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1. Knowledge Graph Prompting for Multi-Document Question Answering

   https://doi.org/10.1609/aaai.v38i17.29889  

   Wang, Yu; Lipka, Nedim; Rossi, Ryan A; Siu, Alexa; Zhang, Ruiyi; Derr, Tyler (March 2024, Proceedings of the AAAI Conference on Artificial Intelligence)

   The `pre-train, prompt, predict' paradigm of large language models (LLMs) has achieved remarkable success in open-domain question answering (OD-QA). However, few works explore this paradigm in multi-document question answering (MD-QA), a task demanding a thorough understanding of the logical associations among the contents and structures of documents. To fill this crucial gap, we propose a Knowledge Graph Prompting (KGP) method to formulate the right context in prompting LLMs for MD-QA, which consists of a graph construction module and a graph traversal module. For graph construction, we create a knowledge graph (KG) over multiple documents with nodes symbolizing passages or document structures (e.g., pages/tables), and edges denoting the semantic/lexical similarity between passages or document structural relations. For graph traversal, we design an LLM-based graph traversal agent that navigates across nodes and gathers supporting passages assisting LLMs in MD-QA. The constructed graph serves as the global ruler that regulates the transitional space among passages and reduces retrieval latency. Concurrently, the graph traversal agent acts as a local navigator that gathers pertinent context to progressively approach the question and guarantee retrieval quality. Extensive experiments underscore the efficacy of KGP for MD-QA, signifying the potential of leveraging graphs in enhancing the prompt design and retrieval augmented generation for LLMs. Our code: https://github.com/YuWVandy/KG-LLM-MDQA. 

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2. GRIL: Knowledge Graph Retrieval-Integrated Learning with Large Language Models

   Chen, Jialin; Zhang, Houyu; Yun, Seongjun; Mottini, Alejandro; Ying, Rex; Song, Xiang; Ioannidis, Vassilis_N; Li, Zheng; Cui, Qingjun (November 2025, Association for Computational Linguistics)

   Retrieval-Augmented Generation (RAG) has significantly mitigated the hallucinations of Large Language Models (LLMs) by grounding the generation with external knowledge. Recent extensions of RAG to graph-based retrieval offer a promising direction, leveraging the structural knowledge for multi-hop reasoning. However, existing graph RAG typically decouples retrieval and reasoning processes, which prevents the retriever from adapting to the reasoning needs of the LLM. They also struggle with scalability when performing multi-hop expansion over large-scale graphs, or depend heavily on annotated ground-truth entities, which are often unavailable in opendomain settings. To address these challenges, we propose a novel graph retriever trained endto-end with LLM, which features an attentionbased growing and pruning mechanism, adaptively navigating multi-hop relevant entities while filtering out noise. Within the extracted subgraph, structural knowledge and semantic features are encoded via soft tokens and the verbalized graph, respectively, which are infused into the LLM together, thereby enhancing its reasoning capability and facilitating interactive joint training of the graph retriever and the LLM reasoner. Experimental results across three QA benchmarks show that our approach consistently achieves state-of-the-art performance, validating the strength of joint graph–LLM optimization for complex reasoning tasks. Notably, our framework eliminates the need for predefined ground-truth entities by directly optimizing the retriever using LLM logits as implicit feedback, making it especially effective in open-domain settings. 

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3. Biomedical knowledge graph-optimized prompt generation for large language models

   https://doi.org/10.1093/bioinformatics/btae560  

   Soman, Karthik; Rose, Peter W; Morris, John H; Akbas, Rabia E; Smith, Brett; Peetoom, Braian; Villouta-Reyes, Catalina; Cerono, Gabriel; Shi, Yongmei; Rizk-Jackson, Angela; et al (September 2024, Bioinformatics)

   Robinson, Peter (Ed.)

