TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average
TraitGym Complex traits with zero-shot score.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
57 recorded evaluations, 57 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
57 evaluations · 57 results. Different protocols are not a single leaderboard.
Protocol: TraitGym Complex traits, zero-shot, 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 57 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_absLLR.plus.score (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.103 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.002443845069261043 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDO.DNA_absLLR.plus.score on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_absLLR.plus.score.csv, column 'score' (standard error in column 'se') |
| Configuration: AIDO.DNA_Embeddings.minus.inner_product (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.109 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.003903483581716696 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDO.DNA_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.minus.inner_product.csv, column 'score' (standard error in column 'se') |
| Configuration: AIDO.DNA_Embeddings.plus.cosine_distance (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.102 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.002738296601032076 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDO.DNA_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.plus.cosine_distance.csv, column 'score' (standard error in column 'se') |
| Configuration: AIDO.DNA_Embeddings.plus.euclidean_distance (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.102 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0026672414045521594 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDO.DNA_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.plus.euclidean_distance.csv, column 'score' (standard error in column 'se') |
| Configuration: AIDO.DNA_LLR.minus.score (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.106 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0025182734251406966 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAIDO.DNA_LLR.minus.score on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_LLR.minus.score.csv, column 'score' (standard error in column 'se') |
| Configuration: Borzoi_L2_L2.plus.all (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.236 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.009154607334170136 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBorzoi_L2_L2.plus.all on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_L2_L2.plus.all.csv, column 'score' (standard error in column 'se') |
| Configuration: CADD.plus.RawScore (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.25 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.01018346234907977 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD.plus.RawScore on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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.plus.RawScore.csv, column 'score' (standard error in column 'se') |
| Configuration: Caduceus_absLLR.plus.score (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.0971 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0019689455982978867 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus_absLLR.plus.score on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_absLLR.plus.score.csv, column 'score' (standard error in column 'se') |
| Configuration: Caduceus_Embeddings.minus.inner_product (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.117 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.006248675945733252 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.minus.inner_product.csv, column 'score' (standard error in column 'se') |
| Configuration: Caduceus_Embeddings.plus.cosine_distance (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.115 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0037614076427251136 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.plus.cosine_distance.csv, column 'score' (standard error in column 'se') |
| Configuration: Caduceus_Embeddings.plus.euclidean_distance (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.115 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.00366295980291948 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.plus.euclidean_distance.csv, column 'score' (standard error in column 'se') |
| Configuration: Caduceus_LLR.minus.score (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.0983 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0018751240045551348 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus_LLR.minus.score on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_LLR.minus.score.csv, column 'score' (standard error in column 'se') |
| Configuration: Enformer_L2_L2.plus.all (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.245 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.007670187349607077 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer_L2_L2.plus.all on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_L2_L2.plus.all.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_1b_base_absLLR.plus.score (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.0976 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.002187413511062486 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_1b_base_absLLR.plus.score on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_absLLR.plus.score.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_1b_base_Embeddings.minus.inner_product (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.122 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0045420079807488535 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_1b_base_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.minus.inner_product.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_1b_base_Embeddings.plus.cosine_distance (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.105 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.002057172765313782 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_1b_base_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.plus.cosine_distance.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_1b_base_Embeddings.plus.euclidean_distance (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.116 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0035650520551844147 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_1b_base_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.plus.euclidean_distance.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_1b_base_LLR.minus.score (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.101 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0020367047500818945 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_1b_base_LLR.minus.score on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_LLR.minus.score.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_40b_absLLR.plus.score (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.139 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.005687240663392772 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_40b_absLLR.plus.score on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_absLLR.plus.score.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_40b_Embeddings.minus.inner_product (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.118 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.004736084564961457 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_40b_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.minus.inner_product.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_40b_Embeddings.plus.cosine_distance (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.108 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.0025126383914997464 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_40b_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.plus.cosine_distance.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_40b_Embeddings.plus.euclidean_distance (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.131 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.00469655237204335 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_40b_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.plus.euclidean_distance.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_40b_LLR.minus.score (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.137 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.006395455552410924 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_40b_LLR.minus.score on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_LLR.minus.score.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_7b_absLLR.plus.score (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.115 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.00416982694719688 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_7b_absLLR.plus.score on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_absLLR.plus.score.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_7b_Embeddings.minus.inner_product (TraitGym) | Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls | 0.123 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.003983951845855774 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_7b_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot 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_Embeddings.minus.inner_product.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_absLLR.plus.score on TraitGym complex_traits_matched_9
- AIDO.DNA_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- AIDO.DNA_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- AIDO.DNA_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- AIDO.DNA_LLR.minus.score on TraitGym complex_traits_matched_9
- Borzoi_L2_L2.plus.all on TraitGym complex_traits_matched_9
- CADD.plus.RawScore on TraitGym complex_traits_matched_9
- Caduceus_absLLR.plus.score on TraitGym complex_traits_matched_9
- Caduceus_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- Caduceus_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- Caduceus_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- Caduceus_LLR.minus.score 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
- 10
- External evaluations
- 47
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Protocol-valid seeded random ranking; no fitting on assay labels
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
Established label-free reference with explicitly permitted sequence/MSA inputs
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
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
0 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|
No evidence rows match these filters. Choose another scope or clear the search.
