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Add FPS recovery figure script #118

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29 changes: 29 additions & 0 deletions scripts/README.md
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Expand Up @@ -195,6 +195,35 @@ manuscript_assets/tables/figure5_fps_spearman_r2_leaderboard.tsv
manuscript_assets/tables/figure5_fps_local_ranks.tsv
```

## Generate Figure 6 FPS Recovery

Run from the repository root:

```bash
uv run python scripts/figure6_fps_recovery.py \
--run-dir results/<results_dir>
```

Figure 6 evaluates practical recovery under the Full Pair Set (FPS), using the
same rank-zero convention for missing predictor scores as Figure 5. It reports
positive-pair recovery by prediction budget, the best per-experiment precision
at a fixed recall target, and the corresponding false positives per true
positive.

This writes:

```text
manuscript_assets/figure6/figure6_fps_recovery_panel_a_recovery_budget.png
manuscript_assets/figure6/figure6_fps_recovery_panel_b_best_precision.png
manuscript_assets/figure6/figure6_fps_recovery_panel_c_validation_burden.png
manuscript_assets/figure6/figure6_fps_recovery_panel_d_legend.png
manuscript_assets/figure6/figure6_fps_recovery_combined.png
manuscript_assets/figure6/figure6_fps_recovery_combined.svg
manuscript_assets/tables/figure6_fps_recovery_by_budget.tsv
manuscript_assets/tables/figure6_fps_precision_at_recall.tsv
manuscript_assets/tables/figure6_fps_best_precision_at_recall.tsv
```

## Generate Supplementary Top-Effect CDF Figure

After running the benchmark with `evaluation.write_top_prediction_cdfs: true`,
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