Index

_

__init_subclass__() (czbenchmarks.datasets.validators.dataset_validator.DatasetValidator class method) (czbenchmarks.datasets.validators.DatasetValidator class method) (czbenchmarks.datasets.validators.single_cell_validator.SingleCellLabeledValidator class method) (czbenchmarks.datasets.validators.SingleCellLabeledValidator class method) (czbenchmarks.tasks.Task class method) (czbenchmarks.tasks.task.Task class method)

__repr__() (czbenchmarks.datasets.Organism method) (czbenchmarks.datasets.types.Organism method) __str__() (czbenchmarks.datasets.Organism method) (czbenchmarks.datasets.types.Organism method) _metrics (czbenchmarks.metrics.types.MetricRegistry attribute)

A

ACCURACY (czbenchmarks.metrics.types.MetricType attribute) ACCURACY_CALCULATION (czbenchmarks.metrics.types.MetricType attribute) adaptive_k (czbenchmarks.tasks.sequential.SequentialOrganizationTaskInput attribute) (czbenchmarks.tasks.SequentialOrganizationTaskInput attribute) adata (czbenchmarks.datasets.single_cell.SingleCellDataset attribute), [1] (czbenchmarks.tasks.PerturbationExpressionPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.perturbation_expression_prediction.PerturbationExpressionPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.PerturbationExpressionPredictionTaskInput attribute) ADJUSTED_RAND_INDEX (czbenchmarks.metrics.types.MetricType attribute) AFRICAN_CLAWED_FROG (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) aggregate_cells_to_samples() (in module czbenchmarks.tasks.utils) aggregate_results() (in module czbenchmarks.metrics.utils)

AggregatedMetricResult (class in czbenchmarks.metrics.types) aggregation_key (czbenchmarks.metrics.types.MetricResult property) (czbenchmarks.tasks.MetricResult property) aggregation_key() (czbenchmarks.metrics.types.MetricResult method) (czbenchmarks.tasks.MetricResult method) aggregation_method (czbenchmarks.tasks.CrossSpeciesLabelPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.cross_species_label_prediction.CrossSpeciesLabelPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesLabelPredictionTaskInput attribute) ANNDATA_REF_PREFIX (in module czbenchmarks.cli.resolve_reference) AnnDataReference (class in czbenchmarks.cli.resolve_reference) AUROC (czbenchmarks.metrics.types.MetricType attribute) available_organisms (czbenchmarks.datasets.validators.single_cell_validator.SingleCellLabeledValidator attribute) (czbenchmarks.datasets.validators.SingleCellLabeledValidator attribute)

B

baseline_params (czbenchmarks.tasks.task.TaskInfo attribute) batch_labels (czbenchmarks.tasks.BatchIntegrationTaskInput attribute) (czbenchmarks.tasks.integration.BatchIntegrationTaskInput attribute) BATCH_SILHOUETTE (czbenchmarks.metrics.types.MetricType attribute) BatchIntegrationOutput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.integration)

BatchIntegrationTask (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.integration) BatchIntegrationTaskInput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.integration) build_task_input_from_predictions() (in module czbenchmarks.tasks.single_cell.perturbation_expression_prediction)

