Munich Institute of Biomedical Engineering, Technical University of Munich, Garching b. München, Germany.
School of Computation, Information and Technology, Technical University of Munich, Garching b. München, Germany.
Rofo. 2024 Sep;196(9):956-965. doi: 10.1055/a-2234-8268. Epub 2024 Jan 31.
PURPOSE: The aim of this study was to develop an algorithm to automatically extract annotations from German thoracic radiology reports to train deep learning-based chest X-ray classification models. MATERIALS AND METHODS: An automatic label extraction model for German thoracic radiology reports was designed based on the CheXpert architecture. The algorithm can extract labels for twelve common chest pathologies, the presence of support devices, and "no finding". For iterative improvements and to generate a ground truth, a web-based multi-reader annotation interface was created. With the proposed annotation interface, a radiologist annotated 1086 retrospectively collected radiology reports from 2020-2021 (data set 1). The effect of automatically extracted labels on chest radiograph classification performance was evaluated on an additional, in-house pneumothorax data set (data set 2), containing 6434 chest radiographs with corresponding reports, by comparing a DenseNet-121 model trained on extracted labels from the associated reports, image-based pneumothorax labels, and publicly available data, respectively. RESULTS: Comparing automated to manual labeling on data set 1: "mention extraction" class-wise F1 scores ranged from 0.8 to 0.995, the "negation detection" F1 scores from 0.624 to 0.981, and F1 scores for "uncertainty detection" from 0.353 to 0.725. Extracted pneumothorax labels on data set 2 had a sensitivity of 0.997 [95 % CI: 0.994, 0.999] and specificity of 0.991 [95 % CI: 0.988, 0.994]. The model trained on publicly available data achieved an area under the receiver operating curve (AUC) for pneumothorax classification of 0.728 [95 % CI: 0.694, 0.760], while the models trained on automatically extracted labels and on manual annotations achieved values of 0.858 [95 % CI: 0.832, 0.882] and 0.934 [95 % CI: 0.918, 0.949], respectively. CONCLUSION: Automatic label extraction from German thoracic radiology reports is a promising substitute for manual labeling. By reducing the time required for data annotation, larger training data sets can be created, resulting in improved overall modeling performance. Our results demonstrated that a pneumothorax classifier trained on automatically extracted labels strongly outperformed the model trained on publicly available data, without the need for additional annotation time and performed competitively compared to manually labeled data. KEY POINTS: · An algorithm for automatic German thoracic radiology report annotation was developed.. · Automatic label extraction is a promising substitute for manual labeling.. · The classifier trained on extracted labels outperformed the model trained on publicly available data.. ZITIERWEISE: · Wollek A, Hyska S, Sedlmeyr T et al. German CheXpert Chest X-ray Radiology Report Labeler. Fortschr Röntgenstr 2024; 196: 956 - 965.
目的:本研究旨在开发一种算法,以自动从德国胸部放射学报告中提取注释,从而训练基于深度学习的胸部 X 射线分类模型。
材料和方法:基于 CheXpert 架构,设计了一种用于德国胸部放射学报告的自动标签提取模型。该算法可以为 12 种常见的胸部病理、支撑设备的存在和“无发现”提取标签。为了进行迭代改进并生成真实标签,创建了一个基于网络的多读者注释界面。利用所提出的注释界面,一名放射科医生对 2020-2021 年回顾性收集的 1086 份放射学报告(数据集 1)进行了注释。通过比较分别使用从相关报告中提取的标签、基于图像的气胸标签和公开数据训练的 DenseNet-121 模型,评估自动提取标签对胸腔 X 射线分类性能的影响,该模型用于内部气胸数据集(数据集 2),该数据集包含 6434 张胸部 X 光片和相应的报告。
结果:与数据集 1 上的手动标注相比,“提及提取”的 F1 得分范围为 0.8 至 0.995,“否定检测”的 F1 得分范围为 0.624 至 0.981,“不确定性检测”的 F1 得分范围为 0.353 至 0.725。数据集 2 上提取的气胸标签的敏感性为 0.997 [95%CI:0.994,0.999],特异性为 0.991 [95%CI:0.988,0.994]。使用公开数据训练的模型在气胸分类的受试者工作特征曲线(AUC)下的面积为 0.728 [95%CI:0.694,0.760],而使用自动提取的标签和手动注释训练的模型的 AUC 值分别为 0.858 [95%CI:0.832,0.882]和 0.934 [95%CI:0.918,0.949]。
结论:从德国胸部放射学报告中自动提取标签是手动标注的有前途的替代方法。通过减少数据注释所需的时间,可以创建更大的训练数据集,从而提高整体建模性能。我们的结果表明,使用自动提取的标签训练的气胸分类器明显优于使用公开数据训练的模型,而无需额外的注释时间,并且与手动标记的数据相比具有竞争力。
关键点: · 开发了一种用于自动德国胸部放射学报告注释的算法。 · 自动标签提取是手动标注的有前途的替代方法。 · 使用提取的标签训练的分类器优于使用公开数据训练的模型。
BMC Med Inform Decis Mak. 2022-4-15