Yiqiao Wang

Single-cell atlases measure each cell once, so a "developmental trajectory" is a population centroid stitched across embryos, not the path of any cell. LADD learns a stochastic developmental vector field from time-series single-cell transcriptomics, computes minimum-action and minimum-time paths with large-deviation theory, and uses a three-layer calibration to separate the generic cost of centroid measurement from genuine path deviation. In the lineage-resolved C. elegans atlas the raw action ratio is 3.79, yet forward-simulated ensembles of the learned model itself score 2.07, leaving a genuine excess of about two-fold; in zebrafish the observed ratio sits entirely at the model's floor.

Single-cell atlases measure each cell once, so a "developmental trajectory" is a population centroid stitched across embryos, not the path of any cell. LADD learns a stochastic developmental vector field from time-series single-cell transcriptomics, computes minimum-action and minimum-time paths with large-deviation theory, and uses a three-layer calibration to separate the generic cost of centroid measurement from genuine path deviation. In the lineage-resolved C. elegans atlas the raw action ratio is 3.79, yet forward-simulated ensembles of the learned model itself score 2.07, leaving a genuine excess of about two-fold; in zebrafish the observed ratio sits entirely at the model's floor.