where a domain-specific tokenizer helps them adapt to various domains. Graph Transformers (GTs) have recently emerged as a leading model in geometric deep learning, outperforming Graph Neural Networks (GNNs) in various graph learning tasks. However, the development of tokenizers for graphs has lagged behind other modalities, with existing approaches relying on heuristics or GNNs co-trained with Transformers. To address this, we introduce GQT (Graph Quantized Tokenizer), which decouples tokenizer training from Transformer training by leveraging multi-task graph self-supervised learning, yielding robust and generalizable graph tokens. Furthermore, the GQT utilizes Residual Vector Quantization (RVQ) to learn hierarchical discrete tokens, resulting in significantly reduced memory requirements and improved generalization capabilities. By combining the GQT with token modulation, a Transformer encoder achieves state-of-the-art performance on 16 out of 18 benchmarks, including large-scale homophilic and heterophilic datasets. The code is available at: https://github.com/limei0307/graph-tokenizer

Recently, large language models (LLMs) have demonstrated superior capabilities in understanding and zero-shot learning on textual data, promising significant advances for many text-related domains. In the graph domain, various real-world scenarios also involve textual data, where tasks and node features can be described by text. These text-attributed graphs (TAGs) have broad applications in social media, recommendation systems, etc. Thus, this paper explores how to utilize LLMs to model TAGs. Previous methods for TAG modeling are based on million-scale LMs. When scaled up to billion-scale LLMs, they face huge challenges in computational costs. Additionally, they also ignore the zero-shot inference capabilities of LLMs. Therefore, we propose GraphAdapter, which uses a graph neural network (GNN) as an efficient adapter in collaboration with LLMs to tackle TAGs. In terms of efficiency, the GNN adapter introduces only a few trainable parameters and can be trained with low computation costs. The entire framework is trained using auto-regression on node text (next token prediction). Once trained, GraphAdapter can be seamlessly fine-tuned with task-specific prompts for various downstream tasks. Through extensive experiments across multiple real-world TAGs, GraphAdapter based on Llama 2 gains an average improvement of approximately 5\% in terms of node classification. Furthermore, GraphAdapter can also adapt to other language models, including RoBERTa, GPT-2. The promising results demonstrate that GNNs can serve as effective adapters for LLMs in TAG modeling.

Over recent decades, significant advancements in cross-modal retrieval are mainly driven by breakthroughs in visual and linguistic modeling. However, a recent study shows that multi-modal data representations tend to cluster within a limited convex cone (as representation degeneration problem), which hinders retrieval performance due to the inseparability of these representations. In our study, we first empirically validate the presence of the representation degeneration problem across multiple cross-modal benchmarks and methods. Next, to address it, we introduce a novel method, called InvGC, a post-processing technique inspired by graph convolution and average pooling. Specifically, InvGC defines the graph topology within the datasets and then applies graph convolution in a subtractive manner. This method effectively separates representations by increasing the distances between data points. To improve the efficiency and effectiveness of InvGC, we propose an advanced graph topology, LocalAdj, which only aims to increase the distances between each data point and its nearest neighbors. To understand why InvGC works, we present a detailed theoretical analysis, proving that the lower bound of recall will be improved after deploying InvGC. Extensive empirical results show that InvGC and InvGC w/LocalAdj significantly mitigate the representation degeneration problem, thereby enhancing retrieval performance. Our code is available at https://github.com/yimuwangcs/Better_Cross_Modal_Retrieval

This paper presents Tag2Text, a vision language pre-training (VLP) framework, which introduces image tagging into vision-language models to guide the learning of visual-linguistic features. In contrast to prior works which utilize object tags either manually labeled or automatically detected with a limited detector, our approach utilizes tags parsed from its paired text to learn an image tagger and meanwhile provides guidance to vision-language models. Given that, Tag2Text can utilize large-scale annotation-free image tags in accordance with image-text pairs, and provides more diverse tag categories beyond objects. As a result, Tag2Text achieves a superior image tag recognition ability by exploiting fine-grained text information. Moreover, by leveraging tagging guidance, Tag2Text effectively enhances the performance of vision-language models on both generation-based and alignment-based tasks. Across a wide range of downstream benchmarks, Tag2Text achieves state-of-the-art or competitive results with similar model sizes and data scales, demonstrating the efficacy of the proposed tagging guidance.

Text-Attributed Graphs (TAGs) augment graph structures with natural language descriptions, facilitating detailed depictions of data and their interconnections across various real-world settings. However, existing TAG datasets predominantly feature textual information only at the nodes, with edges typically represented by mere binary or categorical attributes. This lack of rich textual edge annotations significantly limits the exploration of contextual relationships between entities, hindering deeper insights into graph-structured data. To address this gap, we introduce Textual-Edge Graphs Datasets and Benchmark (TEG-DB), a comprehensive and diverse collection of benchmark textual-edge datasets featuring rich textual descriptions on nodes and edges. The TEG-DB datasets are large-scale and encompass a wide range of domains, from citation networks to social networks. In addition, we conduct extensive benchmark experiments on TEG-DB to assess the extent to which current techniques, including pre-trained language models, graph neural networks, and their combinations, can utilize textual node and edge information. Our goal is to elicit advancements in textual-edge graph research, specifically in developing methodologies that exploit rich textual node and edge descriptions to enhance graph analysis and provide deeper insights into complex real-world networks. The entire TEG-DB project is publicly accessible as an open-source repository on Github, accessible at https://github.com/Zhuofeng-Li/TEG-Benchmark.

Advancements in generative models have sparked significant interest in generating images while adhering to specific structural guidelines. Scene graph to image generation is one such task of generating images which are consistent with the given scene graph. However, the complexity of visual scenes poses a challenge in accurately aligning objects based on specified relations within the scene graph. Existing methods approach this task by first predicting a scene layout and generating images from these layouts using adversarial training. In this work, we introduce a novel approach to generate images from scene graphs which eliminates the need of predicting intermediate layouts. We leverage pre-trained text-to-image diffusion models and CLIP guidance to translate graph knowledge into images. Towards this, we first pre-train our graph encoder to align graph features with CLIP features of corresponding images using a GAN based training. Further, we fuse the graph features with CLIP embedding of object labels present in the given scene graph to create a graph consistent CLIP guided conditioning signal. In the conditioning input, object embeddings provide coarse structure of the image and graph features provide structural alignment based on relationships among objects. Finally, we fine tune a pre-trained diffusion model with the graph consistent conditioning signal with reconstruction and CLIP alignment loss. Elaborate experiments reveal that our method outperforms existing methods on standard benchmarks of COCO-stuff and Visual Genome dataset.

Humans describe complex scenes with compositionality, using simple text descriptions enriched with links and relationships. While vision-language research has aimed to develop models with compositional understanding capabilities, this is not reflected yet in existing datasets which, for the most part, still use plain text to describe images. In this work, we propose a new annotation strategy, graph-based captioning (GBC) that describes an image using a labelled graph structure, with nodes of various types. The nodes in GBC are created using, in a first stage, object detection and dense captioning tools nested recursively to uncover and describe entity nodes, further linked together in a second stage by highlighting, using new types of nodes, compositions and relations among entities. Since all GBC nodes hold plain text descriptions, GBC retains the flexibility found in natural language, but can also encode hierarchical information in its edges. We demonstrate that GBC can be produced automatically, using off-the-shelf multimodal LLMs and open-vocabulary detection models, by building a new dataset, GBC10M, gathering GBC annotations for about 10M images of the CC12M dataset. We use GBC10M to showcase the wealth of node captions uncovered by GBC, as measured with CLIP training. We show that using GBC nodes' annotations -- notably those stored in composition and relation nodes -- results in significant performance boost on downstream models when compared to other dataset formats. To further explore the opportunities provided by GBC, we also propose a new attention mechanism that can leverage the entire GBC graph, with encouraging experimental results that show the extra benefits of incorporating the graph structure. Our datasets are released at https://huggingface.co/graph-based-captions.

Although graph neural networks (GNNs) have achieved impressive achievements in graph classification, they often need abundant task-specific labels, which could be extensively costly to acquire. A credible solution is to explore additional labeled graphs to enhance unsupervised learning on the target domain. However, how to apply GNNs to domain adaptation remains unsolved owing to the insufficient exploration of graph topology and the significant domain discrepancy. In this paper, we propose Coupled Contrastive Graph Representation Learning (CoCo), which extracts the topological information from coupled learning branches and reduces the domain discrepancy with coupled contrastive learning. CoCo contains a graph convolutional network branch and a hierarchical graph kernel network branch, which explore graph topology in implicit and explicit manners. Besides, we incorporate coupled branches into a holistic multi-view contrastive learning framework, which not only incorporates graph representations learned from complementary views for enhanced understanding, but also encourages the similarity between cross-domain example pairs with the same semantics for domain alignment. Extensive experiments on popular datasets show that our CoCo outperforms these competing baselines in different settings generally.

