Condition intensity features with log10 to prevent Percolator hijack (v26.7.0)

[maccoss]

Summary

Lands the intensity-feature log10 conditioning on main (decoupled from the WIP percolator-streaming-only branch), with a defensive floor, tests, docs, and a 26.7.0 release cut. Supersedes #53, which targeted the WIP branch.

peak_apex, peak_area, and peak_sharpness reached the first-pass Percolator SVM as raw, linear, heavy-tailed intensities. Because a single experiment-wide standardizer and one linear model score every peak across all runs, a lone high-intensity DIA interference standardizes to a z-score of 100-300 that dominates the discriminant, letting intensity outliers (a random mix of target / decoy / entrapment) hijack the top of the score ranking. On SEA-AD Astral-DIA entrapment runs this floored the achievable q-value, produced a top-of-ranking FDP spike, and at 1:1 entrapment collapsed a whole run to zero IDs.

What changed

• Single source of truth for the transform. All three features now route through condition_intensity_feature(x) = log10(max(0, x) + 1) at their one computation point (compute_features_at_peak), matching Skyline mProphet's MQuestIntensityCalc and the paired ProteoWizard/pwiz #4412.
• Defensive floor with zero cross-impl cost. max(0.0) is the exact identity on the non-negative real data (intensities/areas are >= 0), so output is bit-identical to the un-floored form and to Condition intensity features with log10 to prevent Percolator hijack #53 / pwiz; the floor only changes the impossible-today negative case and keeps peak_sharpness finite when an override/CWT apex sits below an edge and yields a negative mean slope. peak.area stays raw for quantification.
• Point-1 cache fix = version bump to 26.7.0. Feature semantics changed, so the version bump doubles as the cache-invalidation mechanism: validate_scores_cache exact-matches the version (26.6.x .scores.parquet caches go stale and are re-scored on first run), and cross-impl --join-only aborts on minor-version mismatch rather than silently mixing raw and logged scales.
• Release notes. RELEASE_NOTES_v26.7.0.md documents all 18 unreleased commits since v26.6.1 plus this change; RELEASE_NOTES_next.md reset to a clean draft.
• Docs. docs/README.md, docs/07-fdr-control.md, docs/12-intermediate-files.md note the conditioning and the cache invalidation.

Tests

• 5 new unit tests: zero -> 0, decade scaling, monotonicity, negative/NaN flooring, and floor-is-identity-on-non-negative (the cross-impl parity guarantee).
• cargo fmt --check, cargo clippy --all-targets --all-features -- -D warnings, and the full suite (141 passed / 0 failed) all pass locally.

Cross-impl follow-up

OspreySharp should mirror the uniform max(0, x) floor (correct even before that, since it is bit-identical on the non-negative range) and bump to 26.7.0 so cross-impl joins line up.

🤖 Generated with Claude Code

https://claude.ai/code/session_0146d9VSgpxxA6xp2r6fE3uz

[Copilot]

Pull request overview

This PR introduces a single, centralized log10(max(0, x) + 1) conditioning transform for intensity-magnitude scoring features to reduce heavy-tail/outlier dominance in Percolator scoring, and cuts a v26.7.0 release with accompanying docs and release notes.

Changes:

• Apply condition_intensity_feature(x) = log10(max(0, x) + 1) to peak_apex, peak_area, and peak_sharpness at the single feature computation point (compute_features_at_peak) and add unit tests for the transform.
• Update documentation to reflect the new feature semantics and the resulting .scores.parquet cache invalidation behavior.
• Bump workspace/package versions to 26.7.0 and add/reset release notes (RELEASE_NOTES_v26.7.0.md, RELEASE_NOTES_next.md).

Reviewed changes

Copilot reviewed 7 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
release-notes/RELEASE_NOTES_v26.7.0.md	Adds v26.7.0 release notes including the intensity-feature conditioning and upgrade guidance.
release-notes/RELEASE_NOTES_next.md	Resets the “next release” draft to an empty placeholder after cutting v26.7.0 notes.
docs/README.md	Documents that peak_apex, peak_area, and peak_sharpness are now log10-conditioned (PIN features only).
docs/12-intermediate-files.md	Notes that the stored peak-shape features in the scores parquet are log10-conditioned.
docs/07-fdr-control.md	Updates the feature list and adds explanation of the conditioning and cache invalidation.
crates/osprey/src/pipeline.rs	Implements condition_intensity_feature, routes the three features through it, and adds unit tests.
Cargo.toml	Bumps workspace version to 26.7.0.
Cargo.lock	Updates workspace crate versions to 26.7.0.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.