{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/a-benchmark-of-domain-adapted-large-language","title":"A Dataset and Benchmark for Hospital Course Summarization with Adapted Large Language Models","arxiv_id":"2403.05720","date":"2024-03-08","proceeding":null,"authors":["Asad Aali","Dave Van Veen","Yamin Ishraq Arefeen","Jason Hom","Christian Bluethgen","Eduardo Pontes Reis","Sergios Gatidis","Namuun Clifford","Joseph Daws","Arash S. Tehrani","Jangwon Kim","Akshay S. Chaudhari"],"abstract":"Brief hospital course (BHC) summaries are clinical documents that summarize a patient's hospital stay. While large language models (LLMs) depict remarkable capabilities in automating real-world tasks, their capabilities for healthcare applications such as synthesizing BHCs from clinical notes have not been shown. We introduce a novel pre-processed dataset, the MIMIC-IV-BHC, encapsulating clinical note and brief hospital course (BHC) pairs to adapt LLMs for BHC synthesis. Furthermore, we introduce a benchmark of the summarization performance of two general-purpose LLMs and three healthcare-adapted LLMs. Using clinical notes as input, we apply prompting-based (using in-context learning) and fine-tuning-based adaptation strategies to three open-source LLMs (Clinical-T5-Large, Llama2-13B, FLAN-UL2) and two proprietary LLMs (GPT-3.5, GPT-4). We evaluate these LLMs across multiple context-length inputs using natural language similarity metrics. We further conduct a clinical study with five clinicians, comparing clinician-written and LLM-generated BHCs across 30 samples, focusing on their potential to enhance clinical decision-making through improved summary quality. We observe that the Llama2-13B fine-tuned LLM outperforms other domain-adapted models given quantitative evaluation metrics of BLEU and BERT-Score. GPT-4 with in-context learning shows more robustness to increasing context lengths of clinical note inputs than fine-tuned Llama2-13B. Despite comparable quantitative metrics, the reader study depicts a significant preference for summaries generated by GPT-4 with in-context learning compared to both Llama2-13B fine-tuned summaries and the original summaries, highlighting the need for qualitative clinical evaluation.","url_abs":"https://arxiv.org/abs/2403.05720v4","url_pdf":"https://arxiv.org/pdf/2403.05720v4.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"a-benchmark-of-domain-adapted-large-language","repo_url":"https://github.com/stanfordmimi/clin-bhc-summ","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"in-context-learning","task_name":"In-Context Learning"}],"methods":[{"method_slug":"absolute-position-encodings","method_name":"Absolute Position Encodings"},{"method_slug":"adam","method_name":"Adam"},{"method_slug":"attention","method_name":"Attention"},{"method_slug":"bpe","method_name":"BPE"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"gpt-4","method_name":"GPT-4"},{"method_slug":"label-smoothing","method_name":"Label Smoothing"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"position-wise-feed-forward-layer","method_name":"Position-Wise Feed-Forward Layer"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"transformer","method_name":"Transformer"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}