{
  "baseline_issue": 270,
  "baselines": [
    {
      "baseline_id": "constant_negative",
      "family": "constant",
      "features": [],
      "holdout_metrics": [
        {
          "ci95": [
            0.5,
            0.5
          ],
          "name": "auroc",
          "value": 0.5
        },
        {
          "ci95": [
            0.0878967586309396,
            0.11732278776602828
          ],
          "name": "average_precision",
          "value": 0.09711645830159216
        },
        {
          "ci95": [
            0.5,
            0.5
          ],
          "name": "balanced_accuracy",
          "value": 0.5
        }
      ],
      "holdout_rows": 3390,
      "selected_direction": "constant",
      "threshold": 0.0,
      "train_metrics": [
        {
          "ci95": [
            0.5,
            0.5
          ],
          "name": "auroc",
          "value": 0.5
        },
        {
          "ci95": [
            0.10008615561676856,
            0.10008615561676856
          ],
          "name": "average_precision",
          "value": 0.10008615561676856
        },
        {
          "ci95": [
            0.5,
            0.5
          ],
          "name": "balanced_accuracy",
          "value": 0.5
        }
      ],
      "train_rows": 8010
    },
    {
      "baseline_id": "label_prior_constant",
      "family": "label_prior",
      "features": [],
      "holdout_metrics": [
        {
          "ci95": [
            0.5,
            0.5
          ],
          "name": "auroc",
          "value": 0.5
        },
        {
          "ci95": [
            0.0878967586309396,
            0.11732278776602828
          ],
          "name": "average_precision",
          "value": 0.09711645830159216
        },
        {
          "ci95": [
            0.5,
            0.5
          ],
          "name": "balanced_accuracy",
          "value": 0.5
        }
      ],
      "holdout_rows": 3390,
      "selected_direction": "constant",
      "threshold": 0.1,
      "train_metrics": [
        {
          "ci95": [
            0.5,
            0.5
          ],
          "name": "auroc",
          "value": 0.5
        },
        {
          "ci95": [
            0.10008615561676856,
            0.10008615561676856
          ],
          "name": "average_precision",
          "value": 0.10008615561676856
        },
        {
          "ci95": [
            0.5,
            0.5
          ],
          "name": "balanced_accuracy",
          "value": 0.5
        }
      ],
      "train_rows": 8010
    },
    {
      "baseline_id": "maf_source_only",
      "family": "source_only",
      "features": [
        "maf"
      ],
      "holdout_metrics": [
        {
          "ci95": [
            0.4731464028455562,
            0.5381588543835771
          ],
          "name": "auroc",
          "value": 0.505679263726096
        },
        {
          "ci95": [
            0.08951094404190417,
            0.12004951945854364
          ],
          "name": "average_precision",
          "value": 0.10238259917649947
        },
        {
          "ci95": [
            0.48506896234667085,
            0.5128472203576593
          ],
          "name": "balanced_accuracy",
          "value": 0.49868895444116684
        }
      ],
      "holdout_rows": 3390,
      "selected_direction": "positive",
      "threshold": 0.43005,
      "train_metrics": [
        {
          "ci95": [
            0.5041754922451804,
            0.5041754922451804
          ],
          "name": "auroc",
          "value": 0.5041754922451804
        },
        {
          "ci95": [
            0.10125234249532197,
            0.10125234249532197
          ],
          "name": "average_precision",
          "value": 0.10125234249532197
        },
        {
          "ci95": [
            0.49993064225273964,
            0.49993064225273964
          ],
          "name": "balanced_accuracy",
          "value": 0.49993064225273964
        }
      ],
      "train_rows": 8010
    },
    {
      "baseline_id": "ld_score_source_only",
      "family": "source_only",
      "features": [
        "ld_score"
      ],
      "holdout_metrics": [
        {
          "ci95": [
            0.47607951911863017,
            0.5417366518768001
          ],
          "name": "auroc",
          "value": 0.5076690364105196
        },
        {
