Index

_

__getitem__() (cellarium.ml.data.DistributedAnnDataCollection method) (cellarium.ml.data.IterableDistributedAnnDataCollectionDataset method)

__iter__() (cellarium.ml.data.IterableDistributedAnnDataCollectionDataset method) __len__() (cellarium.ml.data.IterableDistributedAnnDataCollectionDataset method) __new__() (cellarium.ml.cli.LightningModule__load_from_checkpoint_class method)

A

adata (cellarium.ml.data.LazyAnnData property) AnnDataField (class in cellarium.ml.utilities.data) AnnDataSchema (class in cellarium.ml.data) assert_arrays_equal() (in module cellarium.ml.utilities.testing)

assert_columns_and_array_lengths_equal() (in module cellarium.ml.utilities.testing) assert_nonnegative() (in module cellarium.ml.utilities.testing) assert_positive() (in module cellarium.ml.utilities.testing) assert_slope_equals() (in module cellarium.ml.utilities.testing)

B

bias (cellarium.ml.layers.MuLinear property)

C

cached (cellarium.ml.data.LazyAnnData property) categories_to_codes() (in module cellarium.ml.utilities.data) cellarium.ml.callbacks module cellarium.ml.cli module cellarium.ml.core module cellarium.ml.data module cellarium.ml.distributions module cellarium.ml.layers module cellarium.ml.lr_schedulers module cellarium.ml.models module cellarium.ml.preprocessing module cellarium.ml.transforms module

cellarium.ml.utilities.data module cellarium.ml.utilities.distributed module cellarium.ml.utilities.testing module CellariumAnnDataDataModule (class in cellarium.ml.core) CellariumModel (class in cellarium.ml.models) CellariumModule (class in cellarium.ml.core) CellariumModuleLoadFromCheckpoint (in module cellarium.ml.cli) CellariumPipeline (class in cellarium.ml.core) checkpoint_loader_constructor() (in module cellarium.ml.cli) CheckpointLoader (class in cellarium.ml.cli) collate_fn() (in module cellarium.ml.utilities.data) components_kg (cellarium.ml.models.IncrementalPCA property) compute_n_obs() (in module cellarium.ml.cli) compute_var_names_g() (in module cellarium.ml.cli) compute_y_categories() (in module cellarium.ml.cli) configure_model() (cellarium.ml.core.CellariumModule method) configure_optimizers() (cellarium.ml.core.CellariumModule method) cpu_transforms (cellarium.ml.core.CellariumModule property)

D

densify() (in module cellarium.ml.utilities.data) DistributedAnnDataCollection (class in cellarium.ml.data)

DistributedAnnDataCollectionView (class in cellarium.ml.data) DivideByScale (class in cellarium.ml.transforms)

E

explained_variance_k (cellarium.ml.models.IncrementalPCA property)

F

file_loader_constructor() (in module cellarium.ml.cli) FileLoader (class in cellarium.ml.cli) Filter (class in cellarium.ml.transforms) filter() (cellarium.ml.transforms.Filter method) forward() (cellarium.ml.core.CellariumModule method) (cellarium.ml.layers.GeneExpressionEmbedding method) (cellarium.ml.layers.MetadataEmbedding method) (cellarium.ml.layers.MultiHeadAttention method) (cellarium.ml.layers.MultiHeadReadout method) (cellarium.ml.layers.NormAdd method) (cellarium.ml.layers.PositionWiseFFN method) (cellarium.ml.layers.Transformer method) (cellarium.ml.layers.TransformerBlock method) (cellarium.ml.models.Geneformer method) (cellarium.ml.models.IncrementalPCA method) (cellarium.ml.models.LogisticRegression method) (cellarium.ml.models.OnePassMeanVarStd method) (cellarium.ml.models.ProbabilisticPCA method) (cellarium.ml.models.TDigest method) (cellarium.ml.transforms.DivideByScale method) (cellarium.ml.transforms.Filter method) (cellarium.ml.transforms.Log1p method) (cellarium.ml.transforms.NormalizeTotal method) (cellarium.ml.transforms.ZScore method)

G

GatherLayer (class in cellarium.ml.utilities.distributed) GeneExpressionEmbedding (class in cellarium.ml.layers) Geneformer (class in cellarium.ml.models) geneformer() (in module cellarium.ml.cli)

get_categories() (in module cellarium.ml.utilities.data) get_coord_data() (in module cellarium.ml.utilities.testing) get_highly_variable_genes() (in module cellarium.ml.preprocessing) get_rank_and_num_replicas() (in module cellarium.ml.utilities.distributed) get_worker_info() (in module cellarium.ml.utilities.distributed)

I

incremental_pca() (in module cellarium.ml.cli)

IncrementalPCA (class in cellarium.ml.models) IterableDistributedAnnDataCollectionDataset (class in cellarium.ml.data)

L

L_k (cellarium.ml.models.ProbabilisticPCA property) LazyAnnData (class in cellarium.ml.data) lightning_cli_factory() (in module cellarium.ml.cli) LightningModule__load_from_checkpoint_class (class in cellarium.ml.cli) LinearLR (class in cellarium.ml.lr_schedulers)

