| { |
| "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 |
| } |
| ] |
| } |
|
|
