cz-benchmarks
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cz-benchmarks
Index
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Y
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Z
_
__class_vars__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__eq__() (czbenchmarks.datasets.DataType method)
(czbenchmarks.datasets.types.DataType method)
(czbenchmarks.models.types.ModelType method)
__hash__() (czbenchmarks.datasets.DataType method)
(czbenchmarks.datasets.types.DataType method)
(czbenchmarks.models.types.ModelType method)
__init_subclass__() (czbenchmarks.models.validators.base_model_validator.BaseModelValidator class method)
(czbenchmarks.models.validators.base_single_cell_model_validator.BaseSingleCellValidator class method)
(czbenchmarks.models.validators.BaseModelValidator class method)
(czbenchmarks.models.validators.BaseSingleCellValidator class method)
__private_attributes__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_complete__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_computed_fields__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_core_schema__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_custom_init__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_decorators__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_extra__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_fields__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_fields_set__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_generic_metadata__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_parent_namespace__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_post_init__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_private__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_root_model__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_serializer__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__pydantic_validator__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__repr__() (czbenchmarks.datasets.DataType method)
(czbenchmarks.datasets.Organism method)
(czbenchmarks.datasets.types.DataType method)
(czbenchmarks.datasets.types.Organism method)
(czbenchmarks.models.types.ModelType method)
__signature__ (czbenchmarks.cli.cli_run.CacheOptions attribute)
(czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.metrics.types.MetricResult attribute)
__str__() (czbenchmarks.datasets.DataType method)
(czbenchmarks.datasets.Organism method)
(czbenchmarks.datasets.types.DataType method)
(czbenchmarks.datasets.types.Organism method)
(czbenchmarks.models.types.ModelType method)
A
adata (czbenchmarks.datasets.single_cell.SingleCellDataset property)
(czbenchmarks.datasets.SingleCellDataset property)
add_arguments() (in module czbenchmarks.cli.cli_list)
(in module czbenchmarks.cli.cli_run)
ADJUSTED_RAND_INDEX (czbenchmarks.metrics.types.MetricType attribute)
AFRICAN_CLAWED_FROG (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
AIDO (czbenchmarks.models.types.ModelType attribute)
ANNDATA (czbenchmarks.datasets.DataType attribute)
(czbenchmarks.datasets.types.DataType attribute)
app_mount_dir (czbenchmarks.runner.ContainerRunner attribute)
args (czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.models.implementations.base_model_implementation.BaseModelImplementation attribute)
(czbenchmarks.models.implementations.BaseModelImplementation attribute)
ARTIFACTS_PATH_DOCKER (in module czbenchmarks.constants)
available_organisms (czbenchmarks.models.validators.base_single_cell_model_validator.BaseSingleCellValidator attribute)
(czbenchmarks.models.validators.BaseSingleCellValidator attribute)
B
BaseDataset (class in czbenchmarks.datasets)
(class in czbenchmarks.datasets.base)
BASELINE (czbenchmarks.models.types.ModelType attribute)
baseline_args (czbenchmarks.cli.cli_run.TaskArgs attribute)
