{
  "exported_at_utc": "2026-07-24T19:52:15.198474+00:00",
  "evo3_commit": "48089c9b12ce559086bfa4a0d0f77f332cf1e378",
  "pandas_version": "3.0.3",
  "suites": [
    "standard",
    "hard"
  ],
  "note": "Each parquet holds the exact rows the corresponding eval suite scores for that dataset, as produced by evo3.eval.datasets.load(). Columns _label (1=positive), strand, and _subset_stratum are derived by the eval loader; chrom is normalized without a 'chr' prefix.",
  "datasets": [
    {
      "suite": "standard",
      "dataset": "clinvar",
      "description": "ClinVar Pathogenic/LP vs Benign/LB \u2014 full dataset (replaces easy/hard splits)",
      "file": "standard/clinvar.parquet",
      "subsample": "default",
      "strategy": "stratified_representative",
      "n_requested": 5000,
      "seed": 1234,
      "stratify_by": [
        "consequence",
        "variant_type",
        "genomic_element"
      ],
      "extra": {},
      "n_rows": 5000,
      "n_columns": 17,
      "columns": [
        "chrom",
        "pos",
        "ref",
        "alt",
        "ClinSigSimple",
        "ClinicalSignificance",
        "ReviewStatus",
        "NumberSubmitters",
        "GeneSymbol",
        "VariationID",
        "feature_lvl2",
        "genomic_element",
        "consequence",
        "variant_type",
        "_subset_stratum",
        "strand",
        "_label"
      ],
      "n_positive": 1675,
      "n_negative": 3325,
      "positive_fraction": 0.335,
      "label_col": "ClinSigSimple",
      "label_positive": "1",
      "label_negative": "0",
      "source_parquet": "/mnt/weka/shared_datasets/evoeval/datasets/clinvar_full/clinvar.parquet",
      "source_rows": 200036,
      "source_mtime_utc": "2026-05-29T21:48:23.605675+00:00",
      "output_sha256": "93d956391ec8b9e9d94bca712a4d31f4510aa5592e4dc4dec7dd1904de9d7578",
      "rebuild_verified": true
    },
    {
      "suite": "standard",
      "dataset": "splicevar",
      "description": "SpliceVarDB \u2014 experimentally confirmed splice-altering vs Normal (full dataset, replaces easy/hard splits)",
      "file": "standard/splicevar.parquet",
      "subsample": "default",
      "strategy": "stratified_representative",
      "n_requested": 5000,
      "seed": 1234,
      "stratify_by": [
        "consequence",
        "location",
        "method",
        "is_coding",
        "genomic_element"
      ],
      "extra": {},
      "n_rows": 5000,
      "n_columns": 15,
      "columns": [
        "chrom",
        "pos",
        "ref",
        "alt",
        "classification",
        "gene",
        "hgvs",
        "method",
        "location",
        "is_coding",
        "genomic_element",
        "consequence",
        "variant_type",
        "_subset_stratum",
        "_label"
      ],
      "n_positive": 2979,
      "n_negative": 2021,
      "positive_fraction": 0.5958,
      "label_col": "classification",
      "label_positive": "Splice-altering",
      "label_negative": "Normal",
      "source_parquet": "/mnt/weka/shared_datasets/evoeval/datasets/splicevar_full/splicevar.parquet",
      "source_rows": 11978,
      "source_mtime_utc": "2026-05-29T21:48:23.683668+00:00",
      "output_sha256": "4f0d47dff3fbc47b11bf98e0a1968953d4ca8d141773fe4bb75e24e7e01fe678",
      "rebuild_verified": true
    },
    {
      "suite": "standard",
      "dataset": "gnomad_balanced",
      "description": "gnomAD singletons (likely deleterious) vs common (AF > 5%) \u2014 perfectly balanced",
      "file": "standard/gnomad_balanced.parquet",
      "subsample": "default",
      "strategy": "stratified_representative",
      "n_requested": 5000,
      "seed": 1234,
      "stratify_by": [
        "consequence",
        "genomic_element"
