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cschanhniem merged 2 commits into from
Jun 28, 2026
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docs: update METHODS.md version tag and annotate 7-seed expansion #79

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docs: update METHODS.md version tag and annotate 7-seed synthesis poo…
cschanhniem Jun 28, 2026
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docs: fix AUROC attribution in METHODS.md 7-seed note
cschanhniem Jun 28, 2026
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11 changes: 10 additions & 1 deletion docs/METHODS.md
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@@ -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.

---
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Total: 383 unique variants from 5 seeds (rng_seed=2024).

> **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
or Bayesian sequence optimization.
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