Resources


Software Open Access

De-Identification Software Package

The deid software package includes code and dictionaries for automated location and removal of protected health information (PHI) in free text from medical records.

phi deidentification anonymization

Published: Dec. 18, 2007. Version: 1.1

Database Restricted Access

CXRGraph: Using Information Extraction to Normalize the Training Data for Automatic Radiology Report Generation

Yuxiang Liao, Hoisang Heung, Hantao Liu, et al.

CXRGraph is a structured radiology report dataset built upon RadGraph and tailored for the Automatic Radiology Report Generation task. It can identify more task-relevant information such as abnormalities and hallucinated prior references.

relation extraction information extraction natural language processing named entity recognition structured radiology report

Published: Feb. 3, 2025. Version: 1.0.0

Database Credentialed Access

MIMIC-CXR Database

Alistair Johnson, Tom Pollard, Roger Mark, et al.

Chest radiographs in DICOM format with associated free-text reports.

computer vision chest x-rays natural language processing machine learning radiology mimic

Published: July 23, 2024. Version: 2.1.0

Database Credentialed Access

MIMIC-CXR-JPG - chest radiographs with structured labels

Alistair Johnson, Matthew Lungren, Yifan Peng, et al.

Chest x-rays in JPG format with structured labels derived from the associated radiology report.

computer vision chest x-ray radiology mimic deep learning

Published: March 12, 2024. Version: 2.1.0

Database Credentialed Access

RadCoref: Fine-tuning coreference resolution for different styles of clinical narratives

Yuxiang Liao, Hantao Liu, Irena Spasic

RadCoref is a small subset of MIMIC-CXR with manually annotated coreference mentions and clusters. Based on the annotated data, we fine-tuned a deep neural model and used it to annotate the whole MIMIC-CXR dataset. Both data are available.

natural language processing coreference resolution radiology

Published: Jan. 30, 2024. Version: 1.0.0

Database Credentialed Access

Annotation dataset of social determinants of health from MIMIC-III Clinical Care Database

Marco Guevara, Shan Chen, Spencer Thomas, et al.

Annotation dataset of social determinants of health from MIMC-III Clinical Care Database notes.

natural language processing social determinants of health

Published: Jan. 24, 2024. Version: 1.0.1

Database Credentialed Access

CXR-PRO: MIMIC-CXR with Prior References Omitted

Vignav Ramesh, Nathan Chi, Pranav Rajpurkar

CXR-PRO is an adaptation of the MIMIC-CXR dataset (consisting of chest radiographs and their associated free-text radiology reports) with references to non-existent priors removed.

generation free-text radiology reports references to priors retrieval large language models

Published: Nov. 23, 2022. Version: 1.0.0

Database Credentialed Access

Learning to Ask Like a Physician: a Discharge Summary Clinical Questions (DiSCQ) Dataset

Eric Lehman

Dataset of questions asked by medical experts about patients. Medical experts will read a discharge summary line-by-line and (1) ask any question that they may have and (2) record what in the text "triggered" them to ask their question.

question generation question answering machine learning

Published: July 28, 2022. Version: 1.0

Model Credentialed Access

Clinical BERT Models Trained on Pseudo Re-identified MIMIC-III Notes

Eric Lehman, Sarthak Jain, Karl Pichotta, et al.

We explore recovering sensitive info from BERT trained over non-deidentified EHR. We make our models and data available to further facilitate research.

Published: April 28, 2021. Version: 1.0.0

Database Credentialed Access

Deidentified Medical Text

Margaret Douglass, Bill Long, George Moody, et al.

Gold standard corpus of 2,434 deidentified nursing notes

medical text nursing notes hipaa de-identification

Published: Dec. 18, 2007. Version: 1.0