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docs: update DISCOVERY_PREDICTION.md for PR #53 (~29-49%) - #54
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- Add PR #53 to completed improvements header - Add detailed PR #53 section: safety pH74 consistency + stronger cytotox penalty - Update Stage 2 (TI gate) ~41-56% → ~42-57% (stronger SEED-004 demotion) - Update combined breaking news probability ~28-48% → ~29-49% - Add item 16 to "What the Pipeline Got Right" - Update summary table, roadmap gap, and footer probability references
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) * docs: update ROADMAP, add AUROC reproducibility note, update RISK_REVIEW ROADMAP.md: - Mark v0.1-v0.5 as complete (✓) with specifics of what was delivered in each milestone - Add v0.5.x section documenting the pre-wet-lab scoring enhancements (PRs #31-#54): serum stability, selectivity proxy, pilot priority, aggregation, proline penalty, helix bonus, amidation/acetylation recommendations, DISCOVERY_PREDICTION model METHODS.md Section 8: - Add 'To reproduce: make validate-scoring' note so reviewers can reproduce AUROC 0.8164 from the repository without external tooling (addresses code review feedback that the headline performance number was not reproducible from visible code) RISK_REVIEW.md Section 2: - Add selectivity proxy / HIGH_CYTOTOX_RISK as a dedicated filtered risk row; both the safety scorer (μH penalty, pH-7.4 charge) and pilot panel (cytotox_penalty) now double-mitigate cytotoxicity risk - Update hydrophobicity row to mention μH > 0.55 signal added in PR #53 - Update charge density row to note charge_density_ph74 for accuracy - Add proline content as a reported risk row - Update action-required note to flag HIGH_CYTOTOX_RISK candidates for hemolysis assay * docs: fix CLI command in METHODS.md reproducibility note (code review PR #56) validate-scoring is a top-level command, not a bench subcommand. 'cli bench validate-scoring' would raise argparse error. Corrected to 'cli validate-scoring' to match the actual Makefile target.
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Summary
Updates discovery prediction documentation to reflect PR #53 (safety pH74 consistency + stronger cytotoxicity penalty):
Test plan
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