Shaow/BioHarness_Eval

GeneKnowledgeEval

A unified biomedical question-answering benchmark of 19,474 items across 8 datasets and 7 question types, used to evaluate the XCompass^χ (CARA) framework for gene/biomedical knowledge retrieval and reasoning.

The corpus is a curated subset of widely-used public biomedical QA benchmarks, repackaged into a single schema and a unified type-specific evaluator so that retrieval, knowledge-graph, and agent-style systems can be compared head-to-head.

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Composition

Dataset	n	Question types
bioasq	4,719	factoid 1417, yesno 1271, summary 1130, list 901
scihorizon-gene	2,710	mcq 1680, mcq_multi 420, expression 210, list 200, summary 200
geneturing	1,250	factoid 1250
medmcqa	4,183	mcq 4183
medqa_us	1,273	mcq 1273
medqa_taiwan	1,413	mcq 1413
medqa_mainland	3,426	mcq 3426
pubmedqa_pqal_test	500	yesno 500
Total	19,474	mcq 11,975 / factoid 2,667 / yesno 1,771 / summary 1,330 / list 1,101 / mcq_multi 420 / expression 210

Original sources

• BioASQ — yes/no, factoid, list, summary; https://www.bioasq.org/
• PubMedQA (PQA-L) — yes/no on PubMed abstracts; https://pubmedqa.github.io/
• MedMCQA — multi-choice exam questions; https://medmcqa.github.io/
• MedQA-USMLE / Taiwan / Mainland — MCQ from medical licensing exams; https://github.com/jind11/MedQA
• GeneTuring — gene-fact factoid questions (chromosome, alias, location, etc.); https://github.com/ncbi/GeneTuring
• SciHorizon-HGKB — gene/genomics knowledge with mcq / list / summary / expression sub-tasks; https://github.com/cocacola-lab/SciHorizon-HGKB

All items have been re-scoped, re-typed, and re-packaged into the schema below; original metadata (PubMed PMIDs, MeSH terms, GO terms, SciHorizon batch IDs, etc.) is preserved under each item's metadata field.

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Schema

Each row is one JSON object per line:

{
  "id":            "bioasq_55046d5ff8aee20f27000007",
  "dataset":       "bioasq",
  "question":      "List signaling molecules (ligands) that interact with the receptor EGFR?",
  "question_type": "list",
  "options":       null,
  "context":       ["the epidermal growth factor receptor (EGFR) ligands ...", "..."],
  "answer":        "[[\"epidermal growth factor\"], [\"betacellulin\"], ...]",
  "answer_type":   "list",
  "metadata":      { "documents": [...], "concepts": [...], "ideal_answer": [...], ... }
}

Field	Type	Notes
id	string	Stable, dataset-prefixed unique key
dataset	string	One of the 8 dataset names
question	string	The natural-language question
question_type	string	One of: yesno, mcq, mcq_multi, factoid, list, summary, expression
options	object|null	{"A": "...", "B": "..."} for mcq/mcq_multi, else null
context	list[str]|null	Optional gold/grounding passages (BioASQ provides them; SciHorizon does not)
answer	string	Reference answer (format depends on question_type, see Eval)
answer_type	string|null	Free-form annotation of the answer shape
metadata	object	Original-source-specific extras (PMIDs, MeSH IDs, batch IDs, ideal answers, etc.)

Per-question-type expected answer formats

question_type	answer format	Example
yesno	"yes" / "no" / "maybe" (lowercase)	"yes"
mcq	Single capital letter	"A"
mcq_multi	Comma-separated letters	"A, C"
factoid	Short phrase	"Type 1 deiodinase"
list	JSON array of arrays (synonym groups)	[["EGF"], ["betacellulin"], ...] or comma-separated string
summary	Free text 1–3 sentences	"FGF21 is primarily produced..."
expression	JSON object with tissue list + category	{"tissue_list": ["liver", "kidney"], "category": "Biased expression"}

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Evaluation

Recommended (continuous, comparable across systems)

For new systems, report the per-type continuous metric mean. This is the standard practice across NQ, TriviaQA, HotpotQA, BioASQ, and the SQuAD family.

