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International Conference on Distributed Computing and Internet Technology

ICDCIT 2015: Distributed Computing and Internet Technology pp 134–149Cite as

Host Trait Prediction of Metagenomic Data for Topology-Based Visualization

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Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 8956))

Abstract

Microbiome and metagenomic research continues to grow as well as the size and complexity of the collected data. Additionally, it is understood that the microbiome can have a complex relationship with the environment or host it inhabits, such as in gastrointestinal disease. The goal of this study is to accurately predict a host’s trait using only metagenomic data, by training a statistical model on available metagenome sequencing data. We compare a traditional Support Vector Regression approach to a new non-parametric method developed here, called PKEM, which uses dimensionality reduction combined with Kernel Density Estimation. The results are visualized using methods from Topological Data Analysis. Such representations assist in understanding how the data organizes and can lead to new insights. We apply this visualization-of-prediction technique to cat, dog and human microbiome obtained from fecal samples. In the first two the host trait is irritable bowel syndrome while in the last the host trait is Kwashiorkor, a form of severe malnutrition.

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Author information

Authors and Affiliations

  1. Computational Biology Center, IBM T.J. Watson Research, Yorktown Heights, NY, USA

    Laxmi Parida, Niina Haiminen & David Haws

  2. Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA

    Jan Suchodolski

Authors
  1. Laxmi Parida
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  2. Niina Haiminen
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  3. David Haws
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  4. Jan Suchodolski
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Editor information

Editors and Affiliations

  1. School of Technology and Computer Science, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, 400005, Mumbai, India

    Raja Natarajan

  2. Department of Computer Science and Engineering, Indian Institute of Technology Guwahati, 781039, Guwahati, India

    Gautam Barua

  3. Department of Computer Science,, Berhampur University, 760007, Berhampur, Odisha, India

    Manas Ranjan Patra

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Parida, L., Haiminen, N., Haws, D., Suchodolski, J. (2015). Host Trait Prediction of Metagenomic Data for Topology-Based Visualization. In: Natarajan, R., Barua, G., Patra, M.R. (eds) Distributed Computing and Internet Technology. ICDCIT 2015. Lecture Notes in Computer Science, vol 8956. Springer, Cham. https://doi.org/10.1007/978-3-319-14977-6_8

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  • DOI: https://doi.org/10.1007/978-3-319-14977-6_8

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-14976-9

  • Online ISBN: 978-3-319-14977-6

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