bims-arines 2024-10-27 papers

Issue of 2024–10–27
three papers selected by
Farhad Shokraneh

JMIR Med Inform. 2024 Oct 23. 12 e54653

Accelerating Evidence Synthesis in Observational Studies: Development of a Living Natural Language Processing-Assisted Intelligent Systematic Literature Review System.

Frank J Manion, Jingcheng Du, Dong Wang, Long He, Bin Lin, Jingqi Wang, Siwei Wang, David Eckels, Jan Cervenka, Peter C Fiduccia, Nicole Cossrow, Lixia Yao.

Background: Systematic literature review (SLR), a robust method to identify and summarize evidence from published sources, is considered to be a complex, time-consuming, labor-intensive, and expensive task.
Objective: This study aimed to present a solution based on natural language processing (NLP) that accelerates and streamlines the SLR process for observational studies using real-world data.
Methods: We followed an agile software development and iterative software engineering methodology to build a customized intelligent end-to-end living NLP-assisted solution for observational SLR tasks. Multiple machine learning-based NLP algorithms were adopted to automate article screening and data element extraction processes. The NLP prediction results can be further reviewed and verified by domain experts, following the human-in-the-loop design. The system integrates explainable articificial intelligence to provide evidence for NLP algorithms and add transparency to extracted literature data elements. The system was developed based on 3 existing SLR projects of observational studies, including the epidemiology studies of human papillomavirus-associated diseases, the disease burden of pneumococcal diseases, and cost-effectiveness studies on pneumococcal vaccines.
Results: Our Intelligent SLR Platform covers major SLR steps, including study protocol setting, literature retrieval, abstract screening, full-text screening, data element extraction from full-text articles, results summary, and data visualization. The NLP algorithms achieved accuracy scores of 0.86-0.90 on article screening tasks (framed as text classification tasks) and macroaverage F1 scores of 0.57-0.89 on data element extraction tasks (framed as named entity recognition tasks).
Conclusions: Cutting-edge NLP algorithms expedite SLR for observational studies, thus allowing scientists to have more time to focus on the quality of data and the synthesis of evidence in observational studies. Aligning the living SLR concept, the system has the potential to update literature data and enable scientists to easily stay current with the literature related to observational studies prospectively and continuously.

Keywords: artificial intelligence; data extraction; deep learning; epidemiology; machine learning; natural language processing; software development; systematic literature review

DOI: https://doi.org/10.2196/54653

IEEE J Biomed Health Inform. 2024 Oct 21. PP

Benchmarking Large Language Models in Evidence-Based Medicine.

Jin Li, Yiyan Deng, Qi Sun, Junjie Zhu, Yu Tian, Jingsong Li, Tingting Zhu.

Evidence-based medicine (EBM) represents a paradigm of providing patient care grounded in the most current and rigorously evaluated research. Recent advances in large language models (LLMs) offer a potential solution to transform EBM by automating labor-intensive tasks and thereby improving the efficiency of clinical decision-making. This study explores integrating LLMs into the key stages in EBM, evaluating their ability across evidence retrieval (PICO extraction, biomedical question answering), synthesis (summarizing randomized controlled trials), and dissemination (medical text simplification). We conducted a comparative analysis of seven LLMs, including both proprietary and open-source models, as well as those fine-tuned on medical corpora. Specifically, we benchmarked the performance of various LLMs on each EBM task under zero-shot settings as baselines, and employed prompting techniques, including in-context learning, chain-of-thought reasoning, and knowledge-guided prompting to enhance their capabilities. Our extensive experiments revealed the strengths of LLMs, such as remarkable understanding capabilities even in zero-shot settings, strong summarization skills, and effective knowledge transfer via prompting. Promoting strategies such as knowledge-guided prompting proved highly effective (e.g., improving the performance of GPT-4 by 13.10% over zero-shot in PICO extraction). However, the experiments also showed limitations, with LLM performance falling well below state-of-the-art baselines like PubMedBERT in handling named entity recognition tasks. Moreover, human evaluation revealed persisting challenges with factual inconsistencies and domain inaccuracies, underscoring the need for rigorous quality control before clinical application. This study provides insights into enhancing EBM using LLMs while highlighting critical areas for further research. The code is publicly available on Github.

DOI: https://doi.org/10.1109/JBHI.2024.3483816