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Statistical Machine Learning for Agriculture and Human Health Care Based on Biomedical Big Data

  • Yoshihiro YamanishiEmail author
  • Yasuo Tabei
  • Masaaki Kotera
Conference paper
Part of the Mathematics for Industry book series (MFI, volume 28)

Abstract

The availability of biomedical big data provides an opportunity to develop data-driven approaches in agriculture and human healthcare research. In this study, we investigate statistical machine learning approaches to metabolic pathway reconstruction and the prediction of drug–target interactions, using heterogeneous biomedical big data. We present an \(L_1\)-regularized pairwise support vector machine to predict unknown enzymatic reactions among metabolome-scale compounds, based on chemical transformation patterns of compounds. We also present supervised bipartite graph inference with kernel methods to predict unknown interactions between drugs and target proteins, based on the chemical structures of drugs and the amino acid sequences of proteins. We experimentally demonstrated that these methods could be applied to rational compound synthesis and efficient drug discovery for a range of human diseases. Such methods are expected to increase the productivity of research in food and pharmaceutical industries.

Keywords

Metabolic pathways Drug targets Machine learning Classification Feature extraction Graph inference 

Notes

Acknowledgements

This work is supported by JST PRESTO Grant Number JPMJPR15D8, JSPS KAKENHI Grant Numbers 25700029 and 15K14980, and the Program to Disseminate Tenure Tracking System, MEXT, Japan and Kyushu University Interdisciplinary Programs in Education and Projects in Research Development.

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Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Yoshihiro Yamanishi
    • 1
    • 2
    • 3
    Email author
  • Yasuo Tabei
    • 4
  • Masaaki Kotera
    • 5
  1. 1.Division of System CohortMedical Institute of Bioregulation, Kyushu UniversityFukuokaJapan
  2. 2.Institute for Advanced Study, Kyushu UniversityFukuokaJapan
  3. 3.PRESTO, Japan Science and Technology AgencyKawaguchiJapan
  4. 4.RIKEN Center for Advanced Intelligence ProjectTokyoJapan
  5. 5.School of Life Science and TechnologyTokyo Institute of TechnologyTokyoJapan

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