Transformers, adapted from natural language processing, are emerging as a leading approach for graph representation learning. Contemporary graph transformers often treat nodes or edges as separate tokens. This approach leads to computational challenges for even moderately-sized graphs due to the quadratic scaling of self-attention complexity with token count. In this paper, we introduce SubFormer, a graph transformer that operates on subgraphs that aggregate information by a message-passing mechanism. This approach reduces the number of tokens and enhances learning long-range interactions. We demonstrate SubFormer on benchmarks for predicting molecular properties from chemical structures and show that it is competitive with state-of-the-art graph transformers at a fraction of the computational cost, with training times on the order of minutes on a consumer-grade graphics card. We interpret the attention weights in terms of chemical structures. We show that SubFormer exhibits limited over-smoothing and avoids over-squashing, which is prevalent in traditional graph neural networks.

SubFormer是一种图变换器，通过消息传递机制对子图进行操作，减少了标记数量，增强了学习长距离交互的能力。在预测分子属性和化学结构方面，SubFormer与最先进的图变换器相比，在计算成本的一小部分情况下保持着竞争力，并且在消费级显卡上进行训练的时间仅为几分钟。我们通过对化学结构的注意权重进行解读，展示了SubFormer表现出有限的过度平滑和避免了传统图神经网络常见的过度压缩问题。

Transformers高效分层化化学图学习器