Cellarium ML
Documentation
Callbacks
CLI
Core
Data
Distributions
Layers
LR Schedulers
Models
Transforms
Preprocessing
Utilities
Examples
Example CLI workflow
Tutorials
Part I: Preprocessing
Maximal Update Parametrization (μP) - coordinate checking
Set up pretrained Geneformer model and make predictions
Cellarium ML
Index
Index
_
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A
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B
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C
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D
|
E
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F
|
G
|
H
|
I
|
K
|
L
|
M
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N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
|
Z
_
__del__() (cellarium.ml.callbacks.PredictionWriter method)
__getitem__() (cellarium.ml.data.DistributedAnnDataCollection method)
(cellarium.ml.data.IterableDistributedAnnDataCollectionDataset method)
__init__() (cellarium.ml.transforms.Duplicate 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
batch_mean_bg (cellarium.ml.models.OnePassMeanVarStd property)
batch_representation_from_batch_index() (cellarium.ml.models.SingleCellVariationalInference method)
batch_var_bg (cellarium.ml.models.OnePassMeanVarStd property)
bias (cellarium.ml.layers.MuLinear property)
BinomialResample (class in cellarium.ml.transforms)
C
cached (cellarium.ml.data.LazyAnnData property)
categorical_onehot_from_categorical_index() (cellarium.ml.models.SingleCellVariationalInference method)
categories_to_codes() (in module cellarium.ml.utilities.data)
categories_to_product_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
cellarium_gpt() (in module cellarium.ml.cli)
CellariumAnnDataDataModule (class in cellarium.ml.core)
CellariumGPT (class in cellarium.ml.models)
CellariumGPTTrainTokenizer (class in cellarium.ml.transforms)
CellariumModel (class in cellarium.ml.models)
CellariumModule (class in cellarium.ml.core)
CellariumModuleLoadFromCheckpoint (in module cellarium.ml.cli)
CellariumPipeline (class in cellarium.ml.core)
CenterPerCell (class in cellarium.ml.transforms)
check_disk_space() (cellarium.ml.callbacks.PredictionWriter method)
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_batch_index_n_categories() (in module cellarium.ml.cli)
compute_cell_type_categories() (in module cellarium.ml.cli)
compute_cl_distance_matrix() (in module cellarium.ml.utilities.data)
compute_cl_name_subset() (in module cellarium.ml.cli)
compute_n_cats_per_cov() (in module cellarium.ml.cli)
compute_n_obs() (in module cellarium.ml.cli)
compute_n_vars() (in module cellarium.ml.cli)
compute_var_names_g() (in module cellarium.ml.cli)
compute_y_categories() (in module cellarium.ml.cli)
ComputeNorm (class in cellarium.ml.callbacks)
configure_gradient_clipping() (cellarium.ml.core.CellariumModule method)
configure_model() (cellarium.ml.core.CellariumModule method)
configure_optimizers() (cellarium.ml.core.CellariumModule method)
contrastive_mlp() (in module cellarium.ml.cli)
ContrastiveMLP (class in cellarium.ml.models)
cpu_transforms (cellarium.ml.core.CellariumModule property)
D
Densify (class in cellarium.ml.transforms)
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)
DressedLayer (class in cellarium.ml.layers)
Dropout (class in cellarium.ml.transforms)
Duplicate (class in cellarium.ml.transforms)
E
explained_variance_k (cellarium.ml.models.IncrementalPCA property)
F
file_loader_constructor() (in module cellarium.ml.cli)
file_multi_loader_constructor() (in module cellarium.ml.cli)
FileLoader (class in cellarium.ml.cli)
FileMultiLoader (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.DressedLayer method)
(cellarium.ml.layers.MultiHeadAttention method)
(cellarium.ml.layers.MultiHeadReadout method)
(cellarium.ml.layers.NormAdd method)
(cellarium.ml.layers.PositionWiseFFN method)
(cellarium.ml.layers.TokenEmbedding method)
(cellarium.ml.layers.Transformer method)
(cellarium.ml.layers.TransformerBlock method)
(cellarium.ml.models.ContrastiveMLP 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.SingleCellVariationalInference method)
(cellarium.ml.models.SOCAM method)
(cellarium.ml.models.TDigest method)
(cellarium.ml.transforms.BinomialResample method)
(cellarium.ml.transforms.Densify method)
(cellarium.ml.transforms.DivideByScale method)
(cellarium.ml.transforms.Dropout method)
(cellarium.ml.transforms.Duplicate method)
(cellarium.ml.transforms.Filter method)
(cellarium.ml.transforms.GaussianNoise method)
(cellarium.ml.transforms.Log1p method)
(cellarium.ml.transforms.NormalizeTotal method)
