Resources


Model Credentialed Access

Characterization of Stigmatizing Language in Medical Records

Keith Harrigian, Ayah Zirikly, Brant Chee, Alya Ahmad, Anne Links, Somnath Saha, Mary Catherine Beach, Mark Dredze

A suite of classifiers for detecting three types of stigmatizing language in electronic medical records. Trained on MIMIC-IV discharge notes.

clinical natural language processing domain transfer bias stigmatizing language large language models mimic

Published: Nov. 6, 2023. Version: 1.0.0

Database Contributor Review

CARMEN-I: A resource of anonymized electronic health records in Spanish and Catalan for training and testing NLP tools

Eulalia Farre Maduell, Salvador Lima-Lopez, Santiago Andres Frid, Artur Conesa, Elisa Asensio, Antonio Lopez-Rueda, Helena Arino, Elena Calvo, Maria Jesús Bertran, Maria Angeles Marcos, Montserrat Nofre Maiz, Laura Tañá Velasco, Antonia Marti, Ricardo Farreres, Xavier Pastor, Xavier Borrat Frigola, Martin Krallinger

CARMEN-I is a Spanish corpus of 2,000 clinical records from Hospital Clínic, Barcelona. It covers COVID-19 patients and comorbidities, serving as a resource for training clinical NLP models and researchers in NLP applied to clinical documents.

de-identification clinical ner anonymization

Published: April 20, 2024. Version: 1.0.1

Database Contributor Review

CARMEN-I: A resource of anonymized electronic health records in Spanish and Catalan for training and testing NLP tools

Eulalia Farre Maduell, Salvador Lima-Lopez, Santiago Andres Frid, Artur Conesa, Elisa Asensio, Antonio Lopez-Rueda, Helena Arino, Elena Calvo, Maria Jesús Bertran, Maria Angeles Marcos, Montserrat Nofre Maiz, Laura Tañá Velasco, Antonia Marti, Ricardo Farreres, Xavier Pastor, Xavier Borrat Frigola, Martin Krallinger

CARMEN-I is a Spanish corpus of 2,000 clinical records from Hospital Clínic, Barcelona. It covers COVID-19 patients and comorbidities, serving as a resource for training clinical NLP models and researchers in NLP applied to clinical documents.

de-identification clinical ner anonymization

Published: April 20, 2024. Version: 1.0.1

Model Credentialed Access

What's in a Note? Unpacking Predictive Value in Clinical Note Representations

Tristan Naumann, William Boag

Word vectors corresponding to the AMIA 2018 Informatics Summit paper of the same name.

Published: Jan. 7, 2018. Version: 0.1

Challenge Credentialed Access

ShAReCLEF eHealth 2013: Natural Language Processing and Information Retrieval for Clinical Care

Danielle Mowery

2013 ShARe/CLEF eHealth Evaluation Lab: Natural Language Processing and Information Retrieval for Clinical Care (Tasks 1 and 2).

natural language processing

Published: Feb. 15, 2013. Version: 1.0

Database Credentialed Access

Tasks 1 and 3 from Progress Note Understanding Suite of Tasks: SOAP Note Tagging and Problem List Summarization

Yanjun Gao, John Caskey, Timothy Miller, Brihat Sharma, Matthew Churpek, Dmitriy Dligach, Majid Afshar

We introduce a hierarchical annotation suite of tasks addressing clinical text understanding, reasoning and abstraction over evidence, and diagnosis summarization. One task is section tagging major section and the other task is diagnosis generation.

Published: Sept. 30, 2022. Version: 1.0.0

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

CXR-Align: A Benchmark for CXR-Report Alignment with Negations

Hanbin Ko

CXR-Align is a benchmark dataset created to evaluate vision-language models' capability to interpret negations in chest X-ray (CXR) reports, featuring systematically modified reports from MIMIC-CXR.

Published: Aug. 21, 2025. Version: 1.0.0

Database Credentialed Access

Annotation dataset of problematic opioid use and related contexts from MIMIC-III Critical Care Database discharge summaries

Melissa Poulsen, Vanessa Troiani, Philip Freda, Danielle Mowery, Anahita Davoudi

The database contains a corpus of annotated data from the MIMIC-III Critical Care Database from a study that aimed to develop and apply an annotation schema to characterize opioid use disorder and related contextual factors.

opioid use disorder substance use natural language processing clinical notes

Published: Feb. 8, 2023. Version: 1.0.0

Database Credentialed Access

CLIP: A Dataset for Extracting Action Items for Physicians from Hospital Discharge Notes

James Mullenbach, Yada Pruksachatkun, Sean Adler, Jennifer Seale, Jordan Swartz, T Greg McKelvey, Yi Yang, David Sontag

Clinical action items annotated over MIMIC-III. 718 discharge summaries are labeled at a sentence- and character-level with multiple action labels including Appointment, Lab, Procedure, Medication, Imaging, Patient Instructions, and Other.

Published: June 21, 2021. Version: 1.0.0