add trvae Perturbation prediction notebook

[chelseabright96]

No description provided.

[review-notebook-app]

Check out this pull request on 

See visual diffs & provide feedback on Jupyter Notebooks.

---

Powered by ReviewNB

[Koncopd]

Is this ready?

[M0hammadL]

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]

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