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Analyzing Hemagglutinin Genes of Human H5N1 Virus by Linear Neighborhood Embedding

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Book cover Intelligent Information and Database Systems (ACIIDS 2013)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 7802))

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Abstract

This work proposes using linear neighborhood embedding to visualize the distribution of viral genes in a two-dimensional space. The gradient descent algorithm for the embedding is described and the behavior of the algorithm is analyzed.

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References

  1. Case, S.M.: Biochemical Systematics of Members of the Genus Rana Native to Western North America. Syst. Zool. 27, 299–311 (1978)

    Article  Google Scholar 

  2. Cheng, W.-C.: Visualizing Human Genes on Manifolds Embedded in Three-Dimensional Space. In: Pan, J.-S., Chen, S.-M., Nguyen, N.T. (eds.) ACIIDS 2012, Part II. LNCS, vol. 7197, pp. 421–430. Springer, Heidelberg (2012)

    Chapter  Google Scholar 

  3. Fitch, W.M., Margoliash, E.: Construction of Phylogenetic Trees. Science 155, 279–284 (1967)

    Article  Google Scholar 

  4. Higgins, D.G., Sharp, P.M.: CLUSTAL: a Package for Performing Multiple Sequence Alignment on a Microcomputer. Gene 73, 237–244 (1988)

    Article  Google Scholar 

  5. Krejcar, O., Janckulik, D., Motalova, L.: Complex Biomedical System with Biotelemetric Monitoring of Life Functions. In: Proceedings of the IEEE Eurocon, pp. 138–141 (2009)

    Google Scholar 

  6. Krejcar, O., Janckulik, D., Motalova, L.: Complex Biomedical System with Mobile Clients. In: Dossel, O., Schlegel, W.C. (eds.) WCMPBE 2009, vol. 25/5, pp. 141–144. Springer, Munich (2009)

    Google Scholar 

  7. Liou, C.-Y., Cheng, W.-C.: Visualization of Influenza Protein Segment HA in Manifold Space. In: Nguyen, N.T., Le, M.T., Świątek, J. (eds.) ACIIDS 2010. LNCS, vol. 5990, pp. 150–158. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  8. Paccanaro, A., Hinton, G.E.: Learning Distributed Representations by Mapping Concepts and Relations into a Linear Space. In: Langley, P. (ed.) ICML 2000, pp. 711–718. Stanford University, Morgan Kaufmann Publishers, San Francisco (2000)

    Google Scholar 

  9. Saitou, N., Nei, M.: The Neighbor-joining Method: A New Mothed for Reconstructing Phylogenetic Trees. Mol. Biol. Evol. 4, 406–425 (1987)

    Google Scholar 

  10. Tenenbaum, J.B., de Silva, V., Langford, J.C.: A Global Geometric Framework for Nonlinear Dimensionality Reduction. Science 290, 2319–2323 (2000)

    Article  Google Scholar 

  11. Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-specific Gap Penalties and Weight Matrix Choice. Nucleic Acids Res. 22, 4673–4680 (1994)

    Article  Google Scholar 

  12. Torgerson, W.S.: Multidimensional Scaling, I: Theory and Method. Psychometrika 17, 401–419 (1952)

    Article  MathSciNet  MATH  Google Scholar 

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Cheng, WC. (2013). Analyzing Hemagglutinin Genes of Human H5N1 Virus by Linear Neighborhood Embedding. In: Selamat, A., Nguyen, N.T., Haron, H. (eds) Intelligent Information and Database Systems. ACIIDS 2013. Lecture Notes in Computer Science(), vol 7802. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-36546-1_31

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  • DOI: https://doi.org/10.1007/978-3-642-36546-1_31

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-36545-4

  • Online ISBN: 978-3-642-36546-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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