TraitGym Complex traits, linear-probing, AUPRC by chromosome weighted average
TraitGym Complex traits with ridge logistic regression on extracted features, trained on the other chromosomes.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
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.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
18 evaluations · 18 results. Different protocols are not a single leaderboard.
Protocol: TraitGym Complex traits, linear-probing, AUPRC by chromosome weighted average · Dataset: TraitGym Complex 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.
All 18 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AIDO.DNA.LogisticRegression.chrom (TraitGym) | Protocol: TraitGym Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.152 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.005049713863563956 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDO.DNA.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.297 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.014070612782420427 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBorzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.284 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.012406150330154912 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.351 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0163444581544798 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD+Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.297 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.011590379617788582 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCADD+GPN-MSA.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.362 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.015452234996450652 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCADD+GPN-MSA+Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.151 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.006712807881266443 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.303 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.010447115262766551 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.143 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.005252745453127056 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_1b_base.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.153 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.007042292928569418 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_40b.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.15 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.004981827549333252 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_7b.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.187 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.006975242598920125 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGPN_final.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.269 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.011520107088937664 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGPN-MSA.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.349 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.015400374037865963 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGPN-MSA+Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.136 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.008321382896394669 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.163 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.005949108361581677 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNucleotideTransformer.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.184 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.008017256843127056 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSei.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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 Complex traits, linear-probing, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.185 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.007554667523269251 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSpeciesLM.LogisticRegression.chrom on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-linear-probing Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_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.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- AIDO.DNA.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- CADD.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- CADD+Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- CADD+GPN-MSA.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- CADD+GPN-MSA+Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- Caduceus.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- Enformer.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- evo2_1b_base.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- evo2_40b.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- evo2_7b.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- GPN_final.LogisticRegression.chrom on TraitGym complex_traits_matched_9
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 5
- External evaluations
- 13
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Training-set mean where supervised fitting is permitted
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Simple features with train-only ridge regression
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
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Evidence table
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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/
Technical metadata and extraction receipts
Stable ID: lit-genomics-20261011-traitgym-protocol-complex-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 Complex traits, matched 9 controls
- assessment: AIDO.DNA.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: CADD.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: CADD+Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: CADD+GPN-MSA.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: CADD+GPN-MSA+Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: Caduceus.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: Enformer.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: evo2_1b_base.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: evo2_40b.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: evo2_7b.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: GPN_final.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: GPN-MSA.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: GPN-MSA+Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: HyenaDNA.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: NucleotideTransformer.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: Sei.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessment: SpeciesLM.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- assessed by: Select regulatory variants and genes for functional follow-up