LinkArguments (class in cellarium.ml.cli) load_state_dict() (cellarium.ml.data.IterableDistributedAnnDataCollectionDataset method) Log1p (class in cellarium.ml.transforms) logistic_regression() (in module cellarium.ml.cli) LogisticRegression (class in cellarium.ml.models) LossScaleMonitor (class in cellarium.ml.callbacks)

M

main() (in module cellarium.ml.cli) materialize() (cellarium.ml.data.DistributedAnnDataCollection method) mean_g (cellarium.ml.models.OnePassMeanVarStd property) median_g (cellarium.ml.models.TDigest property) merge_heads() (cellarium.ml.layers.MultiHeadAttention static method) MetadataEmbedding (class in cellarium.ml.layers) model (cellarium.ml.core.CellariumModule property) module cellarium.ml.callbacks cellarium.ml.cli cellarium.ml.core cellarium.ml.data cellarium.ml.distributions cellarium.ml.layers cellarium.ml.lr_schedulers cellarium.ml.models cellarium.ml.preprocessing cellarium.ml.transforms cellarium.ml.utilities.data cellarium.ml.utilities.distributed cellarium.ml.utilities.testing

module_pipeline (cellarium.ml.core.CellariumModule property) MuLinear (class in cellarium.ml.layers) MultiHeadAttention (class in cellarium.ml.layers) MultiHeadReadout (class in cellarium.ml.layers)

N

n_obs (cellarium.ml.data.LazyAnnData property) n_vars (cellarium.ml.data.LazyAnnData property)

NegativeBinomial (class in cellarium.ml.distributions) NormAdd (class in cellarium.ml.layers) NormalizeTotal (class in cellarium.ml.transforms)

O

obs_names (cellarium.ml.data.DistributedAnnDataCollectionView property) (cellarium.ml.data.LazyAnnData property) on_train_batch_end() (cellarium.ml.callbacks.VarianceMonitor method) (cellarium.ml.core.CellariumModule method) on_train_epoch_end() (cellarium.ml.core.CellariumModule method) (cellarium.ml.models.IncrementalPCA method)

on_train_epoch_start() (cellarium.ml.core.CellariumModule method) on_train_start() (cellarium.ml.callbacks.VarianceMonitor method) (cellarium.ml.core.CellariumModule method) onepass_mean_var_std() (in module cellarium.ml.cli) OnePassMeanVarStd (class in cellarium.ml.models)

P

PositionWiseFFN (class in cellarium.ml.layers) predict() (cellarium.ml.models.Geneformer method) (cellarium.ml.models.IncrementalPCA method) (cellarium.ml.models.LogisticRegression method) (cellarium.ml.models.PredictMixin method) (cellarium.ml.models.ProbabilisticPCA method)

predict_dataloader() (cellarium.ml.core.CellariumAnnDataDataModule method) PredictionWriter (class in cellarium.ml.callbacks) PredictMixin (class in cellarium.ml.models) probabilistic_pca() (in module cellarium.ml.cli) ProbabilisticPCA (class in cellarium.ml.models)

R

read_h5ad_file() (in module cellarium.ml.data) read_h5ad_gcs() (in module cellarium.ml.data) read_h5ad_local() (in module cellarium.ml.data)

read_h5ad_url() (in module cellarium.ml.data) record_out_coords() (in module cellarium.ml.utilities.testing) reset_parameters() (cellarium.ml.models.CellariumModel method)

S

set_epoch() (cellarium.ml.data.IterableDistributedAnnDataCollectionDataset method) set_resume_step() (cellarium.ml.data.IterableDistributedAnnDataCollectionDataset method) setup() (cellarium.ml.core.CellariumAnnDataDataModule method)

shape (cellarium.ml.data.LazyAnnData property) sigma_variance (cellarium.ml.models.ProbabilisticPCA property) split_heads() (cellarium.ml.layers.MultiHeadAttention static method) std_g (cellarium.ml.models.OnePassMeanVarStd property)

T

TDigest (class in cellarium.ml.models) tdigest() (in module cellarium.ml.cli) train_dataloader() (cellarium.ml.core.CellariumAnnDataDataModule method)

training_step() (cellarium.ml.core.CellariumModule method) Transformer (class in cellarium.ml.layers) TransformerBlock (class in cellarium.ml.layers) transforms (cellarium.ml.core.CellariumModule property)

U

U_gk (cellarium.ml.models.ProbabilisticPCA property)

V

val_dataloader() (cellarium.ml.core.CellariumAnnDataDataModule method) validate() (cellarium.ml.models.ValidateMixin method) validate_anndata() (cellarium.ml.data.AnnDataSchema method)

ValidateMixin (class in cellarium.ml.models) validation_step() (cellarium.ml.core.CellariumModule method) var_g (cellarium.ml.models.OnePassMeanVarStd property) VarianceMonitor (class in cellarium.ml.callbacks)

W

W_variance (cellarium.ml.models.ProbabilisticPCA property)

weight (cellarium.ml.layers.MuLinear property) wrapped_function() (cellarium.ml.cli.LightningModule__load_from_checkpoint_class method)

Z

ZScore (class in cellarium.ml.transforms)