Choosing number of latent variables

Help scvi-tools
1

Hi,

Is there a way to choose between the number of latent variables when doing scvi integration? Does the hyperparameter tuning provide this option?

Thanks,
Kamalika

2

Yes, of course. You set it when defining the model: SCVI(adata, n_latent=x)

In our hyperparameters tuner, one can do:

run_autotune(
    SCVI,
    adata,
    metrics=["elbo_validation"],
    mode="min",
    search_space={
        "model_params": {
            "n_latent": tune.choice([10, 20]),
        },
    },
    ...)
1 Like
3

Thanks a lot for your response. Do I need anymore dependencies for running autotune? I have used the following

from scvi import autotune
from ray import tune

and

results = autotune.run_autotune(
SCVI,
adata,
metrics=[“elbo_validation”],
mode=“min”,
search_space={
“model_params”: {
“n_latent”: tune.choice([10, 20]),
},
},
…)

It’s throwing an error regarding hyperopt library.

raise ModuleNotFoundError(f"Please install {missing_modules} to use this functionality.")
ModuleNotFoundError: Please install [‘hyperopt’] to use this functionality.

4

You need to install hyperopt:

pip install hyperopt

or originally: pip install scvi-tools[autotune]