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https://github.com/RYDE-WORK/lnp_ml.git
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This commit is contained in:
RYDE-WORK
parent
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commit
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10
Makefile
10
Makefile
@ -74,9 +74,9 @@ data_pretrain: requirements
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$(PYTHON_INTERPRETER) scripts/process_external.py
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## Process CV data for cross-validation pretrain (external/all_amine_split_for_LiON -> processed/cv)
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.PHONY: data_cv
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data_cv: requirements
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$(PYTHON_INTERPRETER) scripts/process_data_cv.py
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.PHONY: data_pretrain_cv
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data_pretrain_cv: requirements
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$(PYTHON_INTERPRETER) scripts/process_external_cv.py
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# MPNN 支持：使用 USE_MPNN=1 启用 MPNN encoder
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# 例如：make pretrain USE_MPNN=1
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@ -106,8 +106,8 @@ pretrain_cv: requirements
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$(PYTHON_INTERPRETER) -m lnp_ml.modeling.pretrain_cv main $(MPNN_FLAG) $(DEVICE_FLAG)
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## Evaluate CV pretrain models on test sets (auto-detects MPNN from checkpoint)
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.PHONY: test_cv
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test_cv: requirements
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.PHONY: test_pretrain_cv
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test_pretrain_cv: requirements
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$(PYTHON_INTERPRETER) -m lnp_ml.modeling.pretrain_cv test $(DEVICE_FLAG)
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## Train model (multi-task, from scratch)
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@ -271,7 +271,7 @@ def create_model(
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@app.command()
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def main(
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data_dir: Path = PROCESSED_DATA_DIR / "cv",
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data_dir: Path = PROCESSED_DATA_DIR / "pretrain_cv",
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output_dir: Path = MODELS_DIR / "pretrain_cv",
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# 模型参数
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d_model: int = 256,
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@ -322,7 +322,7 @@ def main(
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if not fold_dirs:
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logger.error(f"No fold_* directories found in {data_dir}")
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logger.info("Please run 'make data_cv' first to process CV data.")
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logger.info("Please run 'make data_pretrain_cv' first to process CV data.")
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raise typer.Exit(1)
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logger.info(f"Found {len(fold_dirs)} folds: {[d.name for d in fold_dirs]}")
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@ -464,7 +464,7 @@ def main(
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@app.command()
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def test(
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data_dir: Path = PROCESSED_DATA_DIR / "cv",
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data_dir: Path = PROCESSED_DATA_DIR / "pretrain_cv",
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model_dir: Path = MODELS_DIR / "pretrain_cv",
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output_path: Path = MODELS_DIR / "pretrain_cv" / "test_results.json",
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batch_size: int = 64,
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@ -1,310 +1,206 @@
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