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Reseach Article

Study and Analysis of Microarray Denoising using Systholic Boolean Orthonormalizer Network in Wavelet Domain

Published on May 2012 by Vishakha P. S., Supriya S. T.
National Conference on Advancement in Electronics & Telecommunication Engineering
Foundation of Computer Science USA
NCAETE - Number 1
May 2012
Authors: Vishakha P. S., Supriya S. T.
e5a78c8c-c144-4fc6-ad4a-f9d7def8f595

Vishakha P. S., Supriya S. T. . Study and Analysis of Microarray Denoising using Systholic Boolean Orthonormalizer Network in Wavelet Domain. National Conference on Advancement in Electronics & Telecommunication Engineering. NCAETE, 1 (May 2012), 18-23.

@article{
author = { Vishakha P. S., Supriya S. T. },
title = { Study and Analysis of Microarray Denoising using Systholic Boolean Orthonormalizer Network in Wavelet Domain },
journal = { National Conference on Advancement in Electronics & Telecommunication Engineering },
issue_date = { May 2012 },
volume = { NCAETE },
number = { 1 },
month = { May },
year = { 2012 },
issn = 0975-8887,
pages = { 18-23 },
numpages = 6,
url = { /proceedings/ncaete/number1/6590-1080/ },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Proceeding Article
%1 National Conference on Advancement in Electronics & Telecommunication Engineering
%A Vishakha P. S.
%A Supriya S. T.
%T Study and Analysis of Microarray Denoising using Systholic Boolean Orthonormalizer Network in Wavelet Domain
%J National Conference on Advancement in Electronics & Telecommunication Engineering
%@ 0975-8887
%V NCAETE
%N 1
%P 18-23
%D 2012
%I International Journal of Computer Applications
Abstract

In this paper, we present a new approach to deal with the noise inherent in the microarray image processing procedure. The method is based on the following procedure: We apply 1) Bidimentional Discrete Wavelet Transform (DWT-2D) to the Noisy Microarray, 2) scaling and rounding to the coefficients of the highest subbands (to obtain integer and positive coefficients), 3) bit-slicing to the new highest subbands (to obtain bit-planes), 4) then we apply the Systholic Boolean Orthonormalizer Network (SBON) to the input bit-plane set and we obtain two orthonormal otput bit-plane sets (in a Boolean sense), we project a set on the other one, by means of an AND operation, and then, 5) we apply re-assembling, and, 6) rescaling. Finally, 7) we apply Inverse DWT-2D and reconstruct a microarray from the modified wavelet coefficients. Denoising results compare favorably to the most of methods in use at the moment.