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-zero-shot
- areas
- dna-genomes
- contexts
- research
- protocol
- zero-shot score; 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_absLLR.plus.score on TraitGym complex_traits_matched_9
- assessment: AIDO.DNA_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- assessment: AIDO.DNA_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- assessment: AIDO.DNA_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- assessment: AIDO.DNA_LLR.minus.score on TraitGym complex_traits_matched_9
- assessment: Borzoi_L2_L2.plus.all on TraitGym complex_traits_matched_9
- assessment: CADD.plus.RawScore on TraitGym complex_traits_matched_9
- assessment: Caduceus_absLLR.plus.score on TraitGym complex_traits_matched_9
- assessment: Caduceus_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- assessment: Caduceus_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- assessment: Caduceus_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- assessment: Caduceus_LLR.minus.score on TraitGym complex_traits_matched_9
- assessment: Enformer_L2_L2.plus.all on TraitGym complex_traits_matched_9
- assessment: evo2_1b_base_absLLR.plus.score on TraitGym complex_traits_matched_9
- assessment: evo2_1b_base_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- assessment: evo2_1b_base_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- assessment: evo2_1b_base_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- assessment: evo2_1b_base_LLR.minus.score on TraitGym complex_traits_matched_9
- assessment: evo2_40b_absLLR.plus.score on TraitGym complex_traits_matched_9
- assessment: evo2_40b_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- assessment: evo2_40b_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- assessment: evo2_40b_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- assessment: evo2_40b_LLR.minus.score on TraitGym complex_traits_matched_9
- assessment: evo2_7b_absLLR.plus.score on TraitGym complex_traits_matched_9
- assessment: evo2_7b_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- assessment: evo2_7b_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- assessment: evo2_7b_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- assessment: evo2_7b_LLR.minus.score on TraitGym complex_traits_matched_9
- assessment: GPN_final_absLLR.plus.score on TraitGym complex_traits_matched_9
- assessment: GPN_final_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- assessment: GPN_final_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- assessment: GPN_final_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- assessment: GPN_final_LLR.minus.score on TraitGym complex_traits_matched_9
- assessment: GPN-MSA_absLLR.plus.score on TraitGym complex_traits_matched_9
- assessment: GPN-MSA_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- assessment: GPN-MSA_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- assessment: GPN-MSA_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- assessment: GPN-MSA_LLR.minus.score on TraitGym complex_traits_matched_9
- assessment: HyenaDNA_absLLR.plus.score on TraitGym complex_traits_matched_9
- assessment: HyenaDNA_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- assessment: HyenaDNA_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- assessment: HyenaDNA_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- assessment: HyenaDNA_LLR.minus.score on TraitGym complex_traits_matched_9
- assessment: NucleotideTransformer_absLLR.plus.score on TraitGym complex_traits_matched_9
- assessment: NucleotideTransformer_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- assessment: NucleotideTransformer_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- assessment: NucleotideTransformer_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- assessment: NucleotideTransformer_LLR.minus.score on TraitGym complex_traits_matched_9
- assessment: phastCons-43p.plus.score on TraitGym complex_traits_matched_9
- assessment: phyloP-100v.plus.score on TraitGym complex_traits_matched_9
- assessment: phyloP-241m.plus.score on TraitGym complex_traits_matched_9
- assessment: Sei.plus.seqclass_max_absdiff on TraitGym complex_traits_matched_9
- assessment: SpeciesLM_absLLR.plus.score on TraitGym complex_traits_matched_9
- assessment: SpeciesLM_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- assessment: SpeciesLM_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- assessment: SpeciesLM_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- assessment: SpeciesLM_LLR.minus.score on TraitGym complex_traits_matched_9
- assessed by: Select regulatory variants and genes for functional follow-up