BaseModelImplementation (class in czbenchmarks.models.implementations)
(class in czbenchmarks.models.implementations.base_model_implementation)
BaseModelValidator (class in czbenchmarks.models.validators)
(class in czbenchmarks.models.validators.base_model_validator)
BaseSingleCellValidator (class in czbenchmarks.models.validators)
(class in czbenchmarks.models.validators.base_single_cell_model_validator)
BaseTask (class in czbenchmarks.tasks.base)
batch_key (czbenchmarks.tasks.BatchIntegrationTask attribute)
(czbenchmarks.tasks.integration.BatchIntegrationTask attribute)
BATCH_SILHOUETTE (czbenchmarks.metrics.types.MetricType attribute)
BatchIntegrationTask (class in czbenchmarks.tasks)
(class in czbenchmarks.tasks.integration)
C
CacheOptions (class in czbenchmarks.cli.cli_run)
CAENORHABDITIS_ELEGANS (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
CHICKEN (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
CHIMPANZEE (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
cli_args (czbenchmarks.runner.ContainerRunner attribute)
client (czbenchmarks.runner.ContainerRunner attribute)
cluster_embedding() (in module czbenchmarks.tasks.utils)
ClusteringTask (class in czbenchmarks.tasks)
(class in czbenchmarks.tasks.clustering)
compute() (czbenchmarks.metrics.types.MetricRegistry method)
compute_entropy_per_cell() (in module czbenchmarks.metrics.utils)
CONDITION_KEY (czbenchmarks.datasets.DataType attribute)
condition_key (czbenchmarks.datasets.PerturbationSingleCellDataset property)
(czbenchmarks.datasets.single_cell.PerturbationSingleCellDataset property)
CONDITION_KEY (czbenchmarks.datasets.types.DataType attribute)
ContainerRunner (class in czbenchmarks.runner)
CORAL (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
CRAB_EATING_MACAQUE (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
create_parser() (czbenchmarks.models.implementations.base_model_implementation.BaseModelImplementation method)
(czbenchmarks.models.implementations.BaseModelImplementation method)
CrossSpeciesIntegrationTask (class in czbenchmarks.tasks)
(class in czbenchmarks.tasks.single_cell)
(class in czbenchmarks.tasks.single_cell.cross_species)
czbenchmarks
module
czbenchmarks.cli
module
czbenchmarks.cli.cli
module
czbenchmarks.cli.cli_list
module
czbenchmarks.cli.cli_run
module
czbenchmarks.cli.utils
module
czbenchmarks.constants
module
czbenchmarks.datasets
module
czbenchmarks.datasets.base
module
czbenchmarks.datasets.single_cell
module
czbenchmarks.datasets.types
module
czbenchmarks.datasets.utils
module
czbenchmarks.exceptions
module
czbenchmarks.metrics
module
czbenchmarks.metrics.implementations
module
czbenchmarks.metrics.types
module
czbenchmarks.metrics.utils
module
czbenchmarks.models
module
czbenchmarks.models.implementations
module
czbenchmarks.models.implementations.base_model_implementation
module
czbenchmarks.models.types
module
czbenchmarks.models.utils
module
czbenchmarks.models.validators
module
czbenchmarks.models.validators.base_model_validator
module
czbenchmarks.models.validators.base_single_cell_model_validator
module
czbenchmarks.runner
module
czbenchmarks.tasks
module
czbenchmarks.tasks.base
module
czbenchmarks.tasks.clustering
module
czbenchmarks.tasks.constants
module
czbenchmarks.tasks.embedding
module
czbenchmarks.tasks.integration
module
czbenchmarks.tasks.label_prediction
module
czbenchmarks.tasks.single_cell
module
czbenchmarks.tasks.single_cell.cross_species
module
czbenchmarks.tasks.single_cell.perturbation
module
czbenchmarks.tasks.utils
module
czbenchmarks.utils
module
CZBenchmarksException
D
dataset_names (czbenchmarks.cli.cli_run.TaskResult attribute)
dataset_names_display (czbenchmarks.cli.cli_run.TaskResult attribute)
dataset_to_display_name() (in module czbenchmarks.datasets.utils)
