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Clinical Trial Optimization

Optimize clinical trials based on the Mayo Clinic dataset

ingenii

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ingenii

Dustin
brydustin

2

Posted

ClinicalTrial(....) command

I am a little confused how we are supposed to be using "ClinicalTrial(....)" because when I viewed Code/submission/solution.ipynb I see the following:
"Let's look at a simple example. Consider 6 patients, with the following covariates:
Patient 1: w1=58, w2=1718 and w3=12.2
Patient 2: w1=56, w2=7394.8 and w3=10.6
Patient 3: w1=70, w2=516 and w3=12
Patient 4: w1=55, w2=6121 and w3=10.3
Patient 5: w1=38, w2=671 and w3=10.9
Patient 6: w1=66, w2=944 and w3=11

NOTE: The cell below will be replaced with other trials when running aqora test
input = ClinicalTrial( np.array([ [58,1718,12.2], [56,7394.8,10.6], [70,516,12], [55,6121,10.3], [38,671,10.9], [66,944,11] ]), 0.5 ) "
Presumably we should use this data as is, solve the toy model, then submit, and by the NOTE above it seems that "[[58, 1718,....,11]]" will be replaced with the actual data corresponding to the 100 patients. But I don't know what sort of object ClinicalTrial(...) is; presumably we should be using this on the toy model as well. Currently, I am just treating "[[58,...,11]" as an ordinary numpy array.
Is this potentially related to the instructions: "Template You can download a solution template by running the following command:
aqora template ingenii-clinical-trial cd ingenii-clinical-trial aqora install " I ran this and got the following error: "ERROR Whoops! Error sending request to aqora: error decoding response body: expected value at line 2 column 1 (This isn't your fault)
To try and fix this, you can:
  • Check your internet connection "
I ask this because I wonder if ClinicalTrial(...) is defined somehow in the above. I have aqora installed.
To summarize this is two (potentially related questions) (i) What is ClinicalTrial(...) (ii) Can I get it from the aqora commands above and why is that error being generated?

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Jannes Stubbemann

1

Posted by stubbi

Thank you very much for your question. You can find the definition of the Clinical Trial here.
For the second part, the error happens when you execute
aqora template ingenii-clinical-trial
is that correct?

Dustin

1

Posted by brydustin

Thank you! Just seeing this, but I did figure it out. Well, maybe not the second part, but I will! Thank you for the response! :)

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