南方科技大学知识苑(SUSTech KC): Deep learning model to discriminate diverse infection types based on pairwise analysis of host gene expression

题名	Deep learning model to discriminate diverse infection types based on pairwise analysis of host gene expression
作者	Xie, Jize 1,2; Zheng, Xubin 1,3; Yan, Jianlong 1; Li, Qizhi 1,2; Jin, Nana 1,4; Wang, Shuojia 1; Zhao, Pengfei1 ; Li, Shuai 2; Ding, Wanfu 1; Cheng, Lixin 1,4; Geng, Qingshan 1
通讯作者	Ding, Wanfu; Cheng, Lixin; Geng, Qingshan
发表日期	2024-06-21
DOI	10.1016/j.isci.2024.109908
发表期刊	ISCIENCE 影响因子和分区
EISSN	2589-0042
卷号	27 期号:6
摘要	Accurate detection of pathogens, particularly distinguishing between Gram-positive and Gram-negative bacteria, could improve disease treatment. Host gene expression can capture the immune system's response to infections caused by various pathogens. Here, we present a deep neural network model, bvnGPS2, which incorporates the attention mechanism based on a large-scale integrated host transcriptome dataset to precisely identify Gram-positive and Gram-negative bacterial infections as well as viral infections. We performed analysis of 4,949 blood samples across 40 cohorts from 10 countries using our previously designed omics data integration method, iPAGE, to select discriminant gene pairs and train the bvnGPS2. The performance of the model was evaluated on six independent cohorts comprising 374 samples. Overall, our deep neural network model shows robust capability to accurately identify specific infections, paving the way for precise medicine strategies in infection treatment and potentially also for identifying subtypes of other diseases.
相关链接	[来源记录]
收录类别	SCI
语种	英语
学校署名	第一 ; 通讯
资助项目	National Natural Science Foundation of China["32370711","32300554"] ; Shenzhen Medical Research Fund[A2303033] ; Shenzhen Science and Technology Program["JCYJ20220530152409020","RKX20220705152810024"]
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:001244597500001
出版者	CELL PRESS
来源库	Web of Science
引用统计	被引频次[WOS]：1
成果类型	期刊论文
条目标识符	http://sustech.caswiz.com/handle/2SGJ60CL/787970
专题	南方科技大学第一附属医院
作者单位	1.Jinan Univ, Southern Univ Sci & Technol, Shenzhen Peoples Hosp, Affiliated Hosp 1,Clin Med Coll 2,Guangdong Prov C, Shenzhen 518020, Peoples R China 2.Shanghai Jiao Tong Univ, John Hopcroft Ctr Comp Sci, Shanghai, Peoples R China 3.Great Bay Univ, Dongguan, Peoples R China 4.Shenzhen Peoples Hosp, Hlth Data Sci Ctr, Shenzhen 518020, Peoples R China
第一作者单位	南方科技大学第一附属医院
通讯作者单位	南方科技大学第一附属医院
第一作者的第一单位	南方科技大学第一附属医院
推荐引用方式 GB/T 7714	Xie, Jize,Zheng, Xubin,Yan, Jianlong,et al. Deep learning model to discriminate diverse infection types based on pairwise analysis of host gene expression[J]. ISCIENCE,2024,27(6).
APA	Xie, Jize.,Zheng, Xubin.,Yan, Jianlong.,Li, Qizhi.,Jin, Nana.,...&Geng, Qingshan.(2024).Deep learning model to discriminate diverse infection types based on pairwise analysis of host gene expression.ISCIENCE,27(6).
MLA	Xie, Jize,et al."Deep learning model to discriminate diverse infection types based on pairwise analysis of host gene expression".ISCIENCE 27.6(2024).