Extended Data Fig. 5: CONCORD analysis of C. elegans/C.briggsae embryogenesis atlas.

a, 2D and 3D UMAPs of the CONCORD latent space (kNN mode), colored by cell type and inferred embryo time. b, C. elegans lineage tree and its projection onto the CONCORD (hcl) embedding. Lineage annotations from Large et al. were mapped to the C. elegans lineage tree (with some ambiguous mappings due to symmetry). Each lineage is represented by its cluster medoid on the UMAP; lines connect each parent lineage to its daughters following the lineage tree. Subtrees for major lineage groups are shown separately. c, Label refinement in the CONCORD latent space via kNN majority vote. For each cell, we examine its k = 30 nearest neighbors; if ≥50% of neighbors carry expert-curated lineage/cell-type labels, we assign the neighborhood’s majority label to unlabeled cells (and relabel when the majority disagrees). We iterate this procedure twice so newly assigned labels can vote. This recovers labels for many unlabeled cells and flags likely mis-annotations.