PathMind: A Retrieve-Prioritize-Reason Framework for Knowledge Graph Reasoning with Large Language Models

Knowledge base question answering (KBQA) refers to the system that produces answers to user queries by reasoning with a large-scale structured knowledge base. Advanced works have achieved great success either by generating logical forms (LF) or directly generating answers. Although the former typically yields better performance, these generated LF could be inaccurate, e.g., non-executable. In this regard, large language models (LLMs) have shown exciting potential for accurate generation. However, it is challenging to fine-tune LLMs to generate LF. This is because the context retrieved for prediction typically leads to an excessive number of reasoning paths. In this context, LLMs can generate numerous LF corresponding to these reasoning paths, but a few LF can result in correct answers. Thus, fine-tuning LLMs to generate answer-relevant LF would conflict with the prior knowledge of the LLMs. In this work, we propose a novel learning framework, FM-KBQA, to fine-tune LLMs using multi-task learning for KBQA. Specifically, we propose to fine-tune LLMs using an additional objective: generating the index of reasoning paths that lead to correct answers. This will direct LLMs to pay attention to answer-relevant paths among numerous reasoning paths by completing a simple task where the selected reasoning paths can be supplementary for non-executable LF. Directly generating answers can make LLMs pay attention to the answer-relevant reasoning paths, but it is much more challenging than generating the index of reasoning paths. To verify FM-KBQA's effectiveness, we conduct experiments on mainstream benchmarks, such as WebQuestionsSP (WQSP) and ComplexWebQuestions (CWQ). Extensive evaluations across two public benchmark datasets underscore the superiority of FM-KBQA over current state-of-the-art methods.

In today’s rapidly evolving business landscape, Artificial Intelligence (AI), and specifically Large Language Models (LLMs), are redefining how organizations operate, make decisions, and engage with customers. AI-driven technologies have become indispensable, providing businesses with powerful tools to streamline operations, derive actionable insights from vast data, and foster more meaningful customer interactions. For business leaders, scholars, and practitioners alike, understanding the transformative potential of AI isn’t just advantageous—it’s essential to staying competitive in an increasingly data-driven world.This editorial delves into recent scholarly advancements in LLM applications within business contexts, analyzing studies that explore AI’s potential across various domains, from decision support to creative industries. By introducing a structured framework, this editorial highlights key insights and contributions from recent studies, assessing their value to academia and industry. The following comparative analysis sheds light on how these innovations shape our understanding of AI’s role in business while pointing to future research directions.Puyt and Madsen's (2024) study stands out as a foundational exploration of LLM accuracy, assessing ChatGPT-4's ability to recount the history of the SWOT analysis-a vital business strategy tool. Their findings reveal that, while ChatGPT-4 effectively conveys general concepts, it struggles with detailed historical information, often producing inaccuracies or "hallucinations." This gap underscores the need for LLMs to be trained with verified academic data, particularly for strategic business applications that demand precision. This study not only contributes to the literature by proposing methods to evaluate AI accuracy in historical contexts but also highlights the importance of rigorous information vetting in industry settings where reliability is crucial.In contrast, Raikov et al. (2024) explore a hybrid intelligence model that combines LLM capabilities with explainable AI (XAI) principles to enhance human-machine collaboration. Their approach emphasizes cognitive semantics, improving transparency and decision-making efficiency. The hybrid model's real-time adaptability addresses the needs of complex, regulated industries such as finance and healthcare, where trust in AI decisions is paramount. Academically, this study provides a valuable addition to XAI literature by demonstrating how LLMs can bridge the gap between AI autonomy and human oversight, making it a model for future human-AI interactions in complex business environments.Another significant study by Mariotti and colleagues (2024) examines the integration of LLMs with enterprise knowledge graphs to enhance data-driven decision-making. By enabling organizations to leverage knowledge graphs for more accurate and scalable data retrieval, this research provides a robust framework for businesses seeking efficient knowledge management systems. The academic contribution here lies in advancing the dialogue between LLMs and knowledge graphs, emphasizing ethical data handling and quality standards essential for industry applications. For enterprises, the study offers practical solutions to achieve streamlined data management, balancing automation with privacy and security. 2024) take a different approach, investigating LLMs' role in creative industries, specifically within fashion design. They introduce a hybrid intelligence model that supports creative processes, allowing AI to complement rather than replace human ingenuity. While LLMs in this field demonstrate potential in automating repetitive design tasks and enhancing customer personalization, the study reveals limitations in AI's ability to handle spatial and stylistic nuances. This study's academic contribution lies in promoting human-AI co-creation, inspiring further research into AI applications across diverse creative sectors, including media and marketing.Collectively, these studies not only illuminate LLMs' transformative potential in business but also highlight critical ethical and operational considerations. Ensuring accuracy, transparency, and data privacy are vital to responsibly integrating AI into business workflows. Future research should focus on enhancing LLM accuracy, refining hybrid intelligence models, and exploring creative AI applications, all while maintaining ethical standards. As LLMs evolve, interdisciplinary collaborations will be essential to harness their full potential, making AI an ethical, effective, and innovative force in the business world.

