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.

Electronic health records (EHR) and claims data are rich sources of real-world data that reflect patient health status and healthcare utilization. Querying these databases to answer epidemiological questions is challenging due to the intricacy of medical terminology and the need for complex SQL queries. Here, we introduce an end-to-end methodology that combines text-to-SQL generation with retrieval augmented generation (RAG) to answer epidemiological questions using EHR and claims data. We show that our approach, which integrates a medical coding step into the text-to-SQL process, significantly improves the performance over simple prompting. Our findings indicate that although current language models are not yet sufficiently accurate for unsupervised use, RAG offers a promising direction for improving their capabilities, as shown in a realistic industry setting.

Medical coding (MC) is an essential pre-requisite for reliable data retrieval and reporting. Given a free-text reported term (RT) such as “pain of right thigh to the knee”, the task is to identify the matching lowest-level term (LLT) –in this case “unilateral leg pain”– from a very large and continuously growing repository of standardized medical terms. However, automating this task is challenging due to a large number of LLT codes (as of writing over 80\,000), limited availability of training data for long tail/emerging classes, and the general high accuracy demands of the medical domain.With this paper, we introduce the MC task, discuss its challenges, and present a novel approach called xTARS that combines traditional BERT-based classification with a recent zero/few-shot learning approach (TARS). We present extensive experiments that show that our combined approach outperforms strong baselines, especially in the few-shot regime. The approach is developed and deployed at Bayer, live since November 2021. As we believe our approach potentially promising beyond MC, and to ensure reproducibility, we release the code to the research community.

Data-to-text (D2T) generation in the biomedical domain is a promising - yet mostly unexplored - field of research. Here, we apply neural models for D2T generation to a real-world dataset consisting of package leaflets of European medicines. We show that fine-tuned transformers are able to generate realistic, multi-sentence text from data in the biomedical domain, yet have important limitations. We also release a new dataset (BioLeaflets) for benchmarking D2T generation models in the biomedical domain.