Graph Neural Networks (GNNs) have empowered the advance in graph-structured data analysis. Recently, the rise of Large Language Models (LLMs) like GPT-4 has heralded a new era in deep learning. However, their application to graph data poses distinct challenges due to the inherent difficulty of translating graph structures to language. To this end, we introduce the Large Language and Graph Assistant (LLaGA), an innovative model that effectively integrates LLM capabilities to handle the complexities of graph-structured data. LLaGA retains the general-purpose nature of LLMs while adapting graph data into a format compatible with LLM input. LLaGA achieves this by reorganizing graph nodes to structure-aware sequences and then mapping these into the token embedding space through a versatile projector. LLaGA excels in versatility, generalizability and interpretability, allowing it to perform consistently well across different datasets and tasks, extend its ability to unseen datasets or tasks, and provide explanations for graphs. Our extensive experiments across popular graph benchmarks show that LLaGA delivers outstanding performance across four datasets and three tasks using one single model, surpassing state-of-the-art graph models in both supervised and zero-shot scenarios. Our code is available at \url{https://github.com/VITA-Group/LLaGA}.
Graph Neural Networks (GNNs) are prominent in graph machine learning and have shown state-of-the-art performance in Link Prediction (LP) tasks. Nonetheless, recent studies show that GNNs struggle to produce good results on low-degree nodes despite their overall strong performance. In practical applications of LP, like recommendation systems, improving performance on low-degree nodes is critical, as it amounts to tackling the cold-start problem of improving the experiences of users with few observed interactions. In this paper, we investigate improving GNNs' LP performance on low-degree nodes while preserving their performance on high-degree nodes and propose a simple yet surprisingly effective augmentation technique called NodeDup. Specifically, NodeDup duplicates low-degree nodes and creates links between nodes and their own duplicates before following the standard supervised LP training scheme. By leveraging a ''multi-view'' perspective for low-degree nodes, NodeDup shows significant LP performance improvements on low-degree nodes without compromising any performance on high-degree nodes. Additionally, as a plug-and-play augmentation module, NodeDup can be easily applied to existing GNNs with very light computational cost. Extensive experiments show that NodeDup achieves 38.49%, 13.34%, and 6.76% improvements on isolated, low-degree, and warm nodes, respectively, on average across all datasets compared to GNNs and state-of-the-art cold-start methods.
Graph Foundation Model (GFM) is a new trending research topic in the graph domain, aiming to develop a graph model capable of generalizing across different graphs and tasks. However, a versatile GFM has not yet been achieved. The key challenge in building GFM is how to enable positive transfer across graphs with diverse structural patterns. Inspired by the existing foundation models in the CV and NLP domains, we propose a novel perspective for the GFM development by advocating for a "graph vocabulary", in which the basic transferable units underlying graphs encode the invariance on graphs. We ground the graph vocabulary construction from essential aspects including network analysis, theoretical foundations, and stability. Such a vocabulary perspective can potentially advance the future GFM design following the neural scaling laws.
Deep graph models (e.g., graph neural networks and graph transformers) have become important techniques for leveraging knowledge across various types of graphs. Yet, the scaling properties of deep graph models have not been systematically investigated, casting doubt on the feasibility of achieving large graph models through enlarging the model and dataset sizes. In this work, we delve into neural scaling laws on graphs from both model and data perspectives. We first verify the validity of such laws on graphs, establishing formulations to describe the scaling behaviors. For model scaling, we investigate the phenomenon of scaling law collapse and identify overfitting as the potential reason. Moreover, we reveal that the model depth of deep graph models can impact the model scaling behaviors, which differ from observations in other domains such as CV and NLP. For data scaling, we suggest that the number of graphs can not effectively metric the graph data volume in scaling law since the sizes of different graphs are highly irregular. Instead, we reform the data scaling law with the number of edges as the metric to address the irregular graph sizes. We further demonstrate the reformed law offers a unified view of the data scaling behaviors for various fundamental graph tasks including node classification, link prediction, and graph classification. This work provides valuable insights into neural scaling laws on graphs, which can serve as an essential step toward large graph models.
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 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.
Recent studies have shown that graph neural networks (GNNs) exhibit strong biases towards the node degree: they usually perform satisfactorily on high-degree nodes with rich neighbor information but struggle with low-degree nodes. Existing works tackle this problem by deriving either designated GNN architectures or training strategies specifically for low-degree nodes. Though effective, these approaches unintentionally create an artificial out-of-distribution scenario, where models mainly or even only observe low-degree nodes during the training, leading to a downgraded performance for high-degree nodes that GNNs originally perform well at. In light of this, we propose a test-time augmentation framework, namely GraphPatcher, to enhance test-time generalization of any GNNs on low-degree nodes. Specifically, GraphPatcher iteratively generates virtual nodes to patch artificially created low-degree nodes via corruptions, aiming at progressively reconstructing target GNN's predictions over a sequence of increasingly corrupted nodes. Through this scheme, GraphPatcher not only learns how to enhance low-degree nodes (when the neighborhoods are heavily corrupted) but also preserves the original superior performance of GNNs on high-degree nodes (when lightly corrupted). Additionally, GraphPatcher is model-agnostic and can also mitigate the degree bias for either self-supervised or supervised GNNs. Comprehensive experiments are conducted over seven benchmark datasets and GraphPatcher consistently enhances common GNNs' overall performance by up to 3.6% and low-degree performance by up to 6.5%, significantly outperforming state-of-the-art baselines. The source code is publicly available at https://github.com/jumxglhf/GraphPatcher.
Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could have distinct underlying mechanisms of link formation. Evidence in existing literature underscores the absence of a universally best algorithm suitable for all datasets. In this paper, we endeavor to explore principles of link prediction across diverse datasets from a data-centric perspective. We recognize three fundamental factors critical to link prediction: local structural proximity, global structural proximity, and feature proximity. We then unearth relationships among those factors where (i) global structural proximity only shows effectiveness when local structural proximity is deficient. (ii) The incompatibility can be found between feature and structural proximity. Such incompatibility leads to GNNs for Link Prediction (GNN4LP) consistently underperforming on edges where the feature proximity factor dominates. Inspired by these new insights from a data perspective, we offer practical instruction for GNN4LP model design and guidelines for selecting appropriate benchmark datasets for more comprehensive evaluations.