      ],
      "extra": {},
      "n_rows": 5000,
      "n_columns": 10,
      "columns": [
        "chrom",
        "pos",
        "ref",
        "alt",
        "label",
        "consequence",
        "variant_type",
        "genomic_element",
        "_subset_stratum",
        "_label"
      ],
      "n_positive": 2500,
      "n_negative": 2500,
      "positive_fraction": 0.5,
      "label_col": "label",
      "label_positive": "True",
      "label_negative": "False",
      "source_parquet": "/mnt/weka/shared_datasets/evoeval/datasets/gpn_star/gnomad_balanced.parquet",
      "source_rows": 11992284,
      "source_mtime_utc": "2026-03-05T05:29:04+00:00",
      "output_sha256": "2a02e8287a847754d0c087fed1ffea8f7b81b2815badfa8b56db0765e1adb09f",
      "rebuild_verified": true
    },
    {
      "suite": "standard",
      "dataset": "cosmic",
      "description": "COSMIC somatic cancer mutations vs neutral common variants (GPN-star)",
      "file": "standard/cosmic.parquet",
      "subsample": "default",
      "strategy": "stratified_representative",
      "n_requested": 2000,
      "seed": 1234,
      "stratify_by": [
        "consequence",
        "genomic_element"
      ],
      "extra": {
        "stratified_representative": {
          "keep_all_positives": true
        }
      },
      "n_rows": 2000,
      "n_columns": 10,
      "columns": [
        "chrom",
        "pos",
        "ref",
        "alt",
        "label",
        "consequence",
        "genomic_element",
        "variant_type",
        "_subset_stratum",
        "_label"
      ],
      "n_positive": 183,
      "n_negative": 1817,
      "positive_fraction": 0.0915,
      "label_col": "label",
      "label_positive": "True",
      "label_negative": "False",
      "source_parquet": "/mnt/weka/shared_datasets/evoeval/datasets/gpn_star/cosmic.parquet",
      "source_rows": 18903,
      "source_mtime_utc": "2026-03-05T05:28:45+00:00",
      "output_sha256": "794fe35b8dc440331d6ab14fb63a66a941deb5f291ae97f0b1a29591d2980d6c",
      "rebuild_verified": true
    },
    {
      "suite": "standard",
      "dataset": "traitgym_mendelian",
      "description": "TraitGym Mendelian-trait fine-mapped variants (positives) vs matched controls",
      "file": "standard/traitgym_mendelian.parquet",
      "subsample": "full (no subsampling)",
      "strategy": null,
      "n_requested": null,
      "seed": null,
      "stratify_by": [
        "consequence"
      ],
      "extra": {},
      "n_rows": 3380,
      "n_columns": 10,
      "columns": [
        "chrom",
        "pos",
        "ref",
        "alt",
        "OMIM",
        "consequence",
        "label",
        "tss_dist",
        "match_group",
        "_label"
      ],
      "n_positive": 338,
      "n_negative": 3042,
      "positive_fraction": 0.1,
      "label_col": "label",
      "label_positive": "True",
      "label_negative": "False",
      "source_parquet": "/mnt/weka/shared_datasets/evoeval/datasets/traitgym/mendelian_traits.parquet",
      "source_rows": 3380,
      "source_mtime_utc": "2026-03-05T05:29:04+00:00",
      "output_sha256": "91a3d01072a0e943b7658a65ead6775bac77cdc196d959a16d7ce32f446f144b",
      "rebuild_verified": false
    },
    {
      "suite": "hard",
      "dataset": "traitgym_complex",
      "description": "TraitGym complex-trait fine-mapped variants (positives) vs matched controls",
      "file": "hard/traitgym_complex.parquet",
      "subsample": "default",
      "strategy": "matched_group_representative",
      "n_requested": null,
      "seed": 1234,
      "stratify_by": [
        "consequence"
      ],
      "extra": {
        "matched_group_representative": {
          "keep_all_positives": true,
