Irfan Al-Hussaini
2023
Zero-Shot Information Extraction for Clinical Meta-Analysis using Large Language Models
David Kartchner
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Selvi Ramalingam
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Irfan Al-Hussaini
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Olivia Kronick
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Cassie Mitchell
The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks
Meta-analysis of randomized clinical trials (RCTs) plays a crucial role in evidence-based medicine but can be labor-intensive and error-prone. This study explores the use of large language models to enhance the efficiency of aggregating results from randomized clinical trials (RCTs) at scale. We perform a detailed comparison of the performance of these models in zero-shot prompt-based information extraction from a diverse set of RCTs to traditional manual annotation methods. We analyze the results for two different meta-analyses aimed at drug repurposing in cancer therapy pharmacovigilience in chronic myeloid leukemia. Our findings reveal that the best model for the two demonstrated tasks, ChatGPT can generally extract correct information and identify when the desired information is missing from an article. We additionally conduct a systematic error analysis, documenting the prevalence of diverse error types encountered during the process of prompt-based information extraction.
Pathology Dynamics at BioLaySumm: the trade-off between Readability, Relevance, and Factuality in Lay Summarization
Irfan Al-Hussaini
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Austin Wu
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Cassie Mitchell
The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks
Lay summarization aims to simplify complex scientific information for non-expert audiences. This paper investigates the trade-off between readability and relevance in the lay summarization of long biomedical documents. We introduce a two-stage framework that attains the best readability metrics in the first subtask of BioLaySumm 2023, with 8.924 FleschKincaid Grade Level and 9.188 DaleChall Readability Score. However, this comes at the cost of reduced relevance and factuality, emphasizing the inherent challenges of balancing readability and content preservation in lay summarization. The first stage generates summaries using a large language model, such as BART with LSG attention. The second stage uses a zero-shot sentence simplification method to improve the readability of the summaries. In the second subtask, a hybrid dataset is employed to train a model capable of generating both lay summaries and abstracts. This approach achieves the best readability score and shares the top overall rank with other leading methods. Our study underscores the importance of developing effective methods for creating accessible lay summaries while maintaining information integrity. Future work will integrate simplification and summary generation within a joint optimization framework that generates high-quality lay summaries that effectively communicate scientific content to a broader audience.
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