Type	Primary metric (continuous)	Optional secondary
yesno	Accuracy (lowercased exact match)	—
mcq	Accuracy (single-letter match)	—
mcq_multi	Mean macro-F1 (set match)	Subset accuracy (exact set)
factoid	Mean ROUGE-1 F1	Exact match (lenient normalisation)
list	Mean set-F1 (synonym-aware)	MAP, Recall@∞
summary	Mean ROUGE-1 / ROUGE-2 / ROUGE-L F1	—
expression	Mean F1 on tissue_list set	—

Aggregation: report per-type mean of the primary metric, plus an optional macro-mean across types weighting each type equally.

from datasets import load_dataset
from eval.evaluator import MetricsEvaluator

evaluator = MetricsEvaluator()
ds = load_dataset("Shaow/GeneKnowledgeEval", "scihorizon-gene", split="train")

cont_scores = []
for item in ds:
    pred = my_model.generate(item["question"], item["question_type"], item["options"])
    result = evaluator.evaluate(
        predicted=pred,
        ground_truth=item["answer"],
        question_type=item["question_type"],
        options=item["options"],
    )
    cont_scores.append(result.score)            # raw continuous metric
print(f"Mean: {sum(cont_scores)/len(cont_scores):.3f}")

Paper convention (binarised "correct" — XCompass^χ headline only)

The CARA (XCompass^χ) paper reports a single overall accuracy by binarising every per-item score against type-specific thresholds, so all question types reduce to one 0/1 signal that can be summed across the 19 K-item suite. Thresholds:

Type	Score	Threshold (≥ → correct)
yesno, mcq	exact match	binary by definition
mcq_multi	macro-F1	0.50
factoid	ROUGE-1 F1	0.30
list	set-F1	0.30
summary	ROUGE-L F1	0.20
expression	set-F1	0.30

MetricsEvaluator.evaluate(...) returns both fields:

result.score      # continuous (recommended for new systems)
result.correct    # paper-specific binarisation (for XCompass^χ table reproduction)

This binarisation is our convention, not a dataset-level definition. Use it only to compare against published XCompass^χ numbers (76.6 % overall on this 19 K suite); for any other purpose, prefer the continuous metrics above.

Does the binarisation change conclusions?

We checked: across all systems we evaluated (CARA family + 8 retrieval/agent baselines), the top-3 ranking is identical under binary and continuous evaluation. The middle of the table sees ±1 position swaps (e.g., dense ↔ dual-dense, biorag ↔ no-context), but no method's headline conclusion changes. The full per-method binary-vs-continuous table is shipped in eval/overall_continuous.csv.

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Intended use & comparison numbers

This benchmark was used to evaluate the XCompass^χ family in the CARA paper. Headline numbers on this 19 K-item suite (XCompass^χ = v14-cascade-dual-rerank-grounded):

Method	Binary acc (paper)	Continuous mean
No-context LLM (Qwen3.5-35B)	69.30 %	62.51 %
Dense RAG	70.30 %	63.87 %
BioRAG	69.20 %	63.00 %
XCompass^χ	76.68 %	69.20 %
XCompass^χ (forced-agent variant)	76.77 %	69.34 %
XCompass^χ_{+D} (with scRNA atlas grounding, see disco/ in XCompass_Figure)	76.7 % overall, +5.5 pp on expression subset	(subset-only, see disco/data/per_type_lift.csv)

Per-dataset XCompass^χ binary accuracy:

Dataset	acc
pubmedqa_pqal_test	77.0 %
bioasq	74.6 %
geneturing	39.2 %
scihorizon-gene	59.9 %
medmcqa	74.0 %
medqa_us	84.2 %
medqa_taiwan	89.4 %
medqa_mainland	89.6 %

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Loading

from datasets import load_dataset

# Load one configuration:
bioasq = load_dataset("Shaow/GeneKnowledgeEval", "bioasq")

# All eight configs:
configs = ["bioasq", "geneturing", "medmcqa",
           "medqa_us", "medqa_taiwan", "medqa_mainland",
           "pubmedqa_pqal_test", "scihorizon-gene"]
all_items = [item for c in configs
             for item in load_dataset("Shaow/GeneKnowledgeEval", c, split="train")]

If you prefer raw JSONL:

huggingface-cli download Shaow/GeneKnowledgeEval --repo-type dataset --local-dir GeneKnowledgeEval

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Citation

If you use this benchmark, please cite the originating sources (BioASQ, PubMedQA, MedMCQA, MedQA, GeneTuring, SciHorizon-HGKB) and the CARA paper:

@article{xcompass2026,
  title  = {XCompass^χ: Context Assembly with Reasoning Allocation for Biomedical QA},
  author = {Xiao, Meng and ...},
  year   = {2026},
  note   = {Manuscript in preparation}
}

License

CC-BY-4.0. Original datasets retain their respective licences; only the unified packaging and evaluation code in this repository is released under CC-BY-4.0.

Contact

Issues + PRs welcome at https://huggingface.co/datasets/Shaow/GeneKnowledgeEval/discussions.