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Benchmarks

Environment

  • Python 3.8
  • Dependencies:
    • scikit-learn 0.24.1
    • TensorFlow 2.6.0
    • xgboost 1.5.0
  • CPU Install
conda create -n transmed_benchmarks python=3.8
conda activate transmed_benchmarks
pip install -r environment/benchmarks/benchmarks.cpu.requirements.txt

Gated Recurrent Unit (GRU)

python benchmarks/main_gru.py \
    --data_dir 'data/mimic' \
    --infile 'readmission_mimic_lookahead1_numts2.pkl' \
    --task 'readmission' \
    --base_path 'mimic' \
    --num_timesteps 2 \
    --lookahead 1 \
    --features 'dx_pr_rx_demo' \
    --run 9 \
    --results_dir "benchmarks_results/lr_results/mimic/outcome_readmission" \
    --outcome_var "outcome_readmission" \
    --epochs 10

Logistic Regression (LR)

python benchmarks/main_lr.py \
    --data_dir 'data/mimic' \
    --infile 'readmission_mimic_lookahead1_numts2.pkl' \
    --task 'readmission' \
    --base_path 'mimic' \
    --num_timesteps 2 \
    --lookahead 1 \
    --features 'dx_pr_rx_demo' \
    --run 9 \
    --results_dir "benchmarks_results/lr_results/mimic/outcome_readmission" \
    --outcome_var "outcome_readmission"

Multilayer Perceptron (MLP)

python benchmarks/main_mlp.py \
    --data_dir 'data/mimic' \
    --infile 'readmission_mimic_lookahead1_numts2.pkl' \
    --task 'readmission' \
    --base_path 'mimic' \
    --num_timesteps 2 \
    --lookahead 1 \
    --features 'dx_pr_rx_demo' \
    --run 9 \
    --results_dir "benchmarks_results/lr_results/mimic/outcome_readmission" \
    --outcome_var "outcome_readmission" \
    --embedding_method "one_hot" \
    --epochs 10

Random Forest (RF)

python benchmarks/main_rf.py \
    --data_dir 'data/mimic' \
    --infile 'readmission_mimic_lookahead1_numts2.pkl' \
    --task 'readmission' \
    --base_path 'mimic' \
    --num_timesteps 2 \
    --lookahead 1 \
    --features 'dx_pr_rx_demo' \
    --run 9 \
    --results_dir "benchmarks_results/lr_results/mimic/outcome_readmission" \
    --outcome_var "outcome_readmission"

XGBoost (XGB)

python benchmarks/main_xgb.py \
    --data_dir 'data/mimic' \
    --infile 'readmission_mimic_lookahead1_numts2.pkl' \
    --task 'readmission' \
    --base_path 'mimic' \
    --num_timesteps 2 \
    --lookahead 1 \
    --features 'dx_pr_rx_demo' \
    --run 9 \
    --results_dir "benchmarks_results/lr_results/mimic/outcome_readmission" \
    --outcome_var "outcome_readmission"