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nyuad-cai / MedFuse

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Needs clarity in runing the shell script #11

Closed AmudhaTK closed 2 months ago

AmudhaTK commented 1 year ago

Hi @farahshamout, I can understand the situation of not sharing the original protected datasets. But with your help I come to know how to get preprocessed data from raw datasets. After getting proper system up-gradation, I started downloading the raw data from MIMIC IV and MIMIC-CXR-JPG. Thank you for the proper guidance on the memory needed to download the data.

Now, I am working on the processing of the raw data. I did MIMIC IV data extraction using MIMIC III. I need clarification on this part.

Kindly help me with the details of the output that we can get after the execution of this Shell script:

train the imaging model with 14 radiology labels.

sh ./scripts/radiology/uni_cxr.sh

train LSTM model on extracted time-series EHR data for phenotype task.

sh ./scripts/phenotyping/train/uni_all.sh

train LSTM model for the in-hospital-mortality task

sh ./scripts/mortality/train/uni_all.sh

It is showing error,as needs two positional arguments. Which arguments I should pass to run the shell script? It would be helpful to know the proper output of the above command.

thank you, Amudha T K

ShazaElsharief commented 7 months ago

Hi Amudha, you should be able to execute the scripts as specified in this step:

# train the imaging model with 14 radiology labels.
sh ./scripts/radiology/uni_cxr.sh
# train LSTM model on extracted time-series EHR data for phenotype task.
sh ./scripts/phenotyping/train/uni_all.sh

# train LSTM model for in-hospital-mortality task
sh ./scripts/mortality/train/uni_all.sh

without additional arguments. Please make sure that you have specified the cxr and ehr data directories before running the scripts, following the steps outlined in the README file.