PhysioNet

Featured Resources

Software Open Access

Software for computing Heart Rate Fragmentation

Madalena Costa

Heart rate fragmentation: a new method for the analysis of cardiac interbeat interval time series. The code provided can be run in Windows, Mac and Linux machines.

heart rate variability aging cardiovascular disease vagal tone time series analysis prediction of atrial fibrillation cardiac autonomic function prediction of cardiovascular events prediction of cognitive decline heart rate fragmentation

Published: Feb. 14, 2024. Version: 1.0.0

Challenge Credentialed Access

SNOMED CT Entity Linking Challenge

Will Hardman, Mark Banks, Rory Davidson, Donna Truran, Nindya Widita Ayuningtyas, Hoa Ngo, Alistair Johnson, Tom Pollard

272 discharge notes from the MIMIC-IV-Note dataset annotated with SNOMED CT concepts.

snomed entity linking clinical annotation

Published: Dec. 19, 2023. Version: 1.0.0

Database Open Access

VitalDB, a high-fidelity multi-parameter vital signs database in surgical patients

Hyung-Chul Lee, Chul-Woo Jung

VitalDB, a high-fidelity multi-parameter vital signs database in surgical patients

waveform anesthesia vitaldb intraoperative biosignal ecg

Published: Sept. 21, 2022. Version: 1.0.0

Database Credentialed Access

MIMIC-IV

Alistair Johnson, Lucas Bulgarelli, Tom Pollard, Steven Horng, Leo Anthony Celi, Roger Mark

Large database of de-identified health information from patients admitted to Beth Israel Deaconess Medical Center

mimic critical care machine learning intensive care unit

Published: Jan. 6, 2023. Version: 2.2

Database Credentialed Access

MIMIC-CXR Database

Alistair Johnson, Tom Pollard, Roger Mark, Seth Berkowitz, Steven Horng

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

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

Published: Sept. 19, 2019. Version: 2.0.0

Database Credentialed Access

BRAX, a Brazilian labeled chest X-ray dataset

Eduardo Pontes Reis, Joselisa Paiva, Maria Carolina Bueno da Silva, Guilherme Alberto Sousa Ribeiro, Victor Fornasiero Paiva, Lucas Bulgarelli, Henrique Lee, Paulo Victor dos Santos, vanessa brito, Lucas Amaral, Gabriel Beraldo, Jorge Nebhan Haidar Filho, Gustavo Teles, Gilberto Szarf, Tom Pollard, Alistair Johnson, Leo Anthony Celi, Edson Amaro

BRAX contains 24,959 chest radiography exams and 40,967 images acquired in a large general Brazilian hospital. All images have been read by trained radiologists and 14 labels were derived from Brazilian Portuguese reports using NLP.

chest x-ray dataset artificial intelligence

Published: June 17, 2022. Version: 1.1.0

Latest Resources

Challenge Credentialed Access

Discharge Me: BioNLP ACL'24 Shared Task on Streamlining Discharge Documentation

Justin Xu

Data for the "Discharge Me!" Shared Task on Streamlining Discharge Documentation for BioNLP ACL'24

generation bionlp acl discharge summary

Published: April 12, 2024. Version: 1.3

Database Credentialed Access

EHRNoteQA: A Patient-Specific Question Answering Benchmark for Evaluating Large Language Models in Clinical Settings

Sunjun Kweon, Jiyoun Kim, Heeyoung Kwak, Dongchul Cha, Hangyul Yoon, Kwang Hyun Kim, Seunghyun Won, Edward Choi

A patient-specific question answering benchmark tailored for evaluating Large Language Models (LLMs) in clinical environments

Published: April 3, 2024. Version: 1.0.0

Database Credentialed Access

RaDialog Instruct Dataset

Chantal Pellegrini, Ege Özsoy, Benjamin Busam, Nassir Navab, Matthias Keicher

Image-based instruct data for Chest X-Ray understanding and analysis.

radiology report generation large vision-language models medical image understaning radiology assistant radiology chatbot

Published: March 25, 2024. Version: 1.0.0

Database Open Access

PADS - Parkinsons Disease Smartwatch dataset

Julian Varghese, Alexander Brenner, Lucas Plagwitz, Catharina van Alen, Michael Fujarski, Tobias Warnecke

The PADS dataset contains smartwatch-based records from interactive neurological assessments of Parkinsons disease patients, differential diagnoses and healthy controls. The data is complemented with non-motor symptoms and medical history information

wearables movement disorders parkinsons disease

Published: March 25, 2024. Version: 1.0.0

Database Open Access

ScientISST MOVE: Annotated Wearable Multimodal Biosignals recorded during Everyday Life Activities in Naturalistic Environments

João Areias Saraiva, Mariana Abreu, Ana Sofia Carmo, Hugo Plácido da Silva, Ana Fred

Multimodal (ECG, EMG, EDA, PPG, TEMP, ACC) biosignal dataset of everyday activities. Created with 3 wearable devices based on ScientISST Sense and Empatica E4.

multimodal wearable greet lift uncontrolled environments run jump gesticulate walk

