Toronto Health Datathon (23-24 February 2023)
March 10, 2023
Over 45 students, academics, clinicians, and engineers gathered at the Google Canada offices on 23-24 February for the Toronto Health Datathon 2023. Participants used anonymized real-world data from Health Data Nexus to develop machine learning models aimed at solving real-world problems facing Canadian healthcare.
Over the past two years, PhysioNet has been collaborating with Temerty Centre for Artificial Intelligence Research and Education in Medicine (T-CAIREM) at the University of Toronto to develop the software that underpins both Health Data Nexus and PhysioNet. We look forward to continuing this collaboration, working towards tight integration between the two platforms.
Read more: https://datathon.healthdatanexus.ai/
Tokyo Datathon on Machine Learning in Healthcare (1-3 Sept 2023)
March 9, 2023
We are excited to be supporting the 3rd Tokyo Datathon on Machine Learning in Healthcare, co-organized by Tokyo Medical and Dental University and MIT Critical Data. The event will be held on 1-3 September 2023 and will bring together experts from across healthcare and data science to tackle clinical questions.
Registration and event details will be posted on the Datathon Website. If you are a Japanese-language speaker with experience with the MIMIC dataset and would be interested in helping as a mentor at the event, please reach out to Leo Anthony Celi.
PhysioNet 2023 Challenge Opening
Feb. 22, 2023
We are delighted to announce the opening of the George B. Moody PhysioNet Challenge 2023. This year’s Challenge invites teams to use electroencephalogram (EEG) recordings to predict the neurological recovery of patients from coma in the hours following resuscitation from cardiac arrest. This Challenge leverages a novel database of over 1,000 subjects from seven hospitals who together underwent over 50,000 hours of EEG monitoring. As always, the team with the best score for this task on the hidden test set wins the Challenge.
We have shared data, example code, and scoring code in both MATLAB and Python, and we will open the scoring system in the coming weeks. As in previous years, we have divided the Challenge into two phases: an unofficial phase and an official phase. The unofficial phase solicits feedback from the research community (i.e., you) to help us to improve the Challenge for the official phase, so we require teams to register and participate in the unofficial phase of the Challenge to be eligible for a prize. Please enter early and often – we need you to look for and share the quirks in our data, our scoring system, and otherwise.
Please see the Challenge website and the Challenge forum for more information, rules and deadlines: https://physionetchallenges.org/2023/
Many thanks again for your continued support of this event, and we hope that you enjoy the 2023 Challenge.
Read more: https://physionetchallenges.org/2023/
Dataworks! Prizes Awarded to PhysioNet Challenge and MIT Critical Data teams
Feb. 22, 2023
We are delighted to announce that the George B. Moody PhysioNet Challenges were awarded the "Distinguished Achievement Award for Data Reuse, as part of the DataWorks! Prize, while MIT Critical Data was awarded "Significant Achievement Award for Data Sharing".
Launched on May 11, 2022, the Data Works! Prize was created in partnership between the NIH Office of Data Science Strategy and the Federation of American Societies for Experimental Biology (FASEB) to highlight the critical role of data sharing and reuse in scientific discovery.
George B. Moody designed and led the Challenges from 2000 to 2015. Prof. Clifford has led the Challenges since 2015 and has been a key contributor to its parent resource, PhysioNet (The Research Resource for Complex Physiologic Signals), for over two decades. Prof. Reyna has co-led the PhysioNet Challenges since 2019, and has been instrumental in the development of its repeatable science standards.
MIT Critical Data, led by the Laboratory for Computational Physiology, builds communities around the world across disciplines to derive knowledge from data routinely collected in the process of care in order to understand health and disease better, and in the local context. Its flagship project is the Medical Information Mart for Intensive Care, or the MIMIC database.
More on the DataWorks! Prize here: https://datascience.nih.gov/director/directors-blog-dataworks-winners-2023 and the PhysioNet Challenges here: https://physionetchallenges.org/faq and MIT Critical Data here: https://criticaldata.mit.edu/.
PhysioNet and MIMIC are supported by the National Institute of Biomedical Imaging and Bioengineering.
Read more: https://datascience.nih.gov/director/directors-blog-dataworks-winners-2023
Opportunity to join the UCSF Hypoxia Lab as Data Analyst
Feb. 8, 2023
Our colleagues at UCSF Department of Anesthesia, The UCSF Hypoxia Lab (hypoxialab.org) and the UCSF Center for Health Equity in Surgery and Anesthesia (chesa.ucsf.edu) are seeking a full-time Data Analyst (with data engineering skills) to join their Open Oximetry project.
This project seeks to understand the potential impact of skin color on accuracy of pulse oximetry and other medical diagnostic devices. The Data Analyst will work at the intersection of health diagnostics, health equity and AI in the world’s leading lab (hypoxialab.org) for this type of research along with a team of experts who have published some of the seminal research on this topic.
