Lit3R: Retrieve-Relate-Read for Evidence-Grounded Question Answering over Scientific Literature

Scientific literature is increasingly used as a knowledge source for language models, retrieval-augmented generation systems, and research assistants, but answering research questions from papers requires more than fluent generation. A reliable system must identify the relevant papers, locate the concrete evidence that supports the answer, and produce a response that is faithful to that evidence. We present LitTraceQA, a benchmark for literature-grounded question answering over scientific papers. Given a research question and a metadata pool of papers, a system must return three connected outputs: canonical paper identifiers, supporting evidence locations, and answers in one or more requested formats, including free-form text, multiple-choice answers, and structured tables. LitTraceQA targets evidence types common in scientific reading: tables, figures, text spans, equations or algorithms, and citation contexts. The public development split contains 55 examples, including 26 hidden-source single-paper questions and 29 multi-paper questions, and provides gold papers, evidence annotations, and answers for local validation. We also analyze a larger final annotation collection with 4,978 unique-question records over 4,859 unique gold papers. By evaluating paper retrieval, evidence grounding, and answer accuracy separately, LitTraceQA provides a testbed for scientific QA systems that produce verifiable answers rather than unsupported summaries.

Large language models are increasingly used to assist scientific reading, but existing evaluation methods often fail to detect whether answers are supported by verifiable citations. We introduce ResearchQA, a benchmark of 6,211 single-paper question-answer pairs from 494 open-access papers spanning eight domains and four question types: lookup, comprehension, multi-hop, and adversarial. ResearchQA is designed for citation-grounded evaluation: it permits multiple valid supporting passages for a claim and rewards grounded refusal when the source paper does not support an answer. We evaluate eight leading closed- and open-weight models in a citation-grounded chat-with-paper setting using a deterministic citation matcher and an LLM-based rubric evaluator. Citation-based metrics separate systems more clearly than LLM-evaluator scores: section coverage and citation accuracy vary substantially across models, while evaluator scores remain tightly compressed. We further find that open-weight models approach the best closed-model citation accuracy while achieving 3 to 6 times lower per-example latency. We release the benchmark, evaluation harness, and evaluator prompt.

Scientific question answering requires a retrieval system to solve two distinct problems: identifying which papers are relevant and locating the supporting evidence within those papers. Conventional retrieval-augmented generation typically addresses both through similarity search over fixed-length passages, flattening document structure and separating scientific claims from their methodological and argumentative context. We present VecTree-RAG, an agentic framework that assigns these tasks to complementary retrieval mechanisms. Vector search ranks compact document and section representations across the corpus, whereas reasoning-guided traversal of source-verified section trees localizes evidence within shortlisted papers. Full text is retained in a page store and exposed progressively only after structural localization. We evaluate VecTree-RAG on 300 QASPER questions, an open-access subset of 54 LitQA2 questions, and 49 multi-document MOSAIC questions. Compared with Dense RAG, reranked Dense RAG, RAPTOR, and Search-o1, VecTree-RAG obtained the highest observed answer score on all three benchmarks, reaching 0.800 LLM-judge correctness on QASPER, 0.925 accuracy on LitQA2, and a 0.547 composite score on MOSAIC. On QASPER, its evidence-page precision was 0.274, compared with 0.046--0.071 for the baselines. LitQA2 ablations further showed that the complete vector--tree architecture required fewer inference tokens than variants without tree navigation or corpus-level vector routing. These results indicate that vector retrieval narrows the corpus-level search space and tree navigation concentrates reading on structurally relevant evidence. Although multi-turn inference remains more expensive than single-call retrieval, VecTree-RAG provides a structure-aware and traceable architecture for scientific literature question answering.