| """Create GenomeQA mcq_carbon by replacing species classification questions.""" |
|
|
| import argparse |
| import json |
| import random |
| from collections import defaultdict |
| from pathlib import Path |
|
|
| from datasets import Dataset, concatenate_datasets, load_dataset |
| from huggingface_hub import CommitOperationAdd, HfApi, hf_hub_download |
|
|
|
|
| DATASET_ID = "HuggingFaceBio/genomeqa" |
| SEED = 42 |
| PARQUET_PATH = "mcq_carbon/train-00000-of-00001.parquet" |
| QUOTAS = {"basic_class": 300, "reverse_search": 100, "odd_one_out": 100} |
| LABEL_KEYS = {"basic_class": "true", "reverse_search": "target", "odd_one_out": "minority"} |
|
|
|
|
| def main() -> None: |
| parser = argparse.ArgumentParser() |
| parser.add_argument("--source-revision", required=True) |
| parser.add_argument("--output-dataset", default=DATASET_ID) |
| parser.add_argument("--output-dir", type=Path, default=Path.cwd()) |
| parser.add_argument("--publish", action="store_true") |
| args = parser.parse_args() |
|
|
| mcq = load_dataset(DATASET_ID, "mcq", split="train", revision=args.source_revision) |
| eukaryote = load_dataset(DATASET_ID, "eukaryote_cls", split="train", revision=args.source_revision) |
| if mcq.features != eukaryote.features: |
| raise ValueError("The source configurations must have matching features") |
|
|
| strata = defaultdict(lambda: defaultdict(list)) |
| for index, metadata_text in enumerate(eukaryote["metadata"]): |
| metadata = json.loads(metadata_text) |
| dimension = metadata["dim"] |
| strata[dimension][metadata[LABEL_KEYS[dimension]]].append(index) |
|
|
| rng = random.Random(SEED) |
| selected = [] |
| for dimension, quota in QUOTAS.items(): |
| groups = strata[dimension] |
| if sum(len(indices) for indices in groups.values()) != 2 * quota: |
| raise ValueError(f"Expected {2 * quota} {dimension} source rows") |
| take = {label: len(indices) // 2 for label, indices in groups.items()} |
| odd_labels = sorted(label for label, indices in groups.items() if len(indices) % 2) |
| rng.shuffle(odd_labels) |
| for label in odd_labels[: quota - sum(take.values())]: |
| take[label] += 1 |
| for label in sorted(groups): |
| selected.extend(rng.sample(groups[label], take[label])) |
| rng.shuffle(selected) |
| replacement = eukaryote.select(selected) |
|
|
| species_positions = [index for index, subtask in enumerate(mcq["subtask"]) if subtask == "3_species_cls"] |
| if len(species_positions) != 500 or species_positions != list(range(species_positions[0], species_positions[-1] + 1)): |
| raise ValueError("Expected one contiguous 500-row 3_species_cls block") |
| start = species_positions[0] |
| combined = concatenate_datasets([mcq.select(range(start)), replacement, mcq.select(range(start + 500, len(mcq)))]) |
|
|
| parquet_path = args.output_dir / PARQUET_PATH |
| parquet_path.parent.mkdir(parents=True, exist_ok=True) |
| combined.to_parquet(parquet_path) |
| materialized = Dataset.from_parquet(str(parquet_path)) |
|
|
| api = HfApi() |
| head = api.repo_info(args.output_dataset, repo_type="dataset").sha |
| card = Path(hf_hub_download(args.output_dataset, "README.md", repo_type="dataset", revision=head)).read_text() |
| info = f"""- config_name: mcq_carbon |
| features: |
| - name: id |
| dtype: int64 |
| - name: subtask |
| dtype: string |
| - name: question |
| dtype: string |
| - name: options |
| list: string |
| - name: answer_index |
| dtype: int64 |
| - name: answer_text |
| dtype: string |
| - name: metadata |
| dtype: string |
| splits: |
| - name: train |
| num_bytes: {materialized.info.splits['train'].num_bytes} |
| num_examples: {len(materialized)} |
| download_size: {parquet_path.stat().st_size} |
| dataset_size: {materialized.info.dataset_size} |
| """ |
| marker = "- config_name: eukaryote_cls\n features:" |
| existing = "- config_name: mcq_carbon\n features:" |
| if existing in card: |
| start = card.index(existing) |
| end = card.index(marker, start) |
| card = card[:start] + info + card[end:] |
| commit_message = "Correct mcq_carbon size metadata" |
| else: |
| card = card.replace(marker, info + marker, 1) |
| commit_message = "Add stratified mcq_carbon configuration" |
| config = """- config_name: mcq_carbon |
| data_files: |
| - split: train |
| path: mcq_carbon/train-* |
| """ |
| card = card.replace("- config_name: eukaryote_cls\n data_files:", config + "- config_name: eukaryote_cls\n data_files:", 1) |
| row = "| `mcq` | 2,600 | Full benchmark in four-option multiple-choice format. |\n" |
| new_row = "| `mcq_carbon` | 2,600 | MCQ benchmark with the 500 `3_species_cls` rows replaced by 500 stratified `eukaryote_cls` rows. |\n" |
| card = card.replace(row, row + new_row, 1) |
| note = f"""The `mcq_carbon` configuration preserves the other `mcq` rows and inserts 500 `eukaryote_cls` questions at the |
| original species-classification position. From source revision `{args.source_revision}`, seed {SEED} selects 300 |
| `basic_class`, 100 `reverse_search`, and 100 `odd_one_out` rows, sampling approximately half of each taxon label |
| within each question type. See [`scripts/create_mcq_carbon.py`](scripts/create_mcq_carbon.py). |
| |
| """ |
| card = card.replace("The `eukaryote_cls` configuration uses the `mcq` feature schema", note + "The `eukaryote_cls` configuration uses the `mcq` feature schema", 1) |
|
|
| if "### mcq_carbon" not in card: |
| card += f""" |
| ### mcq_carbon |
| |
| To rebuild and publish `mcq_carbon` from the pinned source revision, run: |
| |
| ```bash |
| python scripts/create_mcq_carbon.py --source-revision {args.source_revision} --output-dataset {args.output_dataset} --publish |
| ``` |
| |
| The script publishes the Parquet file, this card, and the builder script together. |
| """ |
|
|
| card_path = args.output_dir / "README.md" |
| card_path.write_text(card) |
| print(f"Prepared {len(combined)} rows ({len(replacement)} replacement rows) at {parquet_path}") |
| if args.publish: |
| commit = api.create_commit( |
| repo_id=args.output_dataset, |
| repo_type="dataset", |
| parent_commit=head, |
| commit_message=commit_message, |
| operations=[ |
| CommitOperationAdd(path_in_repo=PARQUET_PATH, path_or_fileobj=parquet_path), |
| CommitOperationAdd(path_in_repo="README.md", path_or_fileobj=card_path), |
| CommitOperationAdd(path_in_repo="scripts/create_mcq_carbon.py", path_or_fileobj=__file__), |
| ], |
| ) |
| print(f"Published {commit.commit_url}") |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
