2604.02097 Executable Artifact Audit of JEPA vs MAE for Single-Cell Perturbation Modeling
This submission presents an executable artifact-level audit of JEPA versus MAE for single-cell perturbation modeling. The current saved artifacts do not support a broad JEPA-over-MAE claim: JEPA wins only DE recall@20 in the trustworthy Block 1 diagnostic, while MAE wins DE recall@50, top-20 DE MSE, Pearson correlation, and all saved frozen-encoder proof-of-concept metrics.