Disentangling Marginal Capacity from Geometry in Optimal-Transport Label Transfer

Optimal transport (OT) is widely used to align distributions and transfer labels between unpaired source and target data, but source–target composition shifts can cause rare classes to be systematically under-predicted even with high transport confidence. We identify a source of this failure in the transport marginal: under the standard uniform weighting of source points, each class has transport capacity proportional to its source frequency, which can be insufficient to meet its target demand even when separated well in the embedding space. We show that displaced mass is preferentially absorbed by high-capacity classes rather than geometrically similar classes, producing confident errors that are difficult to detect from the transport plan. Downstream read-outs, entropic smoothing, and marginal relaxation provide limited recovery, whereas matching the transport marginal to the target composition substantially improves label transfer. On single-cell data, the oracle composition-matched marginal raises macro-F1 from 0.322 to 0.623, and the best deployable estimator closes 69% of the oracle gap. Correcting the marginal also separates a coverage-dependent component of error from residual error associated with class separability, showing that transport capacity and representation geometry are distinct sources of transfer error.