Dataset

TraitGym Mendelian traits, matched 9 controls

TraitGym mendelian_traits_matched_9: causal variants with nine matched negative controls each.

Evaluation results

81 evaluations · 81 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AIDO.DNA_absLLR.plus.score (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.115 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.008869491282593147 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AIDO.DNA_absLLR.plus.score on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/AIDO.DNA_absLLR.plus.score.csv, column 'score' (standard error in column 'se')
Configuration: AIDO.DNA_Embeddings.minus.inner_product (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.173 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.016767200388829374 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AIDO.DNA_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/AIDO.DNA_Embeddings.minus.inner_product.csv, column 'score' (standard error in column 'se')
Configuration: AIDO.DNA_Embeddings.plus.cosine_distance (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.146 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.016225199774343134 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AIDO.DNA_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/AIDO.DNA_Embeddings.plus.cosine_distance.csv, column 'score' (standard error in column 'se')
Configuration: AIDO.DNA_Embeddings.plus.euclidean_distance (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.148 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.016830422431299015 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AIDO.DNA_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/AIDO.DNA_Embeddings.plus.euclidean_distance.csv, column 'score' (standard error in column 'se')
Configuration: AIDO.DNA_LLR.minus.score (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.135 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.012742124387199684 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AIDO.DNA_LLR.minus.score on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/AIDO.DNA_LLR.minus.score.csv, column 'score' (standard error in column 'se')
Configuration: AIDO.DNA.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.179 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.039616777374824476 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AIDO.DNA.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/AIDO.DNA.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: Borzoi_L2_L2.plus.all (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.436 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.051597004283321764 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Borzoi_L2_L2.plus.all on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/Borzoi_L2_L2.plus.all.csv, column 'score' (standard error in column 'se')
Configuration: Borzoi.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.493 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.03387962392290682 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Borzoi.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/Borzoi.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: CADD.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.875 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.03053334830628915 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/CADD.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: CADD+Borzoi.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.757 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.02800090306412582 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD+Borzoi.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/CADD+Borzoi.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: CADD+GPN-MSA.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.846 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.03343976192415707 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CADD+GPN-MSA.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/CADD+GPN-MSA.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: CADD+GPN-MSA+Borzoi.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.74 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.03341660529784681 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CADD+GPN-MSA+Borzoi.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: CADD.plus.RawScore (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.712 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.038447877158699226 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD.plus.RawScore on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/CADD.plus.RawScore.csv, column 'score' (standard error in column 'se')
Configuration: Caduceus_absLLR.plus.score (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.0878 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.005565988958549242 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus_absLLR.plus.score on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/Caduceus_absLLR.plus.score.csv, column 'score' (standard error in column 'se')
Configuration: Caduceus_Embeddings.minus.inner_product (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.131 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.016254752195469967 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/Caduceus_Embeddings.minus.inner_product.csv, column 'score' (standard error in column 'se')
Configuration: Caduceus_Embeddings.plus.cosine_distance (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.135 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.010093335540829028 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/Caduceus_Embeddings.plus.cosine_distance.csv, column 'score' (standard error in column 'se')
Configuration: Caduceus_Embeddings.plus.euclidean_distance (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.135 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.009044707575175105 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/Caduceus_Embeddings.plus.euclidean_distance.csv, column 'score' (standard error in column 'se')
Configuration: Caduceus_InnerProduct.minus.score (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.131 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.01625459735416025 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus_InnerProduct.minus.score on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/Caduceus_InnerProduct.minus.score.csv, column 'score' (standard error in column 'se')
Configuration: Caduceus_LLR.minus.score (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.108 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.005420533606407098 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus_LLR.minus.score on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/Caduceus_LLR.minus.score.csv, column 'score' (standard error in column 'se')
Configuration: Caduceus.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.237 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0659529424131491 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/Caduceus.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: Enformer_L2_L2.plus.all (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.418 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.03675225375188307 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Enformer_L2_L2.plus.all on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/Enformer_L2_L2.plus.all.csv, column 'score' (standard error in column 'se')
Configuration: Enformer.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.446 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.037976767408547156 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Enformer.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/Enformer.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: evo2_1b_base_absLLR.plus.score (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.159 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.031111541939277777 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source evo2_1b_base_absLLR.plus.score on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/evo2_1b_base_absLLR.plus.score.csv, column 'score' (standard error in column 'se')
Configuration: evo2_1b_base_Embeddings.minus.inner_product (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.165 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.03484037341338302 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source evo2_1b_base_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/evo2_1b_base_Embeddings.minus.inner_product.csv, column 'score' (standard error in column 'se')
Configuration: evo2_1b_base_Embeddings.plus.cosine_distance (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.118 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.006145116728818818 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source evo2_1b_base_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/evo2_1b_base_Embeddings.plus.cosine_distance.csv, column 'score' (standard error in column 'se')

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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6 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Population Mendelian traits; nine matched controls per causal variant (baseline AUPRC 0.1) Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ mendelian_traits_matched_9/test.parquet (not downloaded); README Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
Source location mendelian_traits_matched_9/test.parquet (not downloaded); README Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ mendelian_traits_matched_9/test.parquet (not downloaded); README Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
Split Leave-one-chromosome-out for linear probing; all variants scored for zero-shot Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ mendelian_traits_matched_9/test.parquet (not downloaded); README Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
Version Hugging Face revision 1fde19555fe8 Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ mendelian_traits_matched_9/test.parquet (not downloaded); README Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
Description TraitGym mendelian_traits_matched_9: causal variants with nine matched negative controls each. Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ mendelian_traits_matched_9/test.parquet (not downloaded); README Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
Name TraitGym Mendelian traits, matched 9 controls Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ mendelian_traits_matched_9/test.parquet (not downloaded); README Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · Original source · Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-traitgym-data-mendelian-traits-matched-9

areas: dna-genomes
contexts: research
version: Hugging Face revision 1fde19555fe8
split: Leave-one-chromosome-out for linear probing; all variants scored for zero-shot
population: Mendelian traits; nine matched controls per causal variant (baseline AUPRC 0.1)
source locator: mendelian_traits_matched_9/test.parquet (not downloaded); README

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