/CS329D

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CS329D

Course Project: Aligning single-cell RNA sequencing data across experiments

MixMatch and DANN

To reproduce the results run

python train_scnym --dataset {dataset} --config {config} --basedir {path to  save models}

The dataset in the command above can be rat for the Rat dataset and hb for the hPMBC dataset.

The config in the above command controls the models as described below:

  1. no_ssl: Source Only
  2. only_dan: DANN
  3. no_dan: MixMatch
  4. no_new_identity: MixMatch+DANN

The plots can be generated using the scnym_atlas_transfer.ipynb notebook.

Self-supervised learning

To reproduce results run

python coarse_trainer.py
python nocoarse_trainer.py

To produce plots run the following Jupyter notebook

Notebooks/scnym_atlas_transfer-hpbmc-run.ipynb

CycleGAN

to reproduce results, run

python bioTrain.py --gpu_ids=[*gpu -ids here*]

Then go through scnym_atlas_transfer_cycleGAN.ipynb and run cells