C

cache_dir (czbenchmarks.file_utils.CacheManager attribute) CacheManager (class in czbenchmarks.file_utils) CacheOptions (class in czbenchmarks.file_cache) CAENORHABDITIS_ELEGANS (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) cell_index (czbenchmarks.tasks.PerturbationExpressionPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.perturbation_expression_prediction.PerturbationExpressionPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.PerturbationExpressionPredictionTaskInput attribute) cell_representation (czbenchmarks.tasks.BatchIntegrationOutput attribute) (czbenchmarks.tasks.CrossSpeciesIntegrationOutput attribute) (czbenchmarks.tasks.embedding.EmbeddingOutput attribute) (czbenchmarks.tasks.EmbeddingOutput attribute) (czbenchmarks.tasks.integration.BatchIntegrationOutput attribute) (czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationOutput attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationOutput attribute) CellRepresentation (in module czbenchmarks.tasks.types) CHICKEN (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) CHIMPANZEE (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) clean_expired_cache() (czbenchmarks.file_utils.CacheManager method) cluster_embedding() (in module czbenchmarks.tasks.utils) ClusteringOutput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.clustering) ClusteringTask (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.clustering) ClusteringTaskInput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.clustering) compute() (czbenchmarks.metrics.types.MetricRegistry method) compute_baseline() (czbenchmarks.tasks.CrossSpeciesIntegrationTask method) (czbenchmarks.tasks.CrossSpeciesLabelPredictionTask method) (czbenchmarks.tasks.label_prediction.MetadataLabelPredictionTask method) (czbenchmarks.tasks.MetadataLabelPredictionTask method) (czbenchmarks.tasks.PerturbationExpressionPredictionTask method) (czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationTask method) (czbenchmarks.tasks.single_cell.cross_species_label_prediction.CrossSpeciesLabelPredictionTask method) (czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTask method) (czbenchmarks.tasks.single_cell.CrossSpeciesLabelPredictionTask method) (czbenchmarks.tasks.single_cell.perturbation_expression_prediction.PerturbationExpressionPredictionTask method) (czbenchmarks.tasks.single_cell.PerturbationExpressionPredictionTask method) (czbenchmarks.tasks.Task method) (czbenchmarks.tasks.task.Task method) compute_entropy_per_cell() (in module czbenchmarks.metrics.utils) condition_key (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) (czbenchmarks.tasks.PerturbationExpressionPredictionTask attribute) (czbenchmarks.tasks.single_cell.perturbation_expression_prediction.PerturbationExpressionPredictionTask attribute) (czbenchmarks.tasks.single_cell.PerturbationExpressionPredictionTask attribute) control_cells_ids (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute), [1] (czbenchmarks.datasets.SingleCellPerturbationDataset attribute), [1] control_mapping (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset property) (czbenchmarks.datasets.SingleCellPerturbationDataset property) control_name (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) CORAL (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) CRAB_EATING_MACAQUE (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) CrossSpeciesIntegrationOutput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.single_cell) (class in czbenchmarks.tasks.single_cell.cross_species_integration) CrossSpeciesIntegrationTask (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.single_cell) (class in czbenchmarks.tasks.single_cell.cross_species_integration) CrossSpeciesIntegrationTaskInput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.single_cell) (class in czbenchmarks.tasks.single_cell.cross_species_integration) CrossSpeciesLabelPredictionOutput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.single_cell) (class in czbenchmarks.tasks.single_cell.cross_species_label_prediction) CrossSpeciesLabelPredictionTask (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.single_cell) (class in czbenchmarks.tasks.single_cell.cross_species_label_prediction) CrossSpeciesLabelPredictionTaskInput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.single_cell) (class in czbenchmarks.tasks.single_cell.cross_species_label_prediction) czbenchmarks module czbenchmarks.cli module czbenchmarks.cli.cli module

czbenchmarks.cli.cli_list module czbenchmarks.cli.cli_run module czbenchmarks.cli.resolve_reference module czbenchmarks.cli.runner module czbenchmarks.cli.utils module czbenchmarks.constants module czbenchmarks.datasets module czbenchmarks.datasets.dataset module czbenchmarks.datasets.single_cell module czbenchmarks.datasets.single_cell_labeled module czbenchmarks.datasets.single_cell_perturbation module czbenchmarks.datasets.types module czbenchmarks.datasets.utils module czbenchmarks.datasets.utils_single_cell module czbenchmarks.datasets.validators module czbenchmarks.datasets.validators.dataset_validator module czbenchmarks.datasets.validators.single_cell_validator module czbenchmarks.exceptions module czbenchmarks.file_cache module czbenchmarks.file_utils module czbenchmarks.metrics module czbenchmarks.metrics.implementations module czbenchmarks.metrics.types module czbenchmarks.metrics.utils module czbenchmarks.tasks module czbenchmarks.tasks.clustering module czbenchmarks.tasks.constants module czbenchmarks.tasks.embedding module czbenchmarks.tasks.integration module czbenchmarks.tasks.label_prediction module czbenchmarks.tasks.sequential module czbenchmarks.tasks.single_cell module czbenchmarks.tasks.single_cell.cross_species_integration module czbenchmarks.tasks.single_cell.cross_species_label_prediction module czbenchmarks.tasks.single_cell.perturbation_expression_prediction module czbenchmarks.tasks.task module czbenchmarks.tasks.types module czbenchmarks.tasks.utils module czbenchmarks.types module czbenchmarks.utils module CZBenchmarksException