Graph Neural Networks (GNNs) have shown great potential in the field of graph representation learning. Standard GNNs define a local message-passing mechanism which propagates information over the whole graph domain by stacking multiple layers. This paradigm suffers from two major limitations, over-squashing and poor long-range dependencies, that can be solved using global attention but significantly increases the computational cost to quadratic complexity. In this work, we propose an alternative approach to overcome these structural limitations by leveraging the ViT/MLP-Mixer architectures introduced in computer vision. We introduce a new class of GNNs, called Graph ViT/MLP-Mixer, that holds three key properties. First, they capture long-range dependency and mitigate the issue of over-squashing as demonstrated on Long Range Graph Benchmark and TreeNeighbourMatch datasets. Second, they offer better speed and memory efficiency with a complexity linear to the number of nodes and edges, surpassing the related Graph Transformer and expressive GNN models. Third, they show high expressivity in terms of graph isomorphism as they can distinguish at least 3-WL non-isomorphic graphs. We test our architecture on 4 simulated datasets and 7 real-world benchmarks, and show highly competitive results on all of them. The source code is available for reproducibility at: https://github.com/XiaoxinHe/Graph-ViT-MLPMixer.

Proposing an effective and flexible matrix to represent a graph is a fundamental challenge that has been explored from multiple perspectives, e.g., filtering in Graph Fourier Transforms. In this work, we develop a novel and general framework which unifies many existing GNN models from the view of parameterized decomposition and filtering, and show how it helps to enhance the flexibility of GNNs while alleviating the smoothness and amplification issues of existing models. Essentially, we show that the extensively studied spectral graph convolutions with learnable polynomial filters are constrained variants of this formulation, and releasing these constraints enables our model to express the desired decomposition and filtering simultaneously. Based on this generalized framework, we develop models that are simple in implementation but achieve significant improvements and computational efficiency on a variety of graph learning tasks. Code is available at https://github.com/qslim/PDF.

Pre-trained sequence-to-sequence language models have led to widespread success in many natural language generation tasks. However, there has been relatively less work on analyzing their ability to generate structured outputs such as graphs. Unlike natural language, graphs have distinct structural and semantic properties in the context of a downstream NLP task, e.g., generating a graph that is connected and acyclic can be attributed to its structural constraints, while the semantics of a graph can refer to how meaningfully an edge represents the relation between two node concepts. In this work, we study pre-trained language models that generate explanation graphs in an end-to-end manner and analyze their ability to learn the structural constraints and semantics of such graphs. We first show that with limited supervision, pre-trained language models often generate graphs that either violate these constraints or are semantically incoherent. Since curating large amount of human-annotated graphs is expensive and tedious, we propose simple yet effective ways of graph perturbations via node and edge edit operations that lead to structurally and semantically positive and negative graphs. Next, we leverage these graphs in different contrastive learning models with Max-Margin and InfoNCE losses. Our methods lead to significant improvements in both structural and semantic accuracy of explanation graphs and also generalize to other similar graph generation tasks. Lastly, we show that human errors are the best negatives for contrastive learning and also that automatically generating more such human-like negative graphs can lead to further improvements. Our code and models are publicly available at https://github.com/swarnaHub/ExplagraphGen

We present Simplified Text-Attributed Graph Embeddings (STAGE), a straightforward yet effective method for enhancing node features in Graph Neural Network (GNN) models that encode Text-Attributed Graphs (TAGs). Our approach leverages Large-Language Models (LLMs) to generate embeddings for textual attributes. STAGE achieves competitive results on various node classification benchmarks while also maintaining a simplicity in implementation relative to current state-of-the-art (SoTA) techniques. We show that utilizing pre-trained LLMs as embedding generators provides robust features for ensemble GNN training, enabling pipelines that are simpler than current SoTA approaches which require multiple expensive training and prompting stages. We also implement diffusion-pattern GNNs in an effort to make this pipeline scalable to graphs beyond academic benchmarks.

Machine learning on graphs has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To solve this critical challenge, automated machine learning (AutoML) on graphs which combines the strength of graph machine learning and AutoML together, is gaining attention from the research community. Therefore, we comprehensively survey AutoML on graphs in this paper, primarily focusing on hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We further overview libraries related to automated graph machine learning and in-depth discuss AutoGL, the first dedicated open-source library for AutoML on graphs. In the end, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive review of automated machine learning on graphs to the best of our knowledge.

Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose One for All (OFA), the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.

Node features and structural information of a graph are both crucial for semi-supervised node classification problems. A variety of graph neural network (GNN) based approaches have been proposed to tackle these problems, which typically determine output labels through feature aggregation. This can be problematic, as it implies conditional independence of output nodes given hidden representations, despite their direct connections in the graph. To learn the direct influence among output nodes in a graph, we propose the Explicit Pairwise Factorized Graph Neural Network (EPFGNN), which models the whole graph as a partially observed Markov Random Field. It contains explicit pairwise factors to model output-output relations and uses a GNN backbone to model input-output relations. To balance model complexity and expressivity, the pairwise factors have a shared component and a separate scaling coefficient for each edge. We apply the EM algorithm to train our model, and utilize a star-shaped piecewise likelihood for the tractable surrogate objective. We conduct experiments on various datasets, which shows that our model can effectively improve the performance for semi-supervised node classification on graphs.

We define the bicategory of Graph Convolutional Neural Networks GCNN_n for an arbitrary graph with n nodes. We show it can be factored through the already existing categorical constructions for deep learning called Para and Lens with the base category set to the CoKleisli category of the product comonad. We prove that there exists an injective-on-objects, faithful 2-functor GCNN_n to Para(CoKl(R^{n times n} times -)). We show that this construction allows us to treat the adjacency matrix of a GCNN as a global parameter instead of a a local, layer-wise one. This gives us a high-level categorical characterisation of a particular kind of inductive bias GCNNs possess. Lastly, we hypothesize about possible generalisations of GCNNs to general message-passing graph neural networks, connections to equivariant learning, and the (lack of) functoriality of activation functions.

State-of-the-art Graph Neural Networks (GNNs) have limited scalability with respect to the graph and model sizes. On large graphs, increasing the model depth often means exponential expansion of the scope (i.e., receptive field). Beyond just a few layers, two fundamental challenges emerge: 1. degraded expressivity due to oversmoothing, and 2. expensive computation due to neighborhood explosion. We propose a design principle to decouple the depth and scope of GNNs -- to generate representation of a target entity (i.e., a node or an edge), we first extract a localized subgraph as the bounded-size scope, and then apply a GNN of arbitrary depth on top of the subgraph. A properly extracted subgraph consists of a small number of critical neighbors, while excluding irrelevant ones. The GNN, no matter how deep it is, smooths the local neighborhood into informative representation rather than oversmoothing the global graph into "white noise". Theoretically, decoupling improves the GNN expressive power from the perspectives of graph signal processing (GCN), function approximation (GraphSAGE) and topological learning (GIN). Empirically, on seven graphs (with up to 110M nodes) and six backbone GNN architectures, our design achieves significant accuracy improvement with orders of magnitude reduction in computation and hardware cost.

We present FastRP, a scalable and performant algorithm for learning distributed node representations in a graph. FastRP is over 4,000 times faster than state-of-the-art methods such as DeepWalk and node2vec, while achieving comparable or even better performance as evaluated on several real-world networks on various downstream tasks. We observe that most network embedding methods consist of two components: construct a node similarity matrix and then apply dimension reduction techniques to this matrix. We show that the success of these methods should be attributed to the proper construction of this similarity matrix, rather than the dimension reduction method employed. FastRP is proposed as a scalable algorithm for network embeddings. Two key features of FastRP are: 1) it explicitly constructs a node similarity matrix that captures transitive relationships in a graph and normalizes matrix entries based on node degrees; 2) it utilizes very sparse random projection, which is a scalable optimization-free method for dimension reduction. An extra benefit from combining these two design choices is that it allows the iterative computation of node embeddings so that the similarity matrix need not be explicitly constructed, which further speeds up FastRP. FastRP is also advantageous for its ease of implementation, parallelization and hyperparameter tuning. The source code is available at https://github.com/GTmac/FastRP.

