BADGER: biologically-aware interpretable differential gene expression ranking model.

ABSTRACT:

Motivation

Understanding which genes are significantly affected by drugs is crucial for drug repurposing, as drugs targeting specific pathways in one disease might be effective in another with similar genetic profiles. By analyzing gene expression changes in cells before and after drug treatment, we can identify the genes most impacted by drugs.

Results

The Biologically-Aware Interpretable Differential Gene Expression Ranking (BADGER) model is an interpretable model designed to predict gene expression changes resulting from interactions between cancer cell lines and chemical compounds. The model enhances explainability through integration of prior knowledge about drug targets via pathway information, handles novel cancer cell lines through similarity-based embedding, and emp

SUBMITTER: Kim H 

PROVIDER: S-EPMC11978390 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature