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RIKEN Center for Advanced Intelligence Project Molecular Informatics Team

Team Leader: Koji Tsuda (D.Eng.)

Research Summary

Koji  Tsuda(D.Eng.)

Molecular informatics team aims to develop artificial intelligence methods that design functional biomolecules such as proteins and inorganic compounds such as metal, ceramic and nanoparticles. In addition to theoretical studies about automatic design methods such as Bayesian optimization and Monte Carlo tree search, we synthesize designed materials in collaboration with experimental scientists.

Research Subjects:

  • Automatic design methods for molecules and materials
  • Automatic construction of materials science databases from literature
  • Theoretical studies about experimental design

Main Research Fields

  • Informatics

Related Research Fields

  • Complex Systems
  • Intelligent Informatics


  • Machine Learning
  • Materials Informatics

Selected Publications

  • 1. Terayama, K., Sumita, M., Tamura, R., Payne, D.T., Chahal, M.K., Ishihara, S. and Tsuda, K.:
    "Pushing property limits in materials discovery via boundless objective-free exploration"
    Chemical Science, 11, 5959-5968 (2020)
  • 2. Homma, K., Liu, Y., Sumita, M., Tamura, R., Fushimi, N., Iwata, J., Tsuda, K. and Kaneta, C.:
    "Optimization of heterogeneous ternary Li3PO4-Li3BO3-Li2SO4 mixture for Li-ion conductivity by machine learning"
    The Journal of Physical Chemistry C, 124, 12865-12870 (2020)
  • 3. Mehrabi, P., Di Pietrantonio, C., Kim, T.H., Sljoka, A., Taverner, K., Ing, C., Kruglyak, N., Pomès, R., Pai, E.F. and Prosser, R.S.:
    "Substrate-based allosteric regulation of a homodimeric enzyme"
    Journal of the American Chemical Society, 141, 11540-11556 (2019)
  • 4. Saito, Y., Shin, K., Terayama, K., Desai, S., Onga, M., Nakagawa, Y., Itahashi, Y.M., Iwasa, Y., Yamada, M. and Tsuda, K.:
    "Deep-learning-based quality filtering of mechanically exfoliated 2D crystals"
    npj Computational Materials, 5, 124 (2019)
  • 5. Sakurai, A., Yada, K., Simomura, T., Ju, S., Kashiwagi, M., Okada, H., Nagao, T., Tsuda, K. and Shiomi, J.:
    "Ultranarrow-band wavelength-selective thermal emission with aperiodic multilayered metamaterials designed by Bayesian optimization"
    ACS Central Science, 5, 319-326 (2019)
  • 6. Sumita, M., Tamura, R., Homma, K., Kaneta, C. and Tsuda, K.:
    "Li-Ion Conductive Li3PO4-Li3BO3-Li2SO4 Mixture: Prevision through Density Functional Molecular Dynamics and Machine Learning"
    Bulletin of the Chemical Society of Japan, 92, 1100-1106 (2019)
  • 7. Sumita, M., Yang, X., Ishihara, S., Tamura, R. and Tsuda, K.:
    "Hunting for organic molecules with artificial intelligence: molecules optimized for desired excitation energies"
    ACS Central Science, 4, 1126-1133 (2018)
  • 8. Saito, Y., Oikawa, M., Nakazawa, H., Niide, T., Kameda, T., Tsuda, K. and Umetsu, M.:
    "Machine-learning-guided mutagenesis for directed evolution of fluorescent proteins"
    ACS Synthetic Biology, 7, 2014-2022 (2018)
  • 9. Yang, X., Zhang, J., Yoshizoe, K., Terayama, K. and Tsuda, K.:
    "ChemTS: an efficient python library for de novo molecular generation"
    Science and Technology of Advanced Materials, 18, 972-976 (2017)
  • 10. Ju, S., Shiga, T., Feng, L., Hou, Z., Tsuda, K. and Shiomi, J.:
    "Designing nanostructures for phonon transport via Bayesian optimization"
    Physical Review X, 7, 021024 (2017)

Recent Research Results

Related Links

Lab Members

Principal investigator

Koji Tsuda
Team Leader

Core members

Adnan Sljoka
Research Scientist
Masato Sumita
Research Scientist
Kosuke Hamazaki
Special Postdoctoral Researcher
Mitsuo Umetsu
Senior Visiting Scientist
Masaya Kumagai
Visiting Scientist
Kei Terayama
Visiting Scientist
Ryo Tamura
Visiting Scientist
Andrejs Tucs
Visiting Scientist
Kazuki Yoshizoe
Visiting Scientist
Yukari Katsura
Visiting Scientist
Motoki Shiga
Visiting Scientist
Weilin YUAN
Visiting Scientist
Liyao Wang
Research Part-time Worker I
Peiheng Zou
Research Part-time Worker I

Contact Information

5-1-5-CB02, Kashiwanoha,
Kashiwa, Chiba
277-8561, Japan
Email: koji.tsuda [at] riken.jp