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Makefile
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add-3d-coords:
poetry run python scripts/generate-3d-coords.py \
--input-path "ccs-prediction/combined_metlin_ccsbase_train_test_split.parquet" \
> add-3d-coords.out 2>&1
train-metlin-test-metlin:
poetry run python scripts/train-test.py \
--prefix "train-metlin-test-metlin" \
--train-input-file "ccs-prediction/metlin_train_3d.parquet" \
--test-input-file "ccs-prediction/metlin_test_3d.parquet" \
--coordinates-column-name "coordinates" \
--coordinates-present \
--smiles-column-name "smiles" \
--adduct-column-name "adduct" \
--ccs-column-name "ccs" \
--epochs 400 \
--dropout-rate 0.1 \
--train \
> train-metlin-test-metlin.out 2>&1
# train on metlin-train and test on all ccsbase
# so we have to pass the previous model output file and
# the parameter file
train-metlin-test-ccsbase:
poetry run python scripts/train-test.py \
--prefix "train-metlin-test-ccsbase" \
--train-input-file "ccs-prediction/metlin_train_3d.parquet" \
--test-input-file "ccs-prediction/ccsbase_3d.parquet" \
--parameter-path "parameter/parameter-train-metlin-test-metlin.json" \
--model-output-file "model/train-metlin-test-metlin.h5" \
--coordinates-column-name "coordinates" \
--coordinates-present \
--smiles-column-name "smiles" \
--adduct-column-name "adduct" \
--ccs-column-name "ccs" \
--dropout-rate 0.1 \
--epochs 400 \
> train-metlin-test-ccsbase.out 2>&1
train-ccsbase-test-ccsbase:
poetry run python scripts/train-test.py \
--prefix "train-ccsbase-test-ccsbase" \
--train-input-file "ccs-prediction/ccsbase_train_3d.parquet" \
--test-input-file "ccs-prediction/ccsbase_test_3d.parquet" \
--coordinates-column-name "coordinates" \
--coordinates-present \
--smiles-column-name "smiles" \
--adduct-column-name "adduct" \
--ccs-column-name "ccs" \
--dropout-rate 0.1 \
--epochs 400 \
--train \
> train-ccsbase-test-ccsbase.out 2>&1
# train on ccsbase-train and test on all metlin
train-ccsbase-test-metlin:
poetry run python scripts/train-test.py \
--prefix "train-ccsbase-test-metlin" \
--train-input-file "ccs-prediction/ccsbase_train_3d.parquet" \
--test-input-file "ccs-prediction/metlin_3d.parquet" \
--parameter-path "parameter/parameter-train-ccsbase-test-ccsbase.json" \
--model-output-file "model/train-ccsbase-test-ccsbase.h5" \
--coordinates-column-name "coordinates" \
--coordinates-present \
--smiles-column-name "smiles" \
--adduct-column-name "adduct" \
--ccs-column-name "ccs" \
--dropout-rate 0.1 \
--epochs 400 \
> train-ccsbase-test-metlin.out 2>&1
train-combined-test-combined:
poetry run python scripts/train-test.py \
--prefix "train-combined-test-combined" \
--train-input-file "ccs-prediction/metlin_ccsbase_train_3d.parquet" \
--test-input-file "ccs-prediction/metlin_ccsbase_test_3d.parquet" \
--coordinates-column-name "coordinates" \
--smiles-column-name "smiles" \
--adduct-column-name "adduct" \
--ccs-column-name "ccs" \
--epochs 400 \
--dropout-rate 0.1 \
--train \
> train-combined-test-combined.out 2>&1
# grid-search:
# poetry run python scripts/grid-search.py \
# --prefix "grid-search" \
# --train-input-file "ccs-prediction/combined_metlin_ccsbase_train_3d_spilt_0.parquet" \
# --test-input-file "ccs-prediction/combined_metlin_ccsbase_test_3d.parquet" \
# --epochs 300