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CloudNMF:A MapReduce Implementation of Nonnegative Matrix Factorization for Large-scale Biological Datasets 被引量：2

CloudNMF:A MapReduce Implementation of Nonnegative Matrix Factorization for Large-scale Biological Datasets
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摘要 In the past decades,advances in high-throughput technologies have led to the generation of huge amounts of biological data that require analysis and interpretation.Recently,nonnegative matrix factorization （NMF） has been introduced as an efficient way to reduce the complexity of data as well as to interpret them,and has been applied to various fields of biological research.In this paper,we present CloudNMF,a distributed open-source implementation of NMF on a MapReduce framework.Experimental evaluation demonstrated that CloudNMF is scalable and can be used to deal with huge amounts of data,which may enable various kinds of a high-throughput biological data analysis in the cloud.CloudNMF is freely accessible at http：//admis.fudan.edu.cn/projects/CloudNMF.html. In the past decades,advances in high-throughput technologies have led to the generation of huge amounts of biological data that require analysis and interpretation.Recently,nonnegative matrix factorization （NMF） has been introduced as an efficient way to reduce the complexity of data as well as to interpret them,and has been applied to various fields of biological research.In this paper,we present CloudNMF,a distributed open-source implementation of NMF on a MapReduce framework.Experimental evaluation demonstrated that CloudNMF is scalable and can be used to deal with huge amounts of data,which may enable various kinds of a high-throughput biological data analysis in the cloud.CloudNMF is freely accessible at http：//admis.fudan.edu.cn/projects/CloudNMF.html.
作者 Ruiqi Liao Yifan Zhang Jihong Guan Shuigeng Zhou
机构地区 School of Computer Science Department of Computer Science and Technology Shanghai Key Laboratory of Intelligent Information Processing
出处 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2014年第1期48-51,共4页 基因组蛋白质组与生物信息学报（英文版）
基金 financially supported by National High Technology Research and Development Program of China(863 Program Grant No.2012AA020403) National Natural Science Foundation of China(Grant Nos.61173118 and 61272380)
关键词 Nonnegative matrix factorization MAPREDUCE BIOINFORMATICS Nonnegative matrix factorization MapReduce Bioinformatics
分类号 O151.21 [理学—基础数学]
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参考文献17

  • 1Lee DD,Seung HS.Learning the parts of objects by non-negative matrix factorization.Nature 1999;401:788-91.
  • 2Brunet JP,Tamayo P,Golub TR,Mesirov JP.Metagenes and molecular pattern discovery using matrix factorization.Proc Natl Acad Sci U S A 2004;101:4164-9.
  • 3Gao Y,Church G.Improving molecular cancer class discovery through sparse non-negative matrix factorization.Bioinformatics 2005;21:3970-5.
  • 4Carmona-Saez P,Pascual-Marqui RD,Tirado F,Carazo JM,Pascual-Montano A.Biclustering of gene expression data by nonsmooth non-negative matrix factorization.BMC Bioinformatics 2006;7:78.
  • 5Qi Q,Zhao Y,Li M,Simon R.Non-negative matrix factorization of gene expression profiles:a plug-in for BRB-ArrayTools.Bioinformatics 2009;25:545-7.
  • 6Jung I,Kim D.LinkNMF:identification of histone modification modules in the human genome using nonnegative matrix factorization.Gene 2013;518:215-21.
  • 7Chagoyen M,Carmona-Saez P,Shatkay H,Carazo JM,PascualMontano A.Discovering semantic features in the literature:a foundation for building functional associations.BMC Bioinformatics 2006;7:41.
  • 8Tjioe E,Berry MW,Homayouni R.Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization).BMC Bioinformatics 2010;11:S14.
  • 9Zhang S,Liu CC,Li W,Shen H,Laird PW,Zhou XJ.Discovery of multi-dimensional modules by integrative analysis of cancer genomic data.Nucleic Acids Res 2012;40:9379-91.
  • 10Devarajan K.Nonnegative matrix factorization:an analytical and interpretive tool in computational biology.PLoS Comput Biol 2008;4:e1000029.

同被引文献42

  • 1冯云,周淑秋.MPI+OpenMP混合并行编程模型应用研究[J].计算机系统应用,2006,15(2):86-89. 被引量：24
  • 2CHEN Yan, ZHANG Jiemi, CAI Deng, et al. Nonnegative local coordinate factorization for image representation[J]. IEEE Transactions on Image Processing, 2013, 22(3):969-980.
  • 3GUAN Naiyang, TAO Dacheng, LU Zhigang, et al. Manifold regularized discriminative nonnegative matrix factorization with fast gradient descent[J]. IEEE Transactions on Image Processing, 2011, 20(7):2030-2048.
  • 4ZHENG C H, HUANG D S, ZHANG L, et al. Tumor clustering using nonnegative matrix factorization with gene selection[J]. IEEE Transactions on Information Technology in Biomedicine, 2009, 15(2):599-607.
  • 5CAI Deng, HE Xiaofei, HAN Jiawei, et al. Graph regularized non-negative matrix factorization for data representation[J]. IEEE Transactions on Patten Analysis and Machine Intelligence, 2011, 23(6):902-913.
  • 6YOO Jiho, CHOI Seungjin. Orthogonal nonnegative matrix tri-factorization for co-clustering:multiplicative updates on Stiefel manifolds[J]. Information Processing and Management, 2010, 46(5):721-732.
  • 7LEE Seokjin, PARK Sangha, SUNG Koengmo. Beamspace-domain multichannel nonnegative matrix factorization for audio source separation[J]. IEEE Signal Processing Letters, 2012, 19(1):43-47.
  • 8ZHOU Zhou, LIANG Ruiyu, ZHAO Li, et al. Unsupervised learning of phonemes of whispered speech in a noisy environment based on convolutive non-negative matrix factorization[J]. Information Sciences, 2014(257):115-126.
  • 9LU Xiaoqiang, WU Hao, YUAN Yuan, et al. Manifold regularized sparse NMF for hyperspectral unmixing[J]. IEEE Transactions on Geomscience and Remote Sensing, 2013, 51(5):2815-2926.
  • 10ZHAO Miao, BU Jiajun, CHEN Chun, et al. Graph regularized sparse coding for image representation[J]. IEEE Transactions on Image Processing, 2011, 20(5):1327-1337.

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Genomics, Proteomics & Bioinformatics
2014年 第1期

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