TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average
TraitGym Mendelian 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.
63 recorded evaluations, 63 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
63 evaluations · 63 results. Different protocols are not a single leaderboard.
Protocol: TraitGym Mendelian traits, zero-shot, 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.
All 63 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 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 checkedMethods, coverage and sourceAIDO.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 checkedMethods, coverage and sourceAIDO.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 checkedMethods, coverage and sourceAIDO.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 checkedMethods, coverage and sourceAIDO.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 checkedMethods, coverage and sourceAIDO.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: 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 checkedMethods, coverage and sourceBorzoi_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: 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 checkedMethods, coverage and sourceCADD.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 checkedMethods, coverage and sourceCaduceus_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 checkedMethods, coverage and sourceCaduceus_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 checkedMethods, coverage and sourceCaduceus_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 checkedMethods, coverage and sourceCaduceus_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 checkedMethods, coverage and sourceCaduceus_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 checkedMethods, coverage and sourceCaduceus_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: 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 checkedMethods, coverage and sourceEnformer_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: 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 checkedMethods, coverage and sourceevo2_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 checkedMethods, coverage and sourceevo2_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 checkedMethods, coverage and sourceevo2_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') |
| Configuration: evo2_1b_base_Embeddings.plus.euclidean_distance (TraitGym) | Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls | 0.254 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.026158793742882797 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_1b_base_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/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 Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls | 0.188 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.03162438485608758 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_1b_base_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/evo2_1b_base_LLR.minus.score.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_40b_absLLR.plus.score (TraitGym) | Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls | 0.522 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.05270403330295951 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_40b_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_40b_absLLR.plus.score.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_40b_Embeddings.minus.inner_product (TraitGym) | Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls | 0.153 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.03480910115360255 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_40b_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_40b_Embeddings.minus.inner_product.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_40b_Embeddings.plus.cosine_distance (TraitGym) | Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls | 0.128 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.013828466041078366 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_40b_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_40b_Embeddings.plus.cosine_distance.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_40b_Embeddings.plus.euclidean_distance (TraitGym) | Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls | 0.463 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.04992374864833701 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_40b_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/evo2_40b_Embeddings.plus.euclidean_distance.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_40b_LLR.minus.score (TraitGym) | Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls | 0.557 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.05117276390136009 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_40b_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/evo2_40b_LLR.minus.score.csv, column 'score' (standard error in column 'se') |
| Configuration: evo2_7b_absLLR.plus.score (TraitGym) | Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls | 0.34 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.05965517229087366 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceevo2_7b_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_7b_absLLR.plus.score.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 mendelian_traits_matched_9
- AIDO.DNA_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- AIDO.DNA_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- AIDO.DNA_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- AIDO.DNA_LLR.minus.score on TraitGym mendelian_traits_matched_9
- Borzoi_L2_L2.plus.all on TraitGym mendelian_traits_matched_9
- CADD.plus.RawScore on TraitGym mendelian_traits_matched_9
- Caduceus_absLLR.plus.score on TraitGym mendelian_traits_matched_9
- Caduceus_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- Caduceus_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- Caduceus_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- Caduceus_InnerProduct.minus.score on TraitGym mendelian_traits_matched_9
Baseline coverage
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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.
