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fix: Align sample selection with official AF3 - #95

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omrikais merged 1 commit into
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fix/official-ranking-accuracy
Sep 19, 2026
Merged

omrikais merged 1 commit into
mainfrom
fix/official-ranking-accuracy

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Summary

  • restore deterministic parity for the documented seed-42 golden suite
  • align diffusion key selection and output ranking with official AlphaFold 3
  • preserve the calibrated restraint-guidance path and public/private boundary

Changes

  • use the canonical post-trunk Haiku RNG key for ordinary diffusion
  • calculate structure disorder and clash terms from generated coordinates
  • rank complexes by 0.8 * ipTM + 0.2 * pTM + 0.5 * disorder - 100 * clash
  • publish regression tests and refreshed provenance manifest

Test plan

  • Run the public unit/integration suite (964 passed, 61 skipped)
  • Verify deterministic publisher read-back (0 added, 0 updated, 0 deleted)
  • Run all six server golden cases with --seed 42 --num_samples 5 (6/6 passed)
  • Verify unchanged thresholds, including insulin PAE 0.319 and CA RMSD 0.99 Å
  • Complete an independent stable-diff review (no P0-P2 findings)

Publish the deterministic accuracy correction from private development main.
Ordinary inference now follows the official post-trunk Haiku diffusion key,
while restraint-guided inference retains its separately calibrated stream.

Rank samples with the official pTM/ipTM, disorder, and clash formula using
structure metadata reconstructed from the featurized batch. Include regression
coverage for disorder-sensitive selection and clash penalties.

The documented seed-42 six-case server comparison passes 6/6 without relaxing
any threshold. The public unit/integration suite passes with 964 tests and 61
intentional skips.
@omrikais
omrikais requested a lite review from Copilot and removed request for Copilot September 19, 2026 20:20
@omrikais
omrikais merged commit 3d1ce7b into main Sep 19, 2026
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@omrikais
omrikais deleted the fix/official-ranking-accuracy branch September 19, 2026 20:24
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