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README.md
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# Overview
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This
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## Cell2Sentence Links:
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GitHub: <https://github.com/vandijklab/cell2sentence-ft>
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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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For more details, we refer to the paper linked above.
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This model was trained on the immune tissue dataset from [Domínguez et al.](https://www.science.org/doi/10.1126/science.abl5197) using 8 A100 40GB GPUs
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on the following tasks:
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1. conditional cell generation
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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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# Overview
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This is the the Pythia-160m model developed by EleutherAI fine-tuned using Cell2Sentence on *full* scRNA-seq cells.
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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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For more details, we refer to the paper linked below.
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This model was trained on the immune tissue dataset from [Domínguez et al.](https://www.science.org/doi/10.1126/science.abl5197)
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using 8 A100 40GB GPUs for approximately 20 hours on the following tasks:
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1. conditional cell generation
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2. unconditional cell generation
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3. cell type prediction
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## Cell2Sentence Links:
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GitHub: <https://github.com/vandijklab/cell2sentence-ft>
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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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# 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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