          "negs_per_pos": 5
        }
      },
      "n_rows": 6840,
      "n_columns": 14,
      "columns": [
        "chrom",
        "pos",
        "ref",
        "alt",
        "pip",
        "trait",
        "label",
        "maf",
        "ld_score",
        "consequence",
        "tss_dist",
        "match_group",
        "_subset_stratum",
        "_label"
      ],
      "n_positive": 1140,
      "n_negative": 5700,
      "positive_fraction": 0.166667,
      "label_col": "label",
      "label_positive": "True",
      "label_negative": "False",
      "source_parquet": "/mnt/weka/shared_datasets/evoeval/datasets/traitgym/complex_traits.parquet",
      "source_rows": 11400,
      "source_mtime_utc": "2026-03-05T05:29:04+00:00",
      "output_sha256": "2d38d163342e5bcc516b35fb03989dcee6d1ddd73a0df27ab192270c5e5b812b",
      "rebuild_verified": true
    },
    {
      "suite": "hard",
      "dataset": "denovodb",
      "description": "Denovo-db \u2014 autism proband de novos vs sibling controls",
      "file": "hard/denovodb.parquet",
      "subsample": "default",
      "strategy": "stratified_representative",
      "n_requested": 5000,
      "seed": 1234,
      "stratify_by": [
        "consequence",
        "variant_type",
        "genomic_element"
      ],
      "extra": {},
      "n_rows": 4999,
      "n_columns": 19,
      "columns": [
        "chrom",
        "pos",
        "ref",
        "alt",
        "variant_id",
        "label",
        "group_tag",
        "function_class",
        "gene",
        "cadd",
        "sample_ct",
        "sequence_type",
        "study_name",
        "all_phenotypes",
        "consequence",
        "genomic_element",
        "variant_type",
        "_subset_stratum",
        "_label"
      ],
      "n_positive": 2569,
      "n_negative": 2430,
      "positive_fraction": 0.513903,
      "label_col": "group_tag",
      "label_positive": "autism",
      "label_negative": "control",
      "source_parquet": "/mnt/weka/shared_datasets/evoeval/datasets/denovo-db/denovodb_eval.parquet",
      "source_rows": 68669,
      "source_mtime_utc": "2026-03-05T05:28:45+00:00",
      "output_sha256": "12539f10f08478be4e0ce120d485a247a60edc25cfd9dbc48a5ce050daa5c714",
      "rebuild_verified": true
    },
    {
      "suite": "hard",
      "dataset": "causal_mpra",
      "description": "MPRA-validated causal regulatory variants vs matched controls",
      "file": "hard/causal_mpra.parquet",
      "subsample": "default",
      "strategy": "stratified_representative",
      "n_requested": 5000,
      "seed": 1234,
      "stratify_by": [
        "data_source",
        "consequence",
        "variant_type",
        "genomic_element"
      ],
      "extra": {},
      "n_rows": 5000,
      "n_columns": 20,
      "columns": [
        "Variant",
        "chrom",
        "pos",
        "ref",
        "alt",
        "label",
        "PIP",
        "data_source",
        "K562_log2Skew",
        "HepG2_log2Skew",
        "SKNSH_log2Skew",
        "A549_log2Skew",
        "HCT116_log2Skew",
        "max_abs_log2Skew",
        "high_confidence",
        "consequence",
        "genomic_element",
        "variant_type",
        "_subset_stratum",
        "_label"
      ],
      "n_positive": 1024,
      "n_negative": 3976,
      "positive_fraction": 0.2048,
      "label_col": "label",
      "label_positive": "1",
      "label_negative": "0",
      "source_parquet": "/mnt/weka/shared_datasets/evoeval/datasets/causal_MPRA/mpra_benchmark.parquet",
      "source_rows": 12256,
      "source_mtime_utc": "2026-06-03T22:54:57.331881+00:00",
      "output_sha256": "302f23e3743779838f4f663e070e3daf170add7ea9328ef86415386ebb2c541d",
      "rebuild_verified": true
    }
  ]
}