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二阶HMM算法改进及在miRNA靶基因预测中的应用 被引量：5

Improved Algorithms of HMM2 and Applications to MiRNA Target Predictions
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摘要 隐马氏模型在语音识别和生物信息学中有重要的应用.本文研究二阶隐马氏模型(HMM2)的基本算法,利用归一化和递推原理,改进模型的前向-后向算法及Baum-Welch训练算法并给予证明,使得该算法更容易理解和机器实现,并保证数值稳定性.将HMM2应用到miRNA靶基因预测的后期过滤处理中取得了较好的结果. The hidden Markov model has important applications in speech recognition and bioinformatics. This paper studies basic algorithms of the second-order hidden Markov model（HMM2）,improves the forward-backward algorithm and Baum-Welch training algorithm of the model.We provide the proof using normalization and recursion,making them easier to be understood and implemented in programming,and ensuring numerical stability.The HMM2 is applied to miRNA target predictions of post-processing filters with good results.
作者 高松 秦殿刚 冯铁男 马成荣 王翼飞
机构地区 上海大学数学系
出处 《应用科学学报》 EI CAS CSCD 北大核心 2010年第3期307-312,共6页 Journal of Applied Sciences
基金 国家自然科学基金(No.30871341) 上海市重点学科基金(No.S30104) 上海市教委重点学科建设项目基金(No.J50101) 科技部重大科技专项基金(No.2008ZX10002-017,No.2008ZX10002-020,No.2009ZX09103-686)资助
关键词 二阶隐马氏模型 前向-后向算法 Baum-Welch算法 miRNA靶基因 second-order hidden Markov model（HMM2） forward-backward algorithm Baum-Welch algorithm miRNA target gene
分类号 TP13 [自动化与计算机技术—控制理论与控制工程]
  • 相关文献

参考文献16

  • 1BAUM L E,PETRIE T.Statistical inference for probabilistic functions of finite state Markov chains[J].The Annals of Mathematical Statistics,1966,37:1554-1563.
  • 2RABINER L R.A tutorial on hidden Markov models and selected applications in speech recognition[J].Proceedings of the IEEE,1989,77(2):257-286.
  • 3LEVINSON S E.Structural methods in auroraatic speech recognition[J].Proceeding of the IEEE,1985,73:1625-1650.
  • 4GOUGH J,CHOTHIA C.SUPERFIAMILY:HMMs representing all proteins of known structure,SCOP sequence searches,alignments,and genome assignments[J].Nucleic Acids Research,2002,30(1):268-272.
  • 5DEMPSTER A P,LAIRD N M,RUBIN D B.Maximum likelihood from incomplete data via the EM algorithm[J].Journal of the Royal Statistical Society,1977,39:1-38.
  • 6WU C F J.On the convergence properties of the EM algorithm[J].The Annals of Statistics,1983,11(1):95-103.
  • 7LEVINSON S E,RABINER L R,SONDHI M M.An introduction to the application of the theory of probabilistic functions of Markov process to automatic speech recognition[J].Bell System Technical Journal,1983,62(4):1035-1074.
  • 8LI Xiaolin,MARC P,REJEAN P.Training hidden markov models with multiple observations-a combinatorial method[J].IEEE Transactions on PAMI,2000,22(4):371-377.
  • 9MARI J F,HATON J P,KRIOUILE A.Automatic word recognition based on second-order hidden markov models[J].IEEE Transactions on Speech and Audio Processing,1997,5(1):22-25.
  • 10Xu Dong,LIU Haijun,WANG Yifei.BSS-HMM3s:an improved HMM method for identifying transcription factor binding sites[J].DNA Sequence,2005,16(6):403-411.

二级参考文献60

  • 1杨行峻 迟惠生 等.语言信号数字处理[M].北京:电子工业出版社,..
  • 2Bartel B, Barrel D P. MicroRNAs: at the root of plant development? Plant Physiol, 2003, 132(2): 709-717
  • 3Lim L P, Glasner M E, Yekta S, et al. Vertebrate microRNA genes. Science, 2003, 299(5612): 1540
  • 4Lee R C, Feinbaum R L, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 1993, 75(5): 843-854
  • 5Lagos-Quintana M, Rauhut R, Lendeckel W, et al. Identification of novel genes coding for small expressed RNAs. Science, 294(5354): 853-858
  • 6Bartel D P. MicroRNAs: genomJcs, biogenesis, mechanism, and function. Cell, 116(2): 287-297
  • 7Hwang H W, Mendel J T. MicroRNAs in cell proliferation, cell death, and tumorigenesis. Brit J Cancer, 2006, 94(6): 776-780
  • 8Cheng A M, Byrom M W, Shelton J. Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis. Nucleic Acids Res, 2005, 33(4): 1290-1297
  • 9Croce C M, Calin G A. miRNAs, cancer, and stem cell division. Cell, 2005, 122(1): 6-7
  • 10Ma L, Teruya-Feldstein J, Weinberg R A. Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature, 2007, 449(7163): 682-688

共引文献57

同被引文献56

  • 1梁以敏,黄德根.基于完全二阶隐马尔可夫模型的汉语词性标注[J].计算机工程,2005,31(10):177-179. 被引量：25
  • 2杜世平.混合二阶隐马尔可夫模型的Baum-Welch算法[J].云南大学学报（自然科学版）,2006,28(2):98-102. 被引量：5
  • 3BAUM L E, PETRIE T. Statistical inference for probabilistic functions of finite state Markov chains [J]. The Annals of Mathematical Statistics, 1966, 37(6): 1554-1563.
  • 4BAUM L E, PETRIE T, SOULES G, WEISS N. A maximization technique ocurring in the statistical analysis of probabilistic functions of Markov chains [J]. The Annals of Mathematical Statistics, 1970, 41(1): 164-171.
  • 5EPHRAIM YI MERHAV N. Hidden Markov processes [J]. IEEE Transactions on Information Theory, 2002, 48(6): 1518-1569.
  • 6BILMES J A. What HMMs can do? [J]. IEICE Trans- actions on Information and Systems, 2006, E89-D(3): 1-24.
  • 7RABINER L R. A tutorial on hidden Markov models and selected applications in speech recognition [J]. Proceedings of the IEEE, 1989, 77(2): 257-286.
  • 8Xu Dong, LIU Haijun, WANG Yifei. BSS-HMM3s: an improved HMM method for identifying transcription factor binding sites [J]. DNA Sequence, 2005, 16(6): 403-411.
  • 9MARI J F, HATON J P, KRIOUILE A. Automatic word recognition based on second-order hidden markov models [J]. IEEE Transactions on Speech and Audio Processing, 1997, 5(1): 22-25.
  • 10SINHA S, TOMPA M. A statistical method for finding transcription factor binding sites [C]//Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000: 344-354.

引证文献5

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应用科学学报
2010年 第3期

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