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Harden shared empirical E-value fitting for both database types - #35

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DylanYang merged 3 commits into
mainfrom
codex/unified-empirical-evalues
Oct 30, 2026
Merged

DylanYang merged 3 commits into
mainfrom
codex/unified-empirical-evalues

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@Divo-Lee

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Summary

  • Reuse the existing target-aware Gumbel and empirical-map functions for experimental raw-SW and predicted window-20 composition-adjusted SW fitting.
  • Exclude overlapping multi-label Rfam family or clan annotations before cluster maxima; retain iterative US-align leader auditing and within-cluster backfill.
  • Use a continuous endpoint-anchored power tail above the empirical knots, capped by the cluster count. Previously fitted parameter files keep their original behavior.
  • Allow a wider initial E-value audit ceiling and record the highest directly supported reported E-value. Bind cached scores and US-align results to their database and query panel.

This PR changes package algorithms and fitting commands only. It includes no fitted parameters for RNAsolo, PDB-RNA, or NuFold. Each deployed database needs its own new fit and audit. LOFO is the validation protocol; final deployment parameters are fitted on the designated full panels.

Verification

  • Focused empirical E-value tests: 10 passed.
  • Full Windows suite: 89 passed, 2 skipped; one unrelated legacy calibrate CLI test fails because its shell-script US-align fixture cannot execute as a Win32 program (WinError 193).
  • Both fitting CLI entry points start and display the new audit option.

Values beyond the observed empirical range are extrapolations and are not independently validated.

Divo-Lee and others added 3 commits October 26, 2026 22:02
README: keep main's rewritten E-value section and add a short paragraph on
the audit ceiling, the power-law tail above it and --audit-ceiling.

The experimental fit/attach/search test searched with rerank="sw", which
#37 removed; give its fixture coordinates and search in the default mode.
@DylanYang
DylanYang merged commit b2b76db into main Oct 30, 2026
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2 participants