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scCDX: enhancing cancer driver gene identification and model interpretability with single-cell RNA sequencing data and extreme gradient boosting

overview

Installation

conda create -n $ENV_NAME python=3.11
conda activate $ENV_NAME
python -m venv $VENV_PATH
$VENV_PATH/bin/pip install -U pip setuptools
$VENV_PATH/bin/pip install poetry
$VENV_PATH/bin/poetry install

Experiments

Data preprocessing

  • Protein-protein interaction network & scRNA-seq Following command downloads scRNA-seq files under the DISCOtmp/.
python -m src.preprocessing
  • Topological Features Preprocessed topological features file is in the data/feature/TOPO.pkl.
python -m src.deepwalk --num-workers $NUM_WORKERS

Train & Test

Hyperparameter tuning log files will be located under the logs/. Test result files will be located under the test/.

python -W ignore -m src.crossvalid --mode train --model xgb --omics MF+METH+GE+SYS+TOPO+scRaw_all+nonzero_mean
python -W ignore -m src.crossvalid --mode independent --model xgb --omics MF+METH+GE+SYS+TOPO+scRaw_all+nonzero_mean

Baselines

For GNN-based state-of-the-art methods, run the commands in here. You can train and test mlp, tabnet, rf, svm by the following commands:

python -W ignore -m src.crossvalid --mode train --model $MODEL --omics MF+METH+GE+SYS+TOPO+scRaw_all+nonzero_mean
python -W ignore -m src.crossvalid --mode independent --model $MODEL --omics MF+METH+GE+SYS+TOPO+scRaw_all+nonzero_mean

To run TabNet model, you should install different pacakges

conda env create -n $ENV_NAME -f tabnet_env.yml
conda activate $ENV_NAME

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