arXiv:2505.09794cs.CLcs.AI2025-05被引 1

用NLP自动提取肺癌与乳腺癌病历中的关键信息,提升医疗数据效率。

Automated Detection of Clinical Entities in Lung and Breast Cancer Reports Using NLP Techniques

  • 基于RoBERTa模型微调,实现病历文本中临床实体的自动识别。
  • 在乳腺癌和肺癌病历中整体准确率达90%以上,关键实体如MET、PAT识别效果佳。
  • 适合医疗数据工程师、临床研究者用于加速病历信息结构化处理。

癌症研究依赖从临床报告中手动提取信息,该过程耗时且易出错,限制了医疗数据驱动方法的效率。为解决此问题,自然语言处理(NLP)可自动化电子健康记录(EHR)中的数据提取。本研究聚焦高发的肺癌与乳腺癌,因其对公共健康影响重大,早期检测与有效数据管理至关重要。我们采用GMV公司NLP工具uQuery,其擅长识别临床文本中的实体并转化为SNOMED、OMOP等标准格式。uQuery不仅能检测与分类实体,还能关联否定、时间及患者相关信息。研究使用来自La Fe医院健康研究所的200份标注乳腺癌报告与400份肺癌报告,共600份文档,通过Doccano平台人工标注了8类临床实体。针对命名实体识别(NER),我们对基于RoBERTa的生物医学语言模型bsc-bio-ehr-en3进行微调,利用Transformers架构提升识别精度。结果表明,模型整体表现优异,尤其在识别如MET、PAT等高频实体方面效果突出,但低频实体如EVOL仍存在挑战。

原文摘要 · Abstract (English)

Research projects, including those focused on cancer, rely on the manual extraction of information from clinical reports. This process is time-consuming and prone to errors, limiting the efficiency of data-driven approaches in healthcare. To address these challenges, Natural Language Processing (NLP) offers an alternative for automating the extraction of relevant data from electronic health records (EHRs). In this study, we focus on lung and breast cancer due to their high incidence and the significant impact they have on public health. Early detection and effective data management in both types of cancer are crucial for improving patient outcomes. To enhance the accuracy and efficiency of data extraction, we utilized GMV's NLP tool uQuery, which excels at identifying relevant entities in clinical texts and converting them into standardized formats such as SNOMED and OMOP. uQuery not only detects and classifies entities but also associates them with contextual information, including negated entities, temporal aspects, and patient-related details. In this work, we explore the use of NLP techniques, specifically Named Entity Recognition (NER), to automatically identify and extract key clinical information from EHRs related to these two cancers. A dataset from Health Research Institute Hospital La Fe (IIS La Fe), comprising 200 annotated breast cancer and 400 lung cancer reports, was used, with eight clinical entities manually labeled using the Doccano platform. To perform NER, we fine-tuned the bsc-bio-ehr-en3 model, a RoBERTa-based biomedical linguistic model pre-trained in Spanish. Fine-tuning was performed using the Transformers architecture, enabling accurate recognition of clinical entities in these cancer types. Our results demonstrate strong overall performance, particularly in identifying entities like MET and PAT, although challenges remain with less frequent entities like EVOL.

医疗NLP命名实体识别癌症数据RoBERTa

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