dataset_type (czbenchmarks.models.validators.base_model_validator.BaseModelValidator attribute)
(czbenchmarks.models.validators.base_single_cell_model_validator.BaseSingleCellValidator attribute)
(czbenchmarks.models.validators.BaseModelValidator attribute)
(czbenchmarks.models.validators.BaseSingleCellValidator attribute)
datasets (czbenchmarks.models.implementations.base_model_implementation.BaseModelImplementation attribute)
(czbenchmarks.models.implementations.BaseModelImplementation attribute)
DATASETS_CACHE_PATH (in module czbenchmarks.constants)
DataType (class in czbenchmarks.datasets)
(class in czbenchmarks.datasets.types)
(in module czbenchmarks.models.types)
DataTypeSpec (class in czbenchmarks.datasets.types)
DataValue (in module czbenchmarks.datasets)
(in module czbenchmarks.datasets.types)
DEFAULT_OUTPUT_FORMAT (in module czbenchmarks.cli.cli_run)
default_params (czbenchmarks.metrics.types.MetricInfo attribute)
description (czbenchmarks.datasets.DataType property)
(czbenchmarks.datasets.types.DataType property)
(czbenchmarks.datasets.types.DataTypeSpec attribute)
(czbenchmarks.metrics.types.MetricInfo attribute)
deserialize() (czbenchmarks.datasets.base.BaseDataset static method)
(czbenchmarks.datasets.BaseDataset static method)
display_name (czbenchmarks.tasks.base.BaseTask property)
(czbenchmarks.tasks.BatchIntegrationTask property)
(czbenchmarks.tasks.clustering.ClusteringTask property)
(czbenchmarks.tasks.ClusteringTask property)
(czbenchmarks.tasks.CrossSpeciesIntegrationTask property)
(czbenchmarks.tasks.embedding.EmbeddingTask property)
(czbenchmarks.tasks.EmbeddingTask property)
(czbenchmarks.tasks.integration.BatchIntegrationTask property)
(czbenchmarks.tasks.label_prediction.MetadataLabelPredictionTask property)
(czbenchmarks.tasks.MetadataLabelPredictionTask property)
(czbenchmarks.tasks.PerturbationTask property)
(czbenchmarks.tasks.single_cell.cross_species.CrossSpeciesIntegrationTask property)
(czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTask property)
(czbenchmarks.tasks.single_cell.perturbation.PerturbationTask property)
(czbenchmarks.tasks.single_cell.PerturbationTask property)
download_embeddings (czbenchmarks.cli.cli_run.CacheOptions attribute)
download_file_from_remote() (in module czbenchmarks.utils)
download_model_weights() (czbenchmarks.models.implementations.base_model_implementation.BaseModelImplementation method)
(czbenchmarks.models.implementations.BaseModelImplementation method)
dtype (czbenchmarks.datasets.DataType property)
(czbenchmarks.datasets.types.DataType property)
(czbenchmarks.datasets.types.DataTypeSpec attribute)
E
EMBEDDING (czbenchmarks.datasets.DataType attribute)
(czbenchmarks.datasets.types.DataType attribute)
EmbeddingTask (class in czbenchmarks.tasks)
(class in czbenchmarks.tasks.embedding)
ENTROPY_PER_CELL (czbenchmarks.metrics.types.MetricType attribute)
environment (czbenchmarks.runner.ContainerRunner attribute)
F
filter_minimum_class() (in module czbenchmarks.tasks.utils)
flavor (czbenchmarks.tasks.clustering.ClusteringTask attribute)
(czbenchmarks.tasks.ClusteringTask attribute)
FLAVOR (in module czbenchmarks.tasks.constants)
FRESHWATER_SPONGE (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
from_args() (czbenchmarks.cli.cli_run.CacheOptions class method)
FRUIT_FLY (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
func (czbenchmarks.metrics.types.MetricInfo attribute)
G
GENEFORMER (czbenchmarks.models.types.ModelType attribute)
get_base_name() (in module czbenchmarks.constants)
get_info() (czbenchmarks.metrics.types.MetricRegistry method)
get_input() (czbenchmarks.datasets.base.BaseDataset method)
(czbenchmarks.datasets.BaseDataset method)
get_model_arg_permutations() (in module czbenchmarks.cli.cli_run)
get_model_weights_subdir() (czbenchmarks.models.implementations.base_model_implementation.BaseModelImplementation method)