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- Author-reported evaluations
- 13
- External evaluations
- 50
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
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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-mendelian-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 Mendelian traits, matched 9 controls
- assessment: AIDO.DNA_absLLR.plus.score on TraitGym mendelian_traits_matched_9
- assessment: AIDO.DNA_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- assessment: AIDO.DNA_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- assessment: AIDO.DNA_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- assessment: AIDO.DNA_LLR.minus.score on TraitGym mendelian_traits_matched_9
- assessment: Borzoi_L2_L2.plus.all on TraitGym mendelian_traits_matched_9
- assessment: CADD.plus.RawScore on TraitGym mendelian_traits_matched_9
- assessment: Caduceus_absLLR.plus.score on TraitGym mendelian_traits_matched_9
- assessment: Caduceus_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- assessment: Caduceus_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- assessment: Caduceus_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- assessment: Caduceus_InnerProduct.minus.score on TraitGym mendelian_traits_matched_9
- assessment: Caduceus_LLR.minus.score on TraitGym mendelian_traits_matched_9
- assessment: Enformer_L2_L2.plus.all on TraitGym mendelian_traits_matched_9
- assessment: evo2_1b_base_absLLR.plus.score on TraitGym mendelian_traits_matched_9
- assessment: evo2_1b_base_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- assessment: evo2_1b_base_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- assessment: evo2_1b_base_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- assessment: evo2_1b_base_LLR.minus.score on TraitGym mendelian_traits_matched_9
- assessment: evo2_40b_absLLR.plus.score on TraitGym mendelian_traits_matched_9
- assessment: evo2_40b_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- assessment: evo2_40b_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- assessment: evo2_40b_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- assessment: evo2_40b_LLR.minus.score on TraitGym mendelian_traits_matched_9
- assessment: evo2_7b_absLLR.plus.score on TraitGym mendelian_traits_matched_9
- assessment: evo2_7b_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- assessment: evo2_7b_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- assessment: evo2_7b_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- assessment: evo2_7b_LLR.minus.score on TraitGym mendelian_traits_matched_9
- assessment: GPN_final_absLLR.plus.score on TraitGym mendelian_traits_matched_9
- assessment: GPN_final_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- assessment: GPN_final_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- assessment: GPN_final_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- assessment: GPN_final_EuclideanDistance.plus.score on TraitGym mendelian_traits_matched_9
- assessment: GPN_final_InnerProduct.minus.score on TraitGym mendelian_traits_matched_9
- assessment: GPN_final_LLR.minus.score on TraitGym mendelian_traits_matched_9
- assessment: GPN-MSA_absLLR.plus.score on TraitGym mendelian_traits_matched_9
- assessment: GPN-MSA_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- assessment: GPN-MSA_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- assessment: GPN-MSA_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- assessment: GPN-MSA_InnerProduct.minus.score on TraitGym mendelian_traits_matched_9
- assessment: GPN-MSA_LLR.minus.score on TraitGym mendelian_traits_matched_9
- assessment: HyenaDNA_absLLR.plus.score on TraitGym mendelian_traits_matched_9
- assessment: HyenaDNA_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- assessment: HyenaDNA_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- assessment: HyenaDNA_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- assessment: HyenaDNA_InnerProduct.minus.score on TraitGym mendelian_traits_matched_9
- assessment: HyenaDNA_LLR.minus.score on TraitGym mendelian_traits_matched_9
- assessment: NucleotideTransformer_absLLR.plus.score on TraitGym mendelian_traits_matched_9
- assessment: NucleotideTransformer_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- assessment: NucleotideTransformer_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- assessment: NucleotideTransformer_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- assessment: NucleotideTransformer_InnerProduct.minus.score on TraitGym mendelian_traits_matched_9
- assessment: NucleotideTransformer_LLR.minus.score on TraitGym mendelian_traits_matched_9
- assessment: phastCons-43p.plus.score on TraitGym mendelian_traits_matched_9
- assessment: phyloP-100v.plus.score on TraitGym mendelian_traits_matched_9
- assessment: phyloP-241m.plus.score on TraitGym mendelian_traits_matched_9
- assessment: Sei.plus.seqclass_max_absdiff on TraitGym mendelian_traits_matched_9
- assessment: SpeciesLM_absLLR.plus.score on TraitGym mendelian_traits_matched_9
- assessment: SpeciesLM_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- assessment: SpeciesLM_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- assessment: SpeciesLM_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- assessment: SpeciesLM_LLR.minus.score on TraitGym mendelian_traits_matched_9
- assessed by: Select regulatory variants and genes for functional follow-up