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nyuad-cai / MedFuse

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needs help in running the shell scripts #16

Closed AmudhaTK closed 2 months ago

AmudhaTK commented 9 months ago

Dear @farahshamout , Hope you are doing well.

I need help in running the shell scripts. sh ./scripts/phenotype/uni_csr.sh

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

It is showing an error, as it needs two positional arguments. Do you know 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 2 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.