GraphPINE: Graph Importance propagation for interpretable drug response prediction
Yoshitaka Inoue, Tianfan Fu, Augustin Luna. arXiv.org, 2025. Paper
CV
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Education
- Ph.D in Computer Science, University of Minnesota, 2026 (expected)
- M.S. in Information Science, Nara Institute of Science and Technology, 2019
- B.S. in Biology, Kumamoto University, 2017
Work experience
- Jan 2024 - : Pre-Doctoral Research Training Award Fellow
- The National Institutes of Health
- Working on graph with drug discovery
- Supervisor: Dr. Augustin Luna
- May - Sep 2023: Mentor
- Google Summer of Code
- As a mentor, I work with Dr. Augustin Luna to support Favour James in a project, Generate Example Dataset for PyTorch Geometric Based on Pathway Commons and Prototype.
- Supervisor: Dr. Augustin Luna
- Jun - Sep 2022: Mentee
- Google Summer of Code
- Worked on “Create a Pipeline from data extraction to execution of GNN based Drug Response Prediction”.
- Supervisor: Dr. Augustin Luna
- Apr 2019 - Jun 2021: Machine Learning Researcher
- FreakOut, Inc.
- Worked on click-through rate prediction, calibration, and cloud environment management. Using Python, Perl, C++, and Scala, I have been working on implementing some algorithms such as factorization machine and Levenberg–Marquardt algorithm.
- Supervisor: Dr. Masakazu Sano
Skills
- Programming
- Python
- R
- SQL
- Perl
- Scala
- Swift
- Library
- PyTorch
- PyTorch Geometric
- langchain
- Cloud
- AWS
- GCP
Publications
- Auto-updated publication count: 9
Covered years: 2025, 2024, 2023
CellMiner cross-database (CellMinerCDB) version 2.2 for explorations of patient-derived cancer cell line pharmacogenomics.
Fathi Elloumi, William C Reinhold, Sudhir Varma, Yanghsin Wang, Meric Kinali, Yasuhiro Arakawa, Yoshitaka Inoue, M. Aladjem, Y. Pommier, Augustin Luna. Nucleic Acids Research, 2025. Paper
scVGAE: A Novel Approach using ZINB-Based Variational Graph Autoencoder for Single-Cell RNA-Seq Imputation
Yoshitaka Inoue. arXiv.org, 2024. Paper
Protein-Mamba: Biological Mamba Models for Protein Function Prediction
Bohao Xu, Yingzhou Lu, Yoshitaka Inoue, Namkyeong Lee, Tianfan Fu, Jintai Chen. arXiv.org, 2024. Paper
DruGagent: Multi-Agent Large Language Model-Based Reasoning for Drug-Target Interaction Prediction
Yoshitaka Inoue, Tianci Song, Xinling Wang, Augustin Luna, Tianfan Fu. arXiv.org, 2024. Paper
DrugAgent: Explainable Drug Repurposing Agent with Large Language Model-based Reasoning
Yoshitaka Inoue, Tianci Song, Tianfan Fu. arXiv.org, 2024. Paper
drGT: Attention-Guided Gene Assessment of Drug Response Utilizing a Drug-Cell-Gene Heterogeneous Network
Yoshitaka Inoue, Hunmin Lee, Tianfan Fu, Augustin Luna. arXiv.org, 2024. Paper
BiGCN: Leveraging Cell and Gene Similarities for Single-cell Transcriptome Imputation with Bi-Graph Convolutional Networks
Yoshitaka Inoue, Ethan Kulman, Rui Kuang. bioRxiv, 2024. Paper
Machine learning approach in predicting GlutoPeak test parameters from image data with AutoML and transfer learning
Takehiro Murai, Yoshitaka Inoue, Assey Nambirige, G. Annor. Heliyon, 2023. Paper
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