| Getting Started |
| =============== |
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| Installation |
| ------------ |
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| Geneformer installation instructions. |
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| Make sure you have git-lfs installed (https://git-lfs.com). |
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| .. code-block:: bash |
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| git lfs install |
| git clone https://huggingface.co/ctheodoris/Geneformer |
| cd Geneformer |
| pip install . |
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| Tutorials |
| --------- |
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| | 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 |
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| 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. |
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| Tips |
| ---- |
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| 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.). |
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