(czbenchmarks.models.implementations.BaseModelImplementation method)
get_numbered_path() (in module czbenchmarks.constants)
get_output() (czbenchmarks.datasets.base.BaseDataset method)
(czbenchmarks.datasets.BaseDataset method)
get_processed_dataset_cache_filename() (in module czbenchmarks.cli.cli_run)
get_processed_dataset_cache_path() (in module czbenchmarks.cli.cli_run)
get_remote_cache_prefix() (in module czbenchmarks.cli.cli_run)
get_remote_last_modified() (in module czbenchmarks.utils)
get_result_url_for_remote() (in module czbenchmarks.cli.cli_run)
get_version() (in module czbenchmarks.cli.utils)
GORILLA (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
gpu (czbenchmarks.runner.ContainerRunner attribute)
H
HUMAN (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
I
image (czbenchmarks.runner.ContainerRunner attribute)
import_class_from_config() (in module czbenchmarks.utils)
initialize_hydra() (in module czbenchmarks.utils)
INPUT_DATA_PATH_DOCKER (in module czbenchmarks.constants)
inputs (czbenchmarks.datasets.base.BaseDataset property)
(czbenchmarks.datasets.BaseDataset property)
(czbenchmarks.models.validators.base_model_validator.BaseModelValidator property)
(czbenchmarks.models.validators.BaseModelValidator property)
interactive (czbenchmarks.runner.ContainerRunner attribute)
is_input (czbenchmarks.datasets.DataType property)
(czbenchmarks.datasets.types.DataType property)
(czbenchmarks.datasets.types.DataTypeSpec attribute)
is_output (czbenchmarks.datasets.DataType property)
(czbenchmarks.datasets.types.DataType property)
J
JACCARD (czbenchmarks.metrics.types.MetricType attribute)
jaccard_score() (in module czbenchmarks.metrics.utils)
K
key_added (czbenchmarks.tasks.clustering.ClusteringTask attribute)
(czbenchmarks.tasks.ClusteringTask attribute)
KEY_ADDED (in module czbenchmarks.tasks.constants)
kwargs (czbenchmarks.datasets.base.BaseDataset attribute)
(czbenchmarks.datasets.BaseDataset attribute)
L
label_key (czbenchmarks.tasks.BatchIntegrationTask attribute)
(czbenchmarks.tasks.clustering.ClusteringTask attribute)
(czbenchmarks.tasks.ClusteringTask attribute)
(czbenchmarks.tasks.CrossSpeciesIntegrationTask attribute)
(czbenchmarks.tasks.embedding.EmbeddingTask attribute)
(czbenchmarks.tasks.EmbeddingTask attribute)
(czbenchmarks.tasks.integration.BatchIntegrationTask attribute)
(czbenchmarks.tasks.label_prediction.MetadataLabelPredictionTask attribute)
(czbenchmarks.tasks.MetadataLabelPredictionTask attribute)
(czbenchmarks.tasks.single_cell.cross_species.CrossSpeciesIntegrationTask attribute)
(czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTask attribute)
list_available_datasets() (in module czbenchmarks.datasets)
(in module czbenchmarks.datasets.utils)
list_available_models() (in module czbenchmarks.models)
(in module czbenchmarks.models.utils)
list_metrics() (czbenchmarks.metrics.types.MetricRegistry method)
load_data() (czbenchmarks.datasets.base.BaseDataset method)
(czbenchmarks.datasets.BaseDataset method)
(czbenchmarks.datasets.PerturbationSingleCellDataset method)
(czbenchmarks.datasets.single_cell.PerturbationSingleCellDataset method)
(czbenchmarks.datasets.single_cell.SingleCellDataset method)
(czbenchmarks.datasets.SingleCellDataset method)
load_dataset() (in module czbenchmarks.datasets)
(in module czbenchmarks.datasets.utils)
log (in module czbenchmarks.cli.cli)
(in module czbenchmarks.cli.cli_run)
(in module czbenchmarks.cli.utils)
logger (in module czbenchmarks.datasets.single_cell)
(in module czbenchmarks.models.implementations.base_model_implementation)
(in module czbenchmarks.models.utils)
(in module czbenchmarks.models.validators.base_model_validator)
(in module czbenchmarks.runner)
(in module czbenchmarks.tasks.clustering)
