TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average; Hugging Face revision 1fde19555fe8

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18 recorded evaluations, 18 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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All evaluations

18 evaluations · 18 results. Different protocols are not a single leaderboard.

Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average · Dataset: TraitGym Mendelian traits, matched 9 controls

Sorted by AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all')
CADD.LogisticRegression.chrom (TraitGym)Evaluation	0.875 (best in column)
CADD+GPN-MSA.LogisticRegression.chrom (TraitGym)Evaluation	0.846
CADD+Borzoi.LogisticRegression.chrom (TraitGym)Evaluation	0.757
CADD+GPN-MSA+Borzoi.LogisticRegression.chrom (TraitGym)Evaluation	0.74
GPN-MSA+Borzoi.LogisticRegression.chrom (TraitGym)Evaluation	0.722
GPN-MSA.LogisticRegression.chrom (TraitGym)Evaluation	0.685
Borzoi.LogisticRegression.chrom (TraitGym)Evaluation	0.493
evo2_40b.LogisticRegression.chrom (TraitGym)Evaluation	0.489
Enformer.LogisticRegression.chrom (TraitGym)Evaluation	0.446
GPN_final.LogisticRegression.chrom (TraitGym)Evaluation	0.353
Sei.LogisticRegression.chrom (TraitGym)Evaluation	0.349
evo2_7b.LogisticRegression.chrom (TraitGym)Evaluation	0.339
Caduceus.LogisticRegression.chrom (TraitGym)Evaluation	0.237
SpeciesLM.LogisticRegression.chrom (TraitGym)Evaluation	0.193
AIDO.DNA.LogisticRegression.chrom (TraitGym)Evaluation	0.179
NucleotideTransformer.LogisticRegression.chrom (TraitGym)Evaluation	0.171
HyenaDNA.LogisticRegression.chrom (TraitGym)Evaluation	0.146
evo2_1b_base.LogisticRegression.chrom (TraitGym)Evaluation	0.134

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
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.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: 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.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.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.134 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.017139381662932014 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source evo2_1b_base.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/evo2_1b_base.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: evo2_40b.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.489 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.05317914221924283 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source evo2_40b.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/evo2_40b.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: evo2_7b.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.339 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.06367125219742997 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source evo2_7b.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/evo2_7b.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: GPN_final.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.353 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0583212250339244 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPN_final.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/GPN_final.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: GPN-MSA.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.685 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0674501053545171 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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/GPN-MSA.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: GPN-MSA+Borzoi.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.722 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.040220160541453186 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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/GPN-MSA+Borzoi.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: HyenaDNA.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, 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 0.013889472455416422 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA.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/HyenaDNA.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: NucleotideTransformer.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.171 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.02969380065772309 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NucleotideTransformer.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/NucleotideTransformer.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: Sei.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.349 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.03230521873601639 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Sei.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/Sei.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')
Configuration: SpeciesLM.LogisticRegression.chrom (TraitGym)	Protocol: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.193 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.02116532339560903 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpeciesLM.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/SpeciesLM.LogisticRegression.chrom.csv, column 'score' (standard error in column 'se')

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Author-reported evaluations: 5
External evaluations: 13

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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-protocol-mendelian-traits-matched-9-linear-probing

areas: dna-genomes
contexts: research
protocol: ridge logistic regression on extracted features, trained on the other chromosomes; AUPRC computed per chromosome and averaged with weights by sample size; standard error by bootstrap (paper Appendix B.4).
version: Hugging Face revision 1fde19555fe8
metric: auprc
metric direction: higher
unit: unitless
limitations: Baseline AUPRC is 0.1.; Labels come from fine-mapping (complex traits) and curated pathogenic variants (Mendelian), not experiments.; Benchmark authors developed GPN-MSA and GPN-Promoter.
source locator: File names under AUPRC_by_chrom_weighted_average/all/; paper Section 2 'evaluation metric'

Related records

part of: TraitGym
uses data: TraitGym Mendelian traits, matched 9 controls
assessment: AIDO.DNA.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: Borzoi.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: CADD.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: CADD+Borzoi.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: CADD+GPN-MSA.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: CADD+GPN-MSA+Borzoi.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: Caduceus.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: Enformer.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: evo2_1b_base.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: evo2_40b.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: evo2_7b.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: GPN_final.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: GPN-MSA.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: GPN-MSA+Borzoi.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: HyenaDNA.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: NucleotideTransformer.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: Sei.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessment: SpeciesLM.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
assessed by: Select regulatory variants and genes for functional follow-up