   Abstract MotivationLarge language models (LLMs) are being adopted at an unprecedented rate, yet still face challenges in knowledge-intensive domains such as biomedicine. Solutions such as pretraining and domain-specific fine-tuning add substantial computational overhead, requiring further domain-expertise. Here, we introduce a token-optimized and robust Knowledge Graph-based Retrieval Augmented Generation (KG-RAG) framework by leveraging a massive biomedical KG (SPOKE) with LLMs such as Llama-2-13b, GPT-3.5-Turbo, and GPT-4, to generate meaningful biomedical text rooted in established knowledge. ResultsCompared to the existing RAG technique for Knowledge Graphs, the proposed method utilizes minimal graph schema for context extraction and uses embedding methods for context pruning. This optimization in context extraction results in more than 50% reduction in token consumption without compromising the accuracy, making a cost-effective and robust RAG implementation on proprietary LLMs. KG-RAG consistently enhanced the performance of LLMs across diverse biomedical prompts by generating responses rooted in established knowledge, accompanied by accurate provenance and statistical evidence (if available) to substantiate the claims. Further benchmarking on human curated datasets, such as biomedical true/false and multiple-choice questions (MCQ), showed a remarkable 71% boost in the performance of the Llama-2 model on the challenging MCQ dataset, demonstrating the framework’s capacity to empower open-source models with fewer parameters for domain-specific questions. Furthermore, KG-RAG enhanced the performance of proprietary GPT models, such as GPT-3.5 and GPT-4. In summary, the proposed framework combines explicit and implicit knowledge of KG and LLM in a token optimized fashion, thus enhancing the adaptability of general-purpose LLMs to tackle domain-specific questions in a cost-effective fashion. Availability and implementationSPOKE KG can be accessed at https://spoke.rbvi.ucsf.edu/neighborhood.html. It can also be accessed using REST-API (https://spoke.rbvi.ucsf.edu/swagger/). KG-RAG code is made available at https://github.com/BaranziniLab/KG_RAG. Biomedical benchmark datasets used in this study are made available to the research community in the same GitHub repository. 

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4. Token-Level Precise Attack on RAG: Searching for the Best Alternatives to Mislead Generation

   https://doi.org/10.48448/206t-7r37  

   Li, Zizhong; Zhang, Jiawei; Zhang, Haopeng (January 2026, Underline Science Inc.)

   Abstract: While large language models (LLMs) have achieved remarkable success in providing trustworthy responses for knowledge-intensive tasks, they still face critical limitations such as hallucinations and outdated knowledge. To address these issues, the retrieval-augmented generation (RAG) framework enhances LLMs with access to external knowledge via a retriever, enabling more accurate and real-time outputs about the latest events. However, this integration brings new security vulnerabilities: the risk that malicious content in the external database can be retrieved and used to manipulate model outputs. Although prior work has explored attacks on RAG systems, existing approaches either rely heavily on access to the retriever or fail to jointly consider both retrieval and generation stages, limiting their effectiveness, particularly in black-box scenarios. To overcome these limitations, we propose Token-level Precise Attack on the RAG (TPARAG), a novel framework that targets both white-box and black-box RAG systems. TPARAG leverages a lightweight white-box LLM as an attacker to generate and iteratively optimize malicious passages at the token level, ensuring both retrievability and high attack success in generation. Extensive experiments on open-domain QA datasets demonstrate that TPARAG consistently outperforms previous approaches in retrieval-stage and end-to-end attack effectiveness. These results further reveal critical vulnerabilities in RAG pipelines and offer new insights into improving their robustness. 

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5. Enhancing LLM-Based Short Answer Grading with Retrieval-Augmented Generation

   https://doi.org/10.5281/zenodo.15870304  

   Chu, Yucheng; He, Peng; Li, Hang; Han, Haoyu; Yang, Kaiqi; Xue, Yu; Li, Tingting; Krajcik, Joseph; Tang, Jiliang (July 2025, International Educational Data Mining Society)

   Mills, Caitlin; Alexandron, Giora; Taibi, Davide; Lo_Bosco, Giosuè; Paquette, Luc (Ed.)

   Short answer assessment is a vital component of science education, allowing evaluation of students' complex three-dimensional understanding. Large language models (LLMs) that possess human-like ability in linguistic tasks are increasingly popular in assisting human graders to reduce their workload. However, LLMs' limitations in domain knowledge restrict their understanding in task-specific requirements and hinder their ability to achieve satisfactory performance. Retrieval-augmented generation (RAG) emerges as a promising solution by enabling LLMs to access relevant domain-specific knowledge during assessment. In this work, we propose an adaptive RAG framework for automated grading that dynamically retrieves and incorporates domain-specific knowledge based on the question and student answer context. Our approach combines semantic search and curated educational sources to retrieve valuable reference materials. Experimental results in a science education dataset demonstrate that our system achieves an improvement in grading accuracy compared to baseline LLM approaches. The findings suggest that RAG-enhanced grading systems can serve as reliable support with efficient performance gains. 

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