moscot.base.problems.BirthDeathProblem

class moscot.base.problems.BirthDeathProblem(*args, **kwargs)

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

Notes

If source/target mask is specified, adata_src/adata_tgt will be a view.

Methods

estimate_marginals(adata, source[, ...])
load(path)	Load the model from a file.
prepare(xy, x, y[, a, b, marginal_kwargs])	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, solver_name, 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.

Parameters:

• args (Any)

• kwargs (Any)