Fig. 3: Component addition and pairwise ablations across scales.

A Component addition: for Small (n = 165), Medium (n = 68), and Large (n = 15) groups, LB (low β), IR (irecon bottleneck), and ODE are added sequentially to the Base VAE, and boxplots of eight continuum and eight embedding metrics are shown. Global Friedman tests (reported on the plots) yield p < 0.001 in most cases, indicating systematic differences in metric distributions across configurations. B Pairwise ablations: within each scale, three two-component combinations (LB+IR, LB+ODE, IR+ODE) are compared with the full configuration (LB+IR+ODE). Configurations without the ODE module (LB+IR) display the largest deviations from the full model on continuum and clustering metrics, whereas LB+ODE and IR+ODE remain closer to the full configuration, consistent with a role of the ODE in providing trajectory structure while LB and IR mainly refine geometry and denoising. VAE variational autoencoder, LB low-β regularization, IR irecon bottleneck, ODE ordinary differential equation. Where shown, significance stars denote ^*p < 0.05, ^**p < 0.01, ^***p < 0.001.