From 45c6c0090dd516e73eb0d2ce9b162a5325682894 Mon Sep 17 00:00:00 2001 From: j Date: Sun, 28 Jun 2026 22:25:48 +0700 Subject: [PATCH 1/2] docs: update METHODS.md version tag and annotate 7-seed synthesis pool expansion MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The methods document was last updated for PRs #47-54. Since then the synthesis pool was expanded from 5 to 7 scaffold families (SEED-006 through SEED-009 in expansion PRs; SEED-001 re-entered in PR #72 via face_segregation_bonus). Changes: - Version line: "PRs #47-54" → "PRs #47-78" - Generation section: added blockquote note distinguishing the initial 5-seed benchmark run (383 variants, 87-candidate eval set, AUROC 0.8420) from the current 7-seed synthesis pool (100 candidates) - No scoring formulas or benchmark numbers changed --- docs/METHODS.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/METHODS.md b/docs/METHODS.md index c707b82d..aa926df5 100644 --- a/docs/METHODS.md +++ b/docs/METHODS.md @@ -1,6 +1,6 @@ # OpenAMP Foundry — Methods Appendix -**Version:** 0.2.x (pipeline version); document updated for PRs #47–54 +**Version:** 0.2.x (pipeline version); document updated for PRs #47–78 **Status:** Working draft for expert review. Not a peer-reviewed publication. --- @@ -40,6 +40,14 @@ Three variant strategies were applied: Total: 383 unique variants from 5 seeds (rng_seed=2024). +> **Note (PRs #63–78):** The figures above describe the initial benchmark run that generated +> the 87-sequence evaluation set (43 nominated + 44 held-out) and AUROC 0.8420. The synthesis +> pool generation was subsequently expanded to 7 scaffold families: SEED-006 through SEED-009 +> were added in earlier expansion PRs; SEED-001 (magainin-1) was re-entered in PR #72 after the +> face_segregation_bonus raised its AUROC contribution. Current synthesis pool: **100 candidates +> from 7 scaffold families**. The expanded pool shares the same scoring pipeline and configuration +> (`pipeline.yaml`, `phase3.yaml`) but was generated from a wider seed set. + **Limitation:** This generation strategy produces near-seed variants. It does not explore genuinely novel sequence space. Future work should incorporate protein language model sampling or Bayesian sequence optimization. From ce7118c97e17aef2c52d6654a7812a459005becc Mon Sep 17 00:00:00 2001 From: j Date: Sun, 28 Jun 2026 22:30:24 +0700 Subject: [PATCH 2/2] docs: fix AUROC attribution in METHODS.md 7-seed note AUROC 0.8420 was achieved in PR #72 (face_segregation_bonus), not in the initial 5-seed benchmark generation run. Clarify that the generation section describes the initial corpus and the AUROC figure reflects scoring improvements through PR #72. Also note that the 87-sequence eval set was finalized in PR #66. --- docs/METHODS.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/docs/METHODS.md b/docs/METHODS.md index aa926df5..c205dbf9 100644 --- a/docs/METHODS.md +++ b/docs/METHODS.md @@ -40,13 +40,14 @@ Three variant strategies were applied: Total: 383 unique variants from 5 seeds (rng_seed=2024). -> **Note (PRs #63–78):** The figures above describe the initial benchmark run that generated -> the 87-sequence evaluation set (43 nominated + 44 held-out) and AUROC 0.8420. The synthesis -> pool generation was subsequently expanded to 7 scaffold families: SEED-006 through SEED-009 -> were added in earlier expansion PRs; SEED-001 (magainin-1) was re-entered in PR #72 after the -> face_segregation_bonus raised its AUROC contribution. Current synthesis pool: **100 candidates -> from 7 scaffold families**. The expanded pool shares the same scoring pipeline and configuration -> (`pipeline.yaml`, `phase3.yaml`) but was generated from a wider seed set. +> **Note (PRs #63–78):** The generation strategy above (5 seeds, rng_seed=2024) describes the +> initial variant corpus. Scoring was then improved across PRs #47–72; the current pipeline +> achieves **AUROC 0.8420** on the 87-sequence benchmark set (43 AMPs + 44 background; set +> finalized PR #66). Separately, the synthesis pool was expanded to 7 scaffold families: +> SEED-006 through SEED-009 added in expansion PRs #38–58; SEED-001 (magainin-1) re-entered +> PR #72 after the face_segregation_bonus raised its helix-score contribution. Current synthesis +> pool: **100 candidates from 7 scaffold families**. Same pipeline config (`pipeline.yaml`, +> `phase3.yaml`); wider seed set. **Limitation:** This generation strategy produces near-seed variants. It does not explore genuinely novel sequence space. Future work should incorporate protein language model sampling