Datasets:
File size: 1,853 Bytes
18f68fa | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 | """Create GenomeQA 3_species_cls subsets grouped by target organism."""
import argparse
import json
from pathlib import Path
from datasets import load_dataset
DATASET_ID = "HuggingFaceBio/genomeqa"
SOURCE_REVISION = "d2213306c6cf5b4568a504f87f86ea50b03eeced"
SOURCE_CONFIGS = ("binary", "mcq")
ORGANISMS = ("eukaryote", "prokaryote")
SUBTASK = "3_species_cls"
ORGANISM_KEY_BY_DIMENSION = {
"1_identity": "true",
"basic_class": "true",
"reverse_search": "target",
"odd_one_out": "minority",
}
def get_organism(metadata: str) -> str:
metadata_dict = json.loads(metadata)
dimension = metadata_dict["dim"]
return metadata_dict[ORGANISM_KEY_BY_DIMENSION[dimension]]
def create_subsets(config: str, output_dir: Path) -> None:
dataset = load_dataset(DATASET_ID, config, split="train", revision=SOURCE_REVISION)
species_dataset = dataset.filter(lambda example: example["subtask"] == SUBTASK)
for organism in ORGANISMS:
subset = species_dataset.filter(
lambda example, organism=organism: get_organism(example["metadata"]) == organism
)
if not subset:
raise RuntimeError(f"No {organism} rows found in {config}")
if any(get_organism(metadata) != organism for metadata in subset["metadata"]):
raise RuntimeError(f"Generated {config}_{organism} subset contains another organism")
config_dir = output_dir / f"{config}_{organism}"
config_dir.mkdir(parents=True, exist_ok=True)
subset.to_parquet(config_dir / "train-00000-of-00001.parquet")
def main() -> None:
parser = argparse.ArgumentParser()
parser.add_argument("--output-dir", type=Path, default=Path.cwd())
args = parser.parse_args()
for config in SOURCE_CONFIGS:
create_subsets(config, args.output_dir)
if __name__ == "__main__":
main()
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