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README.md
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license:
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This model uses Cell2Sentence fine-tuning on the Pythia-160m model developed by EleutherAI.
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Cell2Sentence Links:
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GitHub: <https://github.com/vandijklab/cell2sentence-ft>
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Paper: <https://www.biorxiv.org/content/10.1101/2023.09.11.557287v3>
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Pythia Links
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Paper: <https://arxiv.org/abs/2304.01373>
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Hugging Face: <https://huggingface.co/EleutherAI/pythia-160m>
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Cell2Sentence is a novel method for adapting large language models to single-cell transcriptomics.
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We transform single-cell RNA sequencing data into sequences of gene names ordered by expression level, termed "cell sentences".
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2. unconditional cell generation
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3. cell type prediction
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We provide an example of how to use the model to conditionally generate a cell equipped with a post-processing function to remove duplicate and invalid genes.
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Unconditional cell generation and cell type prediction prompts are included as well, but we do not include an example cell sentence to format the prompt.
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license: cc-by-nc-nd-4.0
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# Overview
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This model uses Cell2Sentence fine-tuning on the Pythia-160m model developed by EleutherAI.
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## Cell2Sentence Links:
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GitHub: <https://github.com/vandijklab/cell2sentence-ft>
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Paper: <https://www.biorxiv.org/content/10.1101/2023.09.11.557287v3>
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## Pythia Links:
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GitHub: <https://github.com/EleutherAI/pythia>
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Paper: <https://arxiv.org/abs/2304.01373>
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Hugging Face: <https://huggingface.co/EleutherAI/pythia-160m>
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# Model Details
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Cell2Sentence is a novel method for adapting large language models to single-cell transcriptomics.
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We transform single-cell RNA sequencing data into sequences of gene names ordered by expression level, termed "cell sentences".
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2. unconditional cell generation
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3. cell type prediction
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# Sample Code
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We provide an example of how to use the model to conditionally generate a cell equipped with a post-processing function to remove duplicate and invalid genes.
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Unconditional cell generation and cell type prediction prompts are included as well, but we do not include an example cell sentence to format the prompt.
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