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Model: vandijklab/C2S-Pythia-410m-cell-type-conditioned-cell-generation Source: Original Platform
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README.md
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---
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license: cc-by-4.0
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language:
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- en
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base_model: EleutherAI/pythia-410m
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library_name: transformers
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tags:
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- biology
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- scRNAseq
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---
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# Overview
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This is the C2S-Pythia-410m-cell-type-conditioned-cell-generation model, built on the Pythia-410m architecture developed
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by EleutherAI, fine-tuned using Cell2Sentence (C2S) on a comprehensive collection of single-cell RNA sequencing
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(scRNA-seq) datasets from CellxGene and the Human Cell Atlas. Cell2Sentence is a pioneering technique that adapts
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large language models (LLMs) to single-cell biology by converting scRNA-seq data into "cell sentences" — ordered
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sequences of gene names based on expression levels. This model is specifically trained for cell type-conditioned
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single-cell generation, enabling the generation of realistic single-cell profiles conditioned on specified cell
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types.
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# Training Data
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This model was trained on over 57 million human and mouse cells gathered from over 800 single-cell RNA sequencing
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datasets from CellxGene and the Human Cell Atlas. This dataset covers a broad range of cell types and conditions
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from multiple tissues in both human and mouse.
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This model was trained with the top 200 genes per cell sentence.
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# Tasks
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This model is designed for:
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- Cell type-conditioned single-cell generation: Generating single-cell profiles conditioned on specific cell types, allowing for the creation of synthetic cells that reflect the gene expression patterns of targeted cell types.
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# Cell2Sentence Links
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- GitHub: https://github.com/vandijklab/cell2sentence (Note: Codebase has Apache 2.0 license, weights shared on HuggingFace are CC-by-4.0)
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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/pdf/2304.01373
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- Hugging Face: https://huggingface.co/EleutherAI/pythia-410m
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