(in module czbenchmarks.tasks.embedding)
(in module czbenchmarks.tasks.integration)
(in module czbenchmarks.tasks.label_prediction)
(in module czbenchmarks.tasks.single_cell.perturbation)
(in module czbenchmarks.tasks.utils)
(in module czbenchmarks.utils)
M
main() (in module czbenchmarks.cli.cli)
(in module czbenchmarks.cli.cli_list)
(in module czbenchmarks.cli.cli_run)
MALARIA_PARASITE (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
MARMOSET (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
MEAN_FOLD_ACCURACY (czbenchmarks.metrics.types.MetricType attribute)
MEAN_FOLD_AUROC (czbenchmarks.metrics.types.MetricType attribute)
MEAN_FOLD_F1_SCORE (czbenchmarks.metrics.types.MetricType attribute)
mean_fold_metric() (in module czbenchmarks.metrics.utils)
MEAN_FOLD_PRECISION (czbenchmarks.metrics.types.MetricType attribute)
MEAN_FOLD_RECALL (czbenchmarks.metrics.types.MetricType attribute)
MEAN_SQUARED_ERROR (czbenchmarks.metrics.types.MetricType attribute)
METADATA (czbenchmarks.datasets.DataType attribute)
(czbenchmarks.datasets.types.DataType attribute)
MetadataLabelPredictionTask (class in czbenchmarks.tasks)
(class in czbenchmarks.tasks.label_prediction)
metric_type (czbenchmarks.metrics.types.MetricResult attribute)
MetricInfo (class in czbenchmarks.metrics.types)
MetricRegistry (class in czbenchmarks.metrics.types)
MetricResult (class in czbenchmarks.metrics.types)
metrics (czbenchmarks.cli.cli_run.TaskResult attribute)
metrics_registry (in module czbenchmarks.metrics)
(in module czbenchmarks.metrics.implementations)
MetricType (class in czbenchmarks.metrics.types)
min_class_size (czbenchmarks.tasks.label_prediction.MetadataLabelPredictionTask attribute)
(czbenchmarks.tasks.MetadataLabelPredictionTask attribute)
MIN_CLASS_SIZE (in module czbenchmarks.tasks.constants)
model_args (czbenchmarks.cli.cli_run.TaskResult attribute)
model_config (czbenchmarks.cli.cli_run.TaskArgs attribute)
model_name_display (czbenchmarks.cli.cli_run.TaskResult property)
model_to_display_name() (in module czbenchmarks.models.utils)
model_type (czbenchmarks.cli.cli_run.TaskResult attribute)
(czbenchmarks.models.validators.base_model_validator.BaseModelValidator attribute)
(czbenchmarks.models.validators.BaseModelValidator attribute)
(czbenchmarks.runner.ContainerRunner attribute)
MODEL_WEIGHTS_CACHE_PATH (in module czbenchmarks.constants)
model_weights_dir (czbenchmarks.models.implementations.base_model_implementation.BaseModelImplementation attribute)
(czbenchmarks.models.implementations.BaseModelImplementation attribute)
MODEL_WEIGHTS_PATH_DOCKER (in module czbenchmarks.constants)
ModelArgs (class in czbenchmarks.cli.cli_run)
ModelArgsDict (in module czbenchmarks.cli.cli_run)
ModelOutputs (in module czbenchmarks.models.types)
ModelType (class in czbenchmarks.models.types)
module
czbenchmarks
czbenchmarks.cli
czbenchmarks.cli.cli
czbenchmarks.cli.cli_list
czbenchmarks.cli.cli_run
czbenchmarks.cli.utils
czbenchmarks.constants
czbenchmarks.datasets
czbenchmarks.datasets.base
czbenchmarks.datasets.single_cell
czbenchmarks.datasets.types
czbenchmarks.datasets.utils
czbenchmarks.exceptions
czbenchmarks.metrics
czbenchmarks.metrics.implementations
czbenchmarks.metrics.types
czbenchmarks.metrics.utils
czbenchmarks.models
czbenchmarks.models.implementations
czbenchmarks.models.implementations.base_model_implementation
czbenchmarks.models.types
czbenchmarks.models.utils
czbenchmarks.models.validators
czbenchmarks.models.validators.base_model_validator
czbenchmarks.models.validators.base_single_cell_model_validator
czbenchmarks.runner
czbenchmarks.tasks
czbenchmarks.tasks.base
czbenchmarks.tasks.clustering
czbenchmarks.tasks.constants
czbenchmarks.tasks.embedding
czbenchmarks.tasks.integration
czbenchmarks.tasks.label_prediction
czbenchmarks.tasks.single_cell
