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docs: sync pre-lab documents with 7-scaffold pool state - #77
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- docs/NOMINATION_REPORT.md: add historical-record banner directing readers to current outputs/ for the post-PR #72 synthesis pool - reports/external_predict.py: document Macrel v1.6.0 ONNX model bug where log-softmax scores are compared against 0.5 (causing ALL sequences to be classified as NAMP, including canonical AMPs like magainin-2 and LL-37); recommend web server as reliable alternative and add --keep-negatives flag to CLI instructions
- Use package-documented URL (big-data-biology.org/software/macrel) instead of unverified subdomain - Change "range [-1, 0]" to "always <= 0; observed ~-0.8 to -0.05 on canonical AMPs" (log-softmax is bounded above by 0 but not below) - Update module docstring to match web-server-preferred stance and link to bug note
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Jun 29, 2026
Three fixes: 1. METRICS_CURRENT.md: novelty count corrected to 13/3/1/3 (was 12/4/1/3) 2. create_predictor_results.py: template generator for manual web submission 3. EXTERNAL_PREDICTOR_CONSENSUS.md: updated with submission flow and URLs 4. METRICS_CURRENT.md: test count updated to 1343 External predictors (CAMPR4, AMPScanner, dbAMP, AntiCP2, Macrel) require manual web submission — cannot be automated. Macrel CLI has a known ONNX bug (PR #77). Template + instructions are ready. Co-authored-by: CommandCodeBot <noreply@commandcode.ai>
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Summary
docs/NOMINATION_REPORT.md: Added historical-record banner clarifying this documents the v0.1.0 pipeline state (5 seeds, 89 candidates, pre-PRs fix: resolve CRITICAL pre-wetlab pipeline issues (SEED-008 excluded, benchmark config mismatch) #61–76). Directs readers to currentoutputs/pilot_panel.mdandoutputs/synthesis_readiness_report.mdfor the active 7-scaffold synthesis pool.src/openamp_foundry/reports/external_predict.py: Documented critical Macrel v1.6.0 bug where the ONNX model ships log-softmax scores (range [-1, 0]) but the inference code compares against threshold 0.5, causing ALL sequences — including canonical AMPs magainin-2, LL-37, and melittin — to be classified as NAMP locally. Recommends the official Macrel web server as the reliable alternative, and adds--keep-negativesto the CLI instructions for proper output capture.Outputs updated locally (gitignored, not committed):
outputs/diversity_report.md: regenerated with 7 clusters (was 6, missing SEED-001_VAR_064)outputs/presynth_qc_report.md: regenerated from currentpilot_panel.csv(was from stale pre-PR feat: face segregation bonus in activity scoring (+AUROC 0.8348→0.8420) #72 panel with wrong SEED-008 variants and missing SEED-001)outputs/synthesis_readiness_report.md: updated throughout — 6→7 scaffold families, 6→7 candidate minimal panel, SEED-008_VAR_051→VAR_032 as minimal panel representative, 4×→1 Trp photolability note (all 4 SEED-008 variants have 4 Trp), corrected Met oxidation count 13→11, SPPS difficulty counts correctedTest plan
make ci— 1245 tests, 0 failuresruff check src testsmake cipre-push hook ran and passedmake pilot && make presynth-qcand verify synthesis_readiness_report is consistent with pilot_panel.md before synthesis ordering🤖 Generated with Claude Code