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README.md
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---
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license: mit
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language:
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- en
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tags:
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- biology
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- single-cell
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- scFM
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- Drosophila
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- foundation-model
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- cell-type-annotation
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---
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<div align="start">
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</div>
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**Lemur** is a single-cell foundation model developed specifically for *Drosophila melanogaster*. It achieves fine-tuning-free cell-type annotation using two key innovations:
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- **Comprehensive Pre-training:** Trained on an integrated whole-organism atlas with a unified cell-type annotation schema.
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- **Hierarchical Decoding:** Employs a transformer-based hierarchical cell-type decoder to generate consistent predictions at multiple levels of granularity.
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### Highlights
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- **Fine-Tuning-Free Annotation:** No extra training required on new datasets.
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- **Robust Across Conditions:** Consistent performance across various tissue types, experimental conditions, and sequencing platforms.
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- **Zero-Shot Batch-Effect Correction:** Automatically corrects batch effects without further adjustments.
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- **Broad Applications:** Tailored for the fly research community with potential implications for aging and neurodegenerative disease studies in humans.
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### Status & Availability
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---
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license: mit
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language:
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+
- en
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tags:
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- biology
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- single-cell
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- scFM
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- Drosophila
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- foundation-model
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- cell-type-annotation
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---
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<div align="start">
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</div>
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**Lemur** is a single-cell foundation model developed specifically for *Drosophila melanogaster*. It achieves fine-tuning-free cell-type annotation using two key innovations:
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- **Comprehensive Pre-training:** Trained on an integrated whole-organism atlas with a unified cell-type annotation schema.
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- **Hierarchical Decoding:** Employs a transformer-based hierarchical cell-type decoder to generate consistent predictions at multiple levels of granularity.
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### Highlights β‘οΈ
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- **Fine-Tuning-Free Annotation:** No extra training required on new datasets.
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- **Robust Across Conditions:** Consistent performance across various tissue types, experimental conditions, and sequencing platforms.
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- **Zero-Shot Batch-Effect Correction:** Automatically corrects batch effects without further adjustments.
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- **Broad Applications:** Tailored for the fly research community with potential implications for aging and neurodegenerative disease studies in humans.
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### Status & Availability π
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- **Model Weights:** Available now on the Hugging Face Hub ππ»ββοΈ.
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- **Code:** Soon to be released. Stay tuned! π₯π
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### Publication & Citation ππ
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We're excited to share our manuscript, *Lemur: A Single-Cell Foundation Model with Fine-Tuning-Free Hierarchical Cell-Type Generation for* *Drosophila melanogaster*, which is now available as a preprint on [bioRxiv: 10.1101/123456](https://www.biorxiv.org/content/10.1101/123456)! πβ¨
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If you find our work helpful, please consider citing our preprint as follows:
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```bibtex
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@article{your_citation_key,
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title={Lemur: A Single-Cell Foundation Model with Fine-Tuning-Free Hierarchical Cell-Type Generation for *Drosophila melanogaster*},
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author={Doe, John and Smith, Jane and Collaborators},
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journal={bioRxiv},
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year={2025},
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doi={10.1101/123456}
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}
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```
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