Weaving Multi-Source Evidence for Biomedical Reasoning: The BioMedHop Benchmark and BioWeave Framework

Biomedical question answering (QA) increasingly requires reasoning over interacting entities, where supporting evidence is scattered across biomedical knowledge graphs, literature documents, and web-accessible resources. However, existing biomedical QA benchmarks mainly focus on exam-style knowledge, literature comprehension, or short-range multi-hop inference, leaving source-conditioned graph reasoning and evidence topology construction underexplored. To fill this gap, we introduce BioMedHop, a multi-source graph-grounded benchmark for evaluating biomedical reasoning over structured evidence topologies. BioMedHop contains 10,045 instances across KG, document, web, and hybrid evidence settings, covering shared-neighbor matching, intersection reasoning, path-based reasoning, and counting, with option-based, open-ended, and numeric count renderings. To support this benchmark, we further propose BioWeave, a source-aware reasoning framework that retrieves biomedical KG paths, gathers supporting clues from documents and web sources, assembles them into a unified evidence graph, and verifies answers through entity-level evidence support. Comprehensive experiments show that BioWeave achieves the best overall performance among compared methods on BioMedHop, outperforming the strong hybrid baseline ToG-2 by 10.5% in the overall average. Moreover, BioWeave consistently improves different LLM backbones and enables smaller models, such as Qwen3-4B, to achieve reasoning performance comparable to GPT-4-Turbo.

Trace Only What You Need: Structure-Aware On-Demand Hypergraph Memory for Long-Document Question Answering

Long-document question answering (QA) requires large language models (LLMs) to reason over evidence scattered across lengthy documents, where answers often depend on event order, section-level context, and cross-part evidence connections. Although retrieval-augmented generation (RAG) reduces the input context by retrieving relevant evidence, existing structured RAG methods still face three limitations: costly query-agnostic knowledge organization, insufficient use of original document structure, and no reuse of historical reasoning experience. To address these limitations, we propose DocTrace, a multi-agent RAG framework for long-document QA that supports query-triggered knowledge organization, document-structure-aware and experience-guided reasoning. DocTrace preserves document hierarchy with a lightweight document structural tree index, constructs agent-shared hypergraph-structured working memory on demand during reasoning, and stores successful reasoning plans in graph-structured experience memory for future reuse, enabling adaptive exploration across related long-document questions. Experiments on four long-document QA datasets show that DocTrace achieves the best performance on three datasets, surpassing the strongest baseline, ComoRAG, by up to 8.85% in F1 and 4.40% in EM, while reducing the overall computational cost by 53.32%

PrivGemo: Privacy-Preserving Dual-Tower Graph Retrieval for Empowering LLM Reasoning with Memory Augmentation

Knowledge graphs (KGs) provide structured evidence that can ground large language model (LLM) reasoning for knowledge-intensive question answering. However, many practical KGs are private, and sending retrieved triples or exploration traces to closed-source LLM APIs introduces leakage risk. Existing privacy treatments focus on masking entity names, but they still face four limitations: structural leakage under semantic masking, uncontrollable remote interaction, fragile multi-hop and multi-entity reasoning, and limited experience reuse for stability and efficiency. To address these issues, we propose PrivGemo, a privacy-preserving retrieval-augmented framework for KG-grounded reasoning with memory-guided exposure control. PrivGemo uses a dual-tower design to keep raw KG knowledge local while enabling remote reasoning over an anonymized view that goes beyond name masking to limit both semantic and structural exposure. PrivGemo supports multi-hop, multi-entity reasoning by retrieving anonymized long-hop paths that connect all topic entities, while keeping grounding and verification on the local KG. A hierarchical controller and a privacy-aware experience memory further reduce unnecessary exploration and remote interactions. Comprehensive experiments on six benchmarks show that PrivGemo achieves overall state-of-the-art results, outperforming the strongest baseline by up to 17.1%. Furthermore, PrivGemo enables smaller models (e.g., Qwen3-4B) to achieve reasoning performance comparable to that of GPT-4-Turbo.

