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b/AICare-baselines/train.py |
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import lightning as L |
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from lightning.pytorch.callbacks import EarlyStopping, ModelCheckpoint |
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from lightning.pytorch.loggers import CSVLogger |
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# from configs.experiments_mimic import hparams |
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from configs.exp import hparams |
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from datasets.loader.datamodule import EhrDataModule |
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from datasets.loader.load_los_info import get_los_info |
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from pipelines import DlPipeline, MlPipeline |
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def run_ml_experiment(config): |
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los_config = get_los_info(f'datasets/{config["dataset"]}/processed/fold_{config["fold"]}') |
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config.update({"los_info": los_config}) |
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# data |
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dm = EhrDataModule(f'datasets/{config["dataset"]}/processed/fold_{config["fold"]}', batch_size=config["batch_size"]) |
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# logger |
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checkpoint_filename = f'{config["model"]}-fold{config["fold"]}-seed{config["seed"]}' |
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logger = CSVLogger(save_dir="logs", name=f'train/{config["dataset"]}/{config["task"]}', version=checkpoint_filename) |
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L.seed_everything(config["seed"]) # seed for reproducibility |
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# train/val/test |
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pipeline = MlPipeline(config) |
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trainer = L.Trainer(accelerator="cpu", max_epochs=1, logger=logger, num_sanity_val_steps=0) |
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trainer.fit(pipeline, dm) |
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perf = pipeline.cur_best_performance |
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return perf |
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def run_dl_experiment(config): |
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los_config = get_los_info(f'datasets/{config["dataset"]}/processed/fold_{config["fold"]}') |
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config.update({"los_info": los_config}) |
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# data |
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dm = EhrDataModule(f'datasets/{config["dataset"]}/processed/fold_{config["fold"]}', batch_size=config["batch_size"]) |
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# logger |
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checkpoint_filename = f'{config["model"]}-fold{config["fold"]}-seed{config["seed"]}' |
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if "time_aware" in config and config["time_aware"] == True: |
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checkpoint_filename+="-ta" # time-aware loss applied |
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logger = CSVLogger(save_dir="logs", name=f'train/{config["dataset"]}/{config["task"]}', version=checkpoint_filename) |
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# EarlyStop and checkpoint callback |
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if config["task"] in ["outcome", "multitask"]: |
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early_stopping_callback = EarlyStopping(monitor="auprc", patience=config["patience"], mode="max",) |
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checkpoint_callback = ModelCheckpoint(filename="best", monitor="auprc", mode="max") |
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elif config["task"] == "los": |
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early_stopping_callback = EarlyStopping(monitor="mae", patience=config["patience"], mode="min",) |
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checkpoint_callback = ModelCheckpoint(filename="best", monitor="mae", mode="min") |
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L.seed_everything(config["seed"]) # seed for reproducibility |
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# train/val/test |
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pipeline = DlPipeline(config) |
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trainer = L.Trainer(accelerator="gpu", devices=[1], max_epochs=config["epochs"], logger=logger, callbacks=[early_stopping_callback, checkpoint_callback], num_sanity_val_steps=0) |
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trainer.fit(pipeline, dm) |
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perf = pipeline.cur_best_performance |
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return perf |
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if __name__ == "__main__": |
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best_hparams = hparams # [TO-SPECIFY] |
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for i in range(len(best_hparams)): |
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config = best_hparams[i] |
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run_func = run_ml_experiment if config["model"] in ["RF", "DT", "GBDT", "XGBoost", "CatBoost", "LR", "LightGBM"] else run_dl_experiment |
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seeds = [0] # [0,1,2,3,4] |
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folds = ['nshot'] |
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for fold in folds: |
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config["fold"] = fold |
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for seed in seeds: |
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config["seed"] = seed |
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perf = run_func(config) |
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print(f"{config}, Val Performance: {perf}") |