Hierarchical Feature Extraction from Large Sequence Data by Deep Learning

• Project/Area Number: 26330328
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Life / Health / Medical informatics
• Research Institution: Kanazawa University
• Principal Investigator: SATOU Kenji 金沢大学, 電子情報学系, 教授 (10215783)
• Project Period (FY): 2014-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2014: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: テキスト分類 / 畳み込みニューラルネットワーク / スプライス部位 / プロモータ / 単語埋め込み / 次世代シーケンサ / ゲノム配列決定 / ヒストン修飾 / プロモータ配列 / バイオインフォマティクス / ディープラーニング

Outline of Final Research Achievements

In the field of biological sequence analysis including DNA and amino acid sequence analysis, traditional methods are highly dependent on the knowledge specific to molecular biology, so their ability is limited to the discovery of features easily predicted from domain-specific knowledge. In this study, it is shown that by using various machine learning algorithms including deep learning, it is possible to extract novel and hierarchical features from large sequence data.

Research Products

• [Journal Article] Combined Use of k-Mer Numerical Features and Position-Specific Categorical Features in Fixed-Length DNA Sequence Classification (2017)
  • Author(s): Phan,D., Nguyen,N.G., Lumbanraja,F.R., Faisal,M.R., Abapihi,B., Purnama,B., Delimayanti,M.K., Kubo,M., Satou,K.
  • Journal Title: Journal of Biomedical Science and Engineering Volume: 10 Pages: 390-401
  • Peer Reviewed / Open Access
• [Journal Article] DNA Sequence Classification by Convolutional Neural Network (2016)
  • Author(s): Nguyen,N.G., Tran,V.A., Ngo,D.L., Phan,D., Lumbanraja,F.R., Faisal,M.R., Abapihi,B., Kubo,M., Satou,K.
  • Journal Title: Journal of Biomedical Science and Engineering Volume: 9 Issue: 05 Pages: 280-286
  • DOI: 10.4236/jbise.2016.95021
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Application of Word Embedding to Drug Repositioning (2016)
  • Author(s): Ngo, D.L., Yamamoto, N., Tran, V.A., Nguyen, N.G., Phan, D., Lumbanraja, F.R, Kubo, M., Satou, K.
  • Journal Title: Journal of Biomedical Science and Engineering Volume: 9 Issue: 01 Pages: 7-16
  • DOI: 10.4236/jbise.2016.91002
  • Peer Reviewed / Open Access / Acknowledgement Compliant