References
  1. E. C. Rouchka. (2004, April). Lecture 12: Microarray Image Analysis. [Online] Available: http://kbrin. a-bldg. louisville. edu/CECS694/Lecture12. ppt
  2. X. H. Wang, S. H. Istepanian, and Y. H. Song, "Microarray Image Enhancement by Denoising using Stationary Wavelet Transform," IEEE Transactions on Nanobioscience, vol. 2, no. 4, pp. 184-189, December 2003. [Online]. Available: http://technology. kingston. ac. uk/momed/papers/IEEE_TN_Micorarray_Wavelet%20Denoising. pdf
  3. H. S. Tan. (2001, October). Denoising of Noise Speckle in Radar Image. [Online]. Available: http://innovexpo. itee. uq. edu. au/2001/projects/s804294/thesis. pdf
  4. H. Guo, J. E. Odegard, M. Lang, R. A. Gopinath, I. Selesnick, an C. S. Burrus, "Speckle reduction via wavelet shrinkage with application to SAR based ATD/R," Technical Report CML TR94- 02, CML, Rice University, Houston, 1994.
  5. D. L. Donoho and I. M. Johnstone, "Adapting to unknown smoothness via wavelet shrinkage," Journal of the American Statistical Association, vol. 90, no. 432, pp. 1200-1224, 1995.
  6. S. G. Chang, B. Yu, and M. Vetterli, "Adaptive wavelet thresholding for image denoising and compression," IEEE Transactions on Image Processing, vol. 9, no. 9, pp. 1532-1546, September 2000.
  7. X. -P. Zhang, "Thresholding Neural Network for Adaptive Noise reduction," IEEE Trans. On Neural Networks, vol. 12, no. 3, pp. 567- 584, May 2001.
  8. I. Daubechies, Ten Lectures on Wavelets, SIAM, Philadelphia, 1992.
  9. B. B. Hubbard, The World According to Wavelets: The Story of Mathematical Technique in the Making, A. K. Peter Wellesley, Massachusetts, 1996.
  10. S. G. Mallat, "Multiresolution approximations and wavelet orthonormal bases of L2 (R)," Transactions of the American Mathematical Society, 315(1), pp. 69-87, 1989a.
  11. A. Grossman and J. Morlet, "Decomposition of Hardy Functions into Square Integrable Wavelets of Constant Shape," SIAM J. App Math, 15: pp. 723-736, 1984.
  12. C. Valens. (2004). A really friendly guide to wavelets. [Online]. Available: http://perso. wanadoo. fr/polyvalens/clemens/wavelets/wavelets. html
  13. G. Kaiser, A Friendly Guide To Wavelets, Boston:Birkhauser, 1994.
  14. I. Daubechies, "Different Perspectives on Wavelets," in Proceedings of Symposia in Applied Mathematics, vol. 47, American Mathematical Society, USA, 1993.
  15. J. S. Walker, A Primer on Wavelets and their Scientific Applications, Chapman & Hall/CRC, New York, 1999.
  16. E. J. Stollnitz, T. D. DeRose, and D. H. Salesin, Wavelets for Computer Graphics: Theory and Applications, Morgan Kaufmann Publishers, San Francisco, 1996.
  17. J. Shen and G. Strang, "The zeros of the Daubechies polynomials," in Proc. American Mathematical Society, 1996.
  18. A. K. Jain, Fundamentals of Digital Image Processing, Englewood Cliffs, New Jersey, 1989.
  19. M. Mastriani, "Enhanced Boolean Correlation Matriz Memory", (RNL02), in Proceedings of X RPIC Reunión de Trabajo en Procesamiento de la Información y Control, San Nicolás, Buenos Aires, Argentina, October 8-10, 2003.
  20. G. Delfino and F. Martinez. (2000, March). Watermarking insertion in digital images (spanish). [Online]. Available: http://www. internet. com. uy/fabianm/watermarking. pdf
  21. Y. Yu, and S. T. Acton, "Speckle Reducing Anisotropic Diffusion," IEEE Trans. on Image Processing, vol. 11, no. 11, pp. 1260-1270, 2002.
  22. M. Mastriani and A. Giraldez, "Enhanced Directional Smoothing Algorithm for Edge-Preserving Smoothing of Synthetic-Aperture Radar Images," Journal of Measurement Science Review, vol 4, no. 3, pp. 1-11, 2004. [Online]. Available: http://www. measurement. sk/2004/S3/Mastriani. pdf.
  23. Southern, E. M. : Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98, 503–517 (1975)
  24. Wang Y. , Lu J. , Lee R. , Gu Z. , Clarke R. : Iterative normalization of CDNA microarray data. IEEE Trans. Inf. Technol. Biomed. 6, 29–37 (2000)
  25. O'Neill, P. , Magoulas, G. D. : Improved processing of microarray data using image reconstruction techniques. IEEE Trans. Nanobiosci. 2(4), 176–183, December (2003)
  26. Lukac, R. , Plataniotis, K. N. , Smolka, B. , Venetsanopoulos, A. N. : cDNA microarray image processing using fuzzy vector filtering framework. J. Fuzzy Sets Syst. Special Issue on Fuzzy Sets and Systems in Bioinformatics 152(1), 17–35, May (2005)
  27. Mallat, S. : A theory for multiresolution signal decomposition: the wavelet representation. IEEE Trans. Pattern Anal. Machine Intel. 11, 674–693, July (1989)
  28. Chua,L. O. ,Yang, L. :Cellular neural networks: theory. IEEETrans. Circuits Syst. 35, 1257-1272 (1988)
  29. Zhang, X. Y. , Chen, F. , Zhang, Y. T. , Agner, S. G. , Akay, M. , Lu, Z. H. , Waye, M. M. Y. , Tsui, S. K. W. : Signal processing techniques in genomic engineering. In: Proceedings of the IEEE90(12), 1822–1833, December (2002)
  30. Arena, P. , Bucolo, M. , Fortuna, L. , Occhipinty, L. : Celular neural networks for real-time DNA microarray analysis. IEEE Engl. Med. Biol. 21, 17–25 (2002)
  31. Wang, X. H. , Istepanian, R. S. H. , Song, Y. H. : Microarray image enhancement by denoising using stationary wavelet transform. IEEE Trans. Nanobiosci. 2(4), 184–189, December (2003)
  32. Pesquet, J. C. ,Krim, H. ,Carfantan,H. :Time-invariant Orthonormal Wavelet Representations. IEEE Trans. Signal Process. 44, 1964– 1970, August (1996)
  33. Adjeroh, D. A. , Zhang, Y. , Parthe, R. : On denoising and compression of DNA microarray images. Pattern Recogn. , Special Issue on Bioinformatics, pp. 2478–2493, December (2006)
Index Terms

Computer Science
Information Sciences

Keywords

Systholic Boolean Orthonormalizer Network Microarray Denoising Dwt Sbon