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Comparison of dimensional reduction methods for detecting and visualizing novel patterns in human and marine microbiome

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成果类型:
期刊论文
作者:
Jiang, Xingpeng(蒋兴鹏);Hu, Xiaohua*;Xu, Weiwei;He, Tingting(何婷婷);Park, E. K.
通讯作者:
Hu, Xiaohua
作者机构:
[Jiang, Xingpeng; Hu, Xiaohua] Drexel Univ, Coll Informat Sci & Technol, Philadelphia, PA 19104 USA.
[He, Tingting; Hu, Xiaohua] Cent China Normal Univ, Sch Comp Sci, Wuhan 430079, Hubei, Peoples R China.
[Xu, Weiwei] Wuhan Univ, Int Sch Software, Wuhan 430079, Hubei, Peoples R China.
[Park, E. K.] Calif State Univ Chico, Dept Grad Studies, Chico, CA 95929 USA.
通讯机构:
[Hu, Xiaohua] D
Drexel Univ, Coll Informat Sci & Technol, Philadelphia, PA 19104 USA.
语种:
英文
关键词:
Isomap;metagenomic profile;non-negative matrix factorization;nonlinear dimension reduction;principle component analysis
期刊:
IEEE Transactions on NanoBioscience
ISSN:
1536-1241
年:
2013
卷:
12
期:
3
页码:
199-205
基金类别:
NSFNational Science Foundation (NSF) [CCF 0905291, CCF 1049864, IIP 1160960]; NSFCNational Natural Science Foundation of China (NSFC) [90920005, 61170189]; China National 12-5 plan [2012BAK24B01]
机构署名:
本校为其他机构
院系归属:
计算机学院
摘要:
Using metagenomics to detect the global structure of microbial community remains a significant challenge. The structure of a microbial community and its functions are complicated because of not only the complex interactions among microbes but also their interactions with confounding environmental factors. Recently dimension reduction methods have been employed extensively to investigate the complex structure embedded in metagenomic profiles which summarize the abundance of functional or taxonomic categorizations in metagenomic studies. However,...

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