D

Dataset (class in czbenchmarks.datasets) (class in czbenchmarks.datasets.dataset) dataset_type (czbenchmarks.datasets.validators.dataset_validator.DatasetValidator attribute) (czbenchmarks.datasets.validators.DatasetValidator attribute) (czbenchmarks.datasets.validators.single_cell_validator.SingleCellLabeledValidator attribute) (czbenchmarks.datasets.validators.SingleCellLabeledValidator attribute) DATASETS_CACHE_PATH (in module czbenchmarks.constants) DatasetValidator (class in czbenchmarks.datasets.validators) (class in czbenchmarks.datasets.validators.dataset_validator) de_gene_col (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) de_metric_col (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) de_pval_col (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) de_results (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset property) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset property) default (czbenchmarks.tasks.task.TaskParameter attribute) DEFAULT_CACHE_DIR (in module czbenchmarks.file_utils) DEFAULT_CACHE_EXPIRATION_DAYS (in module czbenchmarks.file_utils) default_params (czbenchmarks.metrics.types.MetricInfo attribute), [1] deg_test_name (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) description (czbenchmarks.metrics.types.MetricInfo attribute), [1] (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.PerturbationExpressionPredictionTask attribute) (czbenchmarks.tasks.sequential.SequentialOrganizationTask attribute) (czbenchmarks.tasks.SequentialOrganizationTask attribute) (czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationTask attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTask attribute) (czbenchmarks.tasks.single_cell.perturbation_expression_prediction.PerturbationExpressionPredictionTask attribute) (czbenchmarks.tasks.single_cell.PerturbationExpressionPredictionTask attribute) (czbenchmarks.tasks.task.TaskInfo attribute)

display_name (czbenchmarks.tasks.BatchIntegrationTask attribute) (czbenchmarks.tasks.clustering.ClusteringTask attribute) (czbenchmarks.tasks.ClusteringTask attribute) (czbenchmarks.tasks.CrossSpeciesIntegrationTask attribute) (czbenchmarks.tasks.CrossSpeciesLabelPredictionTask 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.PerturbationExpressionPredictionTask attribute) (czbenchmarks.tasks.sequential.SequentialOrganizationTask attribute) (czbenchmarks.tasks.SequentialOrganizationTask attribute) (czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationTask attribute) (czbenchmarks.tasks.single_cell.cross_species_label_prediction.CrossSpeciesLabelPredictionTask attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTask attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesLabelPredictionTask attribute) (czbenchmarks.tasks.single_cell.perturbation_expression_prediction.PerturbationExpressionPredictionTask attribute) (czbenchmarks.tasks.single_cell.PerturbationExpressionPredictionTask attribute) (czbenchmarks.tasks.task.TaskInfo attribute) download_embeddings (czbenchmarks.file_cache.CacheOptions attribute), [1] download_file_from_remote() (in module czbenchmarks.file_utils)

E

embedding (czbenchmarks.tasks.sequential.SequentialOrganizationOutput attribute) (czbenchmarks.tasks.SequentialOrganizationOutput attribute) EmbeddingOutput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.embedding) EmbeddingTask (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.embedding)

EmbeddingTaskInput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.embedding) ensure_directory_exists() (czbenchmarks.file_utils.CacheManager method) ENTROPY_PER_CELL (czbenchmarks.metrics.types.MetricType attribute) expiration_days (czbenchmarks.file_utils.CacheManager attribute)

F

F1_CALCULATION (czbenchmarks.metrics.types.MetricType attribute) F1_SCORE (czbenchmarks.metrics.types.MetricType attribute) f1_score_zero_division() (in module czbenchmarks.metrics.implementations) filter_minimum_class() (in module czbenchmarks.tasks.utils) flavor (czbenchmarks.tasks.clustering.ClusteringTaskInput attribute) (czbenchmarks.tasks.ClusteringTaskInput attribute)

FLAVOR (in module czbenchmarks.tasks.constants) FRESHWATER_SPONGE (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) from_args() (czbenchmarks.file_cache.CacheOptions class method) FRUIT_FLY (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) func (czbenchmarks.metrics.types.MetricInfo attribute), [1]

