Participants of the Datathon are added to the Google Group aarhus-critical-2019-participants. Members of this group have access to computation resources through the Google Cloud Platform (GCP) project aarhus-critical-2019-team and to datasets via the GCP project physionet-data.
You can access the datasets directly on GCP:
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Run a query. E.g. count the number of hospital admissions:
SELECT count(*) FROM `physionet-data.mimiciii_clinical.admissions`
You can open the following tutorial notebooks on Colab and get started instantly. Requirements for these notebooks are: (1) you have a Google account, and (2) your Google account has been added to the aarhus-critical-2019-participants Google group.
- 01-accessing-the-data.ipynb
- 02-explore-patients.ipynb
- 03-severity-of-illness.ipynb
- 04-summary-statistics.ipynb
- 05-prediction.ipynb
Datasets can also be queried directly from R. This is exemplified in the following R markdown notebook: mimic-iii-los-aarhus.Rmd
The dataset used in the MIMIC-CXR tutorial is preprocessed for optimal use with Tensorflow. If you use a different library or just want a simpler representation of the data, the MIMIC-CXR dataset is available as JPEG images and CSV tables in the following GCP bucket: gs:https://physionet-data-mimic-cxr-jpg. The URL for the bucket is https://console.cloud.google.com/storage/browser/physionet-data-mimic-cxr-jpg