Clinical abstractive summarization struggles to balance faithfulness and informativeness, sacrificing key information or introducing confabulations. Techniques like in-context learning and fine-tuning have improved overall summary quality orthogonally, without considering the above issue. Conversely, methods aimed at improving faithfulness and informativeness, such as model reasoning and self improvement, have not been systematically evaluated in the clinical domain. We address this gap by first performing a comprehensive benchmark and study of six advanced abstractive summarization methods across three datasets using five reference-based and reference-free metrics, with the latter specifically assessing faithfulness and informativeness. Based on its findings we then develop uMedSum, a modular hybrid framework introducing novel approaches for sequential confabulation removal and key information addition. Our work outperforms previous GPT-4-based state-of-the-art (SOTA) methods in both quantitative metrics and expert evaluations, achieving an 11.8% average improvement in dedicated faithfulness metrics over the previous SOTA. Doctors prefer uMedSum’s summaries 6 times more than previous SOTA in difficult cases containing confabulations or missing information. These results highlight uMedSum’s effectiveness and generalizability across various datasets and metrics, marking a significant advancement in clinical summarization. uMedSum toolkit is made available on GitHub.

Large language models (LLMs) have demonstrated remarkable capabilities across various domains, yet their application to relational deep learning (RDL) remains underexplored. Existing approaches adapt LLMs by traversing relational links between entities in a database and converting the structured data into flat text documents, but this text-based serialization disregards critical relational structures, introduces redundancy, and often exceeds standard LLM context lengths. We introduce Rel-LLM, a novel architecture that employs a graph neural network (GNN) based encoder to create structured relational prompts for LLMs within a retrieval-augmented generation (RAG) framework. Unlike traditional text-based serialization approaches, our method preserves the inherent relational structure of databases while enabling LLMs to effectively process and reason over complex entity relationships. Specifically, the GNN encoder extracts a local subgraph around an entity to build feature representations that contain relevant entity relationships and temporal dependencies. These representations are transformed into structured prompts using a denormalization process, effectively allowing the LLM to reason over relational structures. Through extensive experiments, we demonstrate that Rel-LLM outperforms existing methods on key RDL tasks, offering a scalable and efficient approach to integrating LLMs with structured data sources. Code is available at https://github.com/smiles724/Rel-LLM.

There is vivid research on adapting Large Language Models (LLMs) to perform a variety of tasks in high-stakes domains such as healthcare. Despite their popularity, there is a lack of understanding of the extent and contributing factors that allow LLMs to recall relevant knowledge and combine it with presented information in the clinical and biomedical domain: a fundamental pre-requisite for success on down-stream tasks.Addressing this gap, we use Multiple Choice and Abstractive Question Answering to conduct a large-scale empirical study on 22 datasets in three generalist and three specialist biomedical sub-domains. Our multifaceted analysis of the performance of 15 LLMs, further broken down by sub-domain, source of knowledge and model architecture, uncovers success factors such as instruction tuning that lead to improved recall and comprehension. We further show that while recently proposed domain-adapted models may lack adequate knowledge, directly fine-tuning on our collected medical knowledge datasets shows encouraging results, even generalising to unseen specialist sub-domains. We complement the quantitative results with a skill-oriented manual error analysis, which reveals a significant gap between the models’ capabilities to simply recall necessary knowledge and to integrate it with the presented context.To foster research and collaboration in this field we share M-QALM, our resources, standardised methodology, and evaluation results, with the research community to facilitate further advancements in clinical knowledge representation learning within language models.