G

gene_index (czbenchmarks.tasks.PerturbationExpressionPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.perturbation_expression_prediction.PerturbationExpressionPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.PerturbationExpressionPredictionTaskInput attribute) get_base_name() (in module czbenchmarks.constants) get_cache_path() (czbenchmarks.file_utils.CacheManager method) get_controls() (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset method) (czbenchmarks.datasets.SingleCellPerturbationDataset method) get_datasets() (in module czbenchmarks.cli.utils) get_indices_for() (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset method) (czbenchmarks.datasets.SingleCellPerturbationDataset method)

get_info() (czbenchmarks.metrics.types.MetricRegistry method) get_numbered_path() (in module czbenchmarks.constants) get_task_class() (czbenchmarks.tasks.task.TaskRegistry method) get_task_help() (czbenchmarks.tasks.task.TaskRegistry method) get_task_info() (czbenchmarks.tasks.task.TaskRegistry method) get_version() (in module czbenchmarks.cli.utils) GORILLA (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute)

H

HUMAN (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute)

I

import_class_from_config() (in module czbenchmarks.utils) initialize_hydra() (in module czbenchmarks.utils) input_labels (czbenchmarks.tasks.clustering.ClusteringTaskInput attribute) (czbenchmarks.tasks.ClusteringTaskInput attribute) (czbenchmarks.tasks.embedding.EmbeddingTaskInput attribute) (czbenchmarks.tasks.EmbeddingTaskInput attribute) (czbenchmarks.tasks.sequential.SequentialOrganizationTaskInput attribute) (czbenchmarks.tasks.SequentialOrganizationTaskInput attribute) input_model (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.PerturbationExpressionPredictionTask attribute) (czbenchmarks.tasks.sequential.SequentialOrganizationTask attribute) (czbenchmarks.tasks.SequentialOrganizationTask attribute) (czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationTask attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTask attribute) (czbenchmarks.tasks.single_cell.perturbation_expression_prediction.PerturbationExpressionPredictionTask attribute) (czbenchmarks.tasks.single_cell.PerturbationExpressionPredictionTask attribute)

is_anndata_reference() (in module czbenchmarks.cli.resolve_reference) is_expired() (czbenchmarks.file_utils.CacheManager method) is_not_count_data() (in module czbenchmarks.tasks.utils)

J

JACCARD (czbenchmarks.metrics.types.MetricType attribute)

jaccard_score() (in module czbenchmarks.metrics.utils)

K

k (czbenchmarks.tasks.sequential.SequentialOrganizationTaskInput attribute) (czbenchmarks.tasks.SequentialOrganizationTaskInput attribute) key (czbenchmarks.cli.resolve_reference.AnnDataReference attribute), [1] key_added (czbenchmarks.tasks.clustering.ClusteringTaskInput attribute) (czbenchmarks.tasks.ClusteringTaskInput attribute)

KEY_ADDED (in module czbenchmarks.tasks.constants) kwargs (czbenchmarks.datasets.Dataset attribute) (czbenchmarks.datasets.dataset.Dataset attribute)

L

label_column_key (czbenchmarks.datasets.single_cell_labeled.SingleCellLabeledDataset attribute), [1] (czbenchmarks.datasets.SingleCellLabeledDataset attribute), [1] labels (czbenchmarks.datasets.single_cell_labeled.SingleCellLabeledDataset attribute), [1] (czbenchmarks.datasets.SingleCellLabeledDataset attribute), [1] (czbenchmarks.tasks.BatchIntegrationTaskInput attribute) (czbenchmarks.tasks.CrossSpeciesIntegrationOutput attribute) (czbenchmarks.tasks.CrossSpeciesIntegrationTaskInput attribute) (czbenchmarks.tasks.CrossSpeciesLabelPredictionTaskInput attribute) (czbenchmarks.tasks.integration.BatchIntegrationTaskInput attribute) (czbenchmarks.tasks.label_prediction.MetadataLabelPredictionTaskInput attribute) (czbenchmarks.tasks.MetadataLabelPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationOutput attribute) (czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationTaskInput attribute) (czbenchmarks.tasks.single_cell.cross_species_label_prediction.CrossSpeciesLabelPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationOutput attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTaskInput attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesLabelPredictionTaskInput attribute) list_available_datasets() (in module czbenchmarks.datasets) (in module czbenchmarks.datasets.utils) list_cmd() (in module czbenchmarks.cli.cli_list) list_metrics() (czbenchmarks.metrics.types.MetricRegistry method) list_tasks() (czbenchmarks.tasks.task.TaskRegistry method) ListLike (in module czbenchmarks.types) load_and_filter_deg_results() (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset method) (czbenchmarks.datasets.SingleCellPerturbationDataset method) load_data() (czbenchmarks.datasets.Dataset method) (czbenchmarks.datasets.dataset.Dataset method) (czbenchmarks.datasets.single_cell.SingleCellDataset method) (czbenchmarks.datasets.single_cell_labeled.SingleCellLabeledDataset method) (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset method) (czbenchmarks.datasets.SingleCellLabeledDataset method) (czbenchmarks.datasets.SingleCellPerturbationDataset method)

