add trvae Perturbation prediction notebook

theislab / scarches

Reference mapping for single-cell genomics

https://docs.scarches.org/en/latest/

BSD 3-Clause "New" or "Revised" License

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add trvae Perturbation prediction notebook #243

Closed chelseabright96 closed 1 month ago

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Koncopd commented 4 months ago

Is this ready?

M0hammadL commented 4 months ago

not ready, @chelseabright96 we need to add this predict function as in https://scgen.readthedocs.io/en/stable/tutorials/scgen_perturbation_prediction.html here, and also showing the accuracy of the prediction like R2 plots

chelseabright96 commented 3 months ago

Hi! I have updated the notebook to predict diseased tuft cells from control tuft cells, as was done in the paper. I am getting a lower R2 score for the variance of the expression (0.55 compared to 0.92). The R2 score for the mean is only slightly lower (0.91 vs 0.98). I have played around with the hyperparameters and also used the same as given here https://github.com/theislab/trVAE_reproducibility/blob/master/Jupyter%20Notebooks/Train_Haber.ipynb, but could not get higher scores