BioResearchAgent

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Task D1 · relation extraction

Extract the gene/protein relationship(s) describing how BARD1 relates to BRCA1, with supporting evidence, from the corpus.

Gold evidence

Acceptable answer concepts

  • (BARD1, interacts_with, BRCA1) - obligate binding partner / heterodimerization
  • BRCA1 itself typed as a tumor suppressor protein

Construction note

Structured-extraction counterpart to E1, scored on relation triple correctness rather than free-text answer quality.

How each architecture answered

Baseline 0 · no retrieval

Yuu no Sekai · 438 tokens · 2.9s

(abstained) No evidence passages were retrieved for this question, so no gene/protein relationships describing how BARD1 relates to BRCA1 can be provided.

abstentionverifiedconf 1.00

No evidence passages were retrieved for this question.

run_failed: 0abstention_correct: 0%concept_coverage: 0%

Baseline 1 · retrieve + synthesize

Yuu no Sekai · 2358 tokens · 6.5s
query(ies): Extract the gene/protein relationship(s) describing how BARD1 relates to BRCA1, with supporting evidence, from the corpus.

BARD1 is the obligate binding partner of BRCA1 and plays a critical role in maintaining genome integrity through their heterodimerization. The BRCA1-BARD1 complex is essential for DNA repair, particularly in stimulating long-range DNA end resection during homologous recombination.

factualverifiedconf 0.95

BARD1 is the obligate binding partner of BRCA1.

PMID:42678585Direct support
factualverifiedconf 0.90

The BRCA1-BARD1 complex is essential for DNA repair.

PMID:42678585Direct support
factualverifiedconf 0.90

The BRCA1-BARD1 complex stimulates long-range DNA end resection during homologous recombination.

PMID:42678585Direct support
factualverifiedconf 0.85

The BRCA1-BARD1 complex coordinates accurate DNA repair.

PMID:42693354Direct support
run_failed: 0retrieval_recall_at_k: 100%retrieval_mrr: 100%claim_support_rate: 100%unsupported_claim_rate: 0%citation_precision: 100%source_validity_rate: 100%abstention_correct: 100%concept_coverage: 50%

Agent 1 · planner + retrieve + synthesize

Yuu no Sekai · 211 tokens · 2.3s
Run failed: parse_failure (planner): No JSON object found in planner response: '{"queries": ["BARD1 BRCA1 relationship", "BARD1 BRCA1 interaction", "BARD1 BRCA1 function"]]'