1.split_data

1. Split Data

In this module, we split the training data into training and testing datasets.

Data is split into subsets in split_data.ipynb. The testing dataset is determined by randomly sampling 15% (stratified by phenotypic class) of the single-cell dataset. The training dataset is the subset remaining after the testing samples are removed. We store sample indexes associated with training and testing subsets in indexes/, and we later use these sample indexes to load subsets from labeled data in 0.download_data/data/.

Step 1: Split Data

Use the commands below to create indexes for training and testing data subsets:

# Make sure you are located in 1.split_data
cd 1.split_data

# Activate phenotypic_profiling conda environment
conda activate phenotypic_profiling

# Split data
bash split_data.sh