load_dataset() (in module czbenchmarks.datasets) (in module czbenchmarks.datasets.utils) load_embedding() (in module czbenchmarks.cli.utils) load_local_dataset() (in module czbenchmarks.datasets) (in module czbenchmarks.datasets.utils) log (in module czbenchmarks.cli.utils) (in module czbenchmarks.file_cache) (in module czbenchmarks.file_utils) logger (in module czbenchmarks.cli.runner) (in module czbenchmarks.datasets.single_cell) (in module czbenchmarks.datasets.single_cell_labeled) (in module czbenchmarks.datasets.single_cell_perturbation) (in module czbenchmarks.datasets.utils_single_cell) (in module czbenchmarks.datasets.validators.dataset_validator) (in module czbenchmarks.metrics.utils) (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.sequential) (in module czbenchmarks.tasks.single_cell.cross_species_label_prediction) (in module czbenchmarks.tasks.single_cell.perturbation_expression_prediction) (in module czbenchmarks.tasks.utils) (in module czbenchmarks.utils)

M

main() (in module czbenchmarks.cli.cli) 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) MetadataLabelPredictionOutput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.label_prediction) MetadataLabelPredictionTask (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.label_prediction) MetadataLabelPredictionTaskInput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.label_prediction) metric_column (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset property) (czbenchmarks.datasets.SingleCellPerturbationDataset property) metric_type (czbenchmarks.metrics.types.AggregatedMetricResult attribute), [1] (czbenchmarks.metrics.types.MetricResult attribute), [1] (czbenchmarks.tasks.MetricResult attribute), [1] MetricInfo (class in czbenchmarks.metrics.types) MetricRegistry (class in czbenchmarks.metrics.types) MetricResult (class in czbenchmarks.metrics.types) (class in czbenchmarks.tasks) metrics_registry (in module czbenchmarks.metrics) (in module czbenchmarks.metrics.implementations) MetricType (class in czbenchmarks.metrics.types) min_class_size (czbenchmarks.tasks.label_prediction.MetadataLabelPredictionTaskInput attribute) (czbenchmarks.tasks.MetadataLabelPredictionTaskInput attribute) MIN_CLASS_SIZE (in module czbenchmarks.tasks.constants) min_de_genes_to_mask (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) min_logfoldchange (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) model_config (czbenchmarks.tasks.task.TaskInput attribute) (czbenchmarks.tasks.task.TaskOutput attribute) (czbenchmarks.tasks.TaskInput attribute) (czbenchmarks.tasks.TaskOutput attribute) module czbenchmarks czbenchmarks.cli czbenchmarks.cli.cli czbenchmarks.cli.cli_list czbenchmarks.cli.cli_run czbenchmarks.cli.resolve_reference czbenchmarks.cli.runner czbenchmarks.cli.utils czbenchmarks.constants czbenchmarks.datasets czbenchmarks.datasets.dataset czbenchmarks.datasets.single_cell czbenchmarks.datasets.single_cell_labeled czbenchmarks.datasets.single_cell_perturbation czbenchmarks.datasets.types czbenchmarks.datasets.utils czbenchmarks.datasets.utils_single_cell czbenchmarks.datasets.validators czbenchmarks.datasets.validators.dataset_validator czbenchmarks.datasets.validators.single_cell_validator czbenchmarks.exceptions czbenchmarks.file_cache czbenchmarks.file_utils czbenchmarks.metrics czbenchmarks.metrics.implementations czbenchmarks.metrics.types czbenchmarks.metrics.utils czbenchmarks.tasks czbenchmarks.tasks.clustering czbenchmarks.tasks.constants czbenchmarks.tasks.embedding czbenchmarks.tasks.integration czbenchmarks.tasks.label_prediction czbenchmarks.tasks.sequential czbenchmarks.tasks.single_cell czbenchmarks.tasks.single_cell.cross_species_integration czbenchmarks.tasks.single_cell.cross_species_label_prediction czbenchmarks.tasks.single_cell.perturbation_expression_prediction czbenchmarks.tasks.task czbenchmarks.tasks.types czbenchmarks.tasks.utils czbenchmarks.types 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) mutually_exclusive() (in module czbenchmarks.cli.utils)

