| Getting Started | |
| =============== | |
| Installation | |
| ------------ | |
| Geneformer installation instructions. | |
| Make sure you have git-lfs installed (https://git-lfs.com). | |
| .. code-block:: bash | |
| git lfs install | |
| git clone https://huggingface.co/ctheodoris/Geneformer | |
| cd Geneformer | |
| pip install . | |
| Tutorials | |
| --------- | |
| | See `examples <https://huggingface.co/ctheodoris/Geneformer/tree/main/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 <https://huggingface.co/datasets/ctheodoris/Genecorpus-30M/tree/main/example_input_files>`_ 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.). | |