The recent advent of self-supervised pre-training techniques has led to a surge in the use of multimodal learning in form document understanding. However, existing approaches that extend the mask language modeling to other modalities require careful multi-task tuning, complex reconstruction target designs, or additional pre-training data. In FormNetV2, we introduce a centralized multimodal graph contrastive learning strategy to unify self-supervised pre-training for all modalities in one loss. The graph contrastive objective maximizes the agreement of multimodal representations, providing a natural interplay for all modalities without special customization. In addition, we extract image features within the bounding box that joins a pair of tokens connected by a graph edge, capturing more targeted visual cues without loading a sophisticated and separately pre-trained image embedder. FormNetV2 establishes new state-of-the-art performance on FUNSD, CORD, SROIE and Payment benchmarks with a more compact model size.

Graph Convolutional Neural Networks (GCNs) possess strong capabilities for processing graph data in non-grid domains. They can capture the topological logical structure and node features in graphs and integrate them into nodes' final representations. GCNs have been extensively studied in various fields, such as recommendation systems, social networks, and protein molecular structures. With the increasing application of graph neural networks, research has focused on improving their performance while compressing their size. In this work, a plug-in module named Graph Knowledge Enhancement and Distillation Module (GKEDM) is proposed. GKEDM can enhance node representations and improve the performance of GCNs by extracting and aggregating graph information via multi-head attention mechanism. Furthermore, GKEDM can serve as an auxiliary transferor for knowledge distillation. With a specially designed attention distillation method, GKEDM can distill the knowledge of large teacher models into high-performance and compact student models. Experiments on multiple datasets demonstrate that GKEDM can significantly improve the performance of various GCNs with minimal overhead. Furthermore, it can efficiently transfer distilled knowledge from large teacher networks to small student networks via attention distillation.

Graph representation learning nowadays becomes fundamental in analyzing graph-structured data. Inspired by recent success of contrastive methods, in this paper, we propose a novel framework for unsupervised graph representation learning by leveraging a contrastive objective at the node level. Specifically, we generate two graph views by corruption and learn node representations by maximizing the agreement of node representations in these two views. To provide diverse node contexts for the contrastive objective, we propose a hybrid scheme for generating graph views on both structure and attribute levels. Besides, we provide theoretical justification behind our motivation from two perspectives, mutual information and the classical triplet loss. We perform empirical experiments on both transductive and inductive learning tasks using a variety of real-world datasets. Experimental experiments demonstrate that despite its simplicity, our proposed method consistently outperforms existing state-of-the-art methods by large margins. Moreover, our unsupervised method even surpasses its supervised counterparts on transductive tasks, demonstrating its great potential in real-world applications.

Pre-training convolutional neural networks with weakly-supervised and self-supervised strategies is becoming increasingly popular for several computer vision tasks. However, due to the lack of strong discriminative signals, these learned representations may overfit to the pre-training objective (e.g., hashtag prediction) and not generalize well to downstream tasks. In this work, we present a simple strategy - ClusterFit (CF) to improve the robustness of the visual representations learned during pre-training. Given a dataset, we (a) cluster its features extracted from a pre-trained network using k-means and (b) re-train a new network from scratch on this dataset using cluster assignments as pseudo-labels. We empirically show that clustering helps reduce the pre-training task-specific information from the extracted features thereby minimizing overfitting to the same. Our approach is extensible to different pre-training frameworks -- weak- and self-supervised, modalities -- images and videos, and pre-training tasks -- object and action classification. Through extensive transfer learning experiments on 11 different target datasets of varied vocabularies and granularities, we show that ClusterFit significantly improves the representation quality compared to the state-of-the-art large-scale (millions / billions) weakly-supervised image and video models and self-supervised image models.

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

Deep generative models (DGMs) have been widely developed for graph data. However, much less investigation has been carried out on understanding the latent space of such pretrained graph DGMs. These understandings possess the potential to provide constructive guidelines for crucial tasks, such as graph controllable generation. Thus in this work, we are interested in studying this problem and propose GraphCG, a method for the unsupervised discovery of steerable factors in the latent space of pretrained graph DGMs. We first examine the representation space of three pretrained graph DGMs with six disentanglement metrics, and we observe that the pretrained representation space is entangled. Motivated by this observation, GraphCG learns the steerable factors via maximizing the mutual information between semantic-rich directions, where the controlled graph moving along the same direction will share the same steerable factors. We quantitatively verify that GraphCG outperforms four competitive baselines on two graph DGMs pretrained on two molecule datasets. Additionally, we qualitatively illustrate seven steerable factors learned by GraphCG on five pretrained DGMs over five graph datasets, including two for molecules and three for point clouds.

Deep supervised learning has achieved great success in the last decade. However, its deficiencies of dependence on manual labels and vulnerability to attacks have driven people to explore a better solution. As an alternative, self-supervised learning attracts many researchers for its soaring performance on representation learning in the last several years. Self-supervised representation learning leverages input data itself as supervision and benefits almost all types of downstream tasks. In this survey, we take a look into new self-supervised learning methods for representation in computer vision, natural language processing, and graph learning. We comprehensively review the existing empirical methods and summarize them into three main categories according to their objectives: generative, contrastive, and generative-contrastive (adversarial). We further investigate related theoretical analysis work to provide deeper thoughts on how self-supervised learning works. Finally, we briefly discuss open problems and future directions for self-supervised learning. An outline slide for the survey is provided.

Self-supervised learning (SSL) has been extensively explored in recent years. Particularly, generative SSL has seen emerging success in natural language processing and other AI fields, such as the wide adoption of BERT and GPT. Despite this, contrastive learning-which heavily relies on structural data augmentation and complicated training strategies-has been the dominant approach in graph SSL, while the progress of generative SSL on graphs, especially graph autoencoders (GAEs), has thus far not reached the potential as promised in other fields. In this paper, we identify and examine the issues that negatively impact the development of GAEs, including their reconstruction objective, training robustness, and error metric. We present a masked graph autoencoder GraphMAE that mitigates these issues for generative self-supervised graph pretraining. Instead of reconstructing graph structures, we propose to focus on feature reconstruction with both a masking strategy and scaled cosine error that benefit the robust training of GraphMAE. We conduct extensive experiments on 21 public datasets for three different graph learning tasks. The results manifest that GraphMAE-a simple graph autoencoder with careful designs-can consistently generate outperformance over both contrastive and generative state-of-the-art baselines. This study provides an understanding of graph autoencoders and demonstrates the potential of generative self-supervised pre-training on graphs.

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.

Advances in Visually Rich Document Understanding (VrDU) have enabled information extraction and question answering over documents with complex layouts. Two tropes of architectures have emerged -- transformer-based models inspired by LLMs, and Graph Neural Networks. In this paper, we introduce DocGraphLM, a novel framework that combines pre-trained language models with graph semantics. To achieve this, we propose 1) a joint encoder architecture to represent documents, and 2) a novel link prediction approach to reconstruct document graphs. DocGraphLM predicts both directions and distances between nodes using a convergent joint loss function that prioritizes neighborhood restoration and downweighs distant node detection. Our experiments on three SotA datasets show consistent improvement on IE and QA tasks with the adoption of graph features. Moreover, we report that adopting the graph features accelerates convergence in the learning process during training, despite being solely constructed through link prediction.

Graph Neural Networks (GNNs) have advanced graph structure understanding via recursive information exchange and aggregation among graph nodes. To improve model robustness, self-supervised learning (SSL) has emerged as a promising approach for data augmentation. However, existing methods for generating pre-trained graph embeddings often rely on fine-tuning with specific downstream task labels, which limits their usability in scenarios where labeled data is scarce or unavailable. To address this, our research focuses on advancing the generalization capabilities of graph models in challenging zero-shot learning scenarios. Inspired by the success of large language models (LLMs), we aim to develop a graph-oriented LLM that can achieve high generalization across diverse downstream datasets and tasks, even without any information available from the downstream graph data. In this work, we present the GraphGPT framework that aligns LLMs with graph structural knowledge with a graph instruction tuning paradigm. Our framework incorporates a text-graph grounding component to establish a connection between textual information and graph structures. Additionally, we propose a dual-stage instruction tuning paradigm, accompanied by a lightweight graph-text alignment projector. This paradigm explores self-supervised graph structural signals and task-specific graph instructions, to guide LLMs in understanding complex graph structures and improving their adaptability across different downstream tasks. Our framework is evaluated on supervised and zero-shot graph learning tasks, demonstrating superior generalization and outperforming state-of-the-art baselines.

Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for link prediction (LP). While numerous studies aim to improve the overall LP performance of GNNs, none have explored its varying performance across different nodes and its underlying reasons. To this end, we aim to demystify which nodes will perform better from the perspective of their local topology. Despite the widespread belief that low-degree nodes exhibit poorer LP performance, our empirical findings provide nuances to this viewpoint and prompt us to propose a better metric, Topological Concentration (TC), based on the intersection of the local subgraph of each node with the ones of its neighbors. We empirically demonstrate that TC has a higher correlation with LP performance than other node-level topological metrics like degree and subgraph density, offering a better way to identify low-performing nodes than using cold-start. With TC, we discover a novel topological distribution shift issue in which newly joined neighbors of a node tend to become less interactive with that node's existing neighbors, compromising the generalizability of node embeddings for LP at testing time. To make the computation of TC scalable, We further propose Approximated Topological Concentration (ATC) and theoretically/empirically justify its efficacy in approximating TC and reducing the computation complexity. Given the positive correlation between node TC and its LP performance, we explore the potential of boosting LP performance via enhancing TC by re-weighting edges in the message-passing and discuss its effectiveness with limitations. Our code is publicly available at https://github.com/YuWVandy/Topo_LP_GNN.

Structured representations like graphs and parse trees play a crucial role in many Natural Language Processing systems. In recent years, the advancements in multi-turn user interfaces necessitate the need for controlling and updating these structured representations given new sources of information. Although there have been many efforts focusing on improving the performance of the parsers that map text to graphs or parse trees, very few have explored the problem of directly manipulating these representations. In this paper, we explore the novel problem of graph modification, where the systems need to learn how to update an existing scene graph given a new user's command. Our novel models based on graph-based sparse transformer and cross attention information fusion outperform previous systems adapted from the machine translation and graph generation literature. We further contribute our large graph modification datasets to the research community to encourage future research for this new problem.

Transformers trained with self-supervised learning using self-distillation loss (DINO) have been shown to produce attention maps that highlight salient foreground objects. In this paper, we demonstrate a graph-based approach that uses the self-supervised transformer features to discover an object from an image. Visual tokens are viewed as nodes in a weighted graph with edges representing a connectivity score based on the similarity of tokens. Foreground objects can then be segmented using a normalized graph-cut to group self-similar regions. We solve the graph-cut problem using spectral clustering with generalized eigen-decomposition and show that the second smallest eigenvector provides a cutting solution since its absolute value indicates the likelihood that a token belongs to a foreground object. Despite its simplicity, this approach significantly boosts the performance of unsupervised object discovery: we improve over the recent state of the art LOST by a margin of 6.9%, 8.1%, and 8.1% respectively on the VOC07, VOC12, and COCO20K. The performance can be further improved by adding a second stage class-agnostic detector (CAD). Our proposed method can be easily extended to unsupervised saliency detection and weakly supervised object detection. For unsupervised saliency detection, we improve IoU for 4.9%, 5.2%, 12.9% on ECSSD, DUTS, DUT-OMRON respectively compared to previous state of the art. For weakly supervised object detection, we achieve competitive performance on CUB and ImageNet.

Knowledge graphs enable a wide variety of applications, including question answering and information retrieval. Despite the great effort invested in their creation and maintenance, even the largest (e.g., Yago, DBPedia or Wikidata) remain incomplete. We introduce Relational Graph Convolutional Networks (R-GCNs) and apply them to two standard knowledge base completion tasks: Link prediction (recovery of missing facts, i.e. subject-predicate-object triples) and entity classification (recovery of missing entity attributes). R-GCNs are related to a recent class of neural networks operating on graphs, and are developed specifically to deal with the highly multi-relational data characteristic of realistic knowledge bases. We demonstrate the effectiveness of R-GCNs as a stand-alone model for entity classification. We further show that factorization models for link prediction such as DistMult can be significantly improved by enriching them with an encoder model to accumulate evidence over multiple inference steps in the relational graph, demonstrating a large improvement of 29.8% on FB15k-237 over a decoder-only baseline.

We propose DyGFormer, a new Transformer-based architecture for dynamic graph learning. DyGFormer is conceptually simple and only needs to learn from nodes' historical first-hop interactions by: (1) a neighbor co-occurrence encoding scheme that explores the correlations of the source node and destination node based on their historical sequences; (2) a patching technique that divides each sequence into multiple patches and feeds them to Transformer, allowing the model to effectively and efficiently benefit from longer histories. We also introduce DyGLib, a unified library with standard training pipelines, extensible coding interfaces, and comprehensive evaluating protocols to promote reproducible, scalable, and credible dynamic graph learning research. By performing exhaustive experiments on thirteen datasets for dynamic link prediction and dynamic node classification tasks, we find that DyGFormer achieves state-of-the-art performance on most of the datasets, demonstrating its effectiveness in capturing nodes' correlations and long-term temporal dependencies. Moreover, some results of baselines are inconsistent with previous reports, which may be caused by their diverse but less rigorous implementations, showing the importance of DyGLib. All the used resources are publicly available at https://github.com/yule-BUAA/DyGLib.

Scene graph generation (SGG) models have suffered from inherent problems regarding the benchmark datasets such as the long-tailed predicate distribution and missing annotation problems. In this work, we aim to alleviate the long-tailed problem of SGG by utilizing unannotated triplets. To this end, we introduce a Self-Training framework for SGG (ST-SGG) that assigns pseudo-labels for unannotated triplets based on which the SGG models are trained. While there has been significant progress in self-training for image recognition, designing a self-training framework for the SGG task is more challenging due to its inherent nature such as the semantic ambiguity and the long-tailed distribution of predicate classes. Hence, we propose a novel pseudo-labeling technique for SGG, called Class-specific Adaptive Thresholding with Momentum (CATM), which is a model-agnostic framework that can be applied to any existing SGG models. Furthermore, we devise a graph structure learner (GSL) that is beneficial when adopting our proposed self-training framework to the state-of-the-art message-passing neural network (MPNN)-based SGG models. Our extensive experiments verify the effectiveness of ST-SGG on various SGG models, particularly in enhancing the performance on fine-grained predicate classes.

Natural reading orders of words are crucial for information extraction from form-like documents. Despite recent advances in Graph Convolutional Networks (GCNs) on modeling spatial layout patterns of documents, they have limited ability to capture reading orders of given word-level node representations in a graph. We propose Reading Order Equivariant Positional Encoding (ROPE), a new positional encoding technique designed to apprehend the sequential presentation of words in documents. ROPE generates unique reading order codes for neighboring words relative to the target word given a word-level graph connectivity. We study two fundamental document entity extraction tasks including word labeling and word grouping on the public FUNSD dataset and a large-scale payment dataset. We show that ROPE consistently improves existing GCNs with a margin up to 8.4% F1-score.

Recently, there has been an increasing interest in (supervised) learning with graph data, especially using graph neural networks. However, the development of meaningful benchmark datasets and standardized evaluation procedures is lagging, consequently hindering advancements in this area. To address this, we introduce the TUDataset for graph classification and regression. The collection consists of over 120 datasets of varying sizes from a wide range of applications. We provide Python-based data loaders, kernel and graph neural network baseline implementations, and evaluation tools. Here, we give an overview of the datasets, standardized evaluation procedures, and provide baseline experiments. All datasets are available at www.graphlearning.io. The experiments are fully reproducible from the code available at www.github.com/chrsmrrs/tudataset.

Graph Convolution Network (GCN) has become new state-of-the-art for collaborative filtering. Nevertheless, the reasons of its effectiveness for recommendation are not well understood. Existing work that adapts GCN to recommendation lacks thorough ablation analyses on GCN, which is originally designed for graph classification tasks and equipped with many neural network operations. However, we empirically find that the two most common designs in GCNs -- feature transformation and nonlinear activation -- contribute little to the performance of collaborative filtering. Even worse, including them adds to the difficulty of training and degrades recommendation performance. In this work, we aim to simplify the design of GCN to make it more concise and appropriate for recommendation. We propose a new model named LightGCN, including only the most essential component in GCN -- neighborhood aggregation -- for collaborative filtering. Specifically, LightGCN learns user and item embeddings by linearly propagating them on the user-item interaction graph, and uses the weighted sum of the embeddings learned at all layers as the final embedding. Such simple, linear, and neat model is much easier to implement and train, exhibiting substantial improvements (about 16.0\% relative improvement on average) over Neural Graph Collaborative Filtering (NGCF) -- a state-of-the-art GCN-based recommender model -- under exactly the same experimental setting. Further analyses are provided towards the rationality of the simple LightGCN from both analytical and empirical perspectives.

We propose a simple approach for weighting self-connecting edges in a Graph Convolutional Network (GCN) and show its impact on depression detection from transcribed clinical interviews. To this end, we use a GCN for modeling non-consecutive and long-distance semantics to classify the transcriptions into depressed or control subjects. The proposed method aims to mitigate the limiting assumptions of locality and the equal importance of self-connections vs. edges to neighboring nodes in GCNs, while preserving attractive features such as low computational cost, data agnostic, and interpretability capabilities. We perform an exhaustive evaluation in two benchmark datasets. Results show that our approach consistently outperforms the vanilla GCN model as well as previously reported results, achieving an F1=0.84 on both datasets. Finally, a qualitative analysis illustrates the interpretability capabilities of the proposed approach and its alignment with previous findings in psychology.

