Libraries

A collection of open-source libraries and tools I have developed for computational biology, drug discovery, and bioinformatics.

Research Models

scVGAE

ZINB-Based Variational Graph Autoencoder for Single-Cell RNA-Seq Imputation

• Language: Python
• Topics: Single-cell RNA-seq, Graph Neural Networks, Imputation
• GitHub: https://github.com/inoue0426/scVGAE
• Paper: https://arxiv.org/abs/2403.08959

scBiGCN

Bi-Graph Convolutional Networks for Single-cell Transcriptome Imputation

• Language: Python
• Topics: Single-cell RNA-seq, Graph Convolutional Networks, Imputation
• GitHub: https://github.com/inoue0426/scBiGCN
• Paper: https://doi.org/10.1101/2024.04.05.588342

drGT

Attention-Guided Gene Assessment of Drug Response in a Drug-Cell-Gene Heterogeneous Network

• Language: Python
• Topics: Drug Response Prediction, Graph Neural Networks, Attention Mechanism
• GitHub: https://github.com/inoue0426/drGT
• Paper: https://arxiv.org/abs/2405.08979

GraphPINE

Graph Importance Propagation for Interpretable Drug Response Prediction

• Language: Python
• Topics: Drug Response Prediction, Interpretability, GNN
• GitHub: https://github.com/inoue0426/GraphPINE
• Paper: https://arxiv.org/abs/2504.05454

DrugAgent

Multi-Agent LLM-Based Reasoning for Drug-Target Interaction Prediction

• Language: Python
• Topics: Drug-Target Interaction, Large Language Models, Multi-Agent
• GitHub: https://github.com/inoue0426/DrugAgent-v1
• Paper: https://arxiv.org/abs/2408.13378

Utility Libraries

smiles2graph

Convert SMILES strings to PyTorch Geometric graph objects

• Language: Python
• Topics: Cheminformatics, PyTorch Geometric, Drug Discovery
• GitHub: https://github.com/inoue0426/smiles2graph

PubChemExchanger

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

• Language: Python
• Topics: Cheminformatics, PubChem, Drug Discovery
• GitHub: https://github.com/inoue0426/PubChemExchanger

DrugBankParser

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

• Language: Python
• Topics: DrugBank, Cheminformatics, Data Extraction
• GitHub: https://github.com/inoue0426/DrugBankParser