Knowledge graphs (KGs) have transformed data management within the manufacturing industry, offering effective means for integrating disparate data sources through shared and structured conceptual schemas. However, harnessing the power of KGs can be daunting for non-experts, as it often requires formulating complex SPARQL queries to retrieve specific information. With the advent of Large Language Models (LLMs), there is a growing potential to automatically translate natural language queries into the SPARQL format, thus bridging the gap between user-friendly interfaces and the sophisticated architecture of KGs. The challenge remains in adequately informing LLMs about the relevant context and structure of domain-specific KGs, e.g., in manufacturing, to improve the accuracy of generated queries. In this paper, we evaluate multiple strategies that use LLMs as mediators to facilitate information retrieval from KGs. We focus on the manufacturing domain, particularly on the Bosch Line Information System KG and the I40 Core Information Model. In our evaluation, we compare various approaches for feeding relevant context from the KG to the LLM and analyze their proficiency in transforming real-world questions into SPARQL queries. Our findings show that LLMs can significantly improve their performance on generating correct and complete queries when provided only the adequate context of the KG schema. Such context-aware prompting techniques help LLMs to focus on the relevant parts of the ontology and reduce the risk of hallucination. We anticipate that the proposed techniques help LLMs to democratize access to complex data repositories and empower informed decision-making in manufacturing settings.

This paper investigates the impact of knowledge extraction methods on the effectiveness of RAG (Retrieval-Augmented Generation) systems that utilize knowledge graphs. It highlights that the quality of the knowledge graph, which is formed using various knowledge extraction methods, is crucial for overcoming limitations of large language models (LLMs), such as “hallucinations”. The paper analyzes the architectures of LightRAG and GraphRAG, emphasizing that the selection of an optimal knowledge extraction strategy depends on specific tasks and the subject area. LLMs have advanced significantly, but they have limitations, including generating factually incorrect information (“hallucinations”) and possessing “outdated knowledge”. RAG systems were proposed to address these issues by combining LLMs with external knowledge bases. This approach reduces hallucinations, ensures factual accuracy, solves the problem of outdated knowledge, and increases transparency. Knowledge graphs are powerful tools for structuring information, consisting of entities (nodes) and relations (edges). They enhance RAG systems by enabling more precise and contextually grounded retrieval compared to keyword-based searches. The quality of a knowledge graph depends on the knowledge extraction methods used, which include named entity recognition (NER), relation extraction (RE), entity linking (EL), and event extraction. Different methods, such as rule-based, classical machine learning, and deep learning approaches, have varying trade-offs in terms of accuracy, completeness, and scalability. Entity linking and knowledge graph completion are also crucial for accuracy and richness. LightRAG and GraphRAG are two main graph-based RAG systems. LightRAG uses the knowledge graph as a quick reference, requiring high precision in knowledge extraction to avoid noise degradation. GraphRAG uses the knowledge graph as a domain model, where completeness of extracted knowledge is more critical, though systematic errors are still harmful. Both systems rely on LLMs for knowledge extraction, which makes them dependent on the LLM’s quality and the size of document fragments processed. The theoretical analysis confirms that the effectiveness of RAG systems is critically dependent on knowledge extraction methods. The quality, completeness, and accuracy of the knowledge graph directly influence the RAG system’s ability to provide relevant, accurate, and truthful answers. Different RAG system architectures like LightRAG and GraphRAG have distinct requirements for knowledge graph characteristics, prioritizing either accuracy or completeness in knowledge extraction.

