SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization

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 biomedi...

Full description

Saved in:
Bibliographic Details
Published in:Bioinformatics (Oxford, England) Vol. 37; no. 18; pp. 2988 - 2995
Main Authors: Yu, Yue, Huang, Kexin, Zhang, Chao, Glass, Lucas M, Sun, Jimeng, Xiao, Cao
Format: Journal Article
Language:English
Published: England Oxford University Press 29.09.2021
Subjects:
Drug Interactions
Machine Learning
Neural Networks, Computer
Original Papers
Pattern Recognition, Automated
ISSN:1367-4803, 1367-4811, 1367-4811
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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 existing approaches ignore KGs altogether. Some tries 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 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 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 performance gain is particularly significant in low data relation types. In addition, SumGNN provides interpretable prediction via the generated reasoning paths for each prediction. The code is available in Supplementary Material. Supplementary data are available at Bioinformatics online.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.
ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/btab207