Evaluating and Guarding Citation Faithfulness in Agentic Scientific Synthesis

Abstract

Agentic LLM systems such as OpenScholar and PaperQA2 read the scientific literature and return cited answers, and both they and their benchmarks already check whether those citations hold, with a fixed attribution model or human graders. Neither audits the reliability of that check itself. We show it is not reliable, and that this matters. On identical agent outputs the measured unsupported-citation rate ranges from about 3% to about 18% depending only on the verifier's strictness, and although verifiers agree on which citations are supported, they disagree on which to flag (negative-specific agreement 0.27 to 0.30), so no single flag set is trustworthy and cross-paper comparison is invalid without a named verifier and protocol. We present a gold-anchored evaluation protocol and a deployable guard that make this behavior measurable and bounded. The protocol validates the verifier, measures re-attribution, and calibrates a guarantee against human gold rather than another model's verdict; the verifier is a swappable instrument chosen on cost (recall 0.94 on the supported class, held out), and re-attribution is a commodity step where a deterministic BM25 matches the best open generator. The guard adds a split-conformal layer placing a distribution-free, finite-sample bound on truly unsupported citations that slip past a chosen flagging rule, a guarantee on catch rate rather than conclusion correctness. The bound holds on held-out gold, and we identify and quantify the condition governing its transfer to deployment, calibration-negative difficulty, with a concrete recalibration recipe, left untested by prior conformal-factuality work. Validated across four open 27-35B models and three agentic pipelines on public benchmarks (SciFact, QASA, PubMedQA), with confidence intervals on every headline number, the protocol and guard ship as an open single-GPU kit.