• E-mail: naruki.yoshikawa [at] mail.utoronto.ca
• GitHub: n-yoshikawa
• Google Scholar: Naruki Yoshikawa
• ORCID: 0000-0003-1546-8709

• University of Toronto (2020 - present), 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)

Peer-reviewed journal papers

• 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

• 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

• 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. ChemRxiv, 2024.
• 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. ChemRxiv, 2024.
• 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. ChemRxiv, 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. ChemRxiv, 2024.
• 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. ChemRxiv, 2024.
• 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. arXiv, 2024.
• Naruki Yoshikawa, Kentaro Rikimaru, and Kazuki Z Yamamoto. Sanitize It Yourself: Web-based molecular sanitization for machine-generated chemical structures. ChemRxiv, 2021.

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)

• 加トロント大、LLM使いロボで化学実験　専門知識不要　作業を自動化 (The Nikkan Kogyo Shimbun)
• CS researchers design ‘CLAIRify’ framework to improve chemistry robotics planning (Department of Computer Science, University of Toronto)
• Bots bring chemistry research tools to Twitter (Chemistry World)

• トロント大学日本人コミュニティ (UofT Japanese Community)
• RDKit 日本ユーザー会 (rdkit-users.jp)