TGRA-P: Task-driven Model Predicts 90-Day Mortality from ICU Clinical Notes on Mechanical Ventilation
This repo hosts pretraining and finetuning scripts for TGRA-P.
torch
argparse
copy
tqdm
matplotlib
numpy
pandas
time
sklearn
inspect
Ranger
We provide a notebook (pretrain-xlnet.ipynb) to pretrain your own Clinical model.
python train.py \
--data_dir DATA_FILE\
--config_path CONFIG\
--model_path MORTALITY/PMV_MODEL_PATH \
--save_meta_finetune_path SAVE_PATH \
--prediction_label Mortality\
--Batch_Size_Meta 4 \
--Learning_Rate_Meta 1e-5 \
--Training_Epoch_Meta 4 \
--Batch_Size_Finetune 64 \
--Learning_Rate_Finetune 2e-5 \
--Training_Epoch_Finetune 30 \
--saving_notes_embed_batch_size 16 \
--skip_meta_finetuned
We use MIMIC-III.
-data
-train.csv
-val.csv
-test.csv