Published: March 25, 2024. Version: 1.0.1

Model Credentialed Access

Asclepius-R : Clinical Large Language Model Built On MIMIC-III Discharge Summaries

Sunjun Kweon, Junu Kim, Jiyoun Kim, Sujeong Im, Eunbyeol Cho, Seongsu Bae, Jungwoo Oh, Gyubok Lee, Jong Hak Moon, Seng Chan You, Seungjin Baek, Chang Hoon Han, Yoon Bin Jung, Yohan Jo, Edward Choi

Asclepius: Publicly Available Clinical Large Language Models with Synthetic Clinical Notes Asclepius-R: A instruction-finetuned large language model with MIMIC-III clinical notes

clinical notes large language model synthetic clinical notes synthetic notes asclepius open-source llm clinical llm

Published: March 25, 2024. Version: 1.1.0

More resources

News

Network issues at MIT, impacting the availability of PhysioNet

April 9, 2024

We are currently experiencing network issues at MIT, impacting the availability of PhysioNet services. We apologize for any inconvenience this may cause and are working to resolve the issue as soon as we can.

George B. Moody PhysioNet Challenge 2024: Challenge Update - Partnering with Data Science Africa and

March 14, 2024

We are delighted to announce that the George B. Moody PhysioNet Challenges are partnering with Data Science Africa (DSA) and the IEEE Signal Processing Society's Challenges and Data Collections Committee (CDCC). The IEEE CDCC is supporting this year’s Challenge with additional cash prizes for participating teams from Africa and the Challenge organizers will be running a workshop at this year's annual DSA meeting in Kenya. In connection with this, the Challenge organizers will be running a workshop at DSA in Kenya from June 2-5th 2024. Please note that we are also accepting (and scoring) entries, and there are two deadlines coming up - April 8th to submit a preliminary entry to the Challenge and April 15th to submit a (placeholder) abstract to CinC.

Duke Critical Care Datathon: 13-14 April 2024

Feb. 7, 2024

Our colleagues at Duke are hosting a Critical Care Datathon on April 13-14, 2024. The Datathon is a collaborative two-day event that connects critical care clinicians with data scientists to develop pragmatic data-driven models using de-identified critical care electronic health record datasets.

Using de-identified critical care electronic health record datasets (including MIMIC and the eICU Collaborative Research Database), participants will develop new projects in 36 hours, from problem to abstract (and more)!

Participants will be organized into teams that are half-data science, half-clinical. You do not need to have a team; the organizers will help you find a team. Questions will be crowdsourced. No experience is required.

If you are a clinician, your interest, but not expertise, in data science is required.
If you are a data scientist, your interest, but not expertise, in healthcare and critical care is required.

For more information, see: https://sites.duke.edu/datathon2024/

CHIL 2024: Submit your paper by Friday, 16 February

Feb. 6, 2024

The 2024 Conference on Health, Inference, and Learning (CHIL) invites submissions focused on artificial intelligence and machine learning (AI/ML) techniques that address challenges in health, which includes clinical healthcare, public health, health economics, informatics, and more. For full details, refer to the online Call for Papers: https://www.chilconference.org/call-for-papers.html

This year, CHIL 2024 will accept submissions for three distinct tracks: Models and Methods, Applications and Practice, and Policy, Impact and Society. Accepted papers will be published in the Proceedings of Machine Learning Research (PMLR). We are also offering Best Paper Awards to recognize outstanding work across all tracks.

The deadline for submissions has been extended to: Friday, 16 Feb 2024 at 11:59pm AoE. Submit your paper at: https://openreview.net/group?id=chilconference.org/CHIL/2024/Conference

Conference on Health, Inference, and Learning (CHIL): Submit your paper by Mon 5 Feb, 2024!

Jan. 30, 2024

Submissions are due on February 5th, 11:59 PM EST in the form of anonymized PDF files. All submissions for CHIL 2024 will be managed through the OpenReview system. Similar to last year, we have a full author response period and reviewer discussion period to ensure proper feedback on the work.

Hosted by The Association of Health, Learning, and Inference (AHLI), the CHIL conferences have consistently served as premier scientific meetings, uniting clinicians and researchers from both industry and academia, and weaving a rich tapestry of knowledge and innovation.

Building on a series of conferences and events since 2019, CHIL has persistently set a benchmark in interdisciplinary research within the realms of machine learning and health, demonstrated through its impactful sessions (2020, 2021, 2022, 2023). Following the resounding success of CHIL 2023 at the Broad Institute, Cambridge, we are thrilled to announce that CHIL 2024 will continue fostering insightful discussions and collaborations in the field. The 5th annual conference will take place in-person from June 27-28 at the Verizon Executive Education Center at Cornell Tech in New York City.

Important Dates

Submissions due: Feb 5, 2024 at 11:59pm
Bidding opens for reviewers: Feb 6, 2024 at 11:59pm
Reviews released: Mar 4, 2024 by 11:59pm
Author/Reviewer discussion period: Mar 10-21, 2024
Author notification: Apr 3, 2024 by 11:59pm
CHIL conference: June 27-28, 2024