PaperTrail: A Claim-Evidence Interface for Grounding Provenance in LLM-based Scholarly Q&A

Deep research, or any use of large language models (LLMs) to read a large document collection and produce insights, requires synthesizing information from different sources. In this work, we find that LLMs produce long-form research reports that read as confident syntheses but which fail to accurately reflect the underlying documents. We call this failure smoothing. In collapsing diverse and potentially conflicting sources into a single narrative, the model discards the evidential "jaggedness" of its corpus and asserts conclusions more decisive than the citations can support. We introduce a claim level scoring pipeline, SmoothScore, to quantify this effect. Our pipeline extracts key conclusive claims from model generated reports, then finds evidence relevant to each claim and clusters that evidence along high level aspects. Finally, each claim is scored with respect to the evidence to quantify the degree of smoothing done by the agent. Across 7 systems and 4 datasets, we find that agents consistently produce stronger claims than warranted.

Large Language Models (LLMs) are transforming scholarly tasks like search and summarization, but their reliability remains uncertain. Current evaluation metrics for testing LLM reliability are primarily automated approaches that prioritize efficiency and scalability, but lack contextual nuance and fail to reflect how scientific domain experts assess LLM outputs in practice. We developed and validated a schema for evaluating LLM errors in scholarly question-answering systems that reflects the assessment strategies of practicing scientists. In collaboration with domain experts, we identified 20 error patterns across seven categories through thematic analysis of 68 question-answer pairs. We validated this schema through contextual inquiries with 10 additional scientists, which showed not only which errors experts naturally identify but also how structured evaluation schemas can help them detect previously overlooked issues. Domain experts use systematic assessment strategies, including technical precision testing, value-based evaluation, and meta-evaluation of their own practices. We discuss implications for supporting expert evaluation of LLM outputs, including opportunities for personalized, schema-driven tools that adapt to individual evaluation patterns and expertise levels.

Multimodal Large Language Models (MLLMs) have significantly advanced document understanding, yet current Doc-VQA evaluations score only the final answer and leave the supporting evidence unchecked. This answer-only approach masks a critical failure mode: a model can land on the correct answer while grounding it in the wrong passage---a critical risk in high-stakes domains like law, finance, and medicine, where every conclusion must be traceable to a specific source region. To address this, we introduce CiteVQA, a benchmark that requires models to return element-level bounding-box citations alongside each answer, evaluating both jointly. CiteVQA comprises 1,897 questions across 711 PDFs spanning seven domains and two languages, averaging 40.6 pages per document. To ensure fidelity and scalability, the ground-truth citations are generated by an automated pipeline---which identifies crucial evidence via masking ablation and enforces multi-stage quality control. At the core of our evaluation is Strict Attributed Accuracy (SAA), which credits a prediction only when the answer and the cited region are both correct. Auditing 20 MLLMs reveals a pervasive Attribution Hallucination: models frequently produce the right answer while citing the wrong region. The strongest system (Gemini-3.1-Pro-Preview) achieves an SAA of only 76.0, and the strongest open-source MLLM reaches just 22.5. Ultimately, towards trustworthy document intelligence, CiteVQA exposes a reliability gap that answer-only evaluations overlook, providing the instrumentation needed to close it. Our repository is available at https://github.com/opendatalab/CiteVQA.