Inspected src/ve2e/isup.py, the new scripts/benchmarking/benchmark_isup.py, active edits in src/ve2e/inference.py, the classification metrics, data module, and vxData pipeline steps.
Proposed keeping cohort preparation, one-study eligibility, reference-specific QWK evaluation, PHI handling, and JSON output in the benchmark script.
Proposed reusing the active generic inference functions for ClearML EMA loading, inference datamodule creation, and classification batch iteration, then deleting src/ve2e/isup.py.
Identified behavior risks around outcome-based study selection, validation split filtering, loader coverage, logits-to-row alignment, legacy checkpoint support, and secure result output.
Did not modify the ve2e repository.
Lessons Learned: Pitfalls
The initial clinical workstream path requested by the startup guide does not exist in the knowledge checkout. ve2e is documented under inverse, while older related inbox notes sometimes use clinical.
Repository files changed during inspection because another worker was actively editing src/ve2e/inference.py. Re-reading status and diffs was necessary before giving ownership advice.
Lessons Learned: Improvements
Add a short durable ve2e inference architecture note under wiki/workstreams/inverse/ after the refactor lands. It should distinguish benchmark-specific cohort policy from reusable model and dataloader mechanics.
Clarify in the knowledge index that ve2e/ISUP tasks map to inverse, even when they concern clinical labels and pathology references.
