论文标题
药物与瓦斯恒星对抗自动编码器的知识图嵌入的药物相互作用预测
Drug-Drug Interaction Prediction with Wasserstein Adversarial Autoencoder-based Knowledge Graph Embeddings
论文作者
论文摘要
药理学剂之间的相互作用会触发意外的不良事件。捕获有关药物互动(DDI)的更丰富,更全面的信息是公共卫生和药物开发的关键任务之一。最近,由于其能力将药物和相互作用投入到低维特征空间以预测链接和分类三重序列的低维特征空间中,几种知识图嵌入方法已受到DDI域的越来越多的关注。但是,现有方法仅应用统一的随机模式来构建负样本。结果,这些样品通常太简单了,无法训练有效的模型。在本文中,我们提出了一个新的知识图嵌入框架,该框架通过基于Wasserstein距离和Gumbel-Softmax放松,用于药物毒品相互作用任务。在我们的框架中,使用自动编码器来生成高质量的负样品,并且自动编码器的隐藏矢量被视为合理的候选药物。之后,歧视者基于正和负三重态学习了药物和相互作用的嵌入。同时,为了解决离散表示的消失梯度问题(传统生成模型中的固有缺陷),我们利用Gumbel-Softmax松弛,Wasserstein距离稳定地训练嵌入模型。我们在链接预测和DDI分类的两个任务上经验评估我们的方法。实验结果表明,我们的框架可以取得重大改进,并且明显优于竞争基准。
Interaction between pharmacological agents can trigger unexpected adverse events. Capturing richer and more comprehensive information about drug-drug interactions (DDI) is one of the key tasks in public health and drug development. Recently, several knowledge graph embedding approaches have received increasing attention in the DDI domain due to their capability of projecting drugs and interactions into a low-dimensional feature space for predicting links and classifying triplets. However, existing methods only apply a uniformly random mode to construct negative samples. As a consequence, these samples are often too simplistic to train an effective model. In this paper, we propose a new knowledge graph embedding framework by introducing adversarial autoencoders (AAE) based on Wasserstein distances and Gumbel-Softmax relaxation for drug-drug interactions tasks. In our framework, the autoencoder is employed to generate high-quality negative samples and the hidden vector of the autoencoder is regarded as a plausible drug candidate. Afterwards, the discriminator learns the embeddings of drugs and interactions based on both positive and negative triplets. Meanwhile, in order to solve vanishing gradient problems on the discrete representation--an inherent flaw in traditional generative models--we utilize the Gumbel-Softmax relaxation and the Wasserstein distance to train the embedding model steadily. We empirically evaluate our method on two tasks, link prediction and DDI classification. The experimental results show that our framework can attain significant improvements and noticeably outperform competitive baselines.