Extracting information from unstructured and semi-structured geoscience literature is a crucial step in conducting geological research. The traditional machine learning extraction paradigm requires a substantial amount of high-quality manually annotated data for model training, which is time-consuming, labor-intensive, and not easily transferable to new fields. Recently, large language models (LLMs) (e.g., ChatGPT, GPT-4, and LLaMA), have shown great performance in various natural language processing (NLP) tasks, such as question answering, machine translation, and text generation. A substantial body of work has demonstrated that LLMs possess strong in-context learning (ICL) and even zero-shot learning capabilities to solve downstream tasks without specifically designed supervised fine-tuning. In this paper, we propose utilizing LLMs for geoscience literature information extraction. Specifically, we design a hierarchical PDF parsing pipeline and an automated knowledge extraction process, which can significantly reduce the need for manual data annotation, assisting geoscientists in literature data mining. For the hierarchical PDF parsing pipeline, firstly, a document layout detection model fine-tuned on geoscience literature is employed for layout detection, obtaining layout detection information for the document. Secondly, based on the document layout information, an optical character content parsing model is used for content parsing, obtaining the text structure and plain text corresponding to the content. Finally, the text structure and plain text are combined and reconstructed to ultimately obtain the parsed structured data. For the automated knowledge extraction process, firstly, the parsed long text is segmented into paragraphs to adapt to the input length limit of LLMs. Subsequently, a few-shot prompting method is employed for structured knowledge extraction, encompassing two tasks: attribute value extraction and triplet extraction. In attribute value extraction, prompts are generated automatically by the LLMs based on the subdomain and attribute names, facilitating the location and extraction of values related to subdomain attribute names in the text. For triplet extraction, the LLMs employ a procedural approach to entity extraction, entity type extraction, and relation extraction, following the knowledge graph structure pattern. Finally, the extracted structured knowledge is stored in the form of knowledge graphs, facilitating further analysis and integration of various types of knowledge from the literature. Our proposed approach turns out to be simple, flexible, and highly effective in geoscience literature information extraction. Demonstrations of information extraction in subdomains such as radiolarian fossils and fluvial facies have yielded satisfactory results. The extraction efficiency has significantly improved, and feedback from domain experts indicates a relatively high level of accuracy in the extraction process. The extracted results can be used to construct a foundational knowledge graph for geoscience literature, supporting the comprehensive construction and efficient application of a geoscience knowledge graph.

BackgroundIn recent years, large language models (LLMs) have shown promise in various domains, notably in biomedical sciences. However, their real-world application is often limited by issues like erroneous outputs and hallucinatory responses.ResultsWe developed the knowledge graph–based thought (KGT) framework, an innovative solution that integrates LLMs with knowledge graphs (KGs) to improve their initial responses by utilizing verifiable information from KGs, thus significantly reducing factual errors in reasoning. The KGT framework demonstrates strong adaptability and performs well across various open-source LLMs. Notably, KGT can facilitate the discovery of new uses for existing drugs through potential drug–cancer associations and can assist in predicting resistance by analyzing relevant biomarkers and genetic mechanisms. To evaluate the knowledge graph question answering task within biomedicine, we utilize a pan-cancer knowledge graph to develop a pan-cancer question answering benchmark, named pan-cancer question answering.ConclusionsThe KGT framework substantially improves the accuracy and utility of LLMs in the biomedical field. This study serves as a proof of concept, demonstrating its exceptional performance in biomedical question answering.

