Geneformer Benchmarking

This repository contains reproducible benchmarking scripts for Geneformer-based single-cell RNA-seq cell type classification, including donor-level splits, tokenization, model training, and evaluation for comparing Geneformer models (V1-10M, V2-104M, V2-316M).

Overview

This repository contains:

• Configurable SLURM training scripts for HPC environments
• Jupyter notebooks for data preprocessing and results analysis
• Utilities for fair model comparison with proportional layer freezing

Requirements

• Geneformer package from HuggingFace
• Python 3.11+
• See requirements.txt for dependencies

Usage

See scripts/slurm/README.md for detailed instructions.