Add training scripts for all-future and next-step supervision with DeepHealth
- Implement `train_all_future.py` for training with query-conditioned all-future supervision. - Implement `train_next_step.py` for training with next-token/next-time-point supervision. - Introduce `train_util.py` for shared utility functions including logging, dataset splitting, and model checkpointing. - Enhance argument parsing for both training scripts to accommodate new parameters. - Update loss functions and model configurations to support the new training paradigms.
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@@ -28,6 +28,7 @@ from torch.utils.data import DataLoader, Dataset
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from tqdm.auto import tqdm
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from dataset import HealthDataset
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from eval_data import load_sequence_eval_dataset
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from models import DeepHealth
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from readouts import build_readout
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from targets import CHECKUP_IDX, NO_EVENT_IDX, PAD_IDX
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@@ -1391,11 +1392,14 @@ def main() -> None:
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labels_meta = pd.read_csv(str(labels_meta_path))
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print("Loading dataset...")
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dataset = HealthDataset(
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dataset = load_sequence_eval_dataset(
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model_target_mode=model_target_mode,
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data_prefix=data_prefix,
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labels_file=labels_file,
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no_event_interval_years=float(no_event_interval_years),
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include_no_event_in_uts_target=bool(include_no_event_in_uts_target),
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min_history_events=int(cfg.get("all_future_min_history_events", 1)),
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min_future_events=int(cfg.get("all_future_min_future_events", 1)),
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extra_info_types=parse_int_list(cfg.get("extra_info_types", None)),
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)
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validate_dataset_metadata(dataset, cfg)
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