cmudig / ai-clinician-mimiciv Goto Github PK

1. The Extract function reports an error that the following table does not exist physiionet-data.mimic_hosp.chartevents. The location of chartevents in Mimic iv: physiionet-data.mimic_icu.chartevents
2. There are no fluid_cv.csv and vaso_cv.csv in the generated result of mimic iv, input mv and cv are merged in mimic iv, it is normal that these two files are not generated
3. pd.NA pd does not have the attribute of NA, it is changed to np.nan
4. 05_build_states_and_actions.py TypeError: data type not understood
   Updated pip install --upgrade numpy, pip install --upgrade pandas

I can't find demog.csv and abx.csv in MIMIC IV

After completing BigQuery authentication (including cloud permissions and local setup), running extract.py for the MIMIC-IV dataset results in a Forbidden error:

google.api_core.exceptions.Forbidden: 403 Access Denied: Table physionet-data:mimic_core.admissions: User does not have permission to query table physionet-data:mimic_core.admissions, or perhaps it does not exist in location US.

This issue is caused by a change in the directory structure of the MIMIC-IV dataset. The current dataset uses mimiciv_icu and mimiciv_hospital, while the repository's data_extraction/sql/elixhauser.sql and queries.py still reference mimic_icu and mimic_core. These references need to be updated to match the current MIMIC-IV structure.

If I manage to successfully make these changes, I will submit a pull request to merge my version.