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Examples of training deep learning models in python on OHDSI data?


(Jaan Altosaar) #1

It has been difficult to find examples that are written in python for using pytorch (or other deep learning frameworks) to train models on OHDSI data.

I was pointed to an R package that interfaces with pytorch: https://ohdsi.github.io/PatientLevelPrediction/articles/BuildingDeepLearningModels.html

Are there examples that are purely written in python? A colaboratory notebook would be ideal.

Thank you!
Jaan


(David Sontag) #2

Jaan,
Here is our fully Python deep (and shallow) learning codebase for OMOP:

https://clinicalml.github.io/omop-learn/

The deep model we implement is our AAAI '21 paper https://arxiv.org/abs/2007.05611, but the codebase will make it trivial for you to plug in others.

This is still in beta, so please do keep my lab in the loop as you test it out.
Cheers,
David


(Jaan Altosaar) #3

Fantastic, thanks so much David! Looking forward to reading the paper.


t