Claudio Novella Rausell

Ray.tune for parameter optimization. Included more functionality

9

Hi @adamgayoso and @PierreBoyeau. As we discussed recently via email, in our lab we were able to use the logic in [michael/autotune](https://github.com/scverse/scvi-tools/tree/michael/autotune) to do hyperparameter optimization. I've implemented the changes...

BaseModel.prepare() unexpected behaviour

2

According to the documentation of [BaseModel.prepare()](https://github.com/theislab/cellrank/blob/main/src/cellrank/models/_base_model.py#L298) if there's no Lineage specified, the weights will be set to 1. In such case [Line 366](https://github.com/theislab/cellrank/blob/cabbd348b97661251a7dfa37186b178ff489e746/src/cellrank/models/_base_model.py#L366) ```python probs = Lineage.from_adata(self.adata, backward=backward) ``` throws...

About model covariates

3

I was trying to update a reference scANVI model with a new query dataset. But apparently if the reference model has been trained with categorical covariates included this can't be...