Yuankai Luo

Yuankai Luo, Hongkang Li, Lei Shi et al.

Graph transformers need strong inductive biases to derive meaningful attention scores. Yet, current methods often fall short in capturing longer ranges, hierarchical structures, or community structures, which are common in various graphs such as molecules, social networks, and citation networks. This paper presents a Hierarchical Distance Structural Encoding (HDSE) method to model node distances in a graph, focusing on its multi-level, hierarchical nature. We introduce a novel framework to seamlessly integrate HDSE into the attention mechanism of existing graph transformers, allowing for simultaneous application with other positional encodings. To apply graph transformers with HDSE to large-scale graphs, we further propose a high-level HDSE that effectively biases the linear transformers towards graph hierarchies. We theoretically prove the superiority of HDSE over shortest path distances in terms of expressivity and generalization. Empirically, we demonstrate that graph transformers with HDSE excel in graph classification, regression on 7 graph-level datasets, and node classification on 11 large-scale graphs, including those with up to a billion nodes.

Yuankai Luo, Lei Shi, Xiao-Ming Wu

Message-passing Graph Neural Networks (GNNs) are often criticized for their limited expressiveness, issues like over-smoothing and over-squashing, and challenges in capturing long-range dependencies. Conversely, Graph Transformers (GTs) are regarded as superior due to their employment of global attention mechanisms, which potentially mitigate these challenges. Literature frequently suggests that GTs outperform GNNs in graph-level tasks, especially for graph classification and regression on small molecular graphs. In this study, we explore the untapped potential of GNNs through an enhanced framework, GNN+, which integrates six widely used techniques: edge feature integration, normalization, dropout, residual connections, feed-forward networks, and positional encoding, to effectively tackle graph-level tasks. We conduct a systematic re-evaluation of three classic GNNs (GCN, GIN, and GatedGCN) enhanced by the GNN+ framework across 14 well-known graph-level datasets. Our results reveal that, contrary to prevailing beliefs, these classic GNNs consistently match or surpass the performance of GTs, securing top-three rankings across all datasets and achieving first place in eight. Furthermore, they demonstrate greater efficiency, running several times faster than GTs on many datasets. This highlights the potential of simple GNN architectures, challenging the notion that complex mechanisms in GTs are essential for superior graph-level performance. Our source code is available at https://github.com/LUOyk1999/GNNPlus.