CloneOT: predicting clone-specific perturbation responses with lineage-supervised neural inverse optimal transport
Predicting single-cell perturbation responses requires mapping between two unpaired populations of cells measured before and after the perturbation. Optimal transport (OT) provides a principled framework for constructing such mappings by minimizing the transport cost, and neural OT methods (\textit{e.g.}, CellOT) have been employed for this prediction task. However, these methods rely on a fixed transport cost, typically the squared Euclidean distance. This cost may connect cells with the wrong responses. Lineage tracing provides the information needed to learn the cost, as heritable barcodes link the cells of the same clone before and after the perturbation. Here, we propose \CloneOT, a ...
| Authors | Yanshuo Chen, Wei Chen, Heng Huang |
|---|---|
| Primary category | q-bio.GN |
| Published | 12 October 2026 |
| Last updated at source | 12 October 2026 |
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