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Divide and Conquer Machine Learning for a Genomics Analogy Problem

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Discovery Science (DS 2001)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 2226))

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Abstract

Genomic strings are not of fixed length,but provide one- dimensional spatial data that do not divide for conquering by machine learning into manageable .xed size chunks obeying Dietterich independent and identically distributed assumption.We nonetheless need to divide genomic strings for conquering by machine learning in this case for genomic prediction. Orthologs are genomic strings derived from a common ancestor and having the same biological function.Ortholog detection is biologically interesting since it informs us about protein divergence through evolution, and,in the present context,also has important agricultural applications. In the present paper is indicated means to obtain an associated (fixed size)attribute vector for genomic string data and for dividing and conquering the machine learning problem of ortholog detection herein seen as an analogy problem.The attributes are based on both the typical string similarity measures of bioinformatics and on a large number of differential metrics,many new to bioinformatics.Many of the differential metrics are based on evolutionary considerations,both theoretical and empirically observed,in some cases observed by the authors. C5.0 with AdaBoosting activated was employed and the preliminary results reported herein re complete cDNA strings are very encouraging for eventually and usefully employing the techniques described for ortholog detection on the more readily available EST (incomplete)genomic data.

Machine learning [Mit97,RN95]involves algorithmic techniques for fitting programs to data and for outputting the programs fit for subsequent use in predicting future data. A program so fit to data is said to be learned.

Amino acid sequences fold into 3-D structures,but that,for us,will be taken into account in future work.See Section 6 below.

http://www.usda.gov/news/pubs/fbook98/ch1a.htm

IL-2 is interleukin 2,an immune system protein.

Exons contain the coding portions of genes.

Applying attribute values for both chicken-mouse and chicken-human comparisons improves performance over just employing comparisons between chicken and one of these mammals.

http://www.tigr.org/docs/tigr-scripts/egad scripts/role report.spl

Importantly,the voting weights are bigger for more accurate trees in the sequence of trees.

In the present project we are working only with exons or portions thereof.

Recall from Section 4 above that the ensemble of trees obtained from AdaBoosting makes its decisions by a judiciously weighted majority vote among the decisions of its constituent trees ?ven more usefully subtle decision making than that of any single tree.

http://www.tigr.org/docs/tigr-scripts/egad scripts/role report.spl

http://www.chickest.udel.edu

http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html & http://www.cmpharm.ucsf.edu/ ~nomi/nnpredict-instrucs.html

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Author information

Authors and Affiliations

  1. Environmental and Occupational Health Sciences Institute UMDNJ Robert Wood Johnson Medical School and Rutgers, The State University of New Jersey, 08854, Piscataway, NJ, USA

    Ming Ouyang

  2. Department of CIS, University of Delaware, DE 19716, Newark, USA

    John Case

  3. Department of Animal & Food Sciences, University of Delaware, DE 19716, Newark, USA

    Joan Burnside

Authors
  1. Ming Ouyang
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  2. John Case
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Editor information

Editors and Affiliations

  1. DFKI GmbH Saarbrücken, 66123, Saarbrücken, Germany

    Klaus P. Jantke

  2. Department of Informatics, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, 812-8581, Fukuoka, Japan

    Ayumi Shinohara

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Ouyang, M., Case, J., Burnside, J. (2001). Divide and Conquer Machine Learning for a Genomics Analogy Problem. In: Jantke, K.P., Shinohara, A. (eds) Discovery Science. DS 2001. Lecture Notes in Computer Science(), vol 2226. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45650-3_26

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  • DOI: https://doi.org/10.1007/3-540-45650-3_26

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