Iterative framework radiation hybrid mapping

Raed I. Seetan, Anne M. Denton, Omar Al-Azzam, Ajay Kumar, Jazarai Sturdivant, Shahryar Kianian

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

Building comprehensive radiation hybrid maps for large sets of markers is a computationally expensive process, since the basic mapping problem is equivalent to the traveling salesman problem. The mapping problem is also susceptible to noise, and as a result, it is often beneficial to remove markers that are not trustworthy. The resulting framework maps are typically more reliable but don't provide information about as many markers. We present an approach to mapping most markers by first creating a framework map and then incrementally adding the remaining markers. We consider chromosomes of the human genome, for which the correct ordering is known, and compare the performance of our two-stage algorithm with the Carthagene radiation hybrid mapping software. We show that our approach is not only much faster than mapping the complete genome in one step, but that the quality of the resulting maps is also much higher.

Original languageEnglish (US)
Title of host publicationSIAM International Conference on Data Mining 2014, SDM 2014
EditorsPang Ning-Tan, Arindam Banerjee, Srinivasan Parthasarathy, Zoran Obradovic, Chandrika Kamath, Mohammed Zaki
PublisherSociety for Industrial and Applied Mathematics Publications
Pages1028-1036
Number of pages9
ISBN (Electronic)9781510811515
DOIs
StatePublished - 2014
Event14th SIAM International Conference on Data Mining, SDM 2014 - Philadelphia, United States
Duration: Apr 24 2014Apr 26 2014

Publication series

NameSIAM International Conference on Data Mining 2014, SDM 2014
Volume2

Other

Other14th SIAM International Conference on Data Mining, SDM 2014
CountryUnited States
CityPhiladelphia
Period4/24/144/26/14

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  • Cite this

    Seetan, R. I., Denton, A. M., Al-Azzam, O., Kumar, A., Sturdivant, J., & Kianian, S. (2014). Iterative framework radiation hybrid mapping. In P. Ning-Tan, A. Banerjee, S. Parthasarathy, Z. Obradovic, C. Kamath, & M. Zaki (Eds.), SIAM International Conference on Data Mining 2014, SDM 2014 (pp. 1028-1036). (SIAM International Conference on Data Mining 2014, SDM 2014; Vol. 2). Society for Industrial and Applied Mathematics Publications. https://doi.org/10.1137/1.9781611973440.117