论文标题

sumgnn:通过有效知识图摘要的多型药物相互作用预测

SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization

论文作者

Yu, Yue, Huang, Kexin, Zhang, Chao, Glass, Lucas M., Sun, Jimeng, Xiao, Cao

论文摘要

由于药物相互作用(DDI)数据集和大型生物医学知识图(kgs)的可用性不断提高,因此可以使用机器学习模型准确检测不良DDI。但是,这在很大程度上仍然是一个开放的问题,如何有效利用大型和嘈杂的生物医学kg进行DDI检测。由于其在公斤中的大小和噪声量,将kg与其他较小但较高质量的数据(例如,实验数据)直接整合在一起通常不太有益。大多数现有方法完全忽略了公斤。有些人试图通过图形神经网络将KG与其他数据直接集成,成功。此外,大多数以前的作品都集中在二进制DDI预测上,而多型DDI药理学效应预测是一项更有意义但更艰巨的任务。 To fill the gaps, we propose a new method SumGNN: knowledge summarization graph neural network, which is enabled by a subgraph extraction module that can efficiently anchor on relevant subgraphs from a KG, a self-attention based subgraph summarization scheme to generate a reasoning path within the subgraph, and a multi-channel knowledge and data integration module that utilizes massive external biomedical knowledge for significantly improved multi-typed DDI预测。 SUMGNN的表现优于最佳基线高达5.54 \%,并且在低数据关系类型中,性能增长尤其重要。此外,SUMGNN通过每个预测的生成的推理路径提供了可解释的预测。

Thanks to the increasing availability of drug-drug interactions (DDI) datasets and large biomedical knowledge graphs (KGs), accurate detection of adverse DDI using machine learning models becomes possible. However, it remains largely an open problem how to effectively utilize large and noisy biomedical KG for DDI detection. Due to its sheer size and amount of noise in KGs, it is often less beneficial to directly integrate KGs with other smaller but higher quality data (e.g., experimental data). Most of the existing approaches ignore KGs altogether. Some try to directly integrate KGs with other data via graph neural networks with limited success. Furthermore, most previous works focus on binary DDI prediction whereas the multi-typed DDI pharmacological effect prediction is a more meaningful but harder task. To fill the gaps, we propose a new method SumGNN: knowledge summarization graph neural network, which is enabled by a subgraph extraction module that can efficiently anchor on relevant subgraphs from a KG, a self-attention based subgraph summarization scheme to generate a reasoning path within the subgraph, and a multi-channel knowledge and data integration module that utilizes massive external biomedical knowledge for significantly improved multi-typed DDI predictions. SumGNN outperforms the best baseline by up to 5.54\%, and the performance gain is particularly significant in low data relation types. In addition, SumGNN provides interpretable prediction via the generated reasoning paths for each prediction.

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