N

n_folds (czbenchmarks.tasks.CrossSpeciesLabelPredictionTaskInput attribute) (czbenchmarks.tasks.label_prediction.MetadataLabelPredictionTaskInput attribute) (czbenchmarks.tasks.MetadataLabelPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.cross_species_label_prediction.CrossSpeciesLabelPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesLabelPredictionTaskInput attribute) N_FOLDS (in module czbenchmarks.tasks.constants) n_iterations (czbenchmarks.tasks.clustering.ClusteringTaskInput attribute) (czbenchmarks.tasks.ClusteringTaskInput attribute) N_ITERATIONS (in module czbenchmarks.tasks.constants)

n_values (czbenchmarks.metrics.types.AggregatedMetricResult attribute), [1] NAKED_MOLE_RAT (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) name (czbenchmarks.datasets.Organism property) (czbenchmarks.datasets.types.Organism property) (czbenchmarks.tasks.task.TaskInfo attribute) nearest_neighbors_hnsw() (in module czbenchmarks.metrics.utils) normalize (czbenchmarks.tasks.sequential.SequentialOrganizationTaskInput attribute) (czbenchmarks.tasks.SequentialOrganizationTaskInput attribute) NORMALIZED_MUTUAL_INFO (czbenchmarks.metrics.types.MetricType attribute)

O

obs (czbenchmarks.tasks.clustering.ClusteringTaskInput attribute) (czbenchmarks.tasks.ClusteringTaskInput attribute) (czbenchmarks.tasks.sequential.SequentialOrganizationTaskInput attribute) (czbenchmarks.tasks.SequentialOrganizationTaskInput attribute) 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.Dataset attribute), [1] (czbenchmarks.datasets.dataset.Dataset attribute), [1] organism_list (czbenchmarks.tasks.CrossSpeciesIntegrationTaskInput attribute) (czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationTaskInput attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTaskInput attribute) organisms (czbenchmarks.tasks.CrossSpeciesLabelPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.cross_species_label_prediction.CrossSpeciesLabelPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesLabelPredictionTaskInput attribute)

P

params (czbenchmarks.metrics.types.AggregatedMetricResult attribute), [1] (czbenchmarks.metrics.types.MetricResult attribute), [1] (czbenchmarks.tasks.MetricResult attribute), [1] parse() (czbenchmarks.cli.resolve_reference.AnnDataReference static method) path (czbenchmarks.datasets.Dataset attribute), [1] (czbenchmarks.datasets.dataset.Dataset attribute), [1] PEARSON_CORRELATION (czbenchmarks.metrics.types.MetricType attribute) percent_genes_to_mask (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) PerturbationExpressionPredictionOutput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.single_cell) (class in czbenchmarks.tasks.single_cell.perturbation_expression_prediction) PerturbationExpressionPredictionTask (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.single_cell) (class in czbenchmarks.tasks.single_cell.perturbation_expression_prediction) PerturbationExpressionPredictionTaskInput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.single_cell) (class in czbenchmarks.tasks.single_cell.perturbation_expression_prediction) PLATYPUS (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute)

PRECISION (czbenchmarks.metrics.types.MetricType attribute) PRECISION_CALCULATION (czbenchmarks.metrics.types.MetricType attribute) precision_score_zero_division() (in module czbenchmarks.metrics.implementations) pred_effect_operation (czbenchmarks.tasks.PerturbationExpressionPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.perturbation_expression_prediction.PerturbationExpressionPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.PerturbationExpressionPredictionTaskInput attribute) pred_mean_change_dict (czbenchmarks.tasks.PerturbationExpressionPredictionOutput attribute) (czbenchmarks.tasks.single_cell.perturbation_expression_prediction.PerturbationExpressionPredictionOutput attribute) (czbenchmarks.tasks.single_cell.PerturbationExpressionPredictionOutput attribute) predicted_labels (czbenchmarks.tasks.clustering.ClusteringOutput attribute) (czbenchmarks.tasks.ClusteringOutput attribute) prefix (czbenchmarks.datasets.Organism property) (czbenchmarks.datasets.types.Organism property) print_correlation_metrics_baseline_and_model() (in module czbenchmarks.tasks.utils) print_metrics_summary() (in module czbenchmarks.tasks.utils) PROCESSED_DATASETS_CACHE_PATH (in module czbenchmarks.constants) pval_threshold (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute)

