cellplm 0.1.0.post1

Package of CellPLM: A pretrain-ed cell language model beyond single cells. Paper link: https://www.biorxiv.org/content/10.1101/2023.10.03.560734

CellPLM

This is the official codebase for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.

CellPLM is the first single-Cell Pre-trained Language Model that encodes cell-cell relations and it consistently outperforms existing pre-trained and non-pre-trained models in diverse downstream tasks, with 100x higher inference speed compared to existing pre-trained models.

Installation

We recommend PyPI for quick installation. We recommend using python 3.9 and cuda>=11.7 but they are adjustable.

Quick Installation with PyPI

Make sure gpu version of pytorch (>=1.13.0) has been installed before installing CellPLM.

pip install cellplm

Full Installation (recommended for HPC users and developers)

conda create -n cellplm python=3.9 -y && conda activate cellplm
conda install cudatoolkit=11.7 -c pytorch -c nvidia
pip install -r requirements.txt

The full installation will install the same environment as we used during development. This includes rapids used to accelerate evaluation.

Tutorials

We offer several notebooks for various downstream tasks as introductory tutorials.

We are also working on developing more streamlined protocols for supported tasks and a comprehensive documentation. We aim to release these by the end of the year.

Pretrained CellPLM Model Checkpoints

The checkpoint can be acquired from our dropbox. We might update our checkpoints from time to time.

[10/10/2023] The latest version is 20230926_85M.

Citation

@article{wen2023cellplm,
  title={CellPLM: Pre-training of Cell Language Model Beyond Single Cells},
  author={Wen, Hongzhi and Tang, Wenzhuo and Dai, Xinnan and Ding, Jiayuan and Jin, Wei and Xie, Yuying and Tang, Jiliang},
  journal={bioRxiv},
  pages={2023--10},
  year={2023},
  publisher={Cold Spring Harbor Laboratory}
}