About

I am Yoshitaka Inoue, a PhD candidate in Computer Science at the University of Minnesota under the supervision of Dr. Rui Kuang. I am also a pre-doctoral fellow at the National Library of Medicine and affiliated with the National Cancer Institute, advised by Dr. Augustin Luna.

I am interested in graph neural networks, drug discovery, single cell analysis, and biological networks. My future goal is to understand biological phenomena using computational approaches and to contribute to the development of therapeutics through my research.

I hold an M.S. in Information Science from the Nara Institute of Science and Technology, where I was advised by Dr. Shigehiko Kanaya. During my master’s degree, I studied abroad at UC Davis under the supervision of Dr. Oliver Fiehn.

My Libraries

I develop open-source tools for computational biology and drug discovery. See the full list on the Libraries page.

Research Models:

• scVGAE — ZINB-Based Variational Graph Autoencoder for Single-Cell RNA-Seq Imputation · Paper

• scBiGCN — Bi-Graph Convolutional Networks for Single-cell Transcriptome Imputation · Paper

• drGT — Attention-Guided Gene Assessment of Drug Response in a Drug-Cell-Gene Heterogeneous Network · Paper

• GraphPINE — Graph Importance Propagation for Interpretable Drug Response Prediction · Paper

• DrugAgent — Multi-Agent LLM-Based Reasoning for Drug-Target Interaction Prediction · Paper

Utility Libraries:

• smiles2graph — Convert SMILES strings to PyTorch Geometric graph objects

• PubChemExchanger — Retrieve and exchange chemical identifiers (SMILES, CID, SID, NSC, etc.) from PubChem

• DrugBankParser — Parse DrugBank XML files to extract drug names, CID, SMILES, targets, and UniProt IDs

Other Pages

• Awesome Computational Biology — A curated list of computational biology resources.
• Paper Reading — Notes and summaries from paper reading sessions.

Publications Snapshot

• Total publications: 10

• Latest publication year: 2026

Recent Publications

Abstract 3138: CellMiner Cross-Database (CellMinerCDB) for Exploration of Patient-Derived Cancer Cell Line Pharmacogenomics (2026)

Fathi Elloumi, William C Reinhold, Sudhir Varma, Yanghsin Wang, Meric Kinali, Yashuhiro Arakawa, Yoshitaka Inoue, M. Aladjem, Y. Pommier, Augustin Luna · Paper

GraphPINE: Graph Importance propagation for interpretable drug response prediction (2025)

Yoshitaka Inoue, Tianfan Fu, Augustin Luna · Paper

CellMiner cross-database (CellMinerCDB) version 2.2 for explorations of patient-derived cancer cell line pharmacogenomics. (2025)

Fathi Elloumi, William C Reinhold, Sudhir Varma, Yanghsin Wang, Meric Kinali, Yasuhiro Arakawa, Yoshitaka Inoue, M. Aladjem, Y. Pommier, Augustin Luna · Paper

scVGAE: A Novel Approach using ZINB-Based Variational Graph Autoencoder for Single-Cell RNA-Seq Imputation (2024)

Yoshitaka Inoue · Paper

Protein-Mamba: Biological Mamba Models for Protein Function Prediction (2024)

Bohao Xu, Yingzhou Lu, Yoshitaka Inoue, Namkyeong Lee, Tianfan Fu, Jintai Chen · Paper