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Calibration of scANVI confidence under the cohort shift, with temperature scaling fitted on reference patients (scmap.calibration, scripts/16_calibration_shift.py).
Two-hospital site-shift experiment repeated with scANVI (scripts/15_site_shift_pelka_scanvi.py): a mixed reference raises macro-F1 and restores 90% coverage on both hospitals.
scmap annotate command: maps a new query onto the saved scANVI reference and labels its cells with confidence and the pre-committed abstention flag.
Reference-size curve repeated with scANVI and scArches mapping (scripts/14_reference_size_scanvi.py); same plateau from six patients as the baseline.