New scvi-tools version using SOLO returns probabilities, how to return logits like in version 1.1.2

Noticed a new warning while predicting doublets with SOLO that it returns probabilities instead of logits, how does one convert back or return the logit values like in previous versions? I have tried using the expit function and logit function to convert but have been unable to recreate data I analyzed in the past.

Not sure if this is the way but have you tried following like here and calculating logit = ln(p/(1-p)) where p are the probabilities?


I did try that, but it did not work as expected. After playing around with it a bit I believe the issue is that the “logits” mentioned in the update are not logits formed from the logit function you link but they are transformed into probabilities using the softmax function.

I’m unsure if the softmax function is invertible but there’s some ideas here i might try. Or i’ll just uninstall and downgrade to 1.1.2 again

Hi, I’ve released scvi-tools 1.1.4 which allows you to pass in return_logits=True to SOLO.predict to replicate the previous (buggy) behavior.

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Thanks for the quick action. Can you elaborate or point to some reference about why the behavior was buggy?

Oh, this is because our documentation for the soft argument says the method should return probabilities, so it was technically a bug on our end.

Thanks for the clarification. FYI, it seems the version now in pypi is 1.1.5?

Yes, I had to make another patch release! Anything >= 1.1.4 will have the new argument.