Index

_

__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)