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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.
chest x-rays
computer vision
natural language processing
radiology
mimic
machine learning
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
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
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Maintained by the MIT Laboratory for Computational Physiology
Supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Heart Lung and Blood Institute (NHLBI), and NIH Office of the Director under NIH grant numbers U24EB037545 and R01EB030362
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