Real PMIDs, Wrong Papers: Harness Design for Biomedical Claim-Verification Agents

Overview & Synopsis

Literature-searching language agents are becoming a standard component of scientific assistants for the life sciences, yet there is little controlled evidence on which parts of their harness matter. We run a controlled ablation on biomedical claim verification (SciFact) with the live PubMed API as the only tool. Holding the backbone and output format fixed, we compare four harnesses: closed-book answering, single-shot retrieval using the claim as the query, a ReAct-style agent that writes its own PubMed queries, and an oracle given the gold abstracts, each with two efficient frontier backbones. Naive single-shot retrieval finds the gold paper for only 6% of claims and turns overconfident errors into abstentions without improving accuracy. Letting the model formulate its own queries triples gold recall and yields the best verdicts (62% accuracy vs. 49-59% for the other realistic harnesses), although these differences are not significant at our sample size and agents use fewer than half of their search budget. With gold abstracts, the same models reach 79-86% accuracy, a significant 17-24 point gap showing that retrieval, not reasoning, is the main bottleneck. Finally, a citation audit shows that closed-book models cite PubMed IDs that almost always exist (327/335) but are almost never relevant: a cross-family LLM judge rates only 3 of 327 existing citations as relevant to the claim, versus 67% for citations produced by the search agent. Existence checks are therefore insufficient safeguards for scientific agents. We release code, prompts, and all cached tool calls at https://github.com/saqlain2204/real-pmids-wrong-papers.