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Add to EdgeHi-GMAE: Hierarchical Graph Masked Autoencoders
May 17, 2024
Graph Masked Autoencoders (GMAEs) have emerged as a notable self-supervised learning approach for graph-structured data. Existing GMAE models primarily focus on reconstructing node-level information, categorizing them as single-scale GMAEs. This methodology, while effective in certain contexts, tends to overlook the complex hierarchical structures inherent in many real-world graphs. For instance, molecular graphs exhibit a clear hierarchical organization in the form of the atoms-functional groups-molecules structure. Hence, the inability of single-scale GMAE models to incorporate these hierarchical relationships often leads to their inadequate capture of crucial high-level graph information, resulting in a noticeable decline in performance. To address this limitation, we propose Hierarchical Graph Masked AutoEncoders (Hi-GMAE), a novel multi-scale GMAE framework designed to handle the hierarchical structures within graphs. First, Hi-GMAE constructs a multi-scale graph hierarchy through graph pooling, enabling the exploration of graph structures across different granularity levels. To ensure masking uniformity of subgraphs across these scales, we propose a novel coarse-to-fine strategy that initiates masking at the coarsest scale and progressively back-projects the mask to the finer scales. Furthermore, we integrate a gradual recovery strategy with the masking process to mitigate the learning challenges posed by completely masked subgraphs. Diverging from the standard graph neural network (GNN) used in GMAE models, Hi-GMAE modifies its encoder and decoder into hierarchical structures. This entails using GNN at the finer scales for detailed local graph analysis and employing a graph transformer at coarser scales to capture global information. Our experiments on 15 graph datasets consistently demonstrate that Hi-GMAE outperforms 17 state-of-the-art self-supervised competitors.
Gradformer: Graph Transformer with Exponential Decay
Apr 24, 2024Graph Transformers (GTs) have demonstrated their advantages across a wide range of tasks. However, the self-attention mechanism in GTs overlooks the graph's inductive biases, particularly biases related to structure, which are crucial for the graph tasks. Although some methods utilize positional encoding and attention bias to model inductive biases, their effectiveness is still suboptimal analytically. Therefore, this paper presents Gradformer, a method innovatively integrating GT with the intrinsic inductive bias by applying an exponential decay mask to the attention matrix. Specifically, the values in the decay mask matrix diminish exponentially, correlating with the decreasing node proximities within the graph structure. This design enables Gradformer to retain its ability to capture information from distant nodes while focusing on the graph's local details. Furthermore, Gradformer introduces a learnable constraint into the decay mask, allowing different attention heads to learn distinct decay masks. Such an design diversifies the attention heads, enabling a more effective assimilation of diverse structural information within the graph. Extensive experiments on various benchmarks demonstrate that Gradformer consistently outperforms the Graph Neural Network and GT baseline models in various graph classification and regression tasks. Additionally, Gradformer has proven to be an effective method for training deep GT models, maintaining or even enhancing accuracy compared to shallow models as the network deepens, in contrast to the significant accuracy drop observed in other GT models.Codes are available at \url{https://github.com/LiuChuang0059/Gradformer}.