Shoichi Ishida

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

Education

Skill

• Ph.D. in Biomedical Sciences
• Pharmacist

Development

• 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.

• Nojima, S., Ishida, S., Terayama, K., Matsumoto, K., Matsui, T., Tahara, S., Ohshima, K., Kiyokawa, H., Kido, K., Ukon, K., Yoshida, S. Y., Mitani, T. T., Doki, Y., Mizushima, T., Okuno, Y., Susaki, E. A., Ueda, H. R., & Morii, E. (2022). A novel three-dimensional imaging system based on polysaccharide staining for accurate histopathological diagnosis of inflammatory bowel diseases. Cellular and Molecular Gastroenterology and Hepatology.
• Ishida, S., Terayama, K., Kojima, R., Takasu, K., & Okuno, Y. (2022). AI-driven synthetic route design incorporated with retrosynthesis knowledge. Journal of Chemical Information and Modeling, 62(6), 1357–1367.
• Tanaka, Y., Kojima, R., Ishida, S., Yamashita, F., & Okuno, Y. (2021). Complex network prediction using deep learning. ArXiv [Physics.Soc-Ph].
• Matsumoto, S.†, Ishida, S.†, Araki, M., Kato, T., Terayama, K., & Okuno, Y. (2021). Extraction of protein dynamics information from cryo-EM maps using deep learning Extraction of protein dynamics information from cryo-EM maps using deep learning. Nature Machine Intelligence, 3(2), 153–160.
• Shibukawa, R.†, Ishida, S.†, Yoshizoe, K., Wasa, K., Takasu, K., Okuno, Y., Terayama, K., & Tsuda, K. (2020). CompRet: A comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration Journal of Cheminformatics, 12(1), 52.
• Kojima, R., Ishida, S., Ohta, M., Iwata, H., Honma, T., & Okuno, Y. (2020). kGCN: a graph-based deep learning framework for chemical structures Journal of Cheminformatics, 12(1), 32.
• Ishida, S., Terayama, K., Kojima, R., Takasu, K., & Okuno, Y. (2019). Prediction and Interpretable Visualization of Retrosynthetic Reactions Using Graph Convolutional Networks Journal of Chemical Information and Modeling, 59(12), 5026–5033.

Conference

• 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.

• 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.