czbenchmarks.tasks.single_cell.cross_species
czbenchmarks.tasks.single_cell.perturbation
czbenchmarks.tasks.utils
czbenchmarks.utils
MOUSE (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
MOUSE_LEMUR (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
MULTI_DATASET_TASK_NAMES (in module czbenchmarks.tasks.utils)
N
n_folds (czbenchmarks.tasks.label_prediction.MetadataLabelPredictionTask attribute)
(czbenchmarks.tasks.MetadataLabelPredictionTask attribute)
N_FOLDS (in module czbenchmarks.tasks.constants)
n_iterations (czbenchmarks.tasks.clustering.ClusteringTask attribute)
(czbenchmarks.tasks.ClusteringTask attribute)
N_ITERATIONS (in module czbenchmarks.tasks.constants)
NAKED_MOLE_RAT (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
name (czbenchmarks.cli.cli_run.ModelArgs attribute)
(czbenchmarks.cli.cli_run.TaskArgs attribute)
(czbenchmarks.datasets.Organism property)
(czbenchmarks.datasets.types.DataTypeSpec attribute)
(czbenchmarks.datasets.types.Organism property)
nearest_neighbors_hnsw() (in module czbenchmarks.metrics.utils)
NORMALIZED_MUTUAL_INFO (czbenchmarks.metrics.types.MetricType attribute)
O
OBSM_KEY (in module czbenchmarks.tasks.constants)
OPOSSUM (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
Organism (class in czbenchmarks.datasets)
(class in czbenchmarks.datasets.types)
ORGANISM (czbenchmarks.datasets.DataType attribute)
organism (czbenchmarks.datasets.single_cell.SingleCellDataset property)
(czbenchmarks.datasets.SingleCellDataset property)
ORGANISM (czbenchmarks.datasets.types.DataType attribute)
OUTPUT_DATA_PATH_DOCKER (in module czbenchmarks.constants)
outputs (czbenchmarks.datasets.base.BaseDataset property)
(czbenchmarks.datasets.BaseDataset property)
(czbenchmarks.models.validators.base_model_validator.BaseModelValidator property)
(czbenchmarks.models.validators.BaseModelValidator property)
P
params (czbenchmarks.metrics.types.MetricResult attribute)
parse_args() (czbenchmarks.models.implementations.base_model_implementation.BaseModelImplementation method)
(czbenchmarks.models.implementations.BaseModelImplementation method)
parse_batch_json() (in module czbenchmarks.cli.cli_run)
parse_model_args() (in module czbenchmarks.cli.cli_run)
parse_task_args() (in module czbenchmarks.cli.cli_run)
path (czbenchmarks.datasets.base.BaseDataset attribute)
(czbenchmarks.datasets.BaseDataset attribute)
PEARSON_CORRELATION (czbenchmarks.metrics.types.MetricType attribute)
PERTURBATION_PRED (czbenchmarks.datasets.DataType attribute)
(czbenchmarks.datasets.types.DataType attribute)
PERTURBATION_TRUTH (czbenchmarks.datasets.DataType attribute)
perturbation_truth (czbenchmarks.datasets.PerturbationSingleCellDataset property)
(czbenchmarks.datasets.single_cell.PerturbationSingleCellDataset property)
PERTURBATION_TRUTH (czbenchmarks.datasets.types.DataType attribute)
PerturbationSingleCellDataset (class in czbenchmarks.datasets)
(class in czbenchmarks.datasets.single_cell)
PerturbationTask (class in czbenchmarks.tasks)
(class in czbenchmarks.tasks.single_cell)
(class in czbenchmarks.tasks.single_cell.perturbation)
PLATYPUS (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
prefix (czbenchmarks.datasets.Organism property)
(czbenchmarks.datasets.types.Organism property)
PROCESSED_DATASETS_CACHE_PATH (in module czbenchmarks.constants)
R
RABBIT (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
random_seed (czbenchmarks.tasks.clustering.ClusteringTask attribute)
(czbenchmarks.tasks.ClusteringTask attribute)
(czbenchmarks.tasks.label_prediction.MetadataLabelPredictionTask attribute)
(czbenchmarks.tasks.MetadataLabelPredictionTask attribute)
RANDOM_SEED (in module czbenchmarks.tasks.constants)
RAT (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
RAW_INPUT_DIR_PATH_DOCKER (in module czbenchmarks.constants)
