diff --git a/Makefile b/Makefile index b3c6b13..e73b512 100644 --- a/Makefile +++ b/Makefile @@ -74,9 +74,9 @@ data_pretrain: requirements $(PYTHON_INTERPRETER) scripts/process_external.py ## Process CV data for cross-validation pretrain (external/all_amine_split_for_LiON -> processed/cv) -.PHONY: data_cv -data_cv: requirements - $(PYTHON_INTERPRETER) scripts/process_data_cv.py +.PHONY: data_pretrain_cv +data_pretrain_cv: requirements + $(PYTHON_INTERPRETER) scripts/process_external_cv.py # MPNN 支持：使用 USE_MPNN=1 启用 MPNN encoder # 例如：make pretrain USE_MPNN=1 @@ -106,8 +106,8 @@ pretrain_cv: requirements $(PYTHON_INTERPRETER) -m lnp_ml.modeling.pretrain_cv main $(MPNN_FLAG) $(DEVICE_FLAG) ## Evaluate CV pretrain models on test sets (auto-detects MPNN from checkpoint) -.PHONY: test_cv -test_cv: requirements +.PHONY: test_pretrain_cv +test_pretrain_cv: requirements $(PYTHON_INTERPRETER) -m lnp_ml.modeling.pretrain_cv test $(DEVICE_FLAG) ## Train model (multi-task, from scratch) diff --git a/data/processed/cv/feature_columns.txt b/data/processed/pretrain_cv/feature_columns.txt similarity index 100% rename from data/processed/cv/feature_columns.txt rename to data/processed/pretrain_cv/feature_columns.txt diff --git a/data/processed/cv/fold_0/test.parquet b/data/processed/pretrain_cv/fold_0/test.parquet similarity index 100% rename from data/processed/cv/fold_0/test.parquet rename to data/processed/pretrain_cv/fold_0/test.parquet diff --git a/data/processed/cv/fold_0/train.parquet b/data/processed/pretrain_cv/fold_0/train.parquet similarity index 100% rename from data/processed/cv/fold_0/train.parquet rename to data/processed/pretrain_cv/fold_0/train.parquet diff --git a/data/processed/cv/fold_0/valid.parquet b/data/processed/pretrain_cv/fold_0/valid.parquet similarity index 100% rename from data/processed/cv/fold_0/valid.parquet rename to data/processed/pretrain_cv/fold_0/valid.parquet diff --git a/data/processed/cv/fold_1/test.parquet b/data/processed/pretrain_cv/fold_1/test.parquet similarity index 100% rename from data/processed/cv/fold_1/test.parquet rename to data/processed/pretrain_cv/fold_1/test.parquet diff --git a/data/processed/cv/fold_1/train.parquet b/data/processed/pretrain_cv/fold_1/train.parquet similarity index 100% rename from data/processed/cv/fold_1/train.parquet rename to data/processed/pretrain_cv/fold_1/train.parquet diff --git a/data/processed/cv/fold_1/valid.parquet b/data/processed/pretrain_cv/fold_1/valid.parquet similarity index 100% rename from data/processed/cv/fold_1/valid.parquet rename to data/processed/pretrain_cv/fold_1/valid.parquet diff --git a/data/processed/cv/fold_2/test.parquet b/data/processed/pretrain_cv/fold_2/test.parquet similarity index 100% rename from data/processed/cv/fold_2/test.parquet rename to data/processed/pretrain_cv/fold_2/test.parquet diff --git a/data/processed/cv/fold_2/train.parquet b/data/processed/pretrain_cv/fold_2/train.parquet similarity index 100% rename from data/processed/cv/fold_2/train.parquet rename to data/processed/pretrain_cv/fold_2/train.parquet diff --git a/data/processed/cv/fold_2/valid.parquet b/data/processed/pretrain_cv/fold_2/valid.parquet similarity index 100% rename from data/processed/cv/fold_2/valid.parquet rename to data/processed/pretrain_cv/fold_2/valid.parquet diff --git a/data/processed/cv/fold_3/test.parquet b/data/processed/pretrain_cv/fold_3/test.parquet similarity index 100% rename from data/processed/cv/fold_3/test.parquet rename to data/processed/pretrain_cv/fold_3/test.parquet diff --git a/data/processed/cv/fold_3/train.parquet b/data/processed/pretrain_cv/fold_3/train.parquet similarity index 100% rename from data/processed/cv/fold_3/train.parquet rename to data/processed/pretrain_cv/fold_3/train.parquet diff --git a/data/processed/cv/fold_3/valid.parquet b/data/processed/pretrain_cv/fold_3/valid.parquet similarity index 100% rename from data/processed/cv/fold_3/valid.parquet rename to data/processed/pretrain_cv/fold_3/valid.parquet diff --git a/data/processed/cv/fold_4/test.parquet b/data/processed/pretrain_cv/fold_4/test.parquet similarity index 100% rename from data/processed/cv/fold_4/test.parquet rename to data/processed/pretrain_cv/fold_4/test.parquet diff --git a/data/processed/cv/fold_4/train.parquet b/data/processed/pretrain_cv/fold_4/train.parquet similarity index 100% rename from data/processed/cv/fold_4/train.parquet rename to data/processed/pretrain_cv/fold_4/train.parquet diff --git a/data/processed/cv/fold_4/valid.parquet b/data/processed/pretrain_cv/fold_4/valid.parquet similarity index 100% rename from data/processed/cv/fold_4/valid.parquet rename to data/processed/pretrain_cv/fold_4/valid.parquet diff --git a/lnp_ml/modeling/pretrain_cv.py b/lnp_ml/modeling/pretrain_cv.py index 33bd9b8..75188f9 100644 --- a/lnp_ml/modeling/pretrain_cv.py +++ b/lnp_ml/modeling/pretrain_cv.py @@ -271,7 +271,7 @@ def create_model( @app.command() def main( - 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