Open Problems – Single-Cell Perturbations 2nd Place Solution

Kaggle's Open Problems – Single-Cell Perturbations competition.

Setup

cuda version - cu121 python 3.8

pip install -r  requirements.txt

To train the models modify config_train.yaml and run:

python train.py --config config_train.yaml

To run the models modify config_test.yaml and run:

python predict.py --config config_test.yaml

Make sure you have a file names sample_submission.csv which is the same as the resulted dataframe but filled with zeros.

Hardware

1x Nvidia RTX 3080 mobile Windows 11 11th Gen Intel(R) Core(TM) i7-11800H

Sources

1. Single Cell Perturbations Kaggle 2nd place solution
2. Lion PyTorch by lucidrains
3. Understanding the Competition - Open Problems
4. OP2 EDA Baseline by alexandervc