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b/AICare-baselines/dl_tune.py |
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import hydra |
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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, WandbLogger |
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from omegaconf import DictConfig, OmegaConf |
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import wandb |
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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 |
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# import os |
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# os.environ['WANDB_MODE'] = 'offline' |
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# os.environ['WANDB_LOG_LEVEL'] = 'debug' |
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project_name = "aicare" |
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hydra.initialize(config_path="configs", version_base=None) |
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cfg = OmegaConf.to_container(hydra.compose(config_name="config")) |
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dataset_config = { |
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'tjh': {'demo_dim': 2, 'lab_dim': 73}, |
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'cdsl': {'demo_dim': 2, 'lab_dim': 97}, |
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'mimic-iii': {'demo_dim': 2, 'lab_dim': 59}, |
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'mimic-iv': {'demo_dim': 2, 'lab_dim': 59}, |
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} |
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sweep_configuration = { |
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'method': 'grid', |
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'name': 'sweep_dl_mimic', |
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'metric': {'goal': 'minimize', 'name': 'val_loss'}, |
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'parameters': |
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{ |
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'task': {'values': ['outcome']}, |
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'dataset': {'values': ['mimic-iii', 'mimic-iv']}, |
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'model': {'values': ['MLP', 'GRU', 'RNN', 'LSTM', 'TCN', 'Transformer', 'AdaCare', 'Agent', 'GRASP', 'RETAIN', 'StageNet', 'MCGRU']}, |
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'batch_size': {'values': [1024]}, |
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'hidden_dim': {'values': [64, 128]}, |
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'learning_rate': {'values': [1e-2, 1e-3, 1e-4]}, |
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'fold': {'values': [0]}, |
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'seed': {'values': [0]}, |
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} |
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} |
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sweep_id = wandb.sweep(sweep_configuration, project=project_name) |
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def run_experiment(): |
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run = wandb.init(project=project_name, config=cfg) |
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wandb_logger = WandbLogger(project=project_name, log_model=True) # log only the last (best) checkpoint |
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config = wandb.config |
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config.update(dataset_config[config['dataset']], allow_val_change=True) |
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los_config = get_los_info(f'datasets/{config["dataset"]}/processed/fold_{config["fold"]}') |
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main_metric = "mae" if config["task"] == "los" else "auprc" |
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config.update({"los_info": los_config, "main_metric": main_metric}) |
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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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# 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(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(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.as_dict()) |
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trainer = L.Trainer(accelerator="gpu", devices=[1], max_epochs=config["epochs"], logger=wandb_logger, callbacks=[early_stopping_callback, checkpoint_callback], num_sanity_val_steps=0) |
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trainer.fit(pipeline, dm) |
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print("Best Score", checkpoint_callback.best_model_score) |
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if __name__ == "__main__": |
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wandb.agent(sweep_id, function=run_experiment, project=project_name) |