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

Redpine Science gives models and agents a single access point to a wide range of peer-reviewed literature, queried directly through the Model Context Protocol (MCP) and an API. This report evaluates Redpine Science on two levels: the relevance of the retrieved chunks, and a model's answer when it has access to Redpine Science compared to web search. Both public and expert-validated benchmarks are used. Public benchmarks are a widely accepted way to test model development and are comparable across labs, but risk saturation and memorization. To address this, we complement them with an expert-validated question set. In total, this report presents four evaluations. On ScholarQABench SciFact, the public answer-quality benchmark reported here, an agent with Redpine Science answers 94.4% of claims correctly against 87.6% with no retrieval. On the expert-validated question set, an agent with Redpine Science states 80.1% of the required claims against 70.2% for an agent restricted to web search. On the 668 queries of a public retrieval benchmark whose gold paper Redpine holds, stripped of any model reasoning, Redpine Science places the correct source paper in its top ten results for 83.1% of queries (Recall@10), against 79.3% for the benchmark's creator. A blinded expert relevance panel places Redpine Science's Precision@5 at 75.2% against 39.8% for the PubMed search tool. We release the expert-validated question set and instructions to reproduce every headline result above, at https://github.com/redpine-ai/benchmarks.

Biomedical fact-checking systems must do more than predict whether a claim is supported, contradicted, or unaddressed: they should also produce evidence that is faithful, complete, and useful for verification. We study this evidence-generation setting on CARE-XAI, a unified benchmark spanning five biomedical and health fact-checking sources. We compare base instruction LLMs, PubMed retrieval-augmented LLMs, fine-tuned LLMs, label-only LLMs, and biomedical encoder classifiers under a shared evaluation protocol. Biomedical classifiers remain strongest for verdict-only prediction, while fine-tuned LLMs are the strongest evidence-generating systems. PubMed retrieval is mixed: it helps PubMed-aligned sources such as PubMedQA and SciFact, but can distract models on broader public-health claims. We introduce Bio-GRACE, a gold-reference-normalized diagnostic for measuring whether retrieved evidence recovers the decision benefit of reference evidence. Bio-GRACE shows that retrieval utility is source-dependent, motivates selective retrieval, and exposes why retrieval recall and lexical evidence overlap are insufficient for biomedical fact-checking.

A working citation looks like proof -- but the fact that a link resolves does not mean the cited paper supports the claim. I find that current agentic models rarely fabricate citations (over $99\%$ resolve), yet roughly $15.9\%$ link to the wrong paper. Existing benchmarks miss this failure mode: when a question has a fixed answer key, a model can reproduce the expected source from that key rather than independently verifying that the source supports the claim. I introduce \openbiorq{}, a retrieval-grounded agentic benchmark of $12{,}553$ unsolved biomedical research questions across $12$ domains that treats open questions as a faithfulness-and-abstention probe. To my knowledge, this is the first biomedical benchmark to combine an agentic setting -- where the model must issue multiple tool calls -- with unsolved questions that have no answer key. Openness is verified against real follow-up evidence rather than a model's parametric knowledge. Difficulty is empirical: I anchor it on questions that three open-weight reference models fail to answer, rather than on subjective hardness labels. On this hardest subset, held-out models from the same lineage as the difficulty anchors solve only ~17%, while three independent frontier agents (Gemini-3-Pro, Opus-4.7, GPT-5.5) span a wide 29-60% range. The benchmark is thus hard, non-saturating (the best agent still leaves ~33-40% unsolved), and discriminating across capability tiers. Beyond difficulty, I observe agentic collapse on the hardest questions, where agents stop using their tools. For the most collapse-prone model, blocking tool access entirely barely changes its score -- so tools stop paying off exactly where they are needed most. A frozen per-question checklist raises inter-judge agreement from Spearman 0.35 to 0.82.