The increasing reliance on Large Language Models (LLMs) for health information seeking can pose severe risks due to the potential for misinformation and the complexity of these topics. This paper introduces KnowNet a visualization system that integrates LLMs with Knowledge Graphs (KG) to provide enhanced accuracy and structured exploration. Specifically, for enhanced accuracy, KnowNet extracts triples (e.g., entities and their relations) from LLM outputs and maps them into the validated information and supported evidence in external KGs. For structured exploration, KnowNet provides next-step recommendations based on the neighborhood of the currently explored entities in KGs, aiming to guide a comprehensive understanding without overlooking critical aspects. To enable reasoning with both the structured data in KGs and the unstructured outputs from LLMs, KnowNet conceptualizes the understanding of a subject as the gradual construction of graph visualization. A progressive graph visualization is introduced to monitor past inquiries, and bridge the current query with the exploration history and next-step recommendations. We demonstrate the effectiveness of our system via use cases and expert interviews.

Entity alignment (EA) facilitates knowledge fusion by matching semantically identical entities in distinct knowledge graphs (KGs). Existing embedding-based methods rely solely on intrinsic KG facts and often struggle with long-tail entities due to insufficient information. Recently, large language models (LLMs), empowered by rich background knowledge and strong reasoning abilities, have shown promise for EA. However, most current LLM-enhanced approaches follow the in-context learning paradigm, requiring multi-round interactions with carefully designed prompts to perform additional auxiliary operations, which leads to substantial computational overhead. Moreover, they fail to fully exploit the complementary strengths of embedding-based small models and LLMs. To address these limitations, we propose HIEA, a novel hierarchical inference framework for entity alignment. By instruction-tuning a generative LLM with a unified and concise prompt and a knowledge adapter, HIEA produces alignment results with a single LLM invocation. Meanwhile, embedding-based small models not only generate candidate entities but also support the LLM through data augmentation and certainty-aware source entity classification, fostering deeper collaboration between small models and LLMs. Extensive experiments on both standard and highly heterogeneous benchmarks demonstrate that HIEA consistently outperforms existing embedding-based and LLM-enhanced methods, achieving absolute Hits@1 improvements of up to 5.6%, while significantly reducing inference cost.

Large Language Models (LLMs) face significant challenges when attempting to utilize knowledge not encoded during pre-training. In-context learning (ICL) addresses this limitation by embedding relevant information directly into prompts, enabling LLMs to leverage external knowledge without updating their parameters. Recent advances have explored integrating knowledge graph (KG) information into prompts, taking advantage of the structured and factual representations of entities and relationships that KGs provide. A common approach involves identifying key concepts in a task, grounding them to KG nodes, extracting ego-subgraphs centered on these concepts, and incorporating them into prompts. However, not all subgraphs are equally relevant to the task, and selecting appropriate knowledge remains a critical challenge, as irrelevant or noisy subgraphs can reduce model accuracy. This study investigates how KG-based information related to task-specific concepts influences LLM performance on multiple-choice question answering (MCQA) tasks. We implement a four-stage pipeline that (1) identifies key concepts from questions and grounds them in the KG, (2) extracts individual ego-subgraphs for each concept, (3) integrates these subgraphs into prompts, and (4) evaluates their impact on LLM reasoning via probability scoring. Our analysis highlights which concept-specific subgraphs enhance performance, which introduce misleading information, and which have neutral effects. We show that carefully selected KG subgraphs can substantially outperform others in semantic relevance. Furthermore, we examine how the size and connectivity of selected KG subgraphs influence model performance. Overall, this work deepens understanding of KG-based knowledge selection in ICL and informs the design of more effective, targeted prompting strategies. This project's source code is publicly available at https://github.com/maryam-ghanbari/InformativenessOfKGs.