          "ci95": [
            0.08943593154690196,
            0.11955200357886864
          ],
          "name": "average_precision",
          "value": 0.1025570642571744
        },
        {
          "ci95": [
            0.4829962176295964,
            0.5201457865678654
          ],
          "name": "balanced_accuracy",
          "value": 0.5013110455588332
        }
      ],
      "holdout_rows": 3390,
      "selected_direction": "negative",
      "threshold": -14.86,
      "train_metrics": [
        {
          "ci95": [
            0.5116374680075485,
            0.5116374680075485
          ],
          "name": "auroc",
          "value": 0.5116374680075485
        },
        {
          "ci95": [
            0.10529046723989412,
            0.10529046723989412
          ],
          "name": "average_precision",
          "value": 0.10529046723989412
        },
        {
          "ci95": [
            0.501317797197947,
            0.501317797197947
          ],
          "name": "balanced_accuracy",
          "value": 0.501317797197947
        }
      ],
      "train_rows": 8010
    },
    {
      "baseline_id": "tss_dist_source_only",
      "family": "source_only",
      "features": [
        "tss_dist"
      ],
      "holdout_metrics": [
        {
          "ci95": [
            0.4775741422366398,
            0.5401160798079878
          ],
          "name": "auroc",
          "value": 0.5088833971936277
        },
        {
          "ci95": [
            0.09191532953505854,
            0.12636936803219723
          ],
          "name": "average_precision",
          "value": 0.10907921673083246
        },
        {
          "ci95": [
            0.4998822925435975,
            0.5390914203262805
          ],
          "name": "balanced_accuracy",
          "value": 0.5188462799082268
        }
      ],
      "holdout_rows": 3390,
      "selected_direction": "negative",
      "threshold": -725.0,
      "train_metrics": [
        {
          "ci95": [
            0.502219361323384,
            0.502219361323384
          ],
          "name": "auroc",
          "value": 0.502219361323384
        },
        {
          "ci95": [
            0.10336161751754755,
            0.10336161751754755
          ],
          "name": "average_precision",
          "value": 0.10336161751754755
        },
        {
          "ci95": [
            0.5027049521431544,
            0.5027049521431544
          ],
          "name": "balanced_accuracy",
          "value": 0.5027049521431544
        }
      ],
      "train_rows": 8010
    },
    {
      "baseline_id": "direct_traitgym_native_borzoi",
      "family": "direct_borzoi",
      "features": [
        "borzoi_score"
      ],
      "holdout_metrics": [
        {
          "ci95": [
            0.608166918891345,
            0.6786897387200743
          ],
          "name": "auroc",
          "value": 0.6446380073654462
        },
        {
          "ci95": [
            0.17943976937550182,
            0.2640719088784513
          ],
          "name": "average_precision",
          "value": 0.2213743948035639
        },
        {
          "ci95": [
            0.5540389937997994,
            0.6005375613338952
          ],
          "name": "balanced_accuracy",
          "value": 0.5789904949196985
        }
      ],
      "holdout_rows": 3390,
      "selected_direction": "positive",
      "threshold": 26.49095916748047,
      "train_metrics": [
        {
          "ci95": [
            0.6453825837414703,
            0.6453825837414703
          ],
          "name": "auroc",
          "value": 0.6453825837414703
        },
        {
          "ci95": [
            0.21645986654070518,
            0.21645986654070518
          ],
          "name": "average_precision",
          "value": 0.21645986654070518
        },
        {
          "ci95": [
            0.6032736856706894,
            0.6032736856706894
          ],
          "name": "balanced_accuracy",
          "value": 0.6032736856706894
        }
      ],
      "train_rows": 8010
    },
    {
      "baseline_id": "source_logistic_probe",
      "family": "source_probe",
      "features": [
        "maf",
        "ld_score",
        "tss_dist"
      ],
      "holdout_metrics": [
        {
          "ci95": [
            0.4735925302675608,
            0.5415496282067285
          ],
          "name": "auroc",
          "value": 0.5093905088423062
        },
        {
          "ci95": [
            0.09122582482004839,
            0.12310435346112567
          ],
          "name": "average_precision",
          "value": 0.10457176928978472
        },
        {
          "ci95": [
            0.5,
            0.5
          ],
          "name": "balanced_accuracy",
          "value": 0.5
        }
      ],
      "holdout_rows": 3390,
      "selected_direction": "fit_on_train",
      "threshold": 0.5,
      "train_metrics": [
        {
          "ci95": [
            0.5111213978781205,
            0.5111213978781205
          ],
          "name": "auroc",
          "value": 0.5111213978781205
        },
        {
          "ci95": [
            0.10476784530316627,
            0.10476784530316627
          ],
          "name": "average_precision",
          "value": 0.10476784530316627
        },
        {
          "ci95": [
            0.5,
            0.5
          ],
          "name": "balanced_accuracy",
          "value": 0.5
        }
      ],
      "train_rows": 8010
    },
    {
      "baseline_id": "borzoi_plus_source_logistic_probe",
      "family": "borzoi_probe",
      "features": [
        "borzoi_score",
        "maf",
        "ld_score",
        "tss_dist"
      ],
      "holdout_metrics": [
        {
          "ci95": [
            0.6144029191243308,
            0.6821100969844257
          ],
          "name": "auroc",
          "value": 0.6494374396324432
        },
        {
          "ci95": [
            0.1799612237853904,
            0.26741550737792813
          ],
          "name": "average_precision",
          "value": 0.2225262018025548
        },
        {
          "ci95": [
            0.5013650958851011,
            0.5152777906689212
          ],
          "name": "balanced_accuracy",
          "value": 0.5080301540478531
        }
      ],
      "holdout_rows": 3390,
      "selected_direction": "fit_on_train",
      "threshold": 0.5,
      "train_metrics": [
        {
          "ci95": [
            0.6438785337166106,
            0.6438785337166106
          ],
          "name": "auroc",
          "value": 0.6438785337166106
        },
        {
          "ci95": [
            0.21687975113010652,
            0.21687975113010652
          ],
          "name": "average_precision",
          "value": 0.21687975113010652
        },
        {
          "ci95": [
            0.5144957691774171,
            0.5144957691774171
          ],
          "name": "balanced_accuracy",
          "value": 0.5144957691774171
        }
      ],
      "train_rows": 8010
    }
  ],
  "blockers": [],
  "cache_manifest": {
    "cache_artifact": {
      "path": "docs/research/fx-borzoi-score-cache.parquet",
      "rows": 11400,
      "sha256": "sha256:74695a87dfd0045e6d3ad161167f765497dbb00d99b396ab9490c7d8ade7b76f",
      "size_bytes": 533055
    },
    "path": "docs/research/fx-borzoi-cache-manifest.json",
    "sha256": "sha256:0d06742aacb9c07043cf2dc4b080c18b2846dc71d3358497e356ebbd30317a24"
  },
  "carbon_baseline_status": "not_applicable_no_carbon_scores_in_cache",
  "claim_boundary": "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.",
  "decision": "go_residual_model",
  "epic_issue": 266,
  "fipip_exact_join_status": "not_run_full_table_not_staged",
  "gate": {
    "bootstrap_samples": 500,
    "bootstrap_seed": 270,
    "holdout_split": "holdout",
    "minimum_direct_borzoi_ap_delta_vs_prior": 0.02,
    "primary_metric": "average_precision",
    "saturation_auroc": 0.9,
    "saturation_average_precision": 0.8
  },
  "generated_at": "2026-06-11T13:00:00Z",
  "generated_by": "tools.research.fx_borzoi_baselines",
  "leakage_audit": {
    "consequence_counts_top": {
      "3_prime_UTR_variant": 520,
      "5_prime_UTR_variant": 420,
      "CTCF-only_flank": 80,
      "PLS": 320,
      "PLS_flank": 150,
      "dELS": 3140,
      "dELS_flank": 1670,
      "intergenic_variant": 1030,
      "intron_variant": 1900,
      "non_coding_transcript_exon_variant": 690,
      "pELS": 1010,
      "pELS_flank": 340
    },
    "duplicate_variant_keys": 0,
    "holdout_chromosomes": [
      "3",
      "11",
      "14",
      "16",
      "17",
      "20"
    ],
    "train_chromosomes": [
      "1",
      "2",
      "4",
      "5",
      "6",
      "7",
      "8",
