AMP: Assembly Matching Pursuit

نویسندگان

  • Surojit Biswas
  • Vladimir Jojic
چکیده

Metagenomics, the study of the total genetic material isolated from a biological host, promises to reveal host-microbe or microbe-microbe interactions that may help to personalize medicine or improve agronomic practice. We introduce a method that discovers metagenomic units (MGUs) relevant for phenotype prediction through sequence-based dictionary learning. The method aggregates patient-specific dictionaries and estimates MGU abundances in order to summarize a whole population and yield universally predictive biomarkers. We analyze the impact of Gaussian, Poisson, and Negative Binomial read count models in guiding dictionary construction by examining classification efficiency on a number of synthetic datasets and a real dataset from Ref. 1. Each outperforms standard methods of dictionary composition, such as random projection and orthogonal matching pursuit. Additionally, the predictive MGUs they recover are biologically relevant.

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عنوان ژورنال:
  • Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

دوره   شماره 

صفحات  -

تاریخ انتشار 2013