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Deep representation learning for drugs and proteins with neural networks

Research Project

Project/Area Number 17H07392
Research Category

Grant-in-Aid for Research Activity Start-up

Allocation TypeSingle-year Grants
Research Field Life / Health / Medical informatics
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

Tsubaki Masashi  国立研究開発法人産業技術総合研究所, 情報・人間工学領域, 研究員 (80803874)

Research Collaborator Asho Hideki  
Kanemura Atsunori  
Project Period (FY) 2017-08-25 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2018: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords深層学習 / 創薬 / 機械学習 / 人工知能
Outline of Final Research Achievements

Received the Best Paper Award at the workshop of Advances in Neural Information Processing Systems (NIPS 2017), the largest international conference in machine learning. It was also adopted by Bioinformatics, an international journal in the field of bioinformatics. At the same time, the developed software was released to the public. In fact, it was decided to conduct joint research with a pharmaceutical company. I was able to create a series of flows from industrial design to the application of the method which is a part of the foundation, to the dissertation and the release of software, and from there to joint research with companies, to industrial applications.

Academic Significance and Societal Importance of the Research Achievements

この研究成果の学術的な意義としては、まず、グラフ構造のような離散データについても、深層学習の有効性を検証できたという点である。特に、これまで特徴量や記述子を使って、データを一旦変換した上で、つまり情報を人間の観点から削減した上で機械学習手法を適用していたものが、データのより原始的な情報を入力として扱えるようになった。また、社会的な意義としては、これまで新薬の開発が難しかった病気などに対して、コンピュータのアプローチから迫ることができる点である。特に、機械学習手法はシュミレーションなどの異なり、予測の精度が非常に速いことが大きな利点である。

Report

(3 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • Research Products

    (9 results)

All 2019 2018 2017 Other

All Journal Article (4 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 4 results,  Open Access: 4 results) Presentation (2 results) (of which Int'l Joint Research: 1 results,  Invited: 1 results) Remarks (3 results)

  • [Journal Article] Quantitative estimation of properties from core-loss spectrum via neural network2019

    • Author(s)
      Shin Kiyohara, Masashi Tsubaki, Kunyen Liao, and Teruyasu Mizoguchi
    • Journal Title

      Journal of Physics: Materials

      Volume: 1 Pages: 1-2

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Compound-protein Interaction Prediction with End-to-end Learning of Neural Networks for Graphs and Sequences2018

    • Author(s)
      Masashi Tsubaki, Kentaro Tomii, and Jun Sese
    • Journal Title

      Bioinformatics

      Volume: 35 Pages: 309-318

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Fast and Accurate Molecular Property Prediction: Learning Atomic Interactions and Potentials with Neural Networks2018

    • Author(s)
      Masashi Tsubaki and Teruyasu Mizoguchi
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 9 Pages: 5733-5741

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Mean-field theory of Graph Neural Networks in Graph Partitioning2018

    • Author(s)
      Tatsuro Kawamoto, Masashi Tsubaki, and Tomoyuki Obuchi
    • Journal Title

      Advances in Neural Information Processing Systems

      Volume: 1 Pages: 1-2

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 深層学習を用いた化合物とタンパク質の相互作用予測2018

    • Author(s)
      椿真史
    • Organizer
      創薬インフォマティクス研究会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] End-to-end Learning of Graph Neural Networks for Latent Molecular Representations2017

    • Author(s)
      Masashi Tsubaki
    • Organizer
      Advances in Neural Information Processing Systems (NIPS 2017) Workshop, Machine Learning for Molecules and Materials,
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Remarks] 化合物の薬剤活性予測ソフトウエア

    • URL

      https://github.com/masashitsubaki/GNN_molecules

    • Related Report
      2018 Annual Research Report
  • [Remarks] 化合物とタンパク質の相互作用予測ソフトウエア

    • URL

      https://github.com/masashitsubaki/CPI_prediction

    • Related Report
      2018 Annual Research Report
  • [Remarks] 化合物の立体構造データからの物性値予測ソフトウエア

    • URL

      https://github.com/masashitsubaki/QuantumGNN_molecules

    • Related Report
      2018 Annual Research Report

URL: 

Published: 2017-08-25   Modified: 2020-03-30  

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