Organizations: Department of Chemistry and Materials Science, Xi’an Jiaotong-Liverpool University, Suzhou 215123, Jiangsu, P. R. China · Suzhou Lab, Suzhou, P. R. China · College of Carbon Neutrality Future Technology, State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing 102249, China · Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
Abstract
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.
Answering complex questions over large document collections requires assembling complementary evidence across sections and documents. GraphRAG offers structured retrieval but typically uses fixed traversal, while agentic RAG operates over weakly structured interfaces. Our key insight is that agents should navigate document structure within and across documents rather than repeatedly search from scratch. We introduce DocNavRAG, which organizes document hierarchies and cross-region relations into a navigable graph, exposes graph operations for locating, navigating, expanding, and fetching, and maintains an evolving evidence state to guide retrieval until sufficient evidence is collected. Across four long- and multi-document QA benchmarks, DocNavRAG improves answer quality and context sufficiency over the strongest baseline by 7.8% and 17.7% on average.
Retrieval-augmented generation (RAG) has become the standard way to ground large language models in external knowledge, but many systems still organize evidence as flat chunks and retrieve it through largely unstructured search. This weak structure becomes a bottleneck for complex retrieval: the system must decide where to search, how to move from coarse topics to entity-relation evidence, which evidence has been verified, and which intermediate artifacts can be reused. We define these intermediate variables as a retrieval state and study RAG as structured state management. EfficientGraph-RAG makes this state explicit through three coupled mechanisms: TAM defines a typed hierarchical state space over evidence, MARS updates and verifies the state through role-specialized agents, and SMP stores reusable state under hierarchy-aware access control. Using one shared framework configuration, EfficientGraph-RAG ranks first on the reported answer-quality metrics averaged over the three evaluated LongBench retrieval-style subsets, matches the strongest agentic baseline on HotpotQA EM while reducing large-model token usage by 3.51×, and provides a low-token DocVQA result among retrieval-organizing cross-modal methods. Component analysis shows role-specific mechanisms: MARS is the main answer-quality driver, TAM supplies the typed traversal state and Adaptive Routing signal, and SMP enables corpus-dependent reuse, with cross-query cache hit rates ranging from 3.77% to 23.18%.
We introduce SciRet, a compute-aware empirical study of retrieval-augmented generation for scientific question answering over CORD-19. Rather than proposing a new model, we evaluate a fixed scientific RAG pipeline across three corpus scales: 1,034 chunks (1K papers), 5,160 chunks (5K papers), and 15,480 chunks (15K papers). The pipeline combines sentence-window chunking, BM25, BGE-M3 dense retrieval, reciprocal rank fusion, optional cross-encoder reranking, and grounded answer generation. Across these settings, hybrid retrieval is more robust than either sparse-only or dense-only retrieval in our setting, reaching Recall@10 of 1.000 at 1K and 15K. In contrast, an MS MARCO-trained cross-encoder reranker reduces precision on the scientific corpus, suggesting that domain mismatch can outweigh the benefits of stronger query-passage interaction. Generation faithfulness measured with RAGAS increases with corpus scale in our setup. Retrieval evaluation uses pseudo-relevance labels derived from the hybrid system, so we treat the results as controlled comparative evidence rather than a benchmark claim. We release code, indexes, and evaluation outputs to support replication and follow-up studies.
Kaysarul Anas Apurba, Md. Hasibul Hasan, Rofiqul Alam Shehab +1