Basic information
Naruki has moved to Computational Drug Discovery and Design Lab , Institute of Science Tokyo (ex-Tokyo Medical and Dental University) since July 1, 2024.
New E-mail: yoshikawa.naruki [at] tmd.ac.jp
Education
University of Toronto (2020 - 2024), Doctor of Philosophy (Department of Computer Science, Advisor: Alán Aspuru-Guzik )The University of Tokyo (2018 - 2020), Master of Science (Department of Computational Biology and Medical Sciences, Advisor: Koji Tsuda )The University of Tokyo (2014 - 2018), Bachelor of Science (Department of Bioinformatics and Systems Biology, Advisor: Koji Tsuda )
Publications
Peer-reviewed journal papers
Naruki Yoshikawa , Gun Deniz Akkoc, Sergio Pablo-García, Yang Cao, Han Hao, Alán Aspuru-Guzik. Does one need to polish electrodes in an eight pattern? Automation provides the answer . Digital Discovery, 2025. (Open Access)Kourosh Darvish*, Marta Skreta*, Yuchi Zhao*, Naruki Yoshikawa , Sagnik Som, Miroslav Bogdanovic, Yang Cao, Han Hao, Haoping Xu, Alán Aspuru-Guzik, Animesh Garg, Florian Shkurti. ORGANA: A robotic assistant for automated chemistry experimentation and characterization . Matter, 2024.
Sergio Pablo-García, Ángel García, Gun Deniz Akkoc, Malcolm Sim, Yang Cao, Maxine Somers, Chance Hattrick, Naruki Yoshikawa , Dominik Dworschak, Han Hao, Alán Aspuru-Guzik. An affordable platform for automated synthesis and electrochemical characterization . Device, 2024. (Open Access)
Rama El-khawaldeh, Abhijoy Mandal, Naruki Yoshikawa , Wenyu Zhang, Ryan Corkery, Paloma Prieto, Alán Aspuru-Guzik, Kourosh Darvish, Jason Hein. From eyes to cameras: Computer vision for high-throughput liquid-liquid separation . Device, 2024. (Open Access)
Martin Seifrid, Felix Strieth-Kalthoff, Mohammad Haddadnia, Tony Wu, Emre Alca, Leticia Bodo, Sebastian Arellano-Rubach, Naruki Yoshikawa , Marta Skreta, Rachel Keunen, Alán Aspuru-Guzik. Chemspyd: an open-source python interface for Chemspeed robotic chemistry and materials platforms . Digital Discovery, 2024. (Open Access)
Naruki Yoshikawa *, Marta Skreta*, Kourosh Darvish*, Sebastian Arellano-Rubach, Zhi Ji, Lasse Bjørn Kristensen, Andrew Zou Li, Yuchi Zhao, Haoping Xu, Artur Kuramshin, Alán Aspuru-Guzik, Florian Shkurti, Animesh Garg. Large language models for chemistry robotics . Autonomous Robots, 2023. (Open Access)Naruki Yoshikawa , Kourosh Darvish, Animesh Garg, Alán Aspuru-Guzik. Digital pipette: open hardware for liquid transfer in self-driving laboratories . Digital Discovery, 2023. (Open Access)Naruki Yoshikawa , Masato Sumita. Automatic Differentiation for the Direct Minimization Approach to the Hartree–Fock Method . The Journal of Physical Chemistry A, 2022. (Link to full text )Naruki Yoshikawa *, Ryuichi Kubo*, and Kazuki Z Yamamoto. Twitter Integration of Chemistry Software Tools . Journal of Cheminformatics, 2021. (Open Access)Masato Sumita and Naruki Yoshikawa . Augmented Lagrangian method for spin-coupled wave function . International Journal of Quantum Chemistry, 2021. (Link to full text )
Naruki Yoshikawa and Geoffrey R. Hutchison. Fast, Efficient Fragment-Based Coordinate Generation for Open Babel . Journal of Cheminformatics, 2019. (Open Access)Naruki Yoshikawa , Kei Terayama, Masato Sumita, Teruki Homma, Kenta Oono, and Koji Tsuda. Population-based De Novo Molecule Generation, Using Grammatical Evolution . Chemistry Letters, 2018. (Open Access)Anish MS Shrestha, Naruki Yoshikawa , and Kiyoshi Asai. Combining probabilistic alignments with read pair information improves accuracy of split-alignments . Bioinformatics, 2018. (Open Access)
Reviews
Gary Tom, Stefan P. Schmid, Sterling G. Baird, Yang Cao, Kourosh Darvish, Han Hao, Stanley Lo, Sergio Pablo-García, Ella M. Rajaonson, Marta Skreta, Naruki Yoshikawa , Samantha Corapi, Gun Deniz Akkoc, Felix Strieth-Kalthoff, Martin Seifrid, Alán Aspuru-Guzik. Self-Driving Laboratories for Chemistry and Materials Science . Chemical Reviews, 2024. (Open Access)
AkshatKumar Nigam, Robert Pollice, Matthew F. D. Hurley, Riley J. Hickman, Matteo Aldeghi, Naruki Yoshikawa , Seyone Chithrananda, Vincent A. Voelz, and Alán Aspuru-Guzik. Assigning Confidence to Molecular Property Prediction . Expert Opinion on Drug Discovery, 2021. (arXiv )
Preprints
Presentations
Kusuri Murakumo, Naruki Yoshikawa , Kentaro Rikimaru, Shogo Nakamura, Kairi Furui, Takamasa Suzuki, Hiroyuki Yamasaki, Yuki Nishigaya, Yuzo Takagi, Masahito Ohue. LLM Drug Discovery Challenge: A Contest as a Feasibility Study on the Utilization of Large Language Models in Medicinal Chemistry . (Poster presentation at NeurIPS AI4Mat Workshop, 2023 and 1st Annual CACHE Challenge Symposium, 2024)
Naruki Yoshikawa *, Andrew Zou Li*, Kourosh Darvish*, Yuchi Zhao*, Haoping Xu*, Artur Kuramshin, Alán Aspuru-Guzik, Animesh Garg, Florian Shkurti. Chemistry Lab Automation via Constrained Task and Motion Planning . (Poster presentation at Accelerate Conference 2023)Kevin Angers, Naruki Yoshikawa , Kourosh Darvish, Mohammad Ghazi Vakili, Animesh Garg, Alán Aspuru-Guzik. Digital pipette: Open hardware for liquid transfer in self-driving laboratories . (Poster presentation at Accelerate Conference 2023, designed by Kevin Angers)
Marta Skreta*, Naruki Yoshikawa *, Sebastian Arellano-Rubach, Zhi Ji, Lasse Bjørn Kristensen, Kourosh Darvish, Alán Aspuru-Guzik, Florian Shkurti, Animesh Garg. CLAIRify: Generating chemistry experiment plans from natural language inputs . (Poster presentation at Molecular ML Conference 2023 and Accelerate Conference 2023, designed by Marta Skreta)
Naruki Yoshikawa , Kei Terayama, Masato Sumita, Teruki Homma, Kenta Oono, and Koji Tsuda. Population-based de novo molecule generation, using grammatical evolution . (Poster presentation at 256th ACS National Meeting)Naruki Yoshikawa , Anish MS Shrestha, and Kiyoshi Asai. Combining probabilistic alignments with read pair information improves accuracy of split-alignments . (Poster presentation at APBC 2018)
Media
Activity