# MVA Evidence Audit

Date: 2026-07-23

## Primary endpoint

The official LIVECell test comparison is complete for four conditions and three training seeds. All runs used 162 official 5% training images, 20 epochs (3,240 optimizer updates), all annotated instances, and `maxDets=3000`. The primary mean mask AP values are:

- COCO-full: 0.2413 +/- 0.0057
- ImageNet+COCO: 0.2222 +/- 0.0054
- SimCLR+COCO: 0.2082 +/- 0.0087
- SupCon+COCO: 0.2063 +/- 0.0057

The three-seed paired table reports effect magnitudes and whether all observed signs agree. It does not provide a hypothesis test. The handoff phrase "all three seeds exclude zero" is invalid and must be replaced by "all three paired seed differences have the same sign."

## Corrected training-step record

Remote `summary.json` and `loss_log.csv` files show 3,240 updates for every seed-44 arm. The handoff counts 12,960 and 32,400 arose from multiplying updates by the number of logged loss components; they are not optimizer-step counts.

## Dense evaluation

Density-stratified AP@3000 and the four-cap `maxDets` response are available for three seeds. Extreme-density AP ranges from 0.1195 to 0.1312. The seed44 cap re-evaluation used the stored formal predictions, and every AP@3000 reproduction gate passed with absolute error 0.0 before lower-cap values were accepted.

## Three-seed factorial control

The complete COCO/SimCLR x 1x/5x matrix is available for seeds 42, 43, and 44. All three seeds show COCO above SimCLR at 1x, SimCLR above COCO at 5x, a negative 5x-minus-1x response for COCO, and a positive response for SimCLR. The observed differences-in-differences are +0.0433, +0.0237, +0.0229. This is a repeated descriptive pattern, not a population interaction significance test.

## External Cellpose evidence

The paired external comparison contains ImageNet backbone and ImageNet+COCO components, each with three seeds. The paired ImageNet+COCO improvement is 0.0208 +/- 0.0121; all three observed differences are positive. A separate COCO-full transferable initialization reaches 0.2667 +/- 0.0011. It transfers all compatible COCO modules, reinitializes the binary predictors, and is not part of the fixed-ImageNet paired ablation. This experiment used one fixed 27-image subset and 68 evaluation images. Seven training images exceeded the 128-instance limit; retaining the largest instances excluded 783/2,886 annotations. Twenty-eight evaluation images exceeded 100 ground-truth instances, so AP@100 is a shared capped transfer comparison rather than an uncapped Cellpose benchmark or a protocol-identical LIVECell replication.

The Cellpose SimCLR evidence is incomplete: two learning-rate attempts became non-finite and one seed42 run at `1e-5` completed with AP 0.0030. It may be reported as a failure analysis in supplementary material, but it must not be pooled with the three-seed external table. No Cellpose SupCon run exists.

## Previously available but unused evidence

- Cross-cell-line A/B/C, full-data, freeze, CKA, and probe results exist and remain useful as supplementary exploratory analyses.
- BBBC039 images and masks are present, but no audited model result exists; the dataset must not be described as an evaluated benchmark.
- MS-CLACL numeric results are excluded because the morphology scale used validation/test annotation statistics and the pretraining budget was not matched.
- Early 2%/4%/5%/25%/50% results used the default detection cap, unequal budgets, and incomplete configuration records; they cannot form a controlled label-fraction curve and are superseded by the final dense protocol.

See `evidence/evidence_registry.csv` for the complete use/exclusion decision.
