czbenchmarks.tasks.single_cell.cross_species_integration

Classes

CrossSpeciesIntegrationTaskInput	Pydantic model for CrossSpeciesIntegrationTask inputs.
CrossSpeciesIntegrationOutput	Output for cross-species integration task.
CrossSpeciesIntegrationTask	Task for evaluating cross-species integration quality.

Module Contents

class czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationTaskInput(/, **data: Any)

Bases: czbenchmarks.tasks.task.TaskInput

Pydantic model for CrossSpeciesIntegrationTask inputs.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

labels: List[czbenchmarks.types.ListLike]

organism_list: List[czbenchmarks.datasets.types.Organism]

class czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationOutput(/, **data: Any)

Bases: czbenchmarks.tasks.task.TaskOutput

Output for cross-species integration task.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

cell_representation: czbenchmarks.tasks.types.CellRepresentation

labels: czbenchmarks.types.ListLike

species: czbenchmarks.types.ListLike

class czbenchmarks.tasks.single_cell.cross_species_integration.CrossSpeciesIntegrationTask(*, random_seed: int = RANDOM_SEED)

Bases: czbenchmarks.tasks.task.Task

Task for evaluating cross-species integration quality.

This task computes metrics to assess how well different species’ data are integrated in the embedding space while preserving biological signals. It operates on multiple datasets from different species.

Parameters:

random_seed (int) – Random seed for reproducibility

display_name = 'Cross-species Integration'

description = 'Evaluate cross-species integration quality using various integration metrics.'

input_model

requires_multiple_datasets = True

abstract compute_baseline(**kwargs)

Set a baseline embedding for cross-species integration.

This method is not implemented for cross-species integration tasks as standard preprocessing workflows are not directly applicable across different species.

Raises:

NotImplementedError – Always raised as baseline is not implemented