register() (czbenchmarks.metrics.types.MetricRegistry method)
remote_cache_url (czbenchmarks.cli.cli_run.CacheOptions attribute)
RemoteStorageError
RemoteStorageObjectAlreadyExists
required_args (czbenchmarks.metrics.types.MetricInfo attribute)
required_inputs (czbenchmarks.tasks.base.BaseTask property)
(czbenchmarks.tasks.BatchIntegrationTask property)
(czbenchmarks.tasks.clustering.ClusteringTask property)
(czbenchmarks.tasks.ClusteringTask property)
(czbenchmarks.tasks.CrossSpeciesIntegrationTask property)
(czbenchmarks.tasks.embedding.EmbeddingTask property)
(czbenchmarks.tasks.EmbeddingTask property)
(czbenchmarks.tasks.integration.BatchIntegrationTask property)
(czbenchmarks.tasks.label_prediction.MetadataLabelPredictionTask property)
(czbenchmarks.tasks.MetadataLabelPredictionTask property)
(czbenchmarks.tasks.PerturbationTask property)
(czbenchmarks.tasks.single_cell.cross_species.CrossSpeciesIntegrationTask property)
(czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTask property)
(czbenchmarks.tasks.single_cell.perturbation.PerturbationTask property)
(czbenchmarks.tasks.single_cell.PerturbationTask property)
required_obs_keys (czbenchmarks.models.validators.base_single_cell_model_validator.BaseSingleCellValidator attribute)
(czbenchmarks.models.validators.BaseSingleCellValidator attribute)
required_outputs (czbenchmarks.tasks.base.BaseTask property)
(czbenchmarks.tasks.BatchIntegrationTask property)
(czbenchmarks.tasks.clustering.ClusteringTask property)
(czbenchmarks.tasks.ClusteringTask property)
(czbenchmarks.tasks.CrossSpeciesIntegrationTask property)
(czbenchmarks.tasks.embedding.EmbeddingTask property)
(czbenchmarks.tasks.EmbeddingTask property)
(czbenchmarks.tasks.integration.BatchIntegrationTask property)
(czbenchmarks.tasks.label_prediction.MetadataLabelPredictionTask property)
(czbenchmarks.tasks.MetadataLabelPredictionTask property)
(czbenchmarks.tasks.PerturbationTask property)
(czbenchmarks.tasks.single_cell.cross_species.CrossSpeciesIntegrationTask property)
(czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTask property)
(czbenchmarks.tasks.single_cell.perturbation.PerturbationTask property)
(czbenchmarks.tasks.single_cell.PerturbationTask property)
required_var_keys (czbenchmarks.models.validators.base_single_cell_model_validator.BaseSingleCellValidator attribute)
(czbenchmarks.models.validators.BaseSingleCellValidator attribute)
requires_multiple_datasets (czbenchmarks.tasks.base.BaseTask property)
(czbenchmarks.tasks.CrossSpeciesIntegrationTask property)
(czbenchmarks.tasks.single_cell.cross_species.CrossSpeciesIntegrationTask property)
(czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTask property)
RHESUS_MACAQUE (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
run() (czbenchmarks.models.implementations.base_model_implementation.BaseModelImplementation method)
(czbenchmarks.models.implementations.BaseModelImplementation method)
(czbenchmarks.runner.ContainerRunner method)
(czbenchmarks.tasks.base.BaseTask method)
(in module czbenchmarks.cli.cli_run)
run_inference() (in module czbenchmarks.runner)
run_inference_or_load_from_cache() (in module czbenchmarks.cli.cli_run)
run_model() (czbenchmarks.models.implementations.base_model_implementation.BaseModelImplementation method)
(czbenchmarks.models.implementations.BaseModelImplementation method)
run_multi_dataset_task() (in module czbenchmarks.cli.cli_run)
run_standard_scrna_workflow() (in module czbenchmarks.tasks.utils)
run_task() (in module czbenchmarks.cli.cli_run)
run_with_inference() (in module czbenchmarks.cli.cli_run)
run_without_inference() (in module czbenchmarks.cli.cli_run)
runtime_metrics (czbenchmarks.cli.cli_run.TaskResult attribute)
RuntimeMetricsDict (in module czbenchmarks.cli.cli_run)
S
SCGENEPT (czbenchmarks.models.types.ModelType attribute)
