Transformers
English
biology
single-cell
scRNA-seq
macrophage
IBD
inflammatory-bowel-disease
perturbation
gene-knockout
scGPT
Instructions to use Pathwit/MacroPert with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use Pathwit/MacroPert with Transformers:
# pip install -U transformers accelerate # Load model directly from transformers import AutoModel model = AutoModel.from_pretrained("Pathwit/MacroPert", device_map="auto") - Notebooks
- Google Colab
- Kaggle
Commit History
-
Fix HF metadata: remove invalid GEO dataset IDs
Ham-KrisUnverified signaturedf4af0e -
Initial release: MacroPert IBD macrophage perturbation model
Ham-KrisUnverified signature- scGPT v2 fine-tuned on IBD macrophage scRNA-seq (GSE134809 + 3 datasets) - Continuous polarization embedding: Pearson r=0.909, IBD AUROC=0.989 - scGPT v1 discrete baseline archived for comparison - In silico KO predictions for 8 IBD target genes (CellOracle + OmniPath)94f83d2