Datasets:
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
License:
File size: 1,975 Bytes
6d1bbc7 | 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 59 60 61 | #!/usr/bin/env python
"""Export GE ML datasets with splits and pair aggregation."""
import argparse
from pathlib import Path
_PROJECT_ROOT = Path(__file__).resolve().parent.parent
def main():
parser = argparse.ArgumentParser(description="Export GE ML datasets")
parser.add_argument("--db-path", type=str, default=None)
parser.add_argument("--output-dir", type=str, default=str(_PROJECT_ROOT / "exports" / "ge"))
parser.add_argument("--seed", type=int, default=42)
args = parser.parse_args()
from negbiodb_depmap.depmap_db import get_connection, refresh_all_ge_pairs
from negbiodb_depmap.export import (
export_ge_negatives,
generate_cold_both_split,
generate_cold_cell_line_split,
generate_cold_gene_split,
generate_degree_balanced_split,
generate_random_split,
)
db_path = Path(args.db_path) if args.db_path else _PROJECT_ROOT / "data" / "negbiodb_depmap.db"
output_dir = Path(args.output_dir)
conn = get_connection(db_path)
try:
# Refresh pair aggregation
print("Refreshing pair aggregation...")
count = refresh_all_ge_pairs(conn)
conn.commit()
print(f" {count:,} gene-cell_line pairs")
# Generate splits
print("\nGenerating splits...")
for name, func in [
("random", generate_random_split),
("cold_gene", generate_cold_gene_split),
("cold_cell_line", generate_cold_cell_line_split),
("cold_both", generate_cold_both_split),
("degree_balanced", generate_degree_balanced_split),
]:
result = func(conn, seed=args.seed)
print(f" {name}: {result['counts']}")
# Export
out_path = output_dir / "negbiodb_ge_pairs.parquet"
n = export_ge_negatives(conn, out_path)
print(f"\nExported {n:,} pairs to {out_path}")
finally:
conn.close()
if __name__ == "__main__":
main()
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