moscot.base.problems.BirthDeathProblem#

class moscot.base.problems.BirthDeathProblem(*args, **kwargs)[source]#

OT problem used to estimate the marginals with the birth-death process.

Parameters:

args (Any) – Positional arguments for OTProblem.
kwargs (Any) – Keyword arguments for OTProblem.

Methods

`estimate_marginals`(adata, source[, ...])	Estimate the source or target marginals based on marker genes, either with the birth-death process, as suggested in [Schiebinger et al., 2019], or with an exponential kernel.
`load`(path)	Load the model from a file.
`prepare`(xy, x, y[, a, b])	Prepare the OT problem.
`pull`([data, subset, normalize, split_mass, ...])	Pull data through the `transport_matrix`.
`push`([data, subset, normalize, split_mass, ...])	Push data through the `transport_matrix`.
`save`(path[, overwrite])	Save the problem to a file.
`score_genes_for_marginals`([...])	Compute gene scores to obtain prior knowledge about proliferation and apoptosis.
`set_graph_x`(data[, cost, t])	Set a graph for the source quadratic term.
`set_graph_xy`(data[, cost, t])	Set a graph for the linear term for graph based distances.
`set_graph_y`(data[, cost, t])	Set a graph for the target quadratic term.
`set_solution`(solution, *[, overwrite])	Set a `solution` to the OT problem.
`set_x`(data, tag)	Set a cost/kernel matrix for the source quadratic term.
`set_xy`(data, tag)	Set a cost/kernel matrix for the linear term.
`set_y`(data, tag)	Set a cost/kernel matrix for the target quadratic term.
`solve`([backend, device])	Solve the OT problem.

Attributes

`a`	Source marginals.
`adata`	Annotated data object.
`adata_src`	Source annotated data object.
`adata_tgt`	Target annotated data object.
`apoptosis_key`	Key in `obs` where cell apoptosis is stored.
`b`	Target marginals.
`delta`	Time difference between the source and the target.
`posterior_growth_rates`	Posterior estimate of the source growth rates.
`prior_growth_rates`	Prior estimate of the source growth rates.
`problem_kind`	Kind of the underlying problem.
`proliferation_key`	Key in `obs` where cell proliferation is stored.
`shape`	Shape of the OT problem.
`solution`	Solution of the OT problem.
`solver`	OT solver.
`stage`	Problem stage.
`x`	Geometry defining the source quadratic term.
`xy`	Geometry defining the linear term.
`y`	Geometry defining the target quadratic term.