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mmr12 / MGP-AttTCN

MGP-AttTCN: An Interpretable Machine Learning Model for the Prediction of Sepsis
MIT License
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How do you run the project? And Error: echodata does not exist #1

Closed la122 closed 3 years ago

la122 commented 4 years ago

Hello,

I think there are some bugs in this repository. I managed to run the project only after changing some code, but still get the error: Relation "mimic3_mrosnati.echodata« does not exist"

Which operating system and python version do you use?

mmr12 commented 3 years ago

Hi I changed the SQL queries so that they don't rely on a schema that you might not have (in this case mimic3_mrosnati) and fixed many errors. The code should now run with Python 3.8.5, TensorFlow 2.3.0

mmr12 commented 3 years ago

PS: I haven't updated the readme yet, but you'll have to pass on a string with your postgres login, eg: "dbname=mimic user=postgres password=postgres host=localhost options=--search_path=mimiciii"

la122 commented 3 years ago

Hi, thank you for the reply and the fixes. I tried it again. Now I am getting some other errors:

1

FileNotFoundError: [Errno 2] No such file or directory: '/cluster/home/mrosnat/MGP-AttTCN/data/interim/19-06-12-detailed-case-labels.csv'

fix

added -p . when starting preprocessing

2

FileNotFoundError: [WinError 3] The system cannot find the path specified: 'logs/20210312-175605'

fix

created logs folder in project root

3

Traceback (most recent call last): File ".\src\mains\main.py", line 172, in main( File ".\src\mains\main.py", line 124, in main trainer.run() File "C:\Users\Artur\projects\MGP-AttTCN\src\trainers\trainer.py", line 135, in run y_true, y_hat, _class = self.dev_eval(dev_batch, step) File "C:\Users\Artur\projects\MGP-AttTCN\src\trainers\trainer.py", line 164, in dev_eval tf.summary.scalar("loss_dev", loss_dev.numpy(), step=step + dev_batch) AttributeError: 'NoneType' object has no attribute 'numpy'

Any idea, how to fix the last one?

la122 commented 3 years ago

Problem 3 seems to be fixed now too but I'm not sure why. I pulled your last changes in the extra_exp branch, reinstalled the requirements and repeated the preprocessing step.

yxddzho commented 1 year ago

python scr/data_processing/main.py [-h] -u SQLUSER -pw SQLPASS -ht HOST -db DBNAME -r SCHEMA_READ_NAME [-w SCHEMA_WRITE_NAME] 会报错usage: main.py [-h] [-c CONNECT_KEY] [-p PATH] main.py: error: argument -h/--help: ignored explicit argument 't'