The advent of Large Language Models (LLMs), such as Chat-GPT and GPT-4, has revolutionized natural language processing, opening avenues for advanced textual understanding.This study explores the application of LLMs in developing Knowledge graphs from textual data.Knowledge graphs offer a structured representation of information, facilitating enhanced comprehension and utilization of unstructured text.We intend to construct Knowledge graphs that capture relationships and entities within diverse textual datasets by harnessing LLMs' contextual understanding and language generation capabilities.The primary goal is to explore and understand how well LLMs can identify and extract relevant entities and relationships from textual data using prompt engineering while contributing to structured knowledge representation.

Drug repurposing (DR) offers a promising alternative to the high cost and low success rate of traditional drug development, especially for complex diseases like Alzheimer’s disease (AD). This study addressed DR for AD from three key angles: (1) demonstrating how disease-specific knowledge graphs can improve DR performance, (2) evaluating the role of large language models (LLMs) in enhancing the usability and efficiency of these graphs, and (3) assessing whether Graph-of-Thoughts (GoT)-enhanced LLMs, when integrated with AD knowledge graphs, can outperform traditional machine learning and LLM-based approaches. We tested five distinct DR strategies (DR1–DR5) for AD: DR1, a machine learning method using TxGNN; DR2, a machine learning model leveraging the Alzheimer’s KnowledgeBase (AlzKB); DR3, an LLM-based chatbot built on AlzKB; DR4, our ESCARGOT framework combining GoT-enhanced LLMs with AlzKB; and DR5, a general reasoning-driven LLM approach. Results showed that AlzKB significantly improved DR outcomes. ESCARGOT further enhanced performance while reducing the need for coding or advanced expertise in knowledge graph analysis. Because the architecture of AlzKB is easily adaptable to other diseases and ESCARGOT can integrate with various knowledge graph platforms, this framework offers a broadly applicable, innovative tool for accelerating drug discovery through repurposing.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13040-025-00466-5.

As large language models (LLMs) continue to grow in size, their abilities to tackle complex tasks have significantly improved. However, issues such as hallucination and the lack of up-to-date knowledge largely remain unresolved. Knowledge graphs (KGs), which serve as symbolic representations of real-world knowledge, offer a reliable source for enhancing reasoning. Integrating KG retrieval into LLMs can therefore strengthen their reasoning by providing dependable knowledge. Nevertheless, due to limited understanding of the underlying knowledge graph, LLMs may struggle with queries that have multiple interpretations. Additionally, the incompleteness and noise within knowledge graphs may result in retrieval failures. To address these challenges, we propose an embedding-based retrieval reasoning framework EMBRAG. In this approach, the model first generates multiple logical rules grounded in knowledge graphs based on the input query. These rules are then applied to reasoning in the embedding space, guided by the knowledge graph, ensuring more robust and accurate reasoning. A reranker model further interprets these rules and refines the results. Extensive experiments on two benchmark KGQA datasets demonstrate that our approach achieves the new state-of-the-art performance in KG reasoning tasks.

Given unstructured text, Large Language Models (LLMs) are adept at answering simple (single-hop) questions. However, as the complexity of the questions increase, the performance of LLMs degrade. We believe this is due to the overhead associated with understanding the complex question followed by filtering and aggregating unstructured information in the raw text. Recent methods try to reduce this burden by integrating structured knowledge triples into the raw text, aiming to provide a structured overview that simplifies information processing. However, this simplistic approach is query-agnostic and the extracted facts are ambiguous as they lack context. To address these drawbacks and to enable LLMs to answer complex (multi-hop) questions with ease, we propose to use a knowledge graph (KG) that is context-aware and is distilled to contain query-relevant information. The use of our compressed distilled KG as input to the LLM results in our method utilizing up to 67% fewer tokens to represent the query relevant information present in the supporting documents, compared to the state-of-the-art (SoTA) method. Our experiments show consistent improvements over the SoTA across several metrics (EM, F1, BERTScore, and Human Eval) on two popular benchmark datasets (HotpotQA and MuSiQue).

