Shoichi Ishida

Project Assistant Professor
Graduate School of Medical Life Science · Yokohama City University

I'm currently studying cheminformatics, bioinformatics, and machine learning. I write blog posts related to my researches and life hacks on my web site.


Kyoto University, Kyoto, Japan

Ph.D. in Pharmacy
April 2017 - March 2021

Kitasato University, Tokyo, Japan

B.S. in Pharmacy
April 2011 - March 2017


Programming Languages & Tools
  • Ph.D. in Biomedical Sciences
  • Pharmacist


  • ChemTSv2: Flexible and Versatile Molecule Generator Based on Reinforcement Learning with Natural Language Processing [GitHub]
  • ReTReK: data-driven ReTrosynthesis planning application using Retrosynthesis Knowledge [GitHub]
  • DEFMap: Dynamics Extraction From cryo-EM Map [GitHub]
  • kGCN: A graph-based deep learning framework for life science [GitHub]
  • CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration [GitHub]
  • Reaction template extractor [GitHub]

Research Interest

  • Computer-aided synthesis planning
  • Application of machine learning for life sciences
  • Cheminformatics
  • Bioinformatics

Research Paper

Dagger (†) denotes these authors contributed equally.


International Conferences and Workshops
  • R. Kojima, H. Iwata, S. Ishida, M. Ikeguchi, Y. Okuno; A Prediction Framework for Drug Discovery Using Graph Convolutional Networks; 5th International Symposium for Medicinal Sciences (ISMS) (poster), March, 2019.
Domestic Conferences and Workshops
  • S. Ishida, K. Terayama, R. Kojima, K. Takasu, Y. Okuno; Interpretable Reaction Prediction using Graph Convolutional Networks; CBI Annual Meeting, 2019/10/22~24, (oral)
  • S. Ishida, K. Terayama, R. Kojima, K. Takasu, Y. Okuno; GCN 記述子とモンテカルロ木探索を用いた合成経路予測; CBI Annual Meeting, 2019/10/22~24, (oral: sponsored session)
  • M. Ikeguchi, S. Ishida, R. Kojima, H. Iwata, Y. Okuno; Prediction of Compound-Protein Interactions and Visualization Based on Graph Convolutional Networks; CBI Annual Meeting, 2019/10/22~24, (poster)
  • R. Shibukawa, S. Ishida, K. Terayama, K. Yoshizoe, Y. Okuno, K. Tsuda; 証明数探索を用いた化合物合成経路列挙アルゴリズム; Information-Based Induction Sciences (IBIS), 2018/11. (oral)

Review Article

  • 寺山慧, 石田祥一, 奥野恭史, 『AIによる逆合成解析に向けて』, 月刊「細胞」, Vol.51, No.7, pp.12-15, 2019/5.
  • 寺山慧, 石田祥一, 奥野恭史, 『囲碁AIから逆合成解析へ−情報科学からのアプローチ』, 化学, Vol.74 No.2, pp.36-40, 2019/1.