(cellarium.ml.transforms.ZScore method)
FullyConnectedLinear (class in cellarium.ml.layers)
G
GatherLayer (class in cellarium.ml.utilities.distributed)
GaussianNoise (class in cellarium.ml.transforms)
Geneformer (class in cellarium.ml.models)
geneformer() (in module cellarium.ml.cli)
generative() (cellarium.ml.models.SingleCellVariationalInference method)
get_categories() (in module cellarium.ml.utilities.data)
get_cl_classes_from_owl() (in module cellarium.ml.utilities.data)
get_cl_descendant_tensor_from_owl() (in module cellarium.ml.utilities.data)
get_cl_names_from_owl() (in module cellarium.ml.utilities.data)
get_coord_data() (in module cellarium.ml.utilities.testing)
get_rank_and_num_replicas() (in module cellarium.ml.utilities.distributed)
get_var_names_g_indices() (in module cellarium.ml.utilities.data)
get_worker_info() (in module cellarium.ml.utilities.distributed)
GetCoordData (class in cellarium.ml.callbacks)
H
hvg_seurat_v3() (in module cellarium.ml.cli)
HVGSeuratV3 (class in cellarium.ml.models)
I
incremental_pca() (in module cellarium.ml.cli)
IncrementalPCA (class in cellarium.ml.models)
inference() (cellarium.ml.models.SingleCellVariationalInference method)
IterableDistributedAnnDataCollectionDataset (class in cellarium.ml.data)
K
keep_sparse() (in module cellarium.ml.utilities.data)
kotliar_compute_highly_variable_genes() (in module cellarium.ml.preprocessing)
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)
median_g (cellarium.ml.models.TDigest property)
merge_heads() (cellarium.ml.layers.MultiHeadAttention static method)
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_before_backward() (cellarium.ml.callbacks.ComputeNorm method)
on_before_optimizer_step() (cellarium.ml.callbacks.ComputeNorm method)
on_train_batch_end() (cellarium.ml.callbacks.VarianceMonitor method)
(cellarium.ml.core.CellariumModule method)
on_train_end() (cellarium.ml.core.CellariumModule method)
(cellarium.ml.models.OnePassMeanVarStd method)
on_train_epoch_end() (cellarium.ml.core.CellariumModule method)
(cellarium.ml.models.HVGSeuratV3 method)
(cellarium.ml.models.IncrementalPCA method)
on_train_epoch_start() (cellarium.ml.core.CellariumModule method)
(cellarium.ml.models.HVGSeuratV3 method)
on_train_start() (cellarium.ml.callbacks.VarianceMonitor method)
(cellarium.ml.core.CellariumModule method)
(cellarium.ml.models.HVGSeuratV3 method)
on_validation_epoch_end() (cellarium.ml.core.CellariumModule method)
on_validation_epoch_start() (cellarium.ml.core.CellariumModule method)
onepass_mean_var_std() (in module cellarium.ml.cli)
OnePassMeanVarStd (class in cellarium.ml.models)
P
PFlogPF (class in cellarium.ml.transforms)
PositionWiseFFN (class in cellarium.ml.layers)
predict() (cellarium.ml.models.CellariumGPT method)
(cellarium.ml.models.ContrastiveMLP method)
(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)
(cellarium.ml.models.SingleCellVariationalInference method)
(cellarium.ml.models.SOCAM 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)
PyTreeDataset (class in cellarium.ml.data)
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)
reconstruct() (cellarium.ml.models.SingleCellVariationalInference method)
reset_parameters() (cellarium.ml.models.CellariumModel method)
S
scvi() (in module cellarium.ml.cli)
series_to_str_list() (in module cellarium.ml.utilities.data)
set_epoch() (cellarium.ml.data.IterableDistributedAnnDataCollectionDataset method)
set_resume_step() (cellarium.ml.data.IterableDistributedAnnDataCollectionDataset method)
setup() (cellarium.ml.core.CellariumAnnDataDataModule method)
seurat_compute_highly_variable_genes() (in module cellarium.ml.preprocessing)
shape (cellarium.ml.data.LazyAnnData property)
sigma_variance (cellarium.ml.models.ProbabilisticPCA property)
SingleCellVariationalInference (class in cellarium.ml.models)
SOCAM (class in cellarium.ml.models)
socam() (in module cellarium.ml.cli)
split_heads() (cellarium.ml.layers.MultiHeadAttention static method)
T
TDigest (class in cellarium.ml.models)
tdigest() (in module cellarium.ml.cli)
test() (cellarium.ml.models.TestMixin method)
test_dataloader() (cellarium.ml.core.CellariumAnnDataDataModule method)
test_step() (cellarium.ml.core.CellariumModule method)
TestMixin (class in cellarium.ml.models)
to_torch_sparse_csr() (in module cellarium.ml.utilities.data)
TokenEmbedding (class in cellarium.ml.layers)
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.SOCAM method)
(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)
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)