R

RABBIT (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) random_seed (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) (czbenchmarks.tasks.Task attribute) (czbenchmarks.tasks.task.Task attribute) RANDOM_SEED (in module czbenchmarks.constants) RAT (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) RECALL (czbenchmarks.metrics.types.MetricType attribute) RECALL_CALCULATION (czbenchmarks.metrics.types.MetricType attribute) recall_score_zero_division() (in module czbenchmarks.metrics.implementations) register() (czbenchmarks.metrics.types.MetricRegistry method) register_task() (czbenchmarks.tasks.task.TaskRegistry method) remote_cache_url (czbenchmarks.file_cache.CacheOptions attribute), [1] RemoteStorageError RemoteStorageObjectAlreadyExists required (czbenchmarks.tasks.task.TaskParameter attribute) required_args (czbenchmarks.metrics.types.MetricInfo attribute), [1] required_obs_keys (czbenchmarks.datasets.validators.single_cell_validator.SingleCellLabeledValidator attribute) (czbenchmarks.datasets.validators.SingleCellLabeledValidator attribute) required_var_keys (czbenchmarks.datasets.validators.single_cell_validator.SingleCellLabeledValidator attribute) (czbenchmarks.datasets.validators.SingleCellLabeledValidator attribute)

requires_multiple_datasets (czbenchmarks.tasks.CrossSpeciesIntegrationTask attribute) (czbenchmarks.tasks.CrossSpeciesLabelPredictionTask attribute) (czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationTask attribute) (czbenchmarks.tasks.single_cell.cross_species_label_prediction.CrossSpeciesLabelPredictionTask attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationTask attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesLabelPredictionTask attribute) (czbenchmarks.tasks.Task attribute) (czbenchmarks.tasks.task.Task attribute) resolve() (czbenchmarks.cli.resolve_reference.AnnDataReference method) resolve_task_parameters() (in module czbenchmarks.cli.resolve_reference) resolve_value_recursively() (in module czbenchmarks.cli.resolve_reference) results (czbenchmarks.tasks.CrossSpeciesLabelPredictionOutput attribute) (czbenchmarks.tasks.label_prediction.MetadataLabelPredictionOutput attribute) (czbenchmarks.tasks.MetadataLabelPredictionOutput attribute) (czbenchmarks.tasks.single_cell.cross_species_label_prediction.CrossSpeciesLabelPredictionOutput attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesLabelPredictionOutput attribute) RHESUS_MACAQUE (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) run() (czbenchmarks.tasks.Task method) (czbenchmarks.tasks.task.Task method) (in module czbenchmarks.cli.cli_run) run_multicondition_dge_analysis() (in module czbenchmarks.datasets.utils_single_cell) run_standard_scrna_workflow() (in module czbenchmarks.tasks.utils) run_task() (in module czbenchmarks.cli.runner)

S

sample_de_genes() (in module czbenchmarks.datasets.single_cell_perturbation) sample_ids (czbenchmarks.tasks.CrossSpeciesLabelPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.cross_species_label_prediction.CrossSpeciesLabelPredictionTaskInput attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesLabelPredictionTaskInput attribute) SEA_LAMPREY (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) SEA_URCHIN (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) SEQUENTIAL_ALIGNMENT (czbenchmarks.metrics.types.MetricType attribute) sequential_alignment() (in module czbenchmarks.metrics.utils) SequentialOrganizationOutput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.sequential) SequentialOrganizationTask (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.sequential) SequentialOrganizationTaskInput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.sequential) set_control_mapping() (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset method) (czbenchmarks.datasets.SingleCellPerturbationDataset method) SILHOUETTE_SCORE (czbenchmarks.metrics.types.MetricType attribute) single_metric() (in module czbenchmarks.metrics.utils)