As part of the project, the team will be setting up robust data collection systems in the lab and the hospital settings as well as creating and managing an open access data repository for diagnostics device data. This repository will contain data from our lab as well as data from collaborating study groups. The data will be shared via portals that facilitate raw data utilization for researchers and industry, as well as visualized data to help lay persons and consumers better understand device technology performance and standards.
The Data Analyst will work closely with the laboratory-based clinical research team to gather, analyze, and interpret a wide variety of research data; Design and conduct research including selecting data, developing research instruments, analyzing collected information according to established statistical methods, and developing recommendations based on research findings; Prepare reports, charts, tables, and other visual aids to interpret and communicate data and results; Create and manage data repositories; work with our AI/ML team to test novel analytic methods with our data. The ideal candidate will be knowledgeable in SQL and Python or R and have a Bachelors or Masters degree in Statistics, Data Science, or adjacent technical field.
This position is for a period of 12 months, though may be longer contingent on further funding. For further details, see the job posting.
Read more: https://sjobs.brassring.com/TGnewUI/Search/Home/Home?partnerid=6495&siteid=5861#jobDetails=3342577_5861
BioNLP Workshop 2023: Problem List Summarization
News from: BioNLP Workshop 2023 Shared Task 1A: Problem List Summarization v1.0.0.
Jan. 19, 2023
We are excited to announce the launch of a shared task on problem list summarization at the BioNLP Workshop 2023. The goal for participants is to generate a list of diagnoses and problems in a patient’s daily care plan using input from the provider’s progress notes during hospitalization. The task contains 768 progress notes for training, and 300 progress notes for evaluation. The goal of this shared task is to attract future research efforts in building NLP models for real-world decision support applications, where a system generating relevant and accurate diagnoses will assist the healthcare providers’ decision-making process and improve the quality of care for patients.
Participants will be tasked with developing NLP systems for EHR summarization. Participants who design novel systems and achieve competitive performance in the shared task, running from January to April 2023, will be invited to present their results at the BioNLP Workshop, which will be held in Toronto, Canada and co-located with ACL 2023. The challenge is open to anyone interested in clinical NLP and medical AI. We encourage individuals, teams, and organizations to participate.
To register for the challenge, please visit: https://forms.gle/geTXN6Z1pyfC55Fn8. More information about the challenge, including the official rules and guidelines, can be found at: https://physionet.org/content/bionlp-workshop-2023-task-1a/. You are welcome to join our google discussion group for newest update: https://groups.google.com/g/bionlp2023problemsumm
SOAP Note Tagging and Problem List Summarization dataset: Files unavailable until July 13th, 2023
News from: Tasks 1 and 3 from Progress Note Understanding Suite of Tasks: SOAP Note Tagging and Problem List Summarization v1.0.0.
Jan. 19, 2023
The SOAP Note Tagging and Problem List Summarization dataset dataset is temporarily unavailable as it is part of an ongoing shared task of BioNLP Workshop 2023: 1A (Problem List Summarization). The dataset will be made available on July 13th, 2023. More details about the workshop and shared task can be found at: https://doi.org/10.13026/s8wk-ja78
We apologize for any inconvenience this may cause and appreciate your understanding. We will provide updates as soon as more information becomes available. A new test set with 300 progress notes will be released along with the original set of 768 notes when the embargo is lifted. If you are interested in signing up the shared task, register here: https://forms.gle/geTXN6Z1pyfC55Fn8
MIMIC-IV-ECG module released to consortium members
News from: MIMIC-IV-ECG - Diagnostic Electrocardiogram Matched Subset v0.1.
Dec. 23, 2022
A beta release of the MIMIC-IV-ECG module is now available to MIT Critical Data Consortium members. The MIMIC-IV-ECG module contains approximately 800,000 diagnostic electrocardiograms across nearly 160,000 unique patients. All of the ECGs for patients who appear in the MIMIC-IV Clinical Database are included. When a cardiologist report is available for a given ECG, it is also provided. The patients in MIMIC-IV-ECG have been matched against the MIMIC-IV Clinical Database, making it possible to link to information across the MIMIC-IV modules.
A public version of this dataset will be released in approximately six months. During the embargo period we will be carrying out additional tests and data quality checks.
Support Our Colleagues in the NIH DataWorks Challenge!
Dec. 6, 2022
Congratulations to our colleagues who have been selected as finalists for the National Institutes of Health DataWorks Challenge!
Please support one of these teams working to share and reuse data in research and scientific discovery (The link will take you directly to the page to submit a vote). Voting is open until December 21, 2022. Unfortunately, you may only vote for one team, but they can both be awarded prizes. Please share and promote awareness to increase our colleagues’ chances!