Graph Neural Networks (GNNs) have demonstrated state-of-the-art performance in various graph representation learning tasks. Recently, studies revealed their vulnerability to adversarial attacks. In this work, we theoretically define the concept of expected robustness in the context of attributed graphs and relate it to the classical definition of adversarial robustness in the graph representation learning literature. Our definition allows us to derive an upper bound of the expected robustness of Graph Convolutional Networks (GCNs) and Graph Isomorphism Networks subject to node feature attacks. Building on these findings, we connect the expected robustness of GNNs to the orthonormality of their weight matrices and consequently propose an attack-independent, more robust variant of the GCN, called the Graph Convolutional Orthonormal Robust Networks (GCORNs). We further introduce a probabilistic method to estimate the expected robustness, which allows us to evaluate the effectiveness of GCORN on several real-world datasets. Experimental experiments showed that GCORN outperforms available defense methods. Our code is publicly available at: https://github.com/Sennadir/GCORN{https://github.com/Sennadir/GCORN}.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

Graph Attention Networks (GATs) are one of the most popular GNN architectures and are considered as the state-of-the-art architecture for representation learning with graphs. In GAT, every node attends to its neighbors given its own representation as the query. However, in this paper we show that GAT computes a very limited kind of attention: the ranking of the attention scores is unconditioned on the query node. We formally define this restricted kind of attention as static attention and distinguish it from a strictly more expressive dynamic attention. Because GATs use a static attention mechanism, there are simple graph problems that GAT cannot express: in a controlled problem, we show that static attention hinders GAT from even fitting the training data. To remove this limitation, we introduce a simple fix by modifying the order of operations and propose GATv2: a dynamic graph attention variant that is strictly more expressive than GAT. We perform an extensive evaluation and show that GATv2 outperforms GAT across 11 OGB and other benchmarks while we match their parametric costs. Our code is available at https://github.com/tech-srl/how_attentive_are_gats . GATv2 is available as part of the PyTorch Geometric library, the Deep Graph Library, and the TensorFlow GNN library.

Network embedding, which maps graphs to distributed representations, is a unified framework for various graph inference tasks. According to the topology properties (e.g., structural roles and community memberships of nodes) to be preserved, it can be categorized into the identity and position embedding. However, existing methods can only capture one type of property. Some approaches can support the inductive inference that generalizes the embedding model to new nodes or graphs but relies on the availability of attributes. Due to the complicated correlations between topology and attributes, it is unclear for some inductive methods which type of property they can capture. In this study, we explore a unified framework for the joint inductive inference of identity and position embeddings without attributes. An inductive random walk embedding (IRWE) method is proposed, which combines multiple attention units to handle the random walk on graph topology and simultaneously derives identity and position embeddings that are jointly optimized. In particular, we demonstrate that some random walk statistics can be informative features to characterize node identities and positions while supporting the inductive embedding inference. Experiments validate the superior performance of IRWE beyond various baselines for the transductive and inductive inference of identity and position embeddings.

Graph Neural Networks (GNNs) have emerged as powerful tools to encode graph-structured data. Due to their broad applications, there is an increasing need to develop tools to explain how GNNs make decisions given graph-structured data. Existing learning-based GNN explanation approaches are task-specific in training and hence suffer from crucial drawbacks. Specifically, they are incapable of producing explanations for a multitask prediction model with a single explainer. They are also unable to provide explanations in cases where the GNN is trained in a self-supervised manner, and the resulting representations are used in future downstream tasks. To address these limitations, we propose a Task-Agnostic GNN Explainer (TAGE) that is independent of downstream models and trained under self-supervision with no knowledge of downstream tasks. TAGE enables the explanation of GNN embedding models with unseen downstream tasks and allows efficient explanation of multitask models. Our extensive experiments show that TAGE can significantly speed up the explanation efficiency by using the same model to explain predictions for multiple downstream tasks while achieving explanation quality as good as or even better than current state-of-the-art GNN explanation approaches. Our code is pubicly available as part of the DIG library at https://github.com/divelab/DIG/tree/main/dig/xgraph/TAGE/.

While Language Models have become workhorses for NLP, their interplay with textual knowledge graphs (KGs) - structured memories of general or domain knowledge - is actively researched. Current embedding methodologies for such graphs typically either (i) linearize graphs for embedding them using sequential Language Models (LMs), which underutilize structural information, or (ii) use Graph Neural Networks (GNNs) to preserve graph structure, while GNNs cannot represent textual features as well as a pre-trained LM could. In this work we introduce a novel language model, the Graph Language Model (GLM), that integrates the strengths of both approaches, while mitigating their weaknesses. The GLM parameters are initialized from a pretrained LM, to facilitate nuanced understanding of individual concepts and triplets. Simultaneously, its architectural design incorporates graph biases, thereby promoting effective knowledge distribution within the graph. Empirical evaluations on relation classification tasks on ConceptNet subgraphs reveal that GLM embeddings surpass both LM- and GNN-based baselines in supervised and zero-shot settings.

Graph Convolutional Networks(GCNs) play a crucial role in graph learning tasks, however, learning graph embedding with few supervised signals is still a difficult problem. In this paper, we propose a novel training algorithm for Graph Convolutional Network, called Multi-Stage Self-Supervised(M3S) Training Algorithm, combined with self-supervised learning approach, focusing on improving the generalization performance of GCNs on graphs with few labeled nodes. Firstly, a Multi-Stage Training Framework is provided as the basis of M3S training method. Then we leverage DeepCluster technique, a popular form of self-supervised learning, and design corresponding aligning mechanism on the embedding space to refine the Multi-Stage Training Framework, resulting in M3S Training Algorithm. Finally, extensive experimental results verify the superior performance of our algorithm on graphs with few labeled nodes under different label rates compared with other state-of-the-art approaches.

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at https://github.com/IBM/EvolveGCN.

Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

Graph neural networks (GNNs) learn the representation of graph-structured data, and their expressiveness can be further enhanced by inferring node relations for propagation. Attention-based GNNs infer neighbor importance to manipulate the weight of its propagation. Despite their popularity, the discussion on deep graph attention and its unique challenges has been limited. In this work, we investigate some problematic phenomena related to deep graph attention, including vulnerability to over-smoothed features and smooth cumulative attention. Through theoretical and empirical analyses, we show that various attention-based GNNs suffer from these problems. Motivated by our findings, we propose AEROGNN, a novel GNN architecture designed for deep graph attention. AERO-GNN provably mitigates the proposed problems of deep graph attention, which is further empirically demonstrated with (a) its adaptive and less smooth attention functions and (b) higher performance at deep layers (up to 64). On 9 out of 12 node classification benchmarks, AERO-GNN outperforms the baseline GNNs, highlighting the advantages of deep graph attention. Our code is available at https://github.com/syleeheal/AERO-GNN.

Graph convolutional neural networks have recently shown great potential for the task of zero-shot learning. These models are highly sample efficient as related concepts in the graph structure share statistical strength allowing generalization to new classes when faced with a lack of data. However, multi-layer architectures, which are required to propagate knowledge to distant nodes in the graph, dilute the knowledge by performing extensive Laplacian smoothing at each layer and thereby consequently decrease performance. In order to still enjoy the benefit brought by the graph structure while preventing dilution of knowledge from distant nodes, we propose a Dense Graph Propagation (DGP) module with carefully designed direct links among distant nodes. DGP allows us to exploit the hierarchical graph structure of the knowledge graph through additional connections. These connections are added based on a node's relationship to its ancestors and descendants. A weighting scheme is further used to weigh their contribution depending on the distance to the node to improve information propagation in the graph. Combined with finetuning of the representations in a two-stage training approach our method outperforms state-of-the-art zero-shot learning approaches.

Due to high utility in many applications, from social networks to blockchain to power grids, deep learning on non-Euclidean objects such as graphs and manifolds, coined Geometric Deep Learning (GDL), continues to gain an ever increasing interest. We propose a new L\'evy Flights Graph Convolutional Networks (LFGCN) method for semi-supervised learning, which casts the L\'evy Flights into random walks on graphs and, as a result, allows both to accurately account for the intrinsic graph topology and to substantially improve classification performance, especially for heterogeneous graphs. Furthermore, we propose a new preferential P-DropEdge method based on the Girvan-Newman argument. That is, in contrast to uniform removing of edges as in DropEdge, following the Girvan-Newman algorithm, we detect network periphery structures using information on edge betweenness and then remove edges according to their betweenness centrality. Our experimental results on semi-supervised node classification tasks demonstrate that the LFGCN coupled with P-DropEdge accelerates the training task, increases stability and further improves predictive accuracy of learned graph topology structure. Finally, in our case studies we bring the machinery of LFGCN and other deep networks tools to analysis of power grid networks - the area where the utility of GDL remains untapped.

