论文标题

跨性别归纳药物 - 基因相互作用预测的交流子图表学习

Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction

论文作者

Rao, Jiahua, Zheng, Shuangjia, Mai, Sijie, Yang, Yuedong

论文摘要

照亮药物和基因之间的互连是药物开发和精确医学的重要主题。当前,药物相互作用的计算预测主要集中于结合相互作用,而无需考虑其他关系类型,例如激动剂,拮抗剂等。此外,现有方法在很大程度上依赖于高质量的领域特征,或者在本质上具有转换性,这限制了模型在培训过程中缺乏外部信息或无法观察到的药物/基因的能力。为了解决这些问题,我们提出了一种新型的交流子图表来学习,用于多种关系诱导的药物 - 基因相互作用预测(Cosmig),其中通过子图模式进行了药物与基因关系的预测,因此自然地诱导了不看到的药物/基因而无需重新训练或利用外部域特征。此外,该模型通过传播机制加强了毒品基因图上的关系。为了评估我们的方法,我们从药品银行和DGIDB编辑了两个新的基准数据集。这两个数据集的全面实验表明,我们的方法在转导场景中优于最先进的基线,并在归纳诱导的情况下取得了卓越的性能。包括LINCS实验验证和文献验证在内的进一步的实验分析也证明了我们模型的价值。

Illuminating the interconnections between drugs and genes is an important topic in drug development and precision medicine. Currently, computational predictions of drug-gene interactions mainly focus on the binding interactions without considering other relation types like agonist, antagonist, etc. In addition, existing methods either heavily rely on high-quality domain features or are intrinsically transductive, which limits the capacity of models to generalize to drugs/genes that lack external information or are unseen during the training process. To address these problems, we propose a novel Communicative Subgraph representation learning for Multi-relational Inductive drug-Gene interactions prediction (CoSMIG), where the predictions of drug-gene relations are made through subgraph patterns, and thus are naturally inductive for unseen drugs/genes without retraining or utilizing external domain features. Moreover, the model strengthened the relations on the drug-gene graph through a communicative message passing mechanism. To evaluate our method, we compiled two new benchmark datasets from DrugBank and DGIdb. The comprehensive experiments on the two datasets showed that our method outperformed state-of-the-art baselines in the transductive scenarios and achieved superior performance in the inductive ones. Further experimental analysis including LINCS experimental validation and literature verification also demonstrated the value of our model.

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