From f082c59b7edd9fb0558433bc544702728968ac4c Mon Sep 17 00:00:00 2001 From: j Date: Sun, 28 Jun 2026 19:20:25 +0700 Subject: [PATCH] docs: update CHANGELOG for PRs #68 and #69 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Documents Stage 3 serum stability documentation improvements (PR #68) and synthesis readiness report refresh for current 20-candidate pilot panel (PR #69). Output files regenerated locally (gitignored): presynth_qc_report.md, diversity_report.md, gold_standard_calibration.md, synthesis_readiness_report.md — all updated to reflect current pilot panel. --- CHANGELOG.md | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1141560f..cbb4568b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,8 +9,23 @@ All notable changes to OpenAMP Foundry are documented here. **Status:** Pipeline frozen for synthesis batch ordering. All changes below were quality improvements made before committing the ~$10k wet-lab synthesis budget. -### Latest fixes (PRs #61–67) - +### Latest fixes (PRs #61–69) + +- **PR #69** — synthesis_readiness_report.md updated for current 20-candidate pilot panel + (AUROC 0.8047; 43 AMPs; 6 seed families; all output files regenerated: presynth_qc_report.md, + diversity_report.md, gold_standard_calibration.md); external predictor gate marked PENDING for + new panel; SEED-007 HIGH SPPS difficulty noted; SEED-008 photolability warning added; + serum stability caveats from PR #68 incorporated; synthesis decision tree and 6-candidate + minimal diverse panel recommendation updated; stale reference to old 16-candidate + confident_panel.csv removed +- **PR #68** — Stage 3 serum stability table updated with actual pilot-panel seed families + (SEED-003/005/006/007/008/009; old SEED-001/002/004 removed as excluded at earlier gates); + probability 28–42% → 30–46% (short/Trp-rich model correction; actual pilot-panel data); + SEED-006/SEED-007 gate labels corrected from Pass to Borderline (scores 0.61–0.67 below + ≥0.70 threshold); SEED-007 slot count corrected 4→5; Root Cause Analysis updated to + acknowledge model uncertainty before citing <40 min estimate; early serum screening protocol + added with time points, concentration, reference control; WET_LAB_HANDOFF.md new section + with SEED-003/005/008 stability model limitation table - **PR #67** — JSONL error handling in `pilot-panel` CLI (CRITICAL: bare crash on malformed line → structured error with line number and preview); synthesis-order CSV header validation; `validate-scoring` stdout now includes `n_positives`, `n_negatives`, `benchmark_type`, `auprc`;