Step 2: Extract Data
Jan 29 - Feb 12 | Extract Data
Jan 29 - Feb 12 | Extract Data
This is the step where coffee breaks will be the most useful (a considerable amount of computation time will be required in this step) .
Images from the MIMIC-CXR-JPG database
Radiology notes from the MIMIC-IV-Note database
Discharge notes from the MIMIC-IV-Note database
Finally, note that the criterion for selecting patients for the Testing Phase (100 alive and 100 deceased after one year) was based on the maximization of the entropy of the distribution of multimodal data over one year.
Once you have submitted the required documents to the MEDomicsLab team, you will receive an email with a link to a drive space, containing a zip folder. Simply download the folder into your documents, and follow the instructions for Step 2 in the video below.
Content
The Testing Phase of MEDomicsLab involves the use of MIMIC data. For the purpose of the Testing Phase, we selected a small subset of patients (200) with the intent of simulating a longitudinal clinical decision support system (CDSS) scenario as in the study of (see Figure 5) using multimodality data (tabular, time series, text, images) acquired from multiple patient visits over a year (i.e. all data from the last year since death or the last visit of a given patient). In the subsequent steps of the Testing Phase, one of the goal will be to predict one-year mortality using this data.
In this step of the Testing Phase, we will extract relevant features from time series, text and imaging data based on the package (time series) and pretrained models from the study of (text and images). More specifically, this includes:
Laboratory events (time series) from the MIMIC-IV database (we considered a subset of events as in the study of )
Chart events (time series) from the MIMIC-IV database (we considered a subset of events as in the study of )
Procedure events (time series) from the MIMIC-IV database (we considered a subset of events as in the study of )
At this point you must have completed the requirements to have access to the data.
For additional informations about the Extraction Module and the extraction types used in our application, please refer to the tutorials of the .
Get data and create your workspace
Extract data from discharge notes
Extract data from radiology notes
Extract data from chart events
Extract data from laboratory events
Extract data from procedure events
Extract data from chest X-Ray images
NOTE: We commonly refer to the study of as the "HAIM study".
