moscot.problems.generic.FGWProblem

class moscot.problems.generic.FGWProblem(adata, **kwargs)[source]

Class for solving the FGW problem.

Methods

add_problem(key, problem, *[, overwrite])

Add a subproblem.

cell_transition(source, target[, ...])

Aggregate the transport matrix.

compute_entropy(source, target[, forward, ...])

Compute the conditional entropy per cell.

compute_feature_correlation(obs_key[, ...])

Compute correlation of push-forward or pull-back distribution with features.

load(path)

Load the model from a file.

prepare(key[, joint_attr, x_attr, y_attr, ...])

Prepare the individual quadratic subproblems.

pull(source, target[, data, subset, ...])

Pull mass from target to source.

push(source, target[, data, subset, ...])

Push mass from source to target.

remove_problem(key)

Remove a subproblem.

save(path[, overwrite])

Save the problem to a file.

solve([alpha, epsilon, tau_a, tau_b, rank, ...])

Solve the individual quadratic subproblems.

Attributes

adata

Annotated data object.

batch_key

Batch key in obs.

problem_kind

Kind of the underlying problem.

problems

OT subproblems that define the biological problem.

solutions

Solutions to the problems.

stage

Problem stage.

Parameters: