{
  "schema_version": "1.0",
  "test_set": {
    "path": "/task/test.parquet",
    "build": "GRCh38/hg38",
    "rows": 44706,
    "unique_exact_tuples": 44706,
    "exact_duplicate_rows": 0
  },
  "labeled_training": {
    "compiled": false,
    "rows_before_test_exclusion": 0,
    "exact_test_overlaps_excluded": 0,
    "rows_after_test_exclusion": 0,
    "note": "No labels were parsed or used for fitting/calibration. Released out-of-chromosome predictions and label-independent annotations were used as features/scores."
  },
  "sources": [
    {
      "name": "TraitGym code",
      "url": "https://github.com/songlab-cal/TraitGym",
      "use": "Inspected scoring workflow and confirmed class_weight=balanced."
    },
    {
      "name": "TraitGym Hugging Face dataset",
      "url": "https://huggingface.co/datasets/songlab/TraitGym",
      "files_touched": [
        "complex_traits_matched_9/test.parquet",
        "complex_traits_matched_9/preds/all/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.parquet",
        "complex_traits_matched_9/features/{CADD,GPN-MSA_absLLR,Borzoi_L2_L2}.parquet",
        "mendelian_traits_matched_9/test.parquet",
        "mendelian_traits_matched_9/preds/all/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.parquet",
        "mendelian_traits_matched_9/features/{CADD,GPN-MSA_absLLR,Borzoi_L2_L2}.parquet",
        "complex_traits_v22_matched_9/test.parquet",
        "complex_traits_all/{test.parquet,features/CADDv1.7.RawScore.parquet,features/GPN-MSA_absLLR.parquet}",
        "mendelian_traits_all/{test.parquet,features/CADDv1.7.RawScore.parquet,features/GPN-MSA_absLLR.parquet}"
      ],
      "dedup": {
        "matched_rows_before_cross_dataset_dedup": 14780,
        "shared_exact_tuples": 27,
        "unique_exact_test_tuples_used": 14753
      },
      "labels_used": false
    },
    {
      "name": "Ensembl VEP REST",
      "url": "https://rest.ensembl.org/vep/homo_sapiens/region",
      "annotations": [
        "CADD",
        "AlphaMissense",
        "SpliceAI",
        "SIFT",
        "PolyPhen",
        "consequence"
      ],
      "input_rows": 44706,
      "unique_input_tuples": 44706,
      "output_rows": 44706,
      "cadd_coverage": 44706,
      "alphamissense_coverage": 7308,
      "spliceai_coverage": 34508,
      "clinical_significance_fields_parsed": false
    },
    {
      "name": "CADD v1.7 GRCh38 prescored SNVs",
      "urls": [
        "https://kircherlab.bihealth.org/download/CADD/v1.7/GRCh38/whole_genome_SNVs.tsv.gz",
        "https://kircherlab.bihealth.org/download/CADD/v1.7/GRCh38/whole_genome_SNVs.tsv.gz.tbi",
        "https://krishna.gs.washington.edu/download/CADD/v1.7/GRCh38/whole_genome_SNVs.tsv.gz",
        "https://krishna.gs.washington.edu/download/CADD/v1.7/GRCh38/whole_genome_SNVs.tsv.gz.tbi"
      ],
      "use": "Remote-tabix feasibility pilot; final CADD values came through Ensembl VEP."
    },
    {
      "name": "MyVariant.info",
      "urls": [
        "https://myvariant.info/v1/variant",
        "https://myvariant.info/v1/query"
      ],
      "use": "Coverage pilot only; rejected and unused in final scoring."
    },
    {
      "name": "EVEE ClinVar prediction resource",
      "urls": [
        "https://zenodo.org/records/19701997/files/manifest.json",
        "https://zenodo.org/records/19701997/files/clean_shard_0.parquet",
        "https://zenodo.org/records/19701997/files/clean_shard_1.parquet",
        "https://zenodo.org/records/19701997/files/clean_shard_2.parquet",
        "https://zenodo.org/records/19701997/files/clean_shard_3.parquet"
      ],
      "rows_annotation_columns_touched": 3372596,
      "exact_test_matches": 1604,
      "labels_read": false,
      "used_in_final": false,
      "reason_rejected": "Conservative avoidance of possible overlap with the supervised ClinVar probe."
    },
    {
      "name": "EVEE variant viewer code",
      "url": "https://github.com/goodfire-ai/variant-viewer",
      "use": "Repository access attempted during schema discovery; no final dependency."
    },
    {
      "name": "AlphaMissense release documentation",
      "urls": [
        "https://storage.googleapis.com/dm_alphamissense/README.pdf",
        "https://zenodo.org/records/8360242"
      ],
      "use": "Documentation consulted; scores were returned by Ensembl VEP."
    }
  ],
  "iterations": [
    {
      "iteration": 1,
      "method": "Input normalization/uniqueness audit",
      "status": "completed",
      "coverage": 1,
      "validation_score": null
    },
    {
      "iteration": 2,
      "method": "MyVariant CADD/dbNSFP lookup",
      "status": "rejected_low_coverage",
      "coverage": null,
      "validation_score": null
    },
    {
      "iteration": 3,
      "method": "Sparse remote-tabix CADD v1.7",
      "status": "rejected_high_latency",
      "coverage": null,
      "validation_score": null
    },
    {
      "iteration": 4,
      "method": "TraitGym released chromosome-held-out ensemble exact join",
      "status": "used",
      "rows": 14753,
      "validation_score": null,
      "published_reference_auprc": {
        "complex_traits": 0.362,
        "mendelian_traits": 0.648
      }
    },
    {
      "iteration": 5,
      "method": "TraitGym all-candidate CADD/GPN sparse extraction",
      "status": "intermediate_fallback_only",
      "unique_test_matches": 16981,
      "validation_score": null
    },
    {
      "iteration": 6,
      "method": "EVEE sparse prediction lookup",
      "status": "rejected_leakage_conservatism",
      "exact_test_matches": 1604,
      "validation_score": null
    },
    {
      "iteration": 7,
      "method": "Final TraitGym ensemble plus VEP consequence-aware clinical ensemble",
      "status": "final",
      "coverage": 1,
      "validation_score": null
    }
  ]
}