scgen.SCGEN.get_marginal_ll¶
- SCGEN.get_marginal_ll(adata=None, indices=None, n_mc_samples=1000, batch_size=None, return_mean=True, **kwargs)¶
Return the marginal LL for the data.
The computation here is a biased estimator of the marginal log likelihood of the data. Note, this is not the negative log likelihood, higher is better.
- Parameters
- adata
AnnData
|None
Optional
[AnnData
] (default:None
) AnnData object with equivalent structure to initial AnnData. If None, defaults to the AnnData object used to initialize the model.
- indices
Sequence
[int
] |None
Optional
[Sequence
[int
]] (default:None
) Indices of cells in adata to use. If None, all cells are used.
- n_mc_samples
int
(default:1000
) Number of Monte Carlo samples to use for marginal LL estimation.
- batch_size
int
|None
Optional
[int
] (default:None
) Minibatch size for data loading into model. Defaults to scvi.settings.batch_size.
- return_mean
bool
|None
Optional
[bool
] (default:True
) If False, return the marginal log likelihood for each observation. Otherwise, return the mmean arginal log likelihood.
- adata
- Return type