PRoH: Dynamic Planning and Reasoning over Knowledge Hypergraphs for Retrieval-Augmented Generation

Knowledge Hypergraphs (KHs) have recently emerged as a knowledge representation for retrieval-augmented generation (RAG), offering a paradigm to model multi-entity relations into a structured form. However, existing KH-based RAG methods suffer from three major limitations: static retrieval planning, non-adaptive retrieval execution, and superficial use of KH structure and semantics, which constrain their ability to perform effective multi-hop question answering. To overcome these limitations, we propose PRoH, a dynamic Planning and Reasoning over Knowledge Hypergraphs framework. PRoH incorporates three core innovations: (i) a context-aware planning module that sketches the local KH neighborhood to guide structurally grounded reasoning plan generation; (ii) a structured question decomposition process that organizes subquestions as a dynamically evolving Directed Acyclic Graph (DAG) to enable adaptive, multi-trajectory exploration; and (iii) an Entity-Weighted Overlap (EWO)-guided reasoning path retrieval algorithm that prioritizes semantically coherent hyperedge traversals. Experiments across multiple domains demonstrate that PRoH achieves state-of-the-art performance, surpassing the prior SOTA model HyperGraphRAG by an average of 19.73% in F1 and 8.41% in Generation Evaluation (G-E) score, while maintaining strong robustness in long-range multi-hop reasoning tasks.

Hydra: Structured Cross-Source Enhanced Large Language Model Reasoning

Retrieval-augmented generation (RAG) enhances large language models (LLMs) by incorporating external knowledge. Current hybrid RAG system retrieves evidence from both knowledge graphs (KGs) and text documents to support LLM reasoning. However, it faces challenges like handling multi-hop reasoning, multi-entity questions, multi-source verification, and effective graph utilization. To address these limitations, we present Hydra, a training-free framework that unifies graph topology, document semantics, and source reliability to support deep, faithful reasoning in LLMs. Hydra handles multi-hop and multi-entity problems through agent-driven exploration that combines structured and unstructured retrieval, increasing both diversity and precision of evidence. To tackle multi-source verification, Hydra uses a tri-factor cross-source verification (source trustworthiness assessment, cross-source corroboration, and entity-path alignment), to balance topic relevance with cross-modal agreement. By leveraging graph structure, Hydra fuses heterogeneous sources, guides efficient exploration, and prunes noise early. Comprehensive experiments on seven benchmark datasets show that Hydra achieves overall state-of-the-art results on all benchmarks with GPT-3.5, outperforming the strong hybrid baseline ToG-2 by an average of 20.3% and up to 30.1%. Furthermore, Hydra enables smaller models (e.g., Llama-3.1-8B) to achieve reasoning performance comparable to that of GPT-4-Turbo.

Paths-over-Graph: Knowledge Graph Empowered Large Language Model Reasoning

Large Language Models (LLMs) have achieved impressive results in various tasks but struggle with hallucination problems and lack of relevant knowledge, especially in deep complex reasoning and knowledge-intensive tasks. Knowledge Graphs (KGs), which capture vast amounts of facts in a structured format, offer a reliable source of knowledge for reasoning. However, existing KG-based LLM reasoning methods face challenges like handling multi-hop reasoning, multi-entity questions, and effectively utilizing graph structures. To address these issues, we propose Paths-over-Graph (PoG), a novel method that enhances LLM reasoning by integrating knowledge reasoning paths from KGs, improving the interpretability and faithfulness of LLM outputs. PoG tackles multi-hop and multi-entity questions through a three-phase dynamic multi-hop path exploration, which combines the inherent knowledge of LLMs with factual knowledge from KGs. In order to improve the efficiency, PoG prunes irrelevant information from the graph exploration first and introduces efficient three-step pruning techniques that incorporate graph structures, LLM prompting, and a pre-trained language model (e.g., SBERT) to effectively narrow down the explored candidate paths. This ensures all reasoning paths contain highly relevant information captured from KGs, making the reasoning faithful and interpretable in problem-solving. PoG innovatively utilizes graph structure to prune the irrelevant noise and represents the first method to implement multi-entity deep path detection on KGs for LLM reasoning tasks. Comprehensive experiments on five benchmark KGQA datasets demonstrate PoG outperforms the state-of-the-art method ToG across GPT-3.5-Turbo and GPT-4, achieving an average accuracy improvement of 18.9%. Notably, PoG with GPT-3.5-Turbo surpasses ToG with GPT-4 by up to 23.9%.