Larissa Pusch

Larissa Pusch, Tim O. F. Conrad

Advancements in natural language processing have revolutionized the way we can interact with digital information systems, such as databases, making them more accessible. However, challenges persist, especially when accuracy is critical, as in the biomedical domain. A key issue is the hallucination problem, where models generate information unsupported by the underlying data, potentially leading to dangerous misinformation. This paper presents a novel approach designed to bridge this gap by combining Large Language Models (LLM) and Knowledge Graphs (KG) to improve the accuracy and reliability of question-answering systems, on the example of a biomedical KG. Built on the LangChain framework, our method incorporates a query checker that ensures the syntactical and semantic validity of LLM-generated queries, which are then used to extract information from a Knowledge Graph, substantially reducing errors like hallucinations. We evaluated the overall performance using a new benchmark dataset of 50 biomedical questions, testing several LLMs, including GPT-4 Turbo and llama3:70b. Our results indicate that while GPT-4 Turbo outperforms other models in generating accurate queries, open-source models like llama3:70b show promise with appropriate prompt engineering. To make this approach accessible, a user-friendly web-based interface has been developed, allowing users to input natural language queries, view generated and corrected Cypher queries, and verify the resulting paths for accuracy. Overall, this hybrid approach effectively addresses common issues such as data gaps and hallucinations, offering a reliable and intuitive solution for question answering systems. The source code for generating the results of this paper and for the user-interface can be found in our Git repository: https://git.zib.de/lpusch/cyphergenkg-gui

Larissa Pusch, Alexandre Courtiol, Tim Conrad

Large Language Models (LLMs) excel at language understanding but remain limited in knowledge-intensive domains due to hallucinations, outdated information, and limited explainability. Text-based retrieval-augmented generation (RAG) helps ground model outputs in external sources but struggles with multi-hop reasoning. Knowledge Graphs (KGs), in contrast, support precise, explainable querying, yet require a knowledge of query languages. This work introduces an interactive framework in which LLMs generate and explain Cypher graph queries and users iteratively refine them through natural language. Applied to real-world KGs, the framework improves accessibility to complex datasets while preserving factual accuracy and semantic rigor and provides insight into how model performance varies across domains. Our core quantitative evaluation is a 90-query benchmark on a synthetic movie KG that measures query explanation quality and fault detection across multiple LLMs, complemented by two smaller real-life query-generation experiments on a Hyena KG and the MaRDI (Mathematical Research Data Initiative) KG.