SingleCellDataset (class in czbenchmarks.datasets.single_cell) SingleCellLabeledDataset (class in czbenchmarks.datasets) (class in czbenchmarks.datasets.single_cell_labeled) SingleCellLabeledValidator (class in czbenchmarks.datasets.validators) (class in czbenchmarks.datasets.validators.single_cell_validator) SingleCellPerturbationDataset (class in czbenchmarks.datasets) (class in czbenchmarks.datasets.single_cell_perturbation) space (czbenchmarks.cli.resolve_reference.AnnDataReference attribute), [1] spearman_correlation() (in module czbenchmarks.metrics.implementations) SPEARMAN_CORRELATION_CALCULATION (czbenchmarks.metrics.types.MetricType attribute) species (czbenchmarks.tasks.CrossSpeciesIntegrationOutput attribute) (czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationOutput attribute) (czbenchmarks.tasks.single_cell.CrossSpeciesIntegrationOutput attribute) store_task_inputs() (czbenchmarks.datasets.Dataset method) (czbenchmarks.datasets.dataset.Dataset method) (czbenchmarks.datasets.single_cell_labeled.SingleCellLabeledDataset method) (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset method) (czbenchmarks.datasets.SingleCellLabeledDataset method) (czbenchmarks.datasets.SingleCellPerturbationDataset method) stringified_type (czbenchmarks.tasks.task.TaskParameter attribute)

T

tags (czbenchmarks.metrics.types.MetricInfo attribute), [1] target_conditions_dict (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute), [1] (czbenchmarks.datasets.SingleCellPerturbationDataset attribute), [1] target_conditions_override (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) target_genes (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset property) (czbenchmarks.datasets.SingleCellPerturbationDataset property) Task (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.task) task_inputs_dir (czbenchmarks.datasets.Dataset attribute), [1] (czbenchmarks.datasets.dataset.Dataset attribute), [1] TASK_NAMES (in module czbenchmarks.tasks.utils) task_params (czbenchmarks.tasks.task.TaskInfo attribute) TASK_REGISTRY (in module czbenchmarks.tasks) (in module czbenchmarks.tasks.task)

TaskInfo (class in czbenchmarks.tasks.task) TaskInput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.task) TaskOutput (class in czbenchmarks.tasks) (class in czbenchmarks.tasks.task) TaskParameter (class in czbenchmarks.tasks.task) TaskRegistry (class in czbenchmarks.tasks.task) TROPICAL_CLAWED_FROG (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute) true_mean_change_dict (czbenchmarks.tasks.PerturbationExpressionPredictionOutput attribute) (czbenchmarks.tasks.single_cell.perturbation_expression_prediction.PerturbationExpressionPredictionOutput attribute) (czbenchmarks.tasks.single_cell.PerturbationExpressionPredictionOutput attribute) type (czbenchmarks.tasks.task.TaskParameter attribute)

U

UNS_CONFIG_KEY (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) UNS_CONTROL_MAP_KEY (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) UNS_DE_RESULTS_KEY (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) UNS_METRIC_COL_KEY (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute)

UNS_RANDOM_SEED_KEY (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) UNS_TARGET_GENES_KEY (czbenchmarks.datasets.single_cell_perturbation.SingleCellPerturbationDataset attribute) (czbenchmarks.datasets.SingleCellPerturbationDataset attribute) upload_embeddings (czbenchmarks.file_cache.CacheOptions attribute), [1] upload_results (czbenchmarks.file_cache.CacheOptions attribute), [1] use_rep (czbenchmarks.tasks.clustering.ClusteringTaskInput attribute) (czbenchmarks.tasks.ClusteringTaskInput attribute)

V

validate() (czbenchmarks.datasets.Dataset method) (czbenchmarks.datasets.dataset.Dataset method) validate_dataset() (czbenchmarks.datasets.validators.dataset_validator.DatasetValidator method) (czbenchmarks.datasets.validators.DatasetValidator method) validate_task_input() (czbenchmarks.tasks.task.TaskRegistry method)

validate_task_parameters() (czbenchmarks.tasks.task.TaskRegistry method) value (czbenchmarks.metrics.types.AggregatedMetricResult attribute), [1] (czbenchmarks.metrics.types.MetricResult attribute), [1] (czbenchmarks.tasks.MetricResult attribute), [1] value_std_dev (czbenchmarks.metrics.types.AggregatedMetricResult attribute), [1] values_raw (czbenchmarks.metrics.types.AggregatedMetricResult attribute), [1]

W

WILD_BOAR (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute)

write_results() (in module czbenchmarks.cli.utils)

Y

YEAST (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute)

Z

ZEBRAFISH (czbenchmarks.datasets.Organism attribute) (czbenchmarks.datasets.types.Organism attribute)