MIT Critical Data
MIT Critical Data builds communities across disciplines to derive knowledge from health records to understand health and disease better. Help them continue to build valuable research resources such as MIMIC and freely accessible educational resources.
The PhysioNet Challenges are annual data science competitions that ask what we can learn from data to improve health and healthcare. Help the team draw out unrealized value from data and advance data reuse and algorithm development.
The Federation of American Societies for Experimental Biology (FASEB) and the National Institutes of Health (NIH) are championing a bold vision of data sharing and reuse. The DataWorks! Prize fuels this vision with an annual challenge that showcases the benefits of research data management while recognizing and rewarding teams whose research demonstrates the power of data sharing or reuse practices to advance scientific discovery and human health. The future of biological and biomedical research hinges on researchers’ ability to share and reuse data. Sharing and reuse had a sizable, catalytic impact on the development of COVID-19 vaccines and treatment protocols. The DataWorks! Prize is an opportunity for the research community to share their stories about the practices, big and small, that lead to scientific discovery.
Read more: https://www.herox.com/dataworks
PhysioNet receives inaugural MIT Prize for Open Data
Nov. 10, 2022
The PhysioNet team were recipients of the inaugural MIT Prize for Open Data in recognition of their work to support health research and education. The award - established to highlight the value of open data at MIT - was presented by School of Science Dean Nergis Mavalvala and MIT Libraries Director Chris Bourg on October 28 in the MIT Hayden Library.
Read more: https://libraries.mit.edu/opendata/open-data-mit-home/mit-prize/
Multimodal Physiological Monitoring During Virtual Reality Piloting Tasks: CogPilot Data Challenge
News from: Multimodal Physiological Monitoring During Virtual Reality Piloting Tasks v1.0.0.
Sept. 8, 2022
We are pleased to announce the publication of a dataset comprising multimodal physiologic, flight performance, and user interaction data streams, collected as participants performed virtual-reality flight tasks of varying difficulty.
With over an hour of highly multimodal physiological and behavioral signals collected on each of the thirty-five participants, the dataset represents a unique opportunity to develop analytics and models linking an individual’s physiology to their behavior and performance in tasks of varying difficulty.
More data are being collected and will be uploaded to PhysioNet periodically. The data underpins the CogPilot Data Challenge, which explores how performance measurements and physiological data can be used to assess the competency of student pilots. To participate in the CogPilot Challenge, visit: https://pilotperformance.mit.edu/
Announcing the MIMIC-IV Waveforms
News from: MIMIC-IV Waveform Database v0.1.0.
Aug. 9, 2022
We are pleased to announce an initial release of a version (0.1.0) of the MIMIC-IV-Waveform module. These waveforms are a rich source of patient information - including ECG, PPG, and Blood Pressure signals - and can be linked to the clinical information in MIMIC-IV. This initial release contains 200 records from 198 patients. An upcoming release will include around 10,000 records.
The dataset was the subject of a workshop at IEEE EMBC in July of 2022, led by Peter Charlton, which demonstrated how to use the WFDB-Python package to extract and analyze waveform features. Executable notebooks and tutorial materials are available at: https://mimic.mit.edu/docs/iv/tutorials/waveform/ieee_workshop/ .
Rethinking Algorithm Performance Metrics for Artificial Intelligence in Diagnostic Medicine
July 29, 2022
Gari Clifford and Matthew Reyna from Emory University and Elaine Nsoesie from Boston University recently published an invited viewpoint in The Journal of the American Medical Association on "Rethinking Algorithm Performance Metrics for Artificial Intelligence in Diagnostic Medicine". The viewpoint focuses on how we often use the wrong optimization targets when applying machine learning to medical data, and how we can address this issue, and is part of the Gordon and Betty Moore Foundation's broader series on Diagnostic Excellence.
Server maintenance between 15-18 July 2022 (https://archive.physionet.org/ will be unavailable)
July 17, 2022
Our servers at MIT are undergoing and testing and maintenance work between Friday 15th and Monday 18th July 2022. PhysioNet (https://physionet.org/) will remain active during this period, but some services may be affected (for example, the archive website https://archive.physionet.org/).
Trust Markers with ORCID
June 30, 2022
Linking an ORCID to your PhysioNet profile can help us to quickly verify your identity, speeding up the process of gaining access to datasets such as MIMIC.
When reviewing an ORCID profile, we look out for “Trust Markers” which are pieces of information added to the profile by groups such publishers and employers.
To find out more about how PhysioNet is working with ORCID, see their blog post on how we are using the Trust Markers to streamline the data credentialing process.
Read more: https://info.orcid.org/a-use-case-for-trust-markers-in-orcid-records-streamlining-the-credentialing-process/
Significant delays are expected to applications for credentialed access to PhysioNet.
