Getting Started

Installation

Geneformer installation instructions.

Make sure you have git-lfs installed (https://git-lfs.com).

git lfs install
git clone https://huggingface.co/ctheodoris/Geneformer
cd Geneformer
pip install .

Tutorials

See examples for:

- tokenizing transcriptomes

- pretraining

- hyperparameter tuning

- fine-tuning

- extracting and plotting cell embeddings

- in silico perturbation

Please note that the fine-tuning examples are meant to be generally applicable and the input datasets and labels will vary dependent on the downstream task. Example input files for a few of the downstream tasks demonstrated in the manuscript are located within the example_input_files directory in the dataset repository, but these only represent a few example fine-tuning applications.

Tips

Please note that GPU resources are required for efficient usage of Geneformer. Additionally, we strongly recommend tuning hyperparameters for each downstream fine-tuning application as this can significantly boost predictive potential in the downstream task (e.g. max learning rate, learning schedule, number of layers to freeze, etc.).