In recent years, the landscape of digital biomedicine and healthcare has been reshaped due to the disruptive breakthroughs in AI-facilitated by tremendous data and high-performance computers, large language models (LLMs) have transformed information technology from accessing data to performing analytical tasks. While demonstrating unprecedented capabilities, LLMs have been found unreliable in tasks requiring factual knowledge and rigorous reasoning. Biomedicine and healthcare, as an important vertical domain rapidly benefitting from progress in AI, necessitates strict requirements on the accuracy, controllability, and interpretability of analytical models, posing critical challenges for LLMs. Despite recent studies addressing the hallucination problem of LLMs, research on empowering LLMs with the ability to plan, reason, and ground with explicit knowledge has also started to prosper, especially in the biomedicine and healthcare domain. On the other hand, biomedical data are enormous and notoriously complex, coming from various sources (e.g., biomedical knowledge bases, online literature, and hospitals) and bearing various modalities (e.g., tables, texts, images and time-series). Healthcare professionals have spent decades collecting, cleaning, and curating various types of data. The processes are extremely costly, producing various datasets with different data schemas, coding systems, and quality standards, many privately owned by the creators, making their integrative analysis and utilization through unified AI techniques still rather challenging. The generalizability of LLMs across different types of data endow them strong promises in automating the processing of large-scale complex healthcare data such as into unified knowledge graphs (KGs). Our goal in this survey is to systematically investigate and summarize recent studies on the unification of LLMs and KGs, towards fully utilizing the value of complex data, unleashing the power of generative AI, and expediting next-generation AI for biomedicine and healthcare applications.

BackgroundGestational diabetes mellitus (GDM) is a prevalent chronic condition that affects maternal and fetal health outcomes worldwide, increasingly in underserved populations. While generative artificial intelligence (AI) and large language models (LLMs) have shown promise in health care, their application in GDM management remains underexplored.ObjectiveThis study aimed to investigate whether retrieval-augmented generation techniques, when combined with knowledge graphs (KGs), could improve the contextual relevance and accuracy of AI-driven clinical decision support. For this, we developed and validated a graph-based retrieval-augmented generation (GraphRAG)–enabled local LLM as a clinical support tool for GDM management, assessing its performance against open-source LLM tools.MethodsA prototype clinical AI assistant was developed using a GraphRAG constructed from 1212 peer-reviewed research articles on GDM interventions, retrieved from the Semantic Scholar API (2000‐2024). The GraphRAG prototype integrated entity extraction, KG construction using Neo4j, and retrieval-augmented response generation. The performance was evaluated in a simulated environment using clinical and layperson prompts, comparing the outputs of the systems against ChatGPT (OpenAI), Claude (Anthropic), and BioMistral models across 5 common natural language generation metrics.ResultsThe GraphRAG-enabled local LLM showed higher accuracy in generating clinically relevant responses. It achieved a bilingual evaluation understudy score of 0.99, Jaccard similarity of 0.98, and BERTScore of 0.98, outperforming the benchmark LLMs. The prototype also produced accurate, evidence-based recommendations for clinicians and patients, demonstrating its feasibility as a clinical support tool.ConclusionsGraphRAG-enabled local LLMs show much potential for improving personalized GDM care by integrating domain-specific evidence and contextual retrieval. Our prototype proof-of-concept serves two purposes: (1) the local LLM architecture gives practitioners from underserved locations access to state-of-the-art medical research in the treatment of chronic conditions and (2) the KG schema may be feasibly built on peer-reviewed, indexed publications, devoid of hallucinations and contextualized with patient data. We conclude that advanced AI techniques such as KGs, retrieval-augmented generation, and local LLMs improve GDM management decisions and other similar conditions and advance equitable health care delivery in resource-constrained health care environments.