A retrieval-augmented generation (RAG) system deployed over a multi-author institutional corpus can give a different answer to the same question depending on which source it retrieves -- a failure mode the dominant single-gold-answer paradigm cannot diagnose. We argue that source-dependence is a missing axis of NLP evaluation, and that auditing it means shifting the unit of evaluation from answer correctness to the inter-source relationship. We make this concrete in transplant patient education, where institutional sources demonstrably disagree, releasing three artefacts: TransplantQA, a benchmark of real patient questions, each answered by grounding generation in multiple institutional handbooks as candidate sources; HERO-QA, a hierarchical retrieval strategy that grounds and audits each answer; and a structured-output judge that scores inter-source relationships on a validated 5-label taxonomy. At scale, better retrieval reveals far more disagreement than prior estimates suggested -- understating its prevalence, not its intensity. The framework is domain-agnostic and transfers to legal and educational RAG: measuring source-dependence is a responsibility for deployed multi-source NLP generally.
LLM-as-a-judge evaluation is widely used for retrieval-augmented generation (RAG), but reusing the same model family as both generator and judge makes self-leniency difficult to identify. We introduce Eval-Pair Matrix, a controlled meta evaluation protocol for source-grounded RAG. Starting from GaRAGe questions and grounding passages, we induce one hidden answer-causal contradiction per record, generate answers from perturbed passages with GPT, Grok, and Gemini models, and then use the same models as blind judges to evaluate each answer against the original passages. The experiment contains 300 core records, 897 labeled generator outputs, and 2,683 judge verdicts in a crossed 3 x 3 matrix; the primary analysis uses 275 fully validated records. Instead of comparing diagonal and off-diagonal cells across different answers, we estimate same-model effects by pairing judges on the exact same candidate answer. This changes the interpretation: diagonal and off diagonal F1 are similar, and the paired same-model recall effect is near zero (-0.5 pp; 95% cluster bootstrap CI [-2.7, +1.7]). The only robust paired gap is lower matching-judge flagging for answers that avoided the induced claim (-4.3 pp). A targeted human evaluation finds that reviewed apparent false positives are alternate source-error detections, mistakes in labeling whether the induced claim was adopted, or unclear cases; none were adjudicated as genuine false alarms. The lesson is methodological: RAG judge studies should report full matrices, answer-paired effects, behavior strata, and label-task alignment.
Medical question answering is a high-stakes setting where factual errors can have serious consequences. Retrieval-augmented generation (RAG) is widely viewed as a promising solution, and prior work has reported substantial gains for large medical QA models. We revisit this assumption across a broad range of open-weight instruction-tuned models spanning 7B to 72B parameters. Across five models, ten biomedical QA datasets, four retrieval methods, and four retrieval corpora, we find that retrieval yields only small and inconsistent improvements over a no-retrieval baseline, typically within 1-2 points. In contrast, the choice of backbone model has a much larger effect than the choice of retriever or corpus, and expert and layman retrieval sources perform similarly in most settings. These results suggest that the main bottleneck is not retrieval quality alone, but the model's limited ability to use retrieved evidence effectively.
Retrieval-augmented generation (RAG) grounds a language model's answers on retrieved external knowledge and returns each answer with citations that identify its sources. Those citations are the user's audit trail: they let a reader verify a claim without trusting the model. Prior security work on RAG asks whether an attacker can corrupt the answer, leaving the citation channel unexplored. We show that this channel is a new and practical attack surface. We propose CiteShade, the first citation laundering attack to RAG, in which an attacker controlling a single source induces a model to produce an attacker-chosen wrong answer and to attribute it to a trusted source that does not support it, while the evidence for the correct answer remains in context. We formulate the attack as an optimization problem, derive three necessary conditions (retrieval, generation, and citation) and construct sources satisfying them without any instruction. On multi-source multi-hop question answering the attack raises the wrong-answer rate from 0.01 to 0.68, and source deletion confirms the malicious source is the causal driver in every measured case. Vulnerability tracks a model's propensity to cite rather than its scale, reaching CLR 0.84 under explicit instruction and 0.64 with no instruction at all on the most citation-prone model tested. We then show that perplexity filtering and citation-support checking are each insufficient, and propose a counterfactual defense that verifies which source actually drove the answer.