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made non-uspto train_size=1
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@dswigh
dswigh committed Feb 4, 2024
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4 changes: 2 additions & 2 deletions Makefile
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Expand Up @@ -310,13 +310,13 @@ clean_orderly_forward:
python -m orderly.clean --output_path="data/orderly/orderly_benchmarks/orderly_forward.parquet" --ord_extraction_path="data/orderly/uspto/extracted_ords" --molecules_to_remove_path="data/orderly/uspto/all_molecule_names.csv" --min_frequency_of_occurrence=0 --map_rare_molecules_to_other=False --num_product=2 --num_reactant=3 --num_solv=3 --num_agent=3 --num_cat=0 --num_reag=0 --consistent_yield=False --scramble=True --train_size=0.9 --remove_reactions_with_no_reactants=True --remove_reactions_with_no_products=True --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=False

clean_orderly_forward_non_uspto:
python -m orderly.clean --output_path="data/orderly/orderly_benchmarks/orderly_forward_non_uspto.parquet" --ord_extraction_path="data/orderly/non_uspto/extracted_ords" --molecules_to_remove_path="data/orderly/non_uspto/all_molecule_names.csv" --min_frequency_of_occurrence=0 --map_rare_molecules_to_other=False --num_product=2 --num_reactant=3 --num_solv=3 --num_agent=3 --num_cat=0 --num_reag=0 --consistent_yield=False --scramble=True --train_size=0.9 --remove_reactions_with_no_reactants=True --remove_reactions_with_no_products=True --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=False
python -m orderly.clean --output_path="data/orderly/orderly_benchmarks/orderly_forward_non_uspto.parquet" --ord_extraction_path="data/orderly/non_uspto/extracted_ords" --molecules_to_remove_path="data/orderly/non_uspto/all_molecule_names.csv" --min_frequency_of_occurrence=0 --map_rare_molecules_to_other=False --num_product=2 --num_reactant=3 --num_solv=3 --num_agent=3 --num_cat=0 --num_reag=0 --consistent_yield=False --scramble=True --train_size=1 --remove_reactions_with_no_reactants=True --remove_reactions_with_no_products=True --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=False

clean_orderly_retro:
python -m orderly.clean --output_path="data/orderly/orderly_benchmarks/orderly_retro.parquet" --ord_extraction_path="data/orderly/uspto/extracted_ords" --molecules_to_remove_path="data/orderly/uspto/all_molecule_names.csv" --min_frequency_of_occurrence=0 --map_rare_molecules_to_other=False --num_product=1 --num_reactant=2 --num_solv=-1 --num_agent=-1 --num_cat=0 --num_reag=0 --consistent_yield=False --scramble=True --train_size=0.9 --remove_reactions_with_no_reactants=True --remove_reactions_with_no_products=True --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=False

clean_orderly_retro_non_uspto:
python -m orderly.clean --output_path="data/orderly/orderly_benchmarks/orderly_retro_non_uspto.parquet" --ord_extraction_path="data/orderly/non_uspto/extracted_ords" --molecules_to_remove_path="data/orderly/non_uspto/all_molecule_names.csv" --min_frequency_of_occurrence=0 --map_rare_molecules_to_other=False --num_product=1 --num_reactant=2 --num_solv=-1 --num_agent=-1 --num_cat=0 --num_reag=0 --consistent_yield=False --scramble=True --train_size=0.9 --remove_reactions_with_no_reactants=True --remove_reactions_with_no_products=True --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=False
python -m orderly.clean --output_path="data/orderly/orderly_benchmarks/orderly_retro_non_uspto.parquet" --ord_extraction_path="data/orderly/non_uspto/extracted_ords" --molecules_to_remove_path="data/orderly/non_uspto/all_molecule_names.csv" --min_frequency_of_occurrence=0 --map_rare_molecules_to_other=False --num_product=1 --num_reactant=2 --num_solv=-1 --num_agent=-1 --num_cat=0 --num_reag=0 --consistent_yield=False --scramble=True --train_size=1 --remove_reactions_with_no_reactants=True --remove_reactions_with_no_products=True --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=False

clean_orderly_yield:
python -m orderly.clean --output_path="data/orderly/orderly_benchmarks/orderly_yield.parquet" --ord_extraction_path="data/orderly/uspto/extracted_ords" --molecules_to_remove_path="data/orderly/uspto/all_molecule_names.csv" --min_frequency_of_occurrence=0 --map_rare_molecules_to_other=False --num_product=1 --num_reactant=2 --num_solv=-1 --num_agent=-1 --num_cat=0 --num_reag=0 --consistent_yield=True --scramble=True --train_size=0.9 --remove_reactions_with_no_reactants=True --remove_reactions_with_no_products=True --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=False
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -188,7 +188,7 @@ First extract all non-USPTO data with the extraction script.

```python -m orderly.extract --name_contains_substring="uspto" --trust_labelling=False --output_path="data/orderly/not_uspto" --consider_molecule_names=False --inverse_substring=True```

Next, simply use the same cleaning script as for USPTO (e.g. ORDerly-retro) for your desired task. The data will then be cleaned in the same way. This is a nice way to create test sets with no leakage.
Next, simply use the same cleaning script as for USPTO (e.g. ORDerly-retro) for your desired task. The data will then be cleaned in the same way. This is a nice way to create test sets with no leakage. Remember to set `--train_size=1` if you don't want the dataset to be split in two.

## Issues?
Submit an [issue](https://github.com/sustainable-processes/ORDerly/issues) or send an email to dsw46@cam.ac.uk.
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