GenoLeWM-FX Borzoi baseline and saturation report¶

Generated by tools.research.fx_borzoi_baselines at 2026-06-11T13:00:00Z.

Parent epic: #266. Baseline gate: #270. Model gate: #271.

Decision: go_residual_model.

This report is a baseline and saturation gate only. It is not a model-quality result, clinical result, deployment-readiness result, broad VEP superiority claim, broad Carbon comparison, useful-planning claim, ground-truth biology claim, or exact fipip overlap claim.

Reproduce¶

uv run python -m tools.research.fx_borzoi_baselines \
  --source-manifest configs/fx/borzoi_rescue_sources.json \
  --cache-manifest docs/research/fx-borzoi-cache-manifest.json \
  --output-json docs/research/fx-borzoi-baseline-report.json \
  --output-md docs/research/fx-borzoi-baseline-report.md

Machine-readable report: fx-borzoi-baseline-report.json.

Baselines¶

Baseline	Family	AUROC	AUPRC	Balanced accuracy
`constant_negative`	constant	0.5000 [0.5000, 0.5000]	0.0971 [0.0879, 0.1173]	0.5000 [0.5000, 0.5000]
`label_prior_constant`	label_prior	0.5000 [0.5000, 0.5000]	0.0971 [0.0879, 0.1173]	0.5000 [0.5000, 0.5000]
`maf_source_only`	source_only	0.5057 [0.4731, 0.5382]	0.1024 [0.0895, 0.1200]	0.4987 [0.4851, 0.5128]
`ld_score_source_only`	source_only	0.5077 [0.4761, 0.5417]	0.1026 [0.0894, 0.1196]	0.5013 [0.4830, 0.5201]
`tss_dist_source_only`	source_only	0.5089 [0.4776, 0.5401]	0.1091 [0.0919, 0.1264]	0.5188 [0.4999, 0.5391]
`direct_traitgym_native_borzoi`	direct_borzoi	0.6446 [0.6082, 0.6787]	0.2214 [0.1794, 0.2641]	0.5790 [0.5540, 0.6005]
`source_logistic_probe`	source_probe	0.5094 [0.4736, 0.5415]	0.1046 [0.0912, 0.1231]	0.5000 [0.5000, 0.5000]
`borzoi_plus_source_logistic_probe`	borzoi_probe	0.6494 [0.6144, 0.6821]	0.2225 [0.1800, 0.2674]	0.5080 [0.5014, 0.5153]

Gate Decision¶

Strongest simple baseline: borzoi_plus_source_logistic_probe with AUPRC 0.2225 and AUROC 0.6494.

Saturation thresholds: AUPRC 0.8, AUROC 0.9.

Leakage Audit¶

Check	Value
Duplicate variant keys	0
Train/holdout key overlap	0
Train chromosomes	`1, 2, 4, 5, 6, 7, 8, 9, 10, 12, 13, 15, 18, 19, 21, 22`
Holdout chromosomes	`3, 11, 14, 16, 17, 20`
fipip exact join status	`not_run_full_table_not_staged`
Carbon baseline status	`not_applicable_no_carbon_scores_in_cache`

Blockers¶

No #270 blockers remain; the residual-model issue may proceed.

Recommended Issue Actions¶

Issue	Action	Reason
#270	`close-completed`	The baseline gate is not saturated and direct Borzoi has holdout signal.
#271	`open-next`	A residual model may proceed against the strongest simple baseline.