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author:

Dai, Yuanfei (Dai, Yuanfei.) [1] | Guo, Chenhao (Guo, Chenhao.) [2] | Guo, Wenzhong (Guo, Wenzhong.) [3] (Scholars:郭文忠) | Eickhoff, Carsten (Eickhoff, Carsten.) [4]

Indexed by:

SCIE

Abstract:

An interaction between pharmacological agents can trigger unexpected adverse events. Capturing richer and more comprehensive information about drug-drug interactions (DDIs) is one of the key tasks in public health and drug development. Recently, several knowledge graph (KG) 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 KG embedding framework by introducing adversarial autoencoders (AAEs) based on Wasserstein distances and Gumbel-Softmax relaxation for DDI 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. Supplementary information: Supplementary data and code are available at https://github.com/dyf0631/AAE_FOR_KG.

Keyword:

adversarial learning drug-drug interaction knowledge graph embedding Wasserstein distance

Community:

  • [ 1 ] [Dai, Yuanfei]Fuzhou Univ, Coll Math & Comp Sci, Fuzhou, Fujian, Peoples R China
  • [ 2 ] [Guo, Wenzhong]Fuzhou Univ, Coll Math & Comp Sci, Fuzhou, Fujian, Peoples R China
  • [ 3 ] [Dai, Yuanfei]Brown Univ, Brown Ctr Biomed Informat, Providence, RI 02912 USA
  • [ 4 ] [Eickhoff, Carsten]Brown Univ, Brown Ctr Biomed Informat, Providence, RI 02912 USA
  • [ 5 ] [Guo, Chenhao]Fuzhou Univ, Fuzhou, Peoples R China

Reprint 's Address:

  • 郭文忠

    [Guo, Wenzhong]Fuzhou Univ, Coll Math & Comp Sci, Fuzhou, Fujian, Peoples R China;;[Eickhoff, Carsten]Brown Univ, Ctr Biomed Informat, Providence, RI 02912 USA

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Source :

BRIEFINGS IN BIOINFORMATICS

ISSN: 1467-5463

Year: 2021

Issue: 4

Volume: 22

1 3 . 9 9 4

JCR@2021

6 . 8 0 0

JCR@2023

ESI Discipline: COMPUTER SCIENCE;

ESI HC Threshold:106

JCR Journal Grade:1

CAS Journal Grade:1

Cited Count:

WoS CC Cited Count: 37

SCOPUS Cited Count: 50

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 5

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