Prediction of microbe–disease association from the integration of neighbor and graph with collaborative recommendation model

doi:10.1186/s12967-017-1304-7

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	Prediction of microbe–disease association from the integration of neighbor and graph with collaborative recommendation model
	Huang,Yu-An 1; You,Zhu-Hong 1; Chen,Xing 2; Huang,Zhi-An 3; Zhang,Shanwen 1; Yan,Gui-Ying4
	2017-10-16
发表期刊	Journal of Translational Medicine
ISSN	1479-5876
卷号	15 期号:1
摘要	AbstractBackgroundAccumulating clinical researches have shown that specific microbes with abnormal levels are closely associated with the development of various human diseases. Knowledge of microbe–disease associations can provide valuable insights for complex disease mechanism understanding as well as the prevention, diagnosis and treatment of various diseases. However, little effort has been made to predict microbial candidates for human complex diseases on a large scale.MethodsIn this work, we developed a new computational model for predicting microbe–disease associations by combining two single recommendation methods. Based on the assumption that functionally similar microbes tend to get involved in the mechanism of similar disease, we adopted neighbor-based collaborative filtering and a graph-based scoring method to compute association possibility of microbe–disease pairs. The promising prediction performance could be attributed to the use of hybrid approach based on two single recommendation methods as well as the introduction of Gaussian kernel-based similarity and symptom-based disease similarity.ResultsTo evaluate the performance of the proposed model, we implemented leave-one-out and fivefold cross validations on the HMDAD database, which is recently built as the first database collecting experimentally-confirmed microbe–disease associations. As a result, NGRHMDA achieved reliable results with AUCs of 0.9023?±?0.0031 and 0.9111 in the validation frameworks of fivefold CV and LOOCV. In addition, 78.2% microbe samples and 66.7% disease samples are found to be consistent with the basic assumption of our work that microbes tend to get involved in the similar disease clusters, and vice versa.ConclusionsCompared with other methods, the prediction results yielded by NGRHMDA demonstrate its effective prediction performance for microbe–disease associations. It is anticipated that NGRHMDA can be used as a useful tool to search the most potential microbial candidates for various diseases, and therefore boosts the medical knowledge and drug development. The codes and dataset of our work can be downloaded from https://github.com/yahuang1991/NGRHMDA.
DOI	10.1186/s12967-017-1304-7
语种	英语
WOS记录号	BMC:10.1186/s12967-017-1304-7
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/390
专题	应用数学研究所
通讯作者	You,Zhu-Hong; Chen,Xing
作者单位	1. 2. 3. 4.
推荐引用方式 GB/T 7714	Huang,Yu-An,You,Zhu-Hong,Chen,Xing,等. Prediction of microbe–disease association from the integration of neighbor and graph with collaborative recommendation model[J]. Journal of Translational Medicine,2017,15(1).
APA	Huang,Yu-An,You,Zhu-Hong,Chen,Xing,Huang,Zhi-An,Zhang,Shanwen,&Yan,Gui-Ying.(2017).Prediction of microbe–disease association from the integration of neighbor and graph with collaborative recommendation model.Journal of Translational Medicine,15(1).
MLA	Huang,Yu-An,et al."Prediction of microbe–disease association from the integration of neighbor and graph with collaborative recommendation model".Journal of Translational Medicine 15.1(2017).