Graph neural networks have been extensively studied for learning with inter-connected data. Despite this, recent evidence has revealed GNNs' deficiencies related to over-squashing, heterophily, handling long-range dependencies, edge incompleteness and particularly, the absence of graphs altogether. While a plausible solution is to learn new adaptive topology for message passing, issues concerning quadratic complexity hinder simultaneous guarantees for scalability and precision in large networks. In this paper, we introduce a novel all-pair message passing scheme for efficiently propagating node signals between arbitrary nodes, as an important building block for a new class of Transformer networks for node classification on large graphs, dubbed as NodeFormer. Specifically, the efficient computation is enabled by a kernerlized Gumbel-Softmax operator that reduces the algorithmic complexity to linearity w.r.t.

Graph neural networks have been extensively studied for learning with inter-connected data. Despite this, recent evidence has revealed GNNs' deficiencies related to over-squashing, heterophily, handling long-range dependencies, edge incompleteness and particularly, the absence of graphs altogether. While a plausible solution is to learn new adaptive topology for message passing, issues concerning quadratic complexity hinder simultaneous guarantees for scalability and precision in large networks. In this paper, we introduce a novel all-pair message passing scheme for efficiently propagating node signals between arbitrary nodes, as an important building block for a new class of Transformer networks for node classification on large graphs, dubbed as NodeFormer. Specifically, the efficient computation is enabled by a kernerlized Gumbel-Softmax operator that reduces the algorithmic complexity to linearity w.r.t.

To improve the performance of Graph Neural Networks (GNNs), Graph Structure Learning (GSL) has been extensively applied to reconstruct or refine original graph structures, effectively addressing issues like heterophily, over-squashing, and noisy structures. While GSL is generally thought to improve GNN performance, it often leads to longer training times and more hyperparameter tuning. Besides, the distinctions among current GSL methods remain ambiguous from the perspective of GNN training, and there is a lack of theoretical analysis to quantify their effectiveness. Recent studies further suggest that, under fair comparisons with the same hyperparameter tuning, GSL does not consistently outperform baseline GNNs. This motivates us to ask a critical question: is GSL really useful for GNNs? To address this question, this paper makes two key contributions. First, we propose a new GSL framework, which includes three steps: GSL base (the representation used for GSL) construction, new structure construction, and view fusion, to better understand the effectiveness of GSL in GNNs. Second, after graph convolution, we analyze the differences in mutual information (MI) between node representations derived from the original topology and those from the newly constructed topology. Surprisingly, our empirical observations and theoretical analysis show that no matter which type of graph structure construction methods are used, after feeding the same GSL bases to the newly constructed graph, there is no MI gain compared to the original GSL bases. To fairly reassess the effectiveness of GSL, we conduct ablation experiments and find that it is the pretrained GSL bases that enhance GNN performance, and in most cases, GSL cannot improve GNN performance. This finding encourages us to rethink the essential components in GNNs, such as self-training and structural encoding, in GNN design rather than GSL.

Recently, building Transformer models for handling graph-structured data has aroused wide interests in the machine learning research community. One critical challenge stems from the quadratic complexity of global attention that hinders Transformers for scaling to large graphs. This work proposes a scalable graph Transformers for large node classification graphs where the node numbers could vary from thousands to millions (or even more). The key module is a kernelized Gumbel-Softmax-based message passing that achieves all-pair feature propagation within O(N) complexity (N for #nodes). The following content will summarize the main idea and results of this work.