Graph clustering discovers groups or communities within networks. Deep learning methods such as autoencoders (AE) extract effective clustering and downstream representations but cannot incorporate rich structural information. While Graph Neural Networks (GNN) have shown great success in encoding graph structure, typical GNNs based on convolution or attention variants suffer from over-smoothing, noise, heterophily, are computationally expensive and typically require the complete graph being present. Instead, we propose Self-Supervised Contrastive Graph Clustering (SCGC), which imposes graph-structure via contrastive loss signals to learn discriminative node representations and iteratively refined soft cluster labels. We also propose SCGC*, with a more effective, novel, Influence Augmented Contrastive (IAC) loss to fuse richer structural information, and half the original model parameters. SCGC(*) is faster with simple linear units, completely eliminate convolutions and attention of traditional GNNs, yet efficiently incorporates structure. It is impervious to layer depth and robust to over-smoothing, incorrect edges and heterophily. It is scalable by batching, a limitation in many prior GNN models, and trivially parallelizable. We obtain significant improvements over state-of-the-art on a wide range of benchmark graph datasets, including images, sensor data, text, and citation networks efficiently. Specifically, 20% on ARI and 18% on NMI for DBLP; overall 55% reduction in training time and overall, 81% reduction on inference time. Our code is available at : https://github.com/gayanku/SCGC

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

Learning visual representations with self-supervised learning has become popular in computer vision. The idea is to design auxiliary tasks where labels are free to obtain. Most of these tasks end up providing data to learn specific kinds of invariance useful for recognition. In this paper, we propose to exploit different self-supervised approaches to learn representations invariant to (i) inter-instance variations (two objects in the same class should have similar features) and (ii) intra-instance variations (viewpoint, pose, deformations, illumination, etc). Instead of combining two approaches with multi-task learning, we argue to organize and reason the data with multiple variations. Specifically, we propose to generate a graph with millions of objects mined from hundreds of thousands of videos. The objects are connected by two types of edges which correspond to two types of invariance: "different instances but a similar viewpoint and category" and "different viewpoints of the same instance". By applying simple transitivity on the graph with these edges, we can obtain pairs of images exhibiting richer visual invariance. We use this data to train a Triplet-Siamese network with VGG16 as the base architecture and apply the learned representations to different recognition tasks. For object detection, we achieve 63.2% mAP on PASCAL VOC 2007 using Fast R-CNN (compare to 67.3% with ImageNet pre-training). For the challenging COCO dataset, our method is surprisingly close (23.5%) to the ImageNet-supervised counterpart (24.4%) using the Faster R-CNN framework. We also show that our network can perform significantly better than the ImageNet network in the surface normal estimation task.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

Graph pooling compresses graph information into a compact representation. State-of-the-art graph pooling methods follow a hierarchical approach, which reduces the graph size step-by-step. These methods must balance memory efficiency with preserving node information, depending on whether they use node dropping or node clustering. Additionally, fixed pooling ratios or numbers of pooling layers are predefined for all graphs, which prevents personalized pooling structures from being captured for each individual graph. In this work, inspired by bottom-up grammar induction, we propose an efficient graph parsing algorithm to infer the pooling structure, which then drives graph pooling. The resulting Graph Parsing Network (GPN) adaptively learns personalized pooling structure for each individual graph. GPN benefits from the discrete assignments generated by the graph parsing algorithm, allowing good memory efficiency while preserving node information intact. Experimental results on standard benchmarks demonstrate that GPN outperforms state-of-the-art graph pooling methods in graph classification tasks while being able to achieve competitive performance in node classification tasks. We also conduct a graph reconstruction task to show GPN's ability to preserve node information and measure both memory and time efficiency through relevant tests.

Graph generative models become increasingly effective for data distribution approximation and data augmentation. While they have aroused public concerns about their malicious misuses or misinformation broadcasts, just as what Deepfake visual and auditory media has been delivering to society. Hence it is essential to regulate the prevalence of generated graphs. To tackle this problem, we pioneer the formulation of the generated graph detection problem to distinguish generated graphs from real ones. We propose the first framework to systematically investigate a set of sophisticated models and their performance in four classification scenarios. Each scenario switches between seen and unseen datasets/generators during testing to get closer to real-world settings and progressively challenge the classifiers. Extensive experiments evidence that all the models are qualified for generated graph detection, with specific models having advantages in specific scenarios. Resulting from the validated generality and oblivion of the classifiers to unseen datasets/generators, we draw a safe conclusion that our solution can sustain for a decent while to curb generated graph misuses.

Recent advances in Graph Neural Networks (GNNs) and Graph Transformers (GTs) have been driven by innovations in architectures and Positional Encodings (PEs), which are critical for augmenting node features and capturing graph topology. PEs are essential for GTs, where topological information would otherwise be lost without message-passing. However, PEs are often tested alongside novel architectures, making it difficult to isolate their effect on established models. To address this, we present a comprehensive benchmark of PEs in a unified framework that includes both message-passing GNNs and GTs. We also establish theoretical connections between MPNNs and GTs and introduce a sparsified GRIT attention mechanism to examine the influence of global connectivity. Our findings demonstrate that previously untested combinations of GNN architectures and PEs can outperform existing methods and offer a more comprehensive picture of the state-of-the-art. To support future research and experimentation in our framework, we make the code publicly available.

Prediction tasks over nodes and edges in networks require careful effort in engineering features used by learning algorithms. Recent research in the broader field of representation learning has led to significant progress in automating prediction by learning the features themselves. However, present feature learning approaches are not expressive enough to capture the diversity of connectivity patterns observed in networks. Here we propose node2vec, an algorithmic framework for learning continuous feature representations for nodes in networks. In node2vec, we learn a mapping of nodes to a low-dimensional space of features that maximizes the likelihood of preserving network neighborhoods of nodes. We define a flexible notion of a node's network neighborhood and design a biased random walk procedure, which efficiently explores diverse neighborhoods. Our algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and we argue that the added flexibility in exploring neighborhoods is the key to learning richer representations. We demonstrate the efficacy of node2vec over existing state-of-the-art techniques on multi-label classification and link prediction in several real-world networks from diverse domains. Taken together, our work represents a new way for efficiently learning state-of-the-art task-independent representations in complex networks.

Graph-structured scene descriptions can be efficiently used in generative models to control the composition of the generated image. Previous approaches are based on the combination of graph convolutional networks and adversarial methods for layout prediction and image generation, respectively. In this work, we show how employing multi-head attention to encode the graph information, as well as using a transformer-based model in the latent space for image generation can improve the quality of the sampled data, without the need to employ adversarial models with the subsequent advantage in terms of training stability. The proposed approach, specifically, is entirely based on transformer architectures both for encoding scene graphs into intermediate object layouts and for decoding these layouts into images, passing through a lower dimensional space learned by a vector-quantized variational autoencoder. Our approach shows an improved image quality with respect to state-of-the-art methods as well as a higher degree of diversity among multiple generations from the same scene graph. We evaluate our approach on three public datasets: Visual Genome, COCO, and CLEVR. We achieve an Inception Score of 13.7 and 12.8, and an FID of 52.3 and 60.3, on COCO and Visual Genome, respectively. We perform ablation studies on our contributions to assess the impact of each component. Code is available at https://github.com/perceivelab/trf-sg2im

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a k-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.

Contrastive learning is an effective unsupervised method in graph representation learning, and the key component of contrastive learning lies in the construction of positive and negative samples. Previous methods usually utilize the proximity of nodes in the graph as the principle. Recently, the data-augmentation-based contrastive learning method has advanced to show great power in the visual domain, and some works extended this method from images to graphs. However, unlike the data augmentation on images, the data augmentation on graphs is far less intuitive and much harder to provide high-quality contrastive samples, which leaves much space for improvement. In this work, by introducing an adversarial graph view for data augmentation, we propose a simple but effective method, Adversarial Graph Contrastive Learning (ARIEL), to extract informative contrastive samples within reasonable constraints. We develop a new technique called information regularization for stable training and use subgraph sampling for scalability. We generalize our method from node-level contrastive learning to the graph level by treating each graph instance as a super-node. ARIEL consistently outperforms the current graph contrastive learning methods for both node-level and graph-level classification tasks on real-world datasets. We further demonstrate that ARIEL is more robust in the face of adversarial attacks.