SCGPT (czbenchmarks.models.types.ModelType attribute)
SCVI (czbenchmarks.models.types.ModelType attribute)
SEA_LAMPREY (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
SEA_URCHIN (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
serialize() (czbenchmarks.datasets.base.BaseDataset method)
(czbenchmarks.datasets.BaseDataset method)
set_baseline (czbenchmarks.cli.cli_run.TaskArgs attribute)
set_baseline() (czbenchmarks.tasks.base.BaseTask method)
(czbenchmarks.tasks.CrossSpeciesIntegrationTask method)
(czbenchmarks.tasks.label_prediction.MetadataLabelPredictionTask method)
(czbenchmarks.tasks.MetadataLabelPredictionTask method)
(czbenchmarks.tasks.PerturbationTask method)
(czbenchmarks.tasks.single_cell.cross_species.CrossSpeciesIntegrationTask method)
(czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTask method)
(czbenchmarks.tasks.single_cell.perturbation.PerturbationTask method)
(czbenchmarks.tasks.single_cell.PerturbationTask method)
set_input() (czbenchmarks.datasets.base.BaseDataset method)
(czbenchmarks.datasets.BaseDataset method)
set_output() (czbenchmarks.datasets.base.BaseDataset method)
(czbenchmarks.datasets.BaseDataset method)
set_processed_datasets_cache() (in module czbenchmarks.cli.cli_run)
SILHOUETTE_SCORE (czbenchmarks.metrics.types.MetricType attribute)
SingleCellDataset (class in czbenchmarks.datasets)
(class in czbenchmarks.datasets.single_cell)
spec (czbenchmarks.datasets.DataType property)
(czbenchmarks.datasets.types.DataType property)
SPLIT_KEY (czbenchmarks.datasets.DataType attribute)
split_key (czbenchmarks.datasets.PerturbationSingleCellDataset property)
(czbenchmarks.datasets.single_cell.PerturbationSingleCellDataset property)
SPLIT_KEY (czbenchmarks.datasets.types.DataType attribute)
sync_s3_to_local() (in module czbenchmarks.utils)
T
tags (czbenchmarks.metrics.types.MetricInfo attribute)
task (czbenchmarks.cli.cli_run.TaskArgs attribute)
task_name (czbenchmarks.cli.cli_run.TaskResult attribute)
task_name_display (czbenchmarks.cli.cli_run.TaskResult attribute)
TASK_NAMES (in module czbenchmarks.tasks.utils)
TaskArgs (class in czbenchmarks.cli.cli_run)
TaskResult (class in czbenchmarks.cli.cli_run)
TaskType (in module czbenchmarks.cli.cli_run)
TRANSCRIPTFORMER (czbenchmarks.models.types.ModelType attribute)
TROPICAL_CLAWED_FROG (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
try_processed_datasets_cache() (in module czbenchmarks.cli.cli_run)
U
UCE (czbenchmarks.models.types.ModelType attribute)
unload_data() (czbenchmarks.datasets.base.BaseDataset method)
(czbenchmarks.datasets.BaseDataset method)
(czbenchmarks.datasets.PerturbationSingleCellDataset method)
(czbenchmarks.datasets.single_cell.PerturbationSingleCellDataset method)
(czbenchmarks.datasets.single_cell.SingleCellDataset method)
(czbenchmarks.datasets.SingleCellDataset method)
upload_blob_to_remote() (in module czbenchmarks.utils)
upload_embeddings (czbenchmarks.cli.cli_run.CacheOptions attribute)
upload_file_to_remote() (in module czbenchmarks.utils)
upload_results (czbenchmarks.cli.cli_run.CacheOptions attribute)
V
VALID_OUTPUT_FORMATS (in module czbenchmarks.cli.cli_run)
validate() (czbenchmarks.datasets.base.BaseDataset method)
(czbenchmarks.datasets.BaseDataset method)
(czbenchmarks.tasks.base.BaseTask method)
validate_dataset() (czbenchmarks.models.validators.base_model_validator.BaseModelValidator method)
(czbenchmarks.models.validators.BaseModelValidator method)
value (czbenchmarks.metrics.types.MetricResult attribute)
W
WILD_BOAR (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
write_results() (in module czbenchmarks.cli.cli_run)
Y
YEAST (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)
Z
ZEBRAFISH (czbenchmarks.datasets.Organism attribute)
(czbenchmarks.datasets.types.Organism attribute)