🚀 斯坦福去标识符工具
斯坦福去标识符工具在多种放射学和生物医学文档上进行训练,旨在自动化去识别过程,同时达到足以投入生产使用的令人满意的准确率。相关论文正在发表中。
🚀 快速开始
斯坦福去标识符工具可用于对放射学和生物医学文档进行去识别处理,以保护患者的健康信息。
✨ 主要特性
- 多类型文档支持:可处理多种放射学和生物医学文档。
- 自动化去识别:能够自动检测受保护的健康信息(PHI)实体,并将其替换为看似合理的替代信息。
- 高准确率:在多个测试集上取得了出色的F1分数,能有效识别和处理PHI信息。
📚 详细文档
示例数据
widget:
- text: "PROCEDURE: Chest xray. COMPARISON: last seen on 1/1/2020 and also record dated of March 1st, 2019. FINDINGS: patchy airspace opacities. IMPRESSION: The results of the chest xray of January 1 2020 are the most concerning ones. The patient was transmitted to another service of UH Medical Center under the responsability of Dr. Perez. We used the system MedClinical data transmitter and sent the data on 2/1/2020, under the ID 5874233. We received the confirmation of Dr Perez. He is reachable at 567-493-1234."
- text: "Dr. Curt Langlotz chose to schedule a meeting on 06/23."
tags:
- token-classification
- sequence-tagger-model
- pytorch
- transformers
- pubmedbert
- uncased
- radiology
- biomedical
datasets:
- radreports
language:
- en
license: mit
关联仓库
关联的GitHub仓库:https://github.com/MIDRC/Stanford_Penn_Deidentifier
引用信息
@article{10.1093/jamia/ocac219,
author = {Chambon, Pierre J and Wu, Christopher and Steinkamp, Jackson M and Adleberg, Jason and Cook, Tessa S and Langlotz, Curtis P},
title = "{Automated deidentification of radiology reports combining transformer and “hide in plain sight” rule-based methods}",
journal = {Journal of the American Medical Informatics Association},
year = {2022},
month = {11},
abstract = "{To develop an automated deidentification pipeline for radiology reports that detect protected health information (PHI) entities and replaces them with realistic surrogates “hiding in plain sight.”In this retrospective study, 999 chest X-ray and CT reports collected between November 2019 and November 2020 were annotated for PHI at the token level and combined with 3001 X-rays and 2193 medical notes previously labeled, forming a large multi-institutional and cross-domain dataset of 6193 documents. Two radiology test sets, from a known and a new institution, as well as i2b2 2006 and 2014 test sets, served as an evaluation set to estimate model performance and to compare it with previously released deidentification tools. Several PHI detection models were developed based on different training datasets, fine-tuning approaches and data augmentation techniques, and a synthetic PHI generation algorithm. These models were compared using metrics such as precision, recall and F1 score, as well as paired samples Wilcoxon tests.Our best PHI detection model achieves 97.9 F1 score on radiology reports from a known institution, 99.6 from a new institution, 99.5 on i2b2 2006, and 98.9 on i2b2 2014. On reports from a known institution, it achieves 99.1 recall of detecting the core of each PHI span.Our model outperforms all deidentifiers it was compared to on all test sets as well as human labelers on i2b2 2014 data. It enables accurate and automatic deidentification of radiology reports.A transformer-based deidentification pipeline can achieve state-of-the-art performance for deidentifying radiology reports and other medical documents.}",
issn = {1527-974X},
doi = {10.1093/jamia/ocac219},
url = {https://doi.org/10.1093/jamia/ocac219},
note = {ocac219},
eprint = {https://academic.oup.com/jamia/advance-article-pdf/doi/10.1093/jamia/ocac219/47220191/ocac219.pdf},
}
📄 许可证
本项目采用MIT许可证。