In this paper, we propose the first framework that enables solving graph learning tasks of all levels (node, edge and graph) and all types (generation, regression and classification) with one model. We first propose Latent Graph Diffusion (LGD), a generative model that can generate node, edge, and graph-level features of all categories simultaneously. We achieve this goal by embedding the graph structures and features into a latent space leveraging a powerful encoder which can also be decoded, then training a diffusion model in the latent space. LGD is also capable of conditional generation through a specifically designed cross-attention mechanism. Then we formulate prediction tasks including regression and classification as (conditional) generation, which enables our LGD to solve tasks of all levels and all types with provable guarantees. We verify the effectiveness of our framework with extensive experiments, where our models achieve state-of-the-art or highly competitive results across generation and regression tasks.

Computer vision has achieved remarkable success by (a) representing images as uniformly-arranged pixel arrays and (b) convolving highly-localized features. However, convolutions treat all image pixels equally regardless of importance; explicitly model all concepts across all images, regardless of content; and struggle to relate spatially-distant concepts. In this work, we challenge this paradigm by (a) representing images as semantic visual tokens and (b) running transformers to densely model token relationships. Critically, our Visual Transformer operates in a semantic token space, judiciously attending to different image parts based on context. This is in sharp contrast to pixel-space transformers that require orders-of-magnitude more compute. Using an advanced training recipe, our VTs significantly outperform their convolutional counterparts, raising ResNet accuracy on ImageNet top-1 by 4.6 to 7 points while using fewer FLOPs and parameters. For semantic segmentation on LIP and COCO-stuff, VT-based feature pyramid networks (FPN) achieve 0.35 points higher mIoU while reducing the FPN module's FLOPs by 6.5x.

Text-attributed graphs have recently garnered significant attention due to their wide range of applications in web domains. Existing methodologies employ word embedding models for acquiring text representations as node features, which are subsequently fed into Graph Neural Networks (GNNs) for training. Recently, the advent of Large Language Models (LLMs) has introduced their powerful capabilities in information retrieval and text generation, which can greatly enhance the text attributes of graph data. Furthermore, the acquisition and labeling of extensive datasets are both costly and time-consuming endeavors. Consequently, few-shot learning has emerged as a crucial problem in the context of graph learning tasks. In order to tackle this challenge, we propose a lightweight paradigm called LLM4NG, which adopts a plug-and-play approach to empower text-attributed graphs through node generation using LLMs. Specifically, we utilize LLMs to extract semantic information from the labels and generate samples that belong to these categories as exemplars. Subsequently, we employ an edge predictor to capture the structural information inherent in the raw dataset and integrate the newly generated samples into the original graph. This approach harnesses LLMs for enhancing class-level information and seamlessly introduces labeled nodes and edges without modifying the raw dataset, thereby facilitating the node classification task in few-shot scenarios. Extensive experiments demonstrate the outstanding performance of our proposed paradigm, particularly in low-shot scenarios. For instance, in the 1-shot setting of the ogbn-arxiv dataset, LLM4NG achieves a 76% improvement over the baseline model.

Transformers for graph data are increasingly widely studied and successful in numerous learning tasks. Graph inductive biases are crucial for Graph Transformers, and previous works incorporate them using message-passing modules and/or positional encodings. However, Graph Transformers that use message-passing inherit known issues of message-passing, and differ significantly from Transformers used in other domains, thus making transfer of research advances more difficult. On the other hand, Graph Transformers without message-passing often perform poorly on smaller datasets, where inductive biases are more crucial. To bridge this gap, we propose the Graph Inductive bias Transformer (GRIT) -- a new Graph Transformer that incorporates graph inductive biases without using message passing. GRIT is based on several architectural changes that are each theoretically and empirically justified, including: learned relative positional encodings initialized with random walk probabilities, a flexible attention mechanism that updates node and node-pair representations, and injection of degree information in each layer. We prove that GRIT is expressive -- it can express shortest path distances and various graph propagation matrices. GRIT achieves state-of-the-art empirical performance across a variety of graph datasets, thus showing the power that Graph Transformers without message-passing can deliver.

Graph Neural Networks (GNNs) have achieved remarkable performance on graph-based tasks. The key idea for GNNs is to obtain informative representation through aggregating information from local neighborhoods. However, it remains an open question whether the neighborhood information is adequately aggregated for learning representations of nodes with few neighbors. To address this, we propose a simple and efficient data augmentation strategy, local augmentation, to learn the distribution of the node features of the neighbors conditioned on the central node's feature and enhance GNN's expressive power with generated features. Local augmentation is a general framework that can be applied to any GNN model in a plug-and-play manner. It samples feature vectors associated with each node from the learned conditional distribution as additional input for the backbone model at each training iteration. Extensive experiments and analyses show that local augmentation consistently yields performance improvement when applied to various GNN architectures across a diverse set of benchmarks. For example, experiments show that plugging in local augmentation to GCN and GAT improves by an average of 3.4\% and 1.6\% in terms of test accuracy on Cora, Citeseer, and Pubmed. Besides, our experimental results on large graphs (OGB) show that our model consistently improves performance over backbones. Code is available at https://github.com/SongtaoLiu0823/LAGNN.

Deployment of Transformer models on edge devices is becoming increasingly challenging due to the exponentially growing inference cost that scales quadratically with the number of tokens in the input sequence. Token pruning is an emerging solution to address this challenge due to its ease of deployment on various Transformer backbones. However, most token pruning methods require computationally expensive fine-tuning, which is undesirable in many edge deployment cases. In this work, we propose Zero-TPrune, the first zero-shot method that considers both the importance and similarity of tokens in performing token pruning. It leverages the attention graph of pre-trained Transformer models to produce an importance distribution for tokens via our proposed Weighted Page Rank (WPR) algorithm. This distribution further guides token partitioning for efficient similarity-based pruning. Due to the elimination of the fine-tuning overhead, Zero-TPrune can prune large models at negligible computational cost, switch between different pruning configurations at no computational cost, and perform hyperparameter tuning efficiently. We evaluate the performance of Zero-TPrune on vision tasks by applying it to various vision Transformer backbones and testing them on ImageNet. Without any fine-tuning, Zero-TPrune reduces the FLOPs cost of DeiT-S by 34.7\% and improves its throughput by 45.3\% with only 0.4\% accuracy loss. Compared with state-of-the-art pruning methods that require fine-tuning, Zero-TPrune not only eliminates the need for fine-tuning after pruning but also does so with only 0.1\% accuracy loss. Compared with state-of-the-art fine-tuning-free pruning methods, Zero-TPrune reduces accuracy loss by up to 49\% with the same or higher throughput.

Graph Neural Networks (GNNs) are popular models for graph learning problems. GNNs show strong empirical performance in many practical tasks. However, the theoretical properties have not been completely elucidated. In this paper, we investigate whether GNNs can exploit the graph structure from the perspective of the expressive power of GNNs. In our analysis, we consider graph generation processes that are controlled by hidden (or latent) node features, which contain all information about the graph structure. A typical example of this framework is kNN graphs constructed from the hidden features. In our main results, we show that GNNs can recover the hidden node features from the input graph alone, even when all node features, including the hidden features themselves and any indirect hints, are unavailable. GNNs can further use the recovered node features for downstream tasks. These results show that GNNs can fully exploit the graph structure by themselves, and in effect, GNNs can use both the hidden and explicit node features for downstream tasks. In the experiments, we confirm the validity of our results by showing that GNNs can accurately recover the hidden features using a GNN architecture built based on our theoretical analysis.

Inferring objects and their relationships from an image in the form of a scene graph is useful in many applications at the intersection of vision and language. We consider a challenging problem of compositional generalization that emerges in this task due to a long tail data distribution. Current scene graph generation models are trained on a tiny fraction of the distribution corresponding to the most frequent compositions, e.g. <cup, on, table>. However, test images might contain zero- and few-shot compositions of objects and relationships, e.g. <cup, on, surfboard>. Despite each of the object categories and the predicate (e.g. 'on') being frequent in the training data, the models often fail to properly understand such unseen or rare compositions. To improve generalization, it is natural to attempt increasing the diversity of the training distribution. However, in the graph domain this is non-trivial. To that end, we propose a method to synthesize rare yet plausible scene graphs by perturbing real ones. We then propose and empirically study a model based on conditional generative adversarial networks (GANs) that allows us to generate visual features of perturbed scene graphs and learn from them in a joint fashion. When evaluated on the Visual Genome dataset, our approach yields marginal, but consistent improvements in zero- and few-shot metrics. We analyze the limitations of our approach indicating promising directions for future research.

