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自然语言处理在放射学报告中的应用的系统评价。

A systematic review of natural language processing applied to radiology reports.

机构信息

School of Literatures, Languages and Cultures (LLC), University of Edinburgh, Edinburgh, Scotland.

Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland.

出版信息

BMC Med Inform Decis Mak. 2021 Jun 3;21(1):179. doi: 10.1186/s12911-021-01533-7.


DOI:10.1186/s12911-021-01533-7
PMID:34082729
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8176715/
Abstract

BACKGROUND: Natural language processing (NLP) has a significant role in advancing healthcare and has been found to be key in extracting structured information from radiology reports. Understanding recent developments in NLP application to radiology is of significance but recent reviews on this are limited. This study systematically assesses and quantifies recent literature in NLP applied to radiology reports. METHODS: We conduct an automated literature search yielding 4836 results using automated filtering, metadata enriching steps and citation search combined with manual review. Our analysis is based on 21 variables including radiology characteristics, NLP methodology, performance, study, and clinical application characteristics. RESULTS: We present a comprehensive analysis of the 164 publications retrieved with publications in 2019 almost triple those in 2015. Each publication is categorised into one of 6 clinical application categories. Deep learning use increases in the period but conventional machine learning approaches are still prevalent. Deep learning remains challenged when data is scarce and there is little evidence of adoption into clinical practice. Despite 17% of studies reporting greater than 0.85 F1 scores, it is hard to comparatively evaluate these approaches given that most of them use different datasets. Only 14 studies made their data and 15 their code available with 10 externally validating results. CONCLUSIONS: Automated understanding of clinical narratives of the radiology reports has the potential to enhance the healthcare process and we show that research in this field continues to grow. Reproducibility and explainability of models are important if the domain is to move applications into clinical use. More could be done to share code enabling validation of methods on different institutional data and to reduce heterogeneity in reporting of study properties allowing inter-study comparisons. Our results have significance for researchers in the field providing a systematic synthesis of existing work to build on, identify gaps, opportunities for collaboration and avoid duplication.

摘要

背景:自然语言处理(NLP)在推进医疗保健方面发挥着重要作用,并且已被证明是从放射学报告中提取结构化信息的关键。了解 NLP 在放射学中的应用的最新进展具有重要意义,但最近对此类主题的综述有限。本研究系统评估和量化了 NLP 在放射学报告中的应用的最新文献。

方法:我们使用自动过滤、元数据丰富步骤和引文搜索相结合的方法进行自动文献搜索,生成了 4836 个结果,并结合手动审查。我们的分析基于 21 个变量,包括放射学特征、NLP 方法、性能、研究和临床应用特征。

结果:我们对检索到的 164 篇出版物进行了全面分析,2019 年的出版物几乎是 2015 年的三倍。每篇出版物都归入 6 个临床应用类别之一。在该时期,深度学习的使用有所增加,但传统的机器学习方法仍然很普遍。在数据稀缺且几乎没有采用到临床实践的证据的情况下,深度学习仍然具有挑战性。尽管有 17%的研究报告的 F1 得分大于 0.85,但由于它们大多使用不同的数据集,因此很难对这些方法进行比较评估。只有 14 项研究提供了数据,15 项研究提供了代码,其中 10 项研究提供了外部验证结果。

结论:自动理解放射学报告的临床描述具有增强医疗保健流程的潜力,我们表明该领域的研究继续增长。如果该领域要将应用程序推向临床应用,则模型的可重复性和可解释性很重要。可以做更多的工作来共享代码,从而能够在不同机构的数据上验证方法,并减少研究属性报告的异质性,从而实现研究之间的比较。我们的研究结果对于该领域的研究人员具有重要意义,为他们提供了对现有工作的系统综合,以建立基础、识别差距、合作机会并避免重复。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d73/8176715/bf0a7a44d864/12911_2021_1533_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d73/8176715/b214d6053ed8/12911_2021_1533_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d73/8176715/7dc545f0118f/12911_2021_1533_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d73/8176715/b01cefc3ed25/12911_2021_1533_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d73/8176715/4cf5c6e6317a/12911_2021_1533_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d73/8176715/bf0a7a44d864/12911_2021_1533_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d73/8176715/b214d6053ed8/12911_2021_1533_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d73/8176715/7dc545f0118f/12911_2021_1533_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d73/8176715/b01cefc3ed25/12911_2021_1533_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d73/8176715/4cf5c6e6317a/12911_2021_1533_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d73/8176715/bf0a7a44d864/12911_2021_1533_Fig5_HTML.jpg

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本文引用的文献

[1]
Explainable automated coding of clinical notes using hierarchical label-wise attention networks and label embedding initialisation.

J Biomed Inform. 2021-4

[2]
tbiExtractor: A framework for extracting traumatic brain injury common data elements from radiology reports.

PLoS One. 2020-7-1

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Machine learning and natural language processing methods to identify ischemic stroke, acuity and location from radiology reports.

PLoS One. 2020-6-19

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Explainable artificial intelligence models using real-world electronic health record data: a systematic scoping review.

J Am Med Inform Assoc. 2020-7-1

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Deep Learning for Natural Language Processing in Radiology-Fundamentals and a Systematic Review.

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J Am Med Inform Assoc. 2020-3-1

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Natural Language Processing to Assess Palliative Care and End-of-Life Process Measures in Patients With Breast Cancer With Leptomeningeal Disease.

Am J Hosp Palliat Care. 2020-5

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Methods Inf Med. 2019-9

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