April 7, 2022
We are currently dealing with a high volume of applications for credentialed access to PhysioNet, so please expect significant delays (up to 45 days) in the review process. We are doing our best to deal with the waitlist quickly, handling applications in the order in which they are received. To help ensure that your application is successful, please remember to:
- Include a copy of your CITI training report (not the certificate).
- Remind your reference to reply promptly when contacted.
- Check your application details are correct before submitting.
- Add an institutional or educational email address as your primary email.
We apologize for the inconvenience. Please bear with us during this busy time!
Interruption to the PhysioNet mail server between the 30th and 31st March 2022
March 31, 2022
Between Wednesday 30 March and Thursday 31 March the PhysioNet mail server suffered an interruption. As a result, if you attempted to register for a new account or reset a password, you may not have received an email.
We are now in the process of resending emails, so please check your mailbox if an expected email did not arrive. We apologize for the inconvenience and we will be taking steps to prevent similar issues issue in the future.
Applying for access to protected datasets such as MIMIC is now a three step process
March 18, 2022
Applying for access to protected datasets such as MIMIC is now a three step process:
- Submit your personal details via the "Credentialing" page of your user profile.
- Submit your training report via the "Training" page of your user profile.
- Once the steps above are complete, sign the Data Use Agreement in the "Files" section of the relevant project. You can view your signed agreements on the "Agreements" page of your user profile.
The change helps us to review data access requests more efficiently and gives us the flexibility to support additional training courses in future.
Forthcoming changes to the credentialing process
Feb. 28, 2022
When applying for access to datasets such as MIMIC, you are currently required to submit a single "credentialing" application that allows us to check both CITI training status and identity.
We will soon be releasing updates to PhysioNet that will require training and identity details to be submitted independently. As a result, a new "Training" tab will be added to your user profile.
This change will allow us to support different types of training for different datasets (for example, an Australian dataset may require training on specific issues relating to Australia). The change will also help us to streamline the review process.
PhysioNet Challenge 2022 Announcement
Jan. 31, 2022
We have two big announcements today. First, at last year’s Computing in Cardiology (CinC) Conference, the Board voted to rename the PhysioNet/Computing in Cardiology Challenges in honor of George Moody, and his life-long contributions to the field, and specifically PhysioNet, the Challenges and CinC. The Challenge is now called the “The George B. Moody PhysioNet Challenge”. For consistency, we will still abbreviate this to the PhysioNet Challenge. We continue to partner with CinC, and will be awarding prizes in Finland in September this year.
Second, we are delighted to also announce the opening of the George B. Moody PhysioNet Challenge 2022. This year’s Challenge aims to identify the presence, absence, or unclear cases of murmur waves in heart sound recordings collected from multiple auscultation locations on the body using a digital stethoscope. Building on our successful Challenge from 2016, together with our generous collaborators at the Universidade Portucalense and Universidade do Porto, we have sourced a database of 5272 recordings from 1568 inhabitants of Pernambuco state, Brazil during two independent cardiac screening campaigns which were designed to support the development of a telemedicine network. More details on the data can be found in a recent publication in the IEEE Journal of Biomedical and Health Informatics.
Demo code in Python and MATLAB is available, and the scoring system will be open later in February - Look out for the announcement very soon!
See here for more information, rules and deadlines: https://moody-challenge.physionet.org/2022/
As with previous years, we have divided the Challenge into two phases. The first (unofficial phase) is to enable the research community (i.e. you) to help us improve the Challenge. We value your input, and it is therefore compulsory to enter the Challenge in this unofficial phase (before 9th April) to be eligible for a prize. This is very important - we need your help! Please enter early and often - the score doesn’t matter and will be wiped from the board for the official phase. We need you to look for quirks in our scoring system, data formats, or anomalies in the raw data that do not make sense to you. We are not perfect, and are bandwidth-limited, and so we rely on the peer-review of our community to improve the quality of the Challenge every year. In particular, this year we strongly encourage suggestions for modifying our scoring function, which we are sure will be controversial.
Please note that you *must* re-register for this Challenge (using the link below) even if you competed last year and have no team changes, and to be eligible for a prize, you must submit at least one successful entry during the unofficial phase.
Quick links for this year's Challenge:
More information will be posted on the PhysioNet Challenge website as it is available. Please check the Challenge forum for real-time updates. Please also post questions and comments in the forum. However, if your question reveals information about your entry, then please email Info [at] physionetchallenge.org. We may post parts of our reply publicly if we feel that all Challengers should benefit from the information contained in our responses. We will not answer emails about the Challenge sent to other email addresses.
Many thanks again for your continued support of this event, and we hope that you enjoy the 2022 Challenge
-Gari, Matt, Ali and the PhysioNet Challenge Team