Pre-training general-purpose visual features with convolutional neural networks without relying on annotations is a challenging and important task. Most recent efforts in unsupervised feature learning have focused on either small or highly curated datasets like ImageNet, whereas using uncurated raw datasets was found to decrease the feature quality when evaluated on a transfer task. Our goal is to bridge the performance gap between unsupervised methods trained on curated data, which are costly to obtain, and massive raw datasets that are easily available. To that effect, we propose a new unsupervised approach which leverages self-supervision and clustering to capture complementary statistics from large-scale data. We validate our approach on 96 million images from YFCC100M, achieving state-of-the-art results among unsupervised methods on standard benchmarks, which confirms the potential of unsupervised learning when only uncurated data are available. We also show that pre-training a supervised VGG-16 with our method achieves 74.9% top-1 classification accuracy on the validation set of ImageNet, which is an improvement of +0.8% over the same network trained from scratch. Our code is available at https://github.com/facebookresearch/DeeperCluster.

The shared topology of human skeletons motivated the recent investigation of graph convolutional network (GCN) solutions for action recognition. However, the existing GCNs rely on the binary connection of two neighbouring vertices (joints) formed by an edge (bone), overlooking the potential of constructing multi-vertex convolution structures. In this paper we address this oversight and explore the merits of a hyper-graph convolutional network (Hyper-GCN) to achieve the aggregation of rich semantic information conveyed by skeleton vertices. In particular, our Hyper-GCN adaptively optimises multi-scale hyper-graphs during training, revealing the action-driven multi-vertex relations. Besides, virtual connections are often designed to support efficient feature aggregation, implicitly extending the spectrum of dependencies within the skeleton. By injecting virtual connections into hyper-graphs, the semantic clues of diverse action categories can be highlighted. The results of experiments conducted on the NTU-60, NTU-120, and NW-UCLA datasets, demonstrate the merits of our Hyper-GCN, compared to the state-of-the-art methods. Specifically, we outperform the existing solutions on NTU-120, achieving 90.2\% and 91.4\% in terms of the top-1 recognition accuracy on X-Sub and X-Set.

Convolutional networks are at the core of most state-of-the-art computer vision solutions for a wide variety of tasks. Since 2014 very deep convolutional networks started to become mainstream, yielding substantial gains in various benchmarks. Although increased model size and computational cost tend to translate to immediate quality gains for most tasks (as long as enough labeled data is provided for training), computational efficiency and low parameter count are still enabling factors for various use cases such as mobile vision and big-data scenarios. Here we explore ways to scale up networks in ways that aim at utilizing the added computation as efficiently as possible by suitably factorized convolutions and aggressive regularization. We benchmark our methods on the ILSVRC 2012 classification challenge validation set demonstrate substantial gains over the state of the art: 21.2% top-1 and 5.6% top-5 error for single frame evaluation using a network with a computational cost of 5 billion multiply-adds per inference and with using less than 25 million parameters. With an ensemble of 4 models and multi-crop evaluation, we report 3.5% top-5 error on the validation set (3.6% error on the test set) and 17.3% top-1 error on the validation set.

Graph Neural Networks (GNNs) are widely deployed in vast fields, but they often struggle to maintain accurate representations as graphs evolve. We theoretically establish a lower bound, proving that under mild conditions, representation distortion inevitably occurs over time. To estimate the temporal distortion without human annotation after deployment, one naive approach is to pre-train a recurrent model (e.g., RNN) before deployment and use this model afterwards, but the estimation is far from satisfactory. In this paper, we analyze the representation distortion from an information theory perspective, and attribute it primarily to inaccurate feature extraction during evolution. Consequently, we introduce Smart, a straightforward and effective baseline enhanced by an adaptive feature extractor through self-supervised graph reconstruction. In synthetic random graphs, we further refine the former lower bound to show the inevitable distortion over time and empirically observe that Smart achieves good estimation performance. Moreover, we observe that Smart consistently shows outstanding generalization estimation on four real-world evolving graphs. The ablation studies underscore the necessity of graph reconstruction. For example, on OGB-arXiv dataset, the estimation metric MAPE deteriorates from 2.19% to 8.00% without reconstruction.

In contrastive learning, the choice of ``view'' controls the information that the representation captures and influences the performance of the model. However, leading graph contrastive learning methods generally produce views via random corruption or learning, which could lead to the loss of essential information and alteration of semantic information. An anchor view that maintains the essential information of input graphs for contrastive learning has been hardly investigated. In this paper, based on the theory of graph information bottleneck, we deduce the definition of this anchor view; put differently, the anchor view with essential information of input graph is supposed to have the minimal structural uncertainty. Furthermore, guided by structural entropy, we implement the anchor view, termed SEGA, for graph contrastive learning. We extensively validate the proposed anchor view on various benchmarks regarding graph classification under unsupervised, semi-supervised, and transfer learning and achieve significant performance boosts compared to the state-of-the-art methods.

Sharing knowledge between information extraction tasks has always been a challenge due to the diverse data formats and task variations. Meanwhile, this divergence leads to information waste and increases difficulties in building complex applications in real scenarios. Recent studies often formulate IE tasks as a triplet extraction problem. However, such a paradigm does not support multi-span and n-ary extraction, leading to weak versatility. To this end, we reorganize IE problems into unified multi-slot tuples and propose a universal framework for various IE tasks, namely Mirror. Specifically, we recast existing IE tasks as a multi-span cyclic graph extraction problem and devise a non-autoregressive graph decoding algorithm to extract all spans in a single step. It is worth noting that this graph structure is incredibly versatile, and it supports not only complex IE tasks, but also machine reading comprehension and classification tasks. We manually construct a corpus containing 57 datasets for model pretraining, and conduct experiments on 30 datasets across 8 downstream tasks. The experimental results demonstrate that our model has decent compatibility and outperforms or reaches competitive performance with SOTA systems under few-shot and zero-shot settings. The code, model weights, and pretraining corpus are available at https://github.com/Spico197/Mirror .

Convolutional networks are powerful visual models that yield hierarchies of features. We show that convolutional networks by themselves, trained end-to-end, pixels-to-pixels, improve on the previous best result in semantic segmentation. Our key insight is to build "fully convolutional" networks that take input of arbitrary size and produce correspondingly-sized output with efficient inference and learning. We define and detail the space of fully convolutional networks, explain their application to spatially dense prediction tasks, and draw connections to prior models. We adapt contemporary classification networks (AlexNet, the VGG net, and GoogLeNet) into fully convolutional networks and transfer their learned representations by fine-tuning to the segmentation task. We then define a skip architecture that combines semantic information from a deep, coarse layer with appearance information from a shallow, fine layer to produce accurate and detailed segmentations. Our fully convolutional network achieves improved segmentation of PASCAL VOC (30% relative improvement to 67.2% mean IU on 2012), NYUDv2, SIFT Flow, and PASCAL-Context, while inference takes one tenth of a second for a typical image.

Graph neural networks aim to learn representations for graph-structured data and show impressive performance, particularly in node classification. Recently, many methods have studied the representations of GNNs from the perspective of optimization goals and spectral graph theory. However, the feature space that dominates representation learning has not been systematically studied in graph neural networks. In this paper, we propose to fill this gap by analyzing the feature space of both spatial and spectral models. We decompose graph neural networks into determined feature spaces and trainable weights, providing the convenience of studying the feature space explicitly using matrix space analysis. In particular, we theoretically find that the feature space tends to be linearly correlated due to repeated aggregations. Motivated by these findings, we propose 1) feature subspaces flattening and 2) structural principal components to expand the feature space. Extensive experiments verify the effectiveness of our proposed more comprehensive feature space, with comparable inference time to the baseline, and demonstrate its efficient convergence capability.

While Graph Neural Networks have gained popularity in multiple domains, graph-structured input remains a major challenge due to (a) over-smoothing, (b) noisy neighbours (heterophily), and (c) the suspended animation problem. To address all these problems simultaneously, we propose a novel graph neural network FDGATII, inspired by attention mechanism's ability to focus on selective information supplemented with two feature preserving mechanisms. FDGATII combines Initial Residuals and Identity Mapping with the more expressive dynamic self-attention to handle noise prevalent from the neighbourhoods in heterophilic data sets. By using sparse dynamic attention, FDGATII is inherently parallelizable in design, whist efficient in operation; thus theoretically able to scale to arbitrary graphs with ease. Our approach has been extensively evaluated on 7 datasets. We show that FDGATII outperforms GAT and GCN based benchmarks in accuracy and performance on fully supervised tasks, obtaining state-of-the-art results on Chameleon and Cornell datasets with zero domain-specific graph pre-processing, and demonstrate its versatility and fairness.