GenePT-tools

Tools to use and expand the capabilities of the original GenePT. This repository contains utilities and notebooks for working with gene embeddings and single-cell RNA sequencing data.

Overview

This project builds upon the GenePT paper and provides tools to:

• Compare different embedding approaches (GenePT vs scGPT)
• Work with large single-cell datasets like Tabula Sapiens
• Generate composable embeddings across different dimensions
• Perform cell type classification using embeddings

Results

The following image shows a detailed summary of the results of the comparison between GenePT and scGPT zero-shot classification so far: We used a Google Sheet to format the output

Setup

Requirements

• Python 3.10 (required for scGPT compatibility)
• Standard scientific Python packages (pandas, numpy, scikit-learn)
• Special dependencies:
  • scGPT
  • AnnData
  • Hugging Face datasets/models

Installation

# Create venv
python -m venv .venv
source .venv/bin/activate  # or .venv\Scripts\activate on Windows

# Install in development mode with all tools
pip install -e ".[dev]"

Running tools

# Format code
black .
isort --gitignore .

# Run tests
pytest

Important files

GenePT-tools/
├── src/        # utility functions
└── notebooks/  # analysis notebooks

Notebooks

Take a look at generate_genept_embeddings.ipynb to see how to generate a GenePT embeddings and dataset and upload them to HuggingFace Hub. create_hf_repos.ipynb will create a new repository for the embeddings and dataset.

Take a look at tabula_sapiens_*.ipynb for a comparison of cell type classification using GenePT and scGPT embeddings.

Notebook	Description
generate_genept_embeddings.ipynb	Generates the GenePT embeddings and dataset for upload to HuggingFace Hub
tabula_sapiens_embed_genept.ipynb	Evaluates GenePT embeddings' cell classification performance on Tabula Sapiens
create_hf_repos.ipynb	Creates the initial HuggingFace repositories for the GenePT embeddings and dataset
tabula_sapiens_eda.ipynb	Exploratory analysis of the Tabula Sapiens single-cell dataset
tabula_sapiens_embed_genept.ipynb	Embed a subset of the Tabula Sapiens dataset using GenePT embeddings
tabula_sapiens_embed_scgpt.ipynb	Embed a subset of the Tabula Sapiens dataset using scGPT embeddings
tabula_sapiens_analysis_all.ipynb	A comparison of GenePT and scGPT embeddings for cell type classification on TS

Data Processing

• Support for loading and processing large sparse AnnData files
• Integration with Hugging Face datasets

Embedding Generation

• GenePT original embeddings
• scGPT embeddings
• Composable embeddings across different dimensions:
  • Associated genes
  • Aging related information
  • Drug interactions
  • Pathways and biological processes

Analysis Tools

• Cell type classification
• Embedding comparison utilities
• Visualization tools for high-dimensional data

Project Status

• Exact comparison between scGPT and GenePT embeddings
• Minimum cell count filtering per cell type
• AnnData integration
• Original GenePT embeddings support
• Prompt improvements
  • Remove aging
  • Add cell type
  • Add tissue type
  • Add dysfunctional cell type
• scGPT with batch tokens
• scGPT with modality tokens
• scGPT with combined batch/modality tokens
• Complete Tabula Sapiens cell embedding
• Cell-document bidirectional lookups
• Cell separation analysis

Contributing

This is a preliminary repository with work in progress. Code is mostly untested but being actively developed. Contributions and collaborations are welcome.

License

This project is licensed under the MIT License. The original GenePT weights are governed by the license of the original GenePT repository.