scCLIP

Multi-modal Single-cell Integration

scCLIP: Multi-modal Single-cell Contrastive Learning Integration Pre-training

scCLIP: Multi-modal Single-cell Contrastive Learning Integration Pre-training

Download data

Download multiome data folder under data/

• dataset:
  • Brain
    • train: AD
    • test: human_brain_3k
  • Fetal
    • train: fetal
    • test:

Install

pip install .
pre-commit install --hook-type pre-push

Run

python train_clip.py --data_dir AD --logit_scale 1

Load Pretrain model

The model should saved under path/lightning_logs/checkpoints/epochxx-stepxx.ckpt

python train_clip.py --data_dir AD --checkpoint model.ckpt

The results will be saved under the same path