      "9",
      "10",
      "12",
      "13",
      "15",
      "18",
      "19",
      "21",
      "22"
    ],
    "train_holdout_key_overlap": 0,
    "trait_counts_top": {
      "": 10260,
      "ALP": 23,
      "Eosino": 28,
      "FEV1FVC": 29,
      "HbA1c": 23,
      "Height": 70,
      "IGF1": 28,
      "Lym": 28,
      "MCH,MCV": 27,
      "Mono": 39,
      "Plt": 54,
      "eBMD": 60
    }
  },
  "model_issue": 271,
  "ok_to_train_residual_model": true,
  "paired_comparisons": [
    {
      "comparison_id": "strongest_vs_label_prior",
      "left": "borzoi_plus_source_logistic_probe",
      "metrics": [
        {
          "ci95": [
            0.11982414369332395,
            0.17950390727417295
          ],
          "delta": 0.14943743963244316,
          "name": "auroc"
        },
        {
          "ci95": [
            0.08374249864649874,
            0.1621392869323911
          ],
          "delta": 0.12540974350096265,
          "name": "average_precision"
        }
      ],
      "right": "label_prior_constant"
    },
    {
      "comparison_id": "strongest_vs_direct_borzoi",
      "left": "borzoi_plus_source_logistic_probe",
      "metrics": [
        {
          "ci95": [
            -0.007858751598811428,
            0.018405185230988406
          ],
          "delta": 0.0047994322669969725,
          "name": "auroc"
        },
        {
          "ci95": [
            -0.0028953845338253884,
            0.005472658413273101
          ],
          "delta": 0.0011518069989908952,
          "name": "average_precision"
        }
      ],
      "right": "direct_traitgym_native_borzoi"
    },
    {
      "comparison_id": "direct_borzoi_vs_label_prior",
      "left": "direct_traitgym_native_borzoi",
      "metrics": [
        {
          "ci95": [
            0.11238496889890592,
            0.1761152834419466
          ],
          "delta": 0.1446380073654462,
          "name": "auroc"
        },
        {
          "ci95": [
            0.08292374659220711,
            0.16038285501933236
          ],
          "delta": 0.12425793650197176,
          "name": "average_precision"
        }
      ],
      "right": "label_prior_constant"
    }
  ],
  "recommended_issue_actions": [
    {
      "action": "close-completed",
      "issue": 270,
      "reason": "The baseline gate is not saturated and direct Borzoi has holdout signal."
    },
    {
      "action": "open-next",
      "issue": 271,
      "reason": "A residual model may proceed against the strongest simple baseline."
    }
  ],
  "schema_version": "1.0.0",
  "source_manifest": {
    "path": "configs/fx/borzoi_rescue_sources.json",
    "sha256": "sha256:59cbdd6176d48192b25127c02eceb41c3cc2867413f095e7d505cbc7c226355f"
  },
  "split_summary": {
    "holdout_negative": 3051,
    "holdout_positive": 339,
    "holdout_rows": 3390,
    "train_negative": 7209,
    "train_positive": 801,
    "train_rows": 8010
  },
  "strongest_simple_baseline": {
    "baseline_id": "borzoi_plus_source_logistic_probe",
    "family": "borzoi_probe",
    "features": [
      "borzoi_score",
      "maf",
      "ld_score",
      "tss_dist"
    ],
    "holdout_metrics": [
      {
        "ci95": [
          0.6144029191243308,
          0.6821100969844257
        ],
        "name": "auroc",
        "value": 0.6494374396324432
      },
      {
        "ci95": [
          0.1799612237853904,
          0.26741550737792813
        ],
        "name": "average_precision",
        "value": 0.2225262018025548
      },
      {
        "ci95": [
          0.5013650958851011,
          0.5152777906689212
        ],
        "name": "balanced_accuracy",
        "value": 0.5080301540478531
      }
    ],
    "holdout_rows": 3390,
    "selected_direction": "fit_on_train",
    "threshold": 0.5,
    "train_metrics": [
      {
        "ci95": [
          0.6438785337166106,
          0.6438785337166106
        ],
        "name": "auroc",
        "value": 0.6438785337166106
      },
      {
        "ci95": [
          0.21687975113010652,
          0.21687975113010652
        ],
        "name": "average_precision",
        "value": 0.21687975113010652
      },
      {
        "ci95": [
          0.5144957691774171,
          0.5144957691774171
        ],
        "name": "balanced_accuracy",
        "value": 0.5144957691774171
      }
    ],
    "train_rows": 8010
  }
}
