Recent advancements in Large Language Models (LLMs) have showcased their proficiency in answering natural language queries. However, their effectiveness is hindered by limited domain-specific knowledge, raising concerns about the reliability of their responses. We introduce a hybrid system that augments LLMs with domain-specific knowledge graphs (KGs), thereby aiming to enhance factual correctness using a KG-based retrieval approach. We focus on a medical KG to demonstrate our methodology, which includes (1) pre-processing, (2) Cypher query generation, (3) Cypher query processing, (4) KG retrieval, and (5) LLM-enhanced response generation. We evaluate our system on a curated dataset of 69 samples, achieving a precision of 78% in retrieving correct KG nodes. Our findings indicate that the hybrid system surpasses a standalone LLM in accuracy and completeness, as verified by an LLM-as-a-Judge evaluation method. This positions the system as a promising tool for applications that demand factual correctness and completeness, such as target identification — a critical process in pinpointing biological entities for disease treatment or crop enhancement. Moreover, its intuitive search interface and ability to provide accurate responses within seconds make it well-suited for time-sensitive, precision-focused research contexts. We publish the source code together with the dataset and the prompt templates used.

Large language models (LLMs) have recently become the leading source of answers for users’ questions online. Despite their ability to offer eloquent answers, their accuracy and reliability can pose a significant challenge. This is especially true for sensitive domains such as biomedicine, where there is a higher need for factually correct answers. This paper introduces a biomedical retrieval-augmented generation (RAG) system designed to enhance the reliability of generated responses. The system is based on a fine-tuned LLM for the referenced question-answering, where retrieved relevant abstracts from PubMed are passed to LLM’s context as input through a prompt. Its output is an answer based on PubMed abstracts, where each statement is referenced accordingly, allowing the users to verify the answer. Our retrieval system achieves an absolute improvement of 23% compared to the PubMed search engine. Based on the manual evaluation on a small sample, our fine-tuned LLM component achieves comparable results to GPT-4 Turbo in referencing relevant abstracts. We make the dataset used to fine-tune the models and the fine-tuned models based on Mistral-7B-instruct-v0.1 and v0.2 publicly available.