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YerevaNN / mimic3-benchmarks

Python suite to construct benchmark machine learning datasets from the MIMIC-III 💊 clinical database.
https://arxiv.org/abs/1703.07771
MIT License
799 stars 328 forks source link

Add benchmark dataset to derived data repository #34

Open alistairewj opened 6 years ago

alistairewj commented 6 years ago

We just launched a repo to host derived data from MIMIC.

A static snapshot of the code is hosted here: https://physionet.org/physiotools/mimic-code/ A static snapshot of the data is hosted on PhysioNetWorks - everyone who has access to MIMIC will have access to the data: https://physionet.org/works/MIMICIIIDerivedDataRepository/

Would be good to make a GitHub release of the code, and upload that zip + the generated data to the PNW repository. Should make it easier for people to use the benchmarks. Also worth it to track this repo with Zenodo so that the releases are automatically assigned a DOI.

turambar commented 6 years ago

@alistairewj sweet. We're working on our "1.0" release to coincide with a journal submission, so we should be ready to contribute within a few weeks at the latest.

turambar commented 6 years ago

^^^^^ @Hrant-Khachatrian @Harhro94

turambar commented 6 years ago

We should do this upload! :)

partizanos commented 2 years ago

Related issue: https://github.com/YerevaNN/mimic3-benchmarks/issues/127

tompollard commented 2 years ago

Since @alistairewj posted the message above, we have entirely rebuilt PhysioNet. It's now fairly straightforward to publish derived datasets with the same permissions as the parent dataset. We'd love to share the benchmark dataset alongside MIMIC.

Instructions for submitting the dataset to PhysioNet are at: https://physionet.org/about/publish/#submission_overview. Essentially the process is:

  1. Go to https://physionet.org/projects/ and click "Create new project"
  2. Follow the instructions to populate the data description, add collaborators, etc.
  3. On the "Access" tab, select the "Credentialed" access policy
  4. On the "Discovery" tab, select "MIMIC" as the parent project.
  5. Click "submit" to submit the dataset to our team for review.

Thanks, and let us know if you need help. It may be tricky to upload a large dataset using the web form. We're working on a new tool for uploads, but for now you can ping us and we can upload on your behalf.