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arXiv · 2501.08589

Molecular Graph Contrastive Learning with Line Graph

Xueyuan Chen·Shangzhe Li·Ruomei Liu·Bowen Shi·Jiaheng Liu·Junran Wu·Ke Xu
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Abstract

Trapped by the label scarcity in molecular property prediction and drug design, graph contrastive learning (GCL) came forward. Leading contrastive learning works show two kinds of view generators, that is, random or learnable data corruption and domain knowledge incorporation. While effective, the two ways also lead to molecular semantics altering and limited generalization capability, respectively. To this end, we relate the \textbf{L}in\textbf{E} graph with \textbf{MO}lecular graph co\textbf{N}trastive learning and propose a novel method termed \textit{LEMON}. Specifically, by contrasting the given graph with the corresponding line graph, the graph encoder can freely encode the molecular semantics without omission. Furthermore, we present a new patch with edge attribute fusion and two local contrastive losses enhance information transmission and tackle hard negative samples. Compared with state-of-the-art (SOTA) methods for view generation, superior performance on molecular property prediction suggests the effectiveness of our proposed framework.

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Xueyuan Chen, Shangzhe Li, Ruomei Liu, Bowen Shi, Jiaheng Liu, Junran Wu, Ke Xu. 2025-01-15. Molecular Graph